FAIRsharing.32b10v; Last edited: Feb. 7, 2021, 7:56 p.m.; Last accessed: Jan 03 2022 7:11 p.m.

Other names: MIAME

MIAME is intended to specify all the information necessary for an unambiguous interpretation of a microarray experiment, and potentially to reproduce it. MIAME defines the content but not the format for this information.

Webpage:

http://www.fged.org/projects/miame/

Publications:

Publications
More detailed information about this field from each metasource.

Minimum information about a microarray experiment (MIAME)-toward standards for microarray data
PMID: 11726920
metasource: Fairsharing.org
version: FAIRsharing.org: MIAME; Minimum Information About a Microarray Experiment; DOI: https://doi.org/10.25504/FAIRsharing.32b10v; Last edited: Feb. 7, 2021, 7:56 p.m.; Last accessed: Jan 03 2022 7:11 p.m.

Minimum Information About a Microarray Experiment (MIAME)--successes, failures, challenges
PMID: 19484163
metasource: Fairsharing.org
version: FAIRsharing.org: MIAME; Minimum Information About a Microarray Experiment; DOI: https://doi.org/10.25504/FAIRsharing.32b10v; Last edited: Feb. 7, 2021, 7:56 p.m.; Last accessed: Jan 03 2022 7:11 p.m.

Minimum information about a microarray experiment (MIAME)-toward standards for microarray data PubMed citations: 1259.

1259 articles citing: Minimum information about a microarray experiment (MIAME)-toward standards for microarray data

Metadata Framework to Support Deployment of Digital Health Technologies in Clinical Trials in Parkinson's Disease. PMID:35336307
Ten quick tips for deep learning in biology. PMID:35324884
Urgent need for consistent standards in functional enrichment analysis. PMID:35263338
Divergent Regulation of Decidual Oxidative-Stress Response by NRF2 and KEAP1 in Preeclampsia with and without Fetal Growth Restriction. PMID:35216082
Data Integration Challenges for Machine Learning in Precision Medicine. PMID:35145977
Minimal Information about MHC Multimers (MIAMM). PMID:35042788
Harnessing the potential of machine learning for advancing "Quality by Design" in biomanufacturing. PMID:35000555
Hepatoprotective Screening of Seriphidium kurramense (Qazilb.) Y.R. Ling. PMID:34912897
Integration of DNA Microarray with Clinical and Genomic Data. PMID:34902132
Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications. PMID:34862503
FAIR data representation in times of eScience: a comparison of instance-based and class-based semantic representations of empirical data using phenotype descriptions as example. PMID:34823588
Sharing Biomedical Data Obtained Through Government-Funded Research and Development Projects in Korea. PMID:34788906
The importance of adherence to international standards for depositing open data in public repositories. PMID:34727971
A framework for validating AI in precision medicine: considerations from the European ITFoC consortium. PMID:34600518
The role of metadata in reproducible computational research. PMID:34553169
Arabidopsis Coexpression Tool: a tool for gene coexpression analysis in Arabidopsis thaliana. PMID:34381973
The SARS-CoV-2 receptor angiotensin-converting enzyme 2 (ACE2) in myalgic encephalomyelitis/chronic fatigue syndrome: A meta-analysis of public DNA methylation and gene expression data. PMID:34341773
Progress towards an OECD reporting framework for transcriptomics and metabolomics in regulatory toxicology. PMID:34333066
DOME: recommendations for supervised machine learning validation in biology. PMID:34316068
Enabling reproducible re-analysis of single-cell data. PMID:34311752
Exposure to TiO2 Nanostructured Aerosol Induces Specific Gene Expression Profile Modifications in the Lungs of Young and Elderly Rats. PMID:34206090
Dengue Detection: Advances in Diagnostic Tools from Conventional Technology to Point of Care. PMID:34201849
Molecular omics resources should require sex annotation: a call for action. PMID:34099934
Empagliflozin Inhibits IL-1β-Mediated Inflammatory Response in Human Proximal Tubular Cells. PMID:34064989
REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology. PMID:34021280
Quality Considerations When Using Tissue Samples for Biomarker Studies in Cancer Research. PMID:33958852
Differential root and shoot magnetoresponses in Arabidopsis thaliana. PMID:33911161
Elevated expression of the adhesion GPCR ADGRL4/ELTD1 promotes endothelial sprouting angiogenesis without activating canonical GPCR signalling. PMID:33893326
An Arabidopsis lipid map reveals differences between tissues and dynamic changes throughout development. PMID:33866624
The transcriptomic responses of Atlantic salmon (Salmo salar) to high temperature stress alone, and in combination with moderate hypoxia. PMID:33845767
The effect of calcium and magnesium on activity, immunogenicity, and efficacy of a recombinant N1/N2 neuraminidase vaccine. PMID:33824333
MicroRNA biomarkers of type 2 diabetes: A protocol for corroborating evidence by computational genomics and meta-analyses. PMID:33822793
Large-scale labeling and assessment of sex bias in publicly available expression data. PMID:33784977
A Minimal Information Model for Potential Drug-Drug Interactions. PMID:33762928
Therapeutic Use of Mesenchymal Stromal Cells: The Need for Inclusive Characterization Guidelines to Accommodate All Tissue Sources and Species. PMID:33665190
Curation of over 10 000 transcriptomic studies to enable data reuse. PMID:33599246
Method comparison studies of telomere length measurement using qPCR approaches: A critical appraisal of the literature. PMID:33471860
Role of miRNAs shuttled by mesenchymal stem cell-derived small extracellular vesicles in modulating neuroinflammation. PMID:33462263
CDH1 is Identified as A Therapeutic Target for Skin Regeneration after Mechanical Loading. PMID:33390855
Comparative Transcriptome Analysis of Iron and Zinc Deficiency in Maize (Zea mays L.). PMID:33371388
Obstacles to the reuse of study metadata in ClinicalTrials.gov. PMID:33339830
SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery. PMID:33268350
KiMoSys 2.0: an upgraded database for submitting, storing and accessing experimental data for kinetic modeling. PMID:33247931
Expanding and Remixing the Metadata Landscape. PMID:33229213
From ArrayExpress to BioStudies. PMID:33211879
Transcriptomic Profiling of the Adaptive and Innate Immune Responses of Atlantic Salmon to Renibacterium salmoninarum Infection. PMID:33193341
A brief guide to the science and art of writing manuscripts in biomedicine. PMID:33167977
Empagliflozin Inhibits Basal and IL-1β-Mediated MCP-1/CCL2 and Endothelin-1 Expression in Human Proximal Tubular Cells. PMID:33139635
Minimum Information for Reporting on the Comet Assay (MIRCA): recommendations for describing comet assay procedures and results. PMID:33106678
A Semi-Automated Workflow for FAIR Maturity Indicators in the Life Sciences. PMID:33092028
Ten simple rules for annotating sequencing experiments. PMID:33017400
Altered Regulation of adipomiR Editing with Aging. PMID:32962255
DLEU2 participates in lymphovascular invasion and inhibits cervical cancer cell proliferation, migration, and invasion. PMID:32922596
Early immune suppression leads to uncontrolled mite proliferation and potent host inflammatory responses in a porcine model of crusted versus ordinary scabies. PMID:32886659
Breast cancer gene expression datasets do not reflect the disease at the population level. PMID:32885043
Best Practices for Making Reproducible Biochemical Models. PMID:32853539
Developing and Using a Data Commons for Understanding the Molecular Characteristics of Germ Cell Tumors. PMID:32852769
A Systematic Approach to Review of in vitro Methods in Brain Tumour Research (SAToRI-BTR): Development of a Preliminary Checklist for Evaluating Quality and Human Relevance. PMID:32850761
The International Collaboration for Cancer Classification and Research. PMID:32818326
Embryonic atrazine exposure and later in life behavioral and brain transcriptomic, epigenetic, and pathological alterations in adult male zebrafish. PMID:32737625
Responsible, practical genomic data sharing that accelerates research. PMID:32694666
The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). PMID:32637990
MINIMAR (MINimum Information for Medical AI Reporting): Developing reporting standards for artificial intelligence in health care. PMID:32594179
Automated Hypothesis Generation to Identify Signals Relevant in the Development of Mammalian Cell and Tissue Bioprocesses, With Validation in a Retinal Culture System. PMID:32582664
Available Software for Meta-analyses of Genome-wide Expression Studies. PMID:32476989
Metabolomics and Multi-Omics Integration: A Survey of Computational Methods and Resources. PMID:32429287
Community standards for open cell migration data. PMID:32396199
Reporting Guidelines to Increase the Reproducibility and Comparability of Research on Microplastics. PMID:32394727
MyoMiner: explore gene co-expression in normal and pathological muscle. PMID:32393257
The Consequences of a Disruption in Cyto-Nuclear Coadaptation on the Molecular Response to a Nitrate Starvation in Arabidopsis. PMID:32369924
Transcriptomics in Toxicogenomics, Part I: Experimental Design, Technologies, Publicly Available Data, and Regulatory Aspects. PMID:32326418
Transcriptomic Profiling in Fins of Atlantic Salmon Parasitized with Sea Lice: Evidence for an Early Imbalance Between Chalimus-Induced Immunomodulation and the Host's Defense Response. PMID:32244468
The CEDAR Workbench: An Ontology-Assisted Environment for Authoring Metadata that Describe Scientific Experiments. PMID:32219223
Ten simple rules for providing effective bioinformatics research support. PMID:32214318
MicroRNAs associated to single drug components of R-CHOP identifies diffuse large B-cell lymphoma patients with poor outcome and adds prognostic value to the international prognostic index. PMID:32192453
Enabling reusability of plant phenomic datasets with MIAPPE 1.1. PMID:32171029
Guidelines for systematic reporting of sequence alignments. PMID:32161811
Understanding the Molecular Mechanisms of Asthma through Transcriptomics. PMID:32141255
GXD's RNA-Seq and Microarray Experiment Search: using curated metadata to reliably find mouse expression studies of interest. PMID:32140729
Identification of hepatic NPC1L1 as an NAFLD risk factor evidenced by ezetimibe-mediated steatosis prevention and recovery. PMID:32123832
Molecular Basis of Growth Inhibition by Acetate of an Adenylate Cyclase-Deficient Mutant of Corynebacterium glutamicum. PMID:32117117
Crosstalk between heterotrimeric G protein-coupled signaling pathways and WRKY transcription factors modulating plant responses to suboptimal micronutrient conditions. PMID:32107545
Whole embryo culture, transcriptomics and RNA interference identify TBX1 and FGF11 as novel regulators of limb development in the mouse. PMID:32107392
Data libraries - the missing element for modeling biological systems. PMID:32100391
Non-Viral in Vitro Gene Delivery: It is Now Time to Set the Bar! PMID:32098191
Autoantibody testing by enzyme-linked immunosorbent assay-a case in which the solid phase decides on success and failure. PMID:31993528
Comparative analysis of lung and blood transcriptomes in mice exposed to multi-walled carbon nanotubes. PMID:31978390
All of gene expression (AOE): An integrated index for public gene expression databases. PMID:31978081
Ontology-driven integrative analysis of omics data through Onassis. PMID:31959844
Discovery of microarray-identified genes associated with the progression of cervical intraepithelial neoplasia. PMID:31949653
Microglia Actively Remodel Adult Hippocampal Neurogenesis through the Phagocytosis Secretome. PMID:31896673
Recommendations for the collection and use of multiplexed functional data for clinical variant interpretation. PMID:31862013
Bacillus amyloliquefaciens MBI600 differentially induces tomato defense signaling pathways depending on plant part and dose of application. PMID:31836790
The CCN1 (CYR61) protein promotes skin growth by enhancing epithelial-mesenchymal transition during skin expansion. PMID:31828970
ADGRL4/ELTD1 Silencing in Endothelial Cells Induces ACLY and SLC25A1 and Alters the Cellular Metabolic Profile. PMID:31775252
TACITuS: transcriptomic data collector, integrator, and selector on big data platform. PMID:31757212
Common Gene Expression Patterns in Environmental Model Organisms Exposed to Engineered Nanomaterials: A Meta-Analysis. PMID:31752483
Rational Design and Methods of Analysis for the Study of Short- and Long-Term Dynamic Responses of Eukaryotic Systems. PMID:31602619
Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. PMID:31602618
Tissue-regenerative potential of the secretome of γ-irradiated peripheral blood mononuclear cells is mediated via TNFRSF1B-induced necroptosis. PMID:31570701
Driver gene alterations and activated signaling pathways toward malignant progression of gastrointestinal stromal tumors. PMID:31553483
Perspective: Dimensions of the scientific method. PMID:31513575
Differences in blastomere totipotency in 2-cell mouse embryos are a maternal trait mediated by asymmetric mRNA distribution. PMID:31504820
Evaluating Chemicals for Thyroid Disruption: Opportunities and Challenges with in Vitro Testing and Adverse Outcome Pathway Approaches. PMID:31487205
Gene Expression Maps in Plants: Current State and Prospects. PMID:31466308
SOCCOMAS: a FAIR web content management system that uses knowledge graphs and that is based on semantic programming. PMID:31392324
Biomarkers of Acute Lung Injury The Individualized Approach: for Phenotyping, Risk Stratification and Treatment Surveillance. PMID:31382587
Mining of Self-Organizing Map Gene-Expression Portraits Reveals Prognostic Stratification of HPV-Positive Head and Neck Squamous Cell Carcinoma. PMID:31357501
Rag1 immunodeficiency-induced early aging and senescence in zebrafish are dependent on chronic inflammation and oxidative stress. PMID:31348603
Identification of microRNA biomarkers in atrial fibrillation: A protocol for systematic review and bioinformatics analysis. PMID:31348272
Towards a standardized bioinformatics infrastructure for N- and O-glycomics. PMID:31332201
Directions for research and training in plant omics: Big Questions and Big Data. PMID:31245771
Gene Expression Profiles Induced by High-dose Ionizing Radiation in MDA-MB-231 Triple-negative Breast Cancer Cell Line. PMID:31243106
Organizing phenotypic data-a semantic data model for anatomy. PMID:31221226
Mitochondrial Transcriptome Control and Intercompartment Cross-Talk During Plant Development. PMID:31200566
Cyberbiosecurity Challenges of Pathogen Genome Databases. PMID:31157218
Mutational burden and signatures in 4000 Japanese cancers provide insights into tumorigenesis and response to therapy. PMID:31152682
Development and Validation of an Esophageal Squamous Cell Carcinoma Detection Model by Large-Scale MicroRNA Profiling. PMID:31125107
Ten simple rules for carrying out and writing meta-analyses. PMID:31095553
Differential Effects of Influenza Virus NA, HA Head, and HA Stalk Antibodies on Peripheral Blood Leukocyte Gene Expression during Human Infection. PMID:31088926
Muscle Gene Sets: a versatile methodological aid to functional genomics in the neuromuscular field. PMID:31053169
MIReAD, a minimum information standard for reporting arthropod abundance data. PMID:31024009
Influenza A Reinfection in Sequential Human Challenge: Implications for Protective Immunity and "Universal" Vaccine Development. PMID:30953061
Genomic Common Data Model for Seamless Interoperation of Biomedical Data in Clinical Practice: Retrospective Study. PMID:30912749
Predictability of human differential gene expression. PMID:30846554
A Tool to Encourage Minimum Reporting Guideline Uptake for Data Analysis in Metabolomics. PMID:30841575
Evaluating visual analytics for health informatics applications: a systematic review from the American Medical Informatics Association Visual Analytics Working Group Task Force on Evaluation. PMID:30840080
Critical review of reporting of the data analysis step in metabolomics. PMID:30830321
Andrographolide induces DNA damage in prostate cancer cells. PMID:30800220
Placental CX3CL1 is Deregulated by Angiotensin II and Contributes to a Pro-Inflammatory Trophoblast-Monocyte Interaction. PMID:30717334
p.E95K mutation in Indian hedgehog causing brachydactyly type A1 impairs IHH/Gli1 downstream transcriptional regulation. PMID:30651074
Real-World Synthetic Biology: Is It Founded on an Engineering Approach, and Should It Be? PMID:30621107
Identification of a serum-based miRNA signature for response of esophageal squamous cell carcinoma to neoadjuvant chemotherapy. PMID:30602370
Mining data and metadata from the gene expression omnibus. PMID:30594974
High-Throughput Sequencing in Respiratory, Critical Care, and Sleep Medicine Research. An Official American Thoracic Society Workshop Report. PMID:30592451
Diversity of cell phenotypes among MT-2 cell lines affects the growth of U937 cells and cytokine production. PMID:30560508
Gene Expression Studies for the Development of Particle Therapy. PMID:30555854
A minimum information standard for reproducing bench-scale bacterial cell growth and productivity. PMID:30534611
A Serum-Induced Transcriptome and Serum Cytokine Signature Obtained at Diagnosis Correlates with the Development of Early Pancreatic Ductal Adenocarcinoma Metastasis. PMID:30530849
Comparative transcriptomic analysis reveals adriamycin-induced apoptosis via p53 signaling pathway in retinal pigment epithelial cells. PMID:30507074
Forms of selenium in vitamin-mineral mixes differentially affect the expression of genes responsible for prolactin, ACTH, and α-MSH synthesis and mitochondrial dysfunction in pituitaries of steers grazing endophyte-infected tall fescue. PMID:30476104
Identification and validation of potential prognostic and predictive miRNAs of epithelial ovarian cancer. PMID:30475821
Saccharomyces cerevisiae adapted to grow in the presence of low-dose rapamycin exhibit altered amino acid metabolism. PMID:30458881
The Reporting Items for Patent Landscapes statement. PMID:30412195
Global Gene Expression Response in Peripheral Blood Cells of Petroleum Workers Exposed to Sub-Ppm Benzene Levels. PMID:30373255
DDBJ update: the Genomic Expression Archive (GEA) for functional genomics data. PMID:30357349
AIRR Community Standardized Representations for Annotated Immune Repertoires. PMID:30323809
The role of miR-106p-5p in cervical cancer: from expression to molecular mechanism. PMID:30275981
A multiple myeloma classification system that associates normal B-cell subset phenotypes with prognosis. PMID:30254104
Integration among databases and data sets to support productive nanotechnology: Challenges and recommendations. PMID:30246165
Minimum information reporting in bio-nano experimental literature. PMID:30190620
The conserved protective cyclic AMP-phosphodiesterase function PDE4B is expressed in the adenoma and adjacent normal colonic epithelium of mammals and silenced in colorectal cancer. PMID:30188895
MCO: towards an ontology and unified vocabulary for a framework-based annotation of microbial growth conditions. PMID:30137210
Kinomics toolbox-A web platform for analysis and viewing of kinomic peptide array data. PMID:30130366
Adenylyl cyclase 6 is involved in the hyposecretory status of experimental colitis. PMID:30094477
Integrative machine learning analysis of multiple gene expression profiles in cervical cancer. PMID:30065881
Analysis of the Long-Lived Responses Induced by Immunostimulants and Their Effects on a Viral Infection in Zebrafish (Danio rerio). PMID:30038625
The Role of Specific Chemokines in the Amelioration of Colitis by Appendicitis and Appendectomy. PMID:30037025
FindSim: A Framework for Integrating Neuronal Data and Signaling Models. PMID:29997492
A Survey of Data Mining and Deep Learning in Bioinformatics. PMID:29956014
Improving the standardization of mRNA measurement by RT-qPCR. PMID:29922589
Sustainable data and metadata management at the BD2K-LINCS Data Coordination and Integration Center. PMID:29917015
Molecular profiling and sequential somatic mutation shift in hypermutator tumours harbouring POLE mutations. PMID:29880869
Wnt Signaling Pathways Are Dysregulated in Rat Female Cerebellum Following Early Methyl Donor Deficiency. PMID:29804229
Minimal Information About an Immuno-Peptidomics Experiment (MIAIPE). PMID:29791771
The down-regulation of the CYP2C19 gene is associated with aggressive tumor potential and the poorer recurrence-free survival of hepatocellular carcinoma. PMID:29774122
AICAR Antiproliferative Properties Involve the AMPK-Independent Activation of the Tumor Suppressors LATS 1 and 2. PMID:29730476
Improving communication for interdisciplinary teams working on storage of digital information in DNA. PMID:29707196
Transcriptomic Studies of Malaria: a Paradigm for Investigation of Systemic Host-Pathogen Interactions. PMID:29695497
Epithelial-Mesenchymal Transition during Metastasis of HPV-Negative Pharyngeal Squamous Cell Carcinoma. PMID:29693014
How measurement science can improve confidence in research results. PMID:29684013
Engineering d-limonene synthase down-regulation in orange fruit induces resistance against the fungus Phyllosticta citricarpa through enhanced accumulation of monoterpene alcohols and activation of defence. PMID:29573543
Viral Fitness Correlates with the Magnitude and Direction of the Perturbation Induced in the Host's Transcriptome: The Tobacco Etch Potyvirus-Tobacco Case Study. PMID:29562354
Subtype assignment of CLL based on B-cell subset associated gene signatures from normal bone marrow - A proof of concept study. PMID:29513759
Improving Reproducibility and Candidate Selection in Transcriptomics Using Meta-analysis. PMID:29511359
Current applications of antibody microarrays. PMID:29507545
When Transcriptomics and Metabolomics Work Hand in Hand: A Case Study Characterizing Plant CDF Transcription Factors. PMID:29495643
Reporting guidelines for oncology research: helping to maximise the impact of your research. PMID:29471308
Glucocorticoids promote apoptosis of proinflammatory monocytes by inhibiting ERK activity. PMID:29449600
Rational cell culture optimization enhances experimental reproducibility in cancer cells. PMID:29445172
Gene master regulators of papillary and anaplastic thyroid cancers. PMID:29416781
Breed-dependent microRNA expression in the primary culture of skeletal muscle cells subjected to myogenic differentiation. PMID:29390965
A call for action: Improve reporting of research studies to increase the scientific basis for regulatory decision-making. PMID:29297199
Data Sharing: Convert Challenges into Opportunities. PMID:29270401
An integrated meta-analysis approach to identifying medications with potential to alter breast cancer risk through connectivity mapping. PMID:29268695
Serum microRNA array analysis identifies miR-140-3p, miR-33b-3p and miR-671-3p as potential osteoarthritis biomarkers involved in metabolic processes. PMID:29255496
Identification of hub genes related to silicone-induced immune response in rats. PMID:29245939
Assessing Public Metabolomics Metadata, Towards Improving Quality. PMID:29236679
A Look Behind the Curtain: Epilepsy Microarray Consortium. PMID:29217985
In vitro to in vivo extrapolation for high throughput prioritization and decision making. PMID:29203341
Updating the MISEV minimal requirements for extracellular vesicle studies: building bridges to reproducibility. PMID:29184626
Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data. PMID:29163494
Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data. PMID:29144493
A generic Transcriptomics Reporting Framework (TRF) for 'omics data processing and analysis. PMID:29113939
CYP3A4 Gene Is a Novel Biomarker for Predicting a Poor Prognosis in Hepatocellular Carcinoma. PMID:29109094
Data Science in Radiology: A Path Forward. PMID:29097379
Transcriptomic data from two primary cell models stimulating human monocytes suggest inhibition of oxidative phosphorylation and mitochondrial function by N. meningitidis which is partially up-regulated by IL-10. PMID:29078758
Correlating Resolving Power, Resolution, and Collision Cross Section: Unifying Cross-Platform Assessment of Separation Efficiency in Ion Mobility Spectrometry. PMID:29039942
MicroRNA expression profiles and type 1 diabetes mellitus: systematic review and bioinformatic analysis. PMID:28986402
Applying 'omics technologies in chemicals risk assessment: Report of an ECETOC workshop. PMID:28958911
Compliance with minimum information guidelines in public metabolomics repositories. PMID:28949328
Cleaning by clustering: methodology for addressing data quality issues in biomedical metadata. PMID:28923003
GlyTouCan: an accessible glycan structure repository. PMID:28922742
Genome build information is an essential part of genomic track files. PMID:28911336
Pituitary genomic expression profiles of steers are altered by grazing of high vs. low endophyte-infected tall fescue forages. PMID:28902910
Transcriptome profiling of antiviral immune and dietary fatty acid dependent responses of Atlantic salmon macrophage-like cells. PMID:28886690
Variant Interpretation: Functional Assays to the Rescue. PMID:28886340
Data Management Rubric for Video Data in Organismal Biology. PMID:28881939
Murine Myocardial Transcriptome Analysis Reveals a Critical Role of COPS8 in the Gene Expression of Cullin-RING Ligase Substrate Receptors and Redox and Vesicle Trafficking Pathways. PMID:28861005
Global analysis of gene expression in maize leaves treated with low temperature. II. Combined effect of severe cold (8 °C) and circadian rhythm. PMID:28828699
Totipotency segregates between the sister blastomeres of two-cell stage mouse embryos. PMID:28811525
Salivary extracellular RNA biomarkers for insulin resistance detection in hispanics. PMID:28802700
Extracellular Matrix and Integrin Expression Profiles in Fuchs Endothelial Corneal Dystrophy Cells and Tissue Model. PMID:28726551
Transcriptomics in toxicology. PMID:28720289
BIG LEAF is a regulator of organ size and adventitious root formation in poplar. PMID:28686626
Nuclear CD24 Drives Tumor Growth and Is Predictive of Poor Patient Prognosis. PMID:28674079
Predicting biomedical metadata in CEDAR: A study of Gene Expression Omnibus (GEO). PMID:28625880
Transcriptomics technologies. PMID:28545146
Reproducible and reusable research: are journal data sharing policies meeting the mark? PMID:28462024
Overexpression of heat-shock factor 1 is associated with a poor prognosis in esophageal squamous cell carcinoma. PMID:28454329
A Systems Biology Approach Using Transcriptomic Data Reveals Genes and Pathways in Porcine Skeletal Muscle Affected by Dietary Lysine. PMID:28430144
Longitudinal peripheral blood transcriptional analysis of a patient with severe Ebola virus disease. PMID:28404864
IL-15 regulates migration, invasion, angiogenesis and genes associated with lipid metabolism and inflammation in prostate cancer. PMID:28379958
Integrated analysis of gene expression and copy number identified potential cancer driver genes with amplification-dependent overexpression in 1,454 solid tumors. PMID:28377632
Poplar MYB115 and MYB134 Transcription Factors Regulate Proanthocyanidin Synthesis and Structure. PMID:28348066
International Standards for Genomes, Transcriptomes, and Metagenomes. PMID:28337071
Inhibition of fat cell differentiation in 3T3-L1 pre-adipocytes by all-trans retinoic acid: Integrative analysis of transcriptomic and phenotypic data. PMID:28331816
Reproducibility of biomedical research - The importance of editorial vigilance. PMID:28331813
How consistent are we? Interlaboratory comparison study in fathead minnows using the model estrogen 17α-ethinylestradiol to develop recommendations for environmental transcriptomics. PMID:28316117
Dose-dependent induction of astrocyte activation and reactive astrogliosis in mouse brain following maternal exposure to carbon black nanoparticle. PMID:28148272
Transcriptome profiling of visceral adipose tissue in a novel obese rat model, WNIN/Ob & its comparison with other animal models. PMID:28139540
Heat-induced masculinization in domesticated zebrafish is family-specific and yields a set of different gonadal transcriptomes. PMID:28115725
Atrazine exposure elicits copy number alterations in the zebrafish genome. PMID:28111253
Informatics and Data Analytics to Support Exposome-Based Discovery for Public Health. PMID:28068484
GB3.0: a platform for plant bio-design that connects functional DNA elements with associated biological data. PMID:28053117
An LRR/Malectin Receptor-Like Kinase Mediates Resistance to Non-adapted and Adapted Powdery Mildew Fungi in Barley and Wheat. PMID:28018377
The minimum information required for a glycomics experiment (MIRAGE) project: improving the standards for reporting glycan microarray-based data. PMID:27993942
How to make Mathematics Biology's next and better microscope. PMID:27920995
Towards an open grapevine information system. PMID:27917288
Consistency in drug response profiling. PMID:27905421
The reproducibility of biomedical research: Sleepers awake! PMID:27896142
Multi-template polymerase chain reaction. PMID:27896140
Immediate-early alcohol-responsive miRNA expression in Drosophila. PMID:27845601
Somatic cancer variant curation and harmonization through consensus minimum variant level data. PMID:27814769
Homogeneous Inflammatory Gene Profiles Induced in Human Dermal Fibroblasts in Response to the Three Main Species of Borrelia burgdorferi sensu lato. PMID:27706261
Characterisation of equine satellite cell transcriptomic profile response to β-hydroxy-β-methylbutyrate (HMB). PMID:27691998
Key Challenges and Opportunities Associated with the Use of In Vitro Models to Detect Human DILI: Integrated Risk Assessment and Mitigation Plans. PMID:27689095
The application of transcriptomic data in the authentication of beef derived from contrasting production systems. PMID:27654331
The minimum information required for a glycomics experiment (MIRAGE) project: sample preparation guidelines for reliable reporting of glycomics datasets. PMID:27654115
Resources and Recommendations for Using Transcriptomics to Address Grand Challenges in Comparative Biology. PMID:27639274
Histological and Transcriptomic Changes in Male Zebrafish Testes Due to Early Life Exposure to Low Level 2,3,7,8-Tetrachlorodibenzo-p-Dioxin. PMID:27618130
Extremes of Interferon-Stimulated Gene Expression Associate with Worse Outcomes in the Acute Respiratory Distress Syndrome. PMID:27606687
Genomic-Wide Analysis with Microarrays in Human Oncology. PMID:27600234
Up-to-Date Applications of Microarrays and Their Way to Commercialization. PMID:27600220
Stereospecific induction of apoptosis in tumor cells via endogenous C16-ceramide and distinct transcripts. PMID:27551447
The PBMC transcriptome profile after intake of oxidized versus high-quality fish oil: an explorative study in healthy subjects. PMID:27551317
Granulocyte macrophage colony-stimulating factor induces CCL17 production via IRF4 to mediate inflammation. PMID:27525438
Methods for Optimizing CRISPR-Cas9 Genome Editing Specificity. PMID:27494557
Effect of a diet enriched with omega-6 and omega-3 fatty acids on the pig liver transcriptome. PMID:27482299
Transcriptomic profile adaptations following exposure of equine satellite cells to nutriactive phytochemical gamma-oryzanol. PMID:27482297
Quality Matters: Systematic Analysis of Endpoints Related to "Cellular Life" in Vitro Data of Radiofrequency Electromagnetic Field Exposure. PMID:27420084
Embryonic Atrazine Exposure Elicits Alterations in Genes Associated with Neuroendocrine Function in Adult Male Zebrafish. PMID:27413107
First Proposal of Minimum Information About a Cellular Assay for Regenerative Medicine. PMID:27405781
NeuroRDF: semantic integration of highly curated data to prioritize biomarker candidates in Alzheimer's disease. PMID:27392431
Protection against doxorubicin-induced myocardial dysfunction in mice by cardiac-specific expression of carboxyl terminus of hsp70-interacting protein. PMID:27323684
Pigment epithelium-derived factor (PEDF): a novel trophoblast-derived factor limiting feto-placental angiogenesis in late pregnancy. PMID:27278471
The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report. PMID:27255532
Germline APOBEC3B deletion is associated with breast cancer risk in an Asian multi-ethnic cohort and with immune cell presentation. PMID:27233495
Gene expression changes in the retina following subretinal injection of human neural progenitor cells into a rodent model for retinal degeneration. PMID:27217715
MicroRNA858 Is a Potential Regulator of Phenylpropanoid Pathway and Plant Development. PMID:27208307
Gene Expression Patterns of Wood Decay Fungi Postia placenta and Phanerochaete chrysosporium Are Influenced by Wood Substrate Composition during Degradation. PMID:27208101
Host-induced aneuploidy and phenotypic diversification in the Sudden Oak Death pathogen Phytophthora ramorum. PMID:27206972
Integrated Systems for NGS Data Management and Analysis: Open Issues and Available Solutions. PMID:27200084
Immunogenic Subtypes of Breast Cancer Delineated by Gene Classifiers of Immune Responsiveness. PMID:27197066
Genetic Approaches to Study Plant Responses to Environmental Stresses: An Overview. PMID:27196939
How should the completeness and quality of curated nanomaterial data be evaluated? PMID:27143028
Ontology-based annotations and semantic relations in large-scale (epi)genomics data. PMID:27142216
An 80-gene set to predict response to preoperative chemoradiotherapy for rectal cancer by principle component analysis. PMID:27123272
Improving the reliability of peer-reviewed publications: We are all in it together. PMID:27077047
A physiome interoperability roadmap for personalized drug development. PMID:27051513
The Gene Expression Omnibus Database. PMID:27008011
Principles of metadata organization at the ENCODE data coordination center. PMID:26980513
Thioridazine inhibits gene expression control of the cell wall signaling pathway (CWI) in the human pathogenic fungus Paracoccidioides brasiliensis. PMID:26956010
Genome-Wide Transcriptional Response of Saccharomyces cerevisiae to Stress-Induced Perturbations. PMID:26925399
Methodological challenges and analytic opportunities for modeling and interpreting Big Healthcare Data. PMID:26918190
Alcohol resistance in Drosophila is modulated by the Toll innate immune pathway. PMID:26916032
Molecular foundations of chilling-tolerance of modern maize. PMID:26897027
An embryonic atrazine exposure results in reproductive dysfunction in adult zebrafish and morphological alterations in their offspring. PMID:26891955
Behçet's: A Disease or a Syndrome? Answer from an Expression Profiling Study. PMID:26890122
Translational bioinformatics in the era of real-time biomedical, health care and wellness data streams. PMID:26876889
The Electron Microscopy eXchange (EMX) initiative. PMID:26873784
Osteogenic Differentiation of MSC through Calcium Signaling Activation: Transcriptomics and Functional Analysis. PMID:26828589
PMD: A Resource for Archiving and Analyzing Protein Microarray data. PMID:26813635
Microarray Meta-Analysis Focused on the Response of Genes Involved in Redox Homeostasis to Diverse Abiotic Stresses in Rice. PMID:26793229
Fenofibrate unexpectedly induces cardiac hypertrophy in mice lacking MuRF1. PMID:26764147
Comparative transcriptional profiling of orange fruit in response to the biocontrol yeast Kloeckera apiculata and its active compounds. PMID:26725242
The evolution of standards and data management practices in systems biology. PMID:26700851
Landscape of gene fusions in epithelial cancers: seq and ye shall find. PMID:26684754
Data standards can boost metabolomics research, and if there is a will, there is a way. PMID:26612985
Transcriptome profiling reveals that feeding wild zooplankton to larval Atlantic cod (Gadus morhua) influences suites of genes involved in oxidation-reduction, mitosis, and selenium homeostasis. PMID:26610852
Analysis of the Secretome of Apoptotic Peripheral Blood Mononuclear Cells: Impact of Released Proteins and Exosomes for Tissue Regeneration. PMID:26567861
From raw data to data-analysis for magnetic resonance spectroscopy--the missing link: jMRUI2XML. PMID:26552737
Global Gene Expression Profiling in Omental Adipose Tissue of Morbidly Obese Diabetic African Americans. PMID:26504501
OpenTein: a database of digital whole-slide images of stem cell-derived teratomas. PMID:26496950
NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases. PMID:26475471
Building an RNA Sequencing Transcriptome of the Central Nervous System. PMID:26463470
Tumor Necrosis Factor Alpha and Insulin-Like Growth Factor 1 Induced Modifications of the Gene Expression Kinetics of Differentiating Skeletal Muscle Cells. PMID:26447881
Experiences in supporting the structured collection of cancer nanotechnology data using caNanoLab. PMID:26425409
Age-Specific Gene Expression Profiles of Rhesus Monkey Ovaries Detected by Microarray Analysis. PMID:26421297
Repertoires: How to Transform a Project into a Research Community. PMID:26412866
An Application of Sequential Meta-Analysis to Gene Expression Studies. PMID:26401096
Isolated Rat Epididymal Basal Cells Share Common Properties with Adult Stem Cells. PMID:26400399
Data integration in biological research: an overview. PMID:26336651
Integrative Analysis of MicroRNA and mRNA Data Reveals an Orchestrated Function of MicroRNAs in Skeletal Myocyte Differentiation in Response to TNF-α or IGF1. PMID:26270642
An Enriched European Eel Transcriptome Sheds Light upon Host-Pathogen Interactions with Vibrio vulnificus. PMID:26207370
SEEK: a systems biology data and model management platform. PMID:26160520
Data analysis: Create a cloud commons. PMID:26156357
Cultured Cells from the Human Oocyte Cumulus Niche Are Efficient Feeders to Propagate Pluripotent Stem Cells. PMID:26153797
Transcriptome and ultrastructural changes in dystrophic Epidermolysis bullosa resemble skin aging. PMID:26143532
The center for expanded data annotation and retrieval. PMID:26112029
DNA microarray integromics analysis platform. PMID:26110022
Gene expression markers of age-related inflammation in two human cohorts. PMID:26087330
BioMiner: Paving the Way for Personalized Medicine. PMID:26005322
Tools and resources for analyzing gene expression changes in glaucomatous neurodegeneration. PMID:25999234
Microarray transcriptional profiling of Arctic Mesorhizobium strain N33 at low temperature provides insights into cold adaption strategies. PMID:25975821
Early maternal alcohol consumption alters hippocampal DNA methylation, gene expression and volume in a mouse model. PMID:25970770
Rethinking Meta-Analysis: Applications for Air Pollution Data and Beyond. PMID:25969128
Lactococcus garvieae: a small bacteria and a big data world. PMID:25960872
Investigation into the annotation of protocol sequencing steps in the sequence read archive. PMID:25960871
Intuitive web-based experimental design for high-throughput biomedical data. PMID:25954760
Comparison of microarray expression profiles between follicular variant of papillary thyroid carcinomas and follicular adenomas of the thyroid. PMID:25923053
Effect of BRAF mutational status on expression profiles in conventional papillary thyroid carcinomas. PMID:25922907
Head and neck cancer subtypes with biological and clinical relevance: Meta-analysis of gene-expression data. PMID:25821127
BioXpress: an integrated RNA-seq-derived gene expression database for pan-cancer analysis. PMID:25819073
Diffuse large B-cell lymphoma classification system that associates normal B-cell subset phenotypes with prognosis. PMID:25800755
Analytical methods in untargeted metabolomics: state of the art in 2015. PMID:25798438
Stratifying risk of recurrence in stage II colorectal cancer using deregulated stromal and epithelial microRNAs. PMID:25788261
Towards the automatic classification of neurons. PMID:25765323
G Protein-Coupled Receptor (GPCR) Expression in Native Cells: "Novel" endoGPCRs as Physiologic Regulators and Therapeutic Targets. PMID:25737495
Integration of metabolic activation with a predictive toxicogenomics signature to classify genotoxic versus nongenotoxic chemicals in human TK6 cells. PMID:25733247
Modifications in stromal extracellular matrix of aged corneas can be induced by ultraviolet A irradiation. PMID:25728164
Development of data representation standards by the human proteome organization proteomics standards initiative. PMID:25726569
Components of the endocannabinoid and dopamine systems are dysregulated in Huntington's disease: analysis of publicly available microarray datasets. PMID:25692022
Gene expression changes during retinal development and rod specification. PMID:25678762
Vision from next generation sequencing: multi-dimensional genome-wide analysis for producing gene regulatory networks underlying retinal development, aging and disease. PMID:25668385
Identification of reference genes in human myelomonocytic cells for gene expression studies in altered gravity. PMID:25654098
Standard reporting requirements for biological samples in metabolomics experiments: microbial and in vitro biology experiments. PMID:25653575
Enabling consistency in pluripotent stem cell-derived products for research and development and clinical applications through material standards. PMID:25650438
Orchestrating high-throughput genomic analysis with Bioconductor. PMID:25633503
TNF-α and IGF1 modify the microRNA signature in skeletal muscle cell differentiation. PMID:25630602
Comparison of toxicogenomics and traditional approaches to inform mode of action and points of departure in human health risk assessment of benzo[a]pyrene in drinking water. PMID:25605026
Virtual Reference Environments: a simple way to make research reproducible. PMID:25433467
Dissecting the organ specificity of insecticide resistance candidate genes in Anopheles gambiae: known and novel candidate genes. PMID:25421852
Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data. PMID:25414366
Fingerprints of a message: integrating positional information on the transcriptome. PMID:25364746
ArrayExpress update--simplifying data submissions. PMID:25361974
Vitamin D receptor and RXR in the post-genomic era. PMID:25335912
High dose ionizing radiation regulates micro RNA and gene expression changes in human peripheral blood mononuclear cells. PMID:25257395
Modulation of interferon activity-associated soluble molecules by appendicitis and appendectomy limits colitis-identification of novel anti-colitic targets. PMID:25243802
Commentary on: "Facilitating transparency in spinal cord injury studies using data standards and ontologies". PMID:25206737
Facilitating transparency in spinal cord injury studies using data standards and ontologies. PMID:25206736
We are all individuals... bioinformatics in the personalized medicine era. PMID:25204962
The concentrations of EGFR, LRG1, ITIH4, and F5 in serum correlate with the number of colonic adenomas in ApcPirc/+ rats. PMID:25200834
Exposure to paper mill effluent at a site in North Central Florida elicits molecular-level changes in gene expression indicative of progesterone and androgen exposure. PMID:25198161
The involvement of cholesterol in sepsis and tolerance to lipopolysaccharide highlighted by the transcriptome analysis of zebrafish (Danio rerio). PMID:25181277
Improved reproducibility by assuring confidence in measurements in biomedical research. PMID:25166868
Microarray R-based analysis of complex lysate experiments with MIRACLE. PMID:25161257
Multiple regulatory roles of the mouse transmembrane adaptor protein NTAL in gene transcription and mast cell physiology. PMID:25153696
pENCODE: a plant encyclopedia of DNA elements. PMID:25149370
Plant disease resistance is augmented in uzu barley lines modified in the brassinosteroid receptor BRI1. PMID:25135116
KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems. PMID:25115331
Toward effective sharing of high-dimensional immunology data. PMID:25101748
Semantic Web repositories for genomics data using the eXframe platform. PMID:25093072
CSEO - the Cigarette Smoke Exposure Ontology. PMID:25093069
Endothelin and vascular remodelling in colitis pathogenesis--appendicitis and appendectomy limit colitis by suppressing endothelin pathways. PMID:25085204
A digital repository with an extensible data model for biobanking and genomic analysis management. PMID:25077808
The quality of methods reporting in parasitology experiments. PMID:25076044
Repeated gestational exposure of mice to chlorpyrifos oxon is associated with paraoxonase 1 (PON1) modulated effects in maternal and fetal tissues. PMID:25070982
STATegra EMS: an Experiment Management System for complex next-generation omics experiments. PMID:25033091
Data integration in the era of omics: current and future challenges. PMID:25032990
Influence of Populus genotype on gene expression by the wood decay fungus Phanerochaete chrysosporium. PMID:25015893
Enhancing reproducibility in cancer drug screening: how do we move forward? PMID:25015668
Improving the transparency of prognosis research: the role of reporting, data sharing, registration, and protocols. PMID:25003600
Clinic-genomic association mining for colorectal cancer using publicly available datasets. PMID:24987669
Upregulation of heat shock proteins and the promotion of damage-associated molecular pattern signals in a colorectal cancer model by modulated electrohyperthermia. PMID:24973890
Identification of microRNA profiles in salivary adenoid cystic carcinoma cells during metastatic progression. PMID:24932284
Ontology-supported research on vaccine efficacy, safety and integrative biological networks. PMID:24909153
Longissimus dorsi transcriptome analysis of purebred and crossbred Iberian pigs differing in muscle characteristics. PMID:24885501
Minimum information about a spinal cord injury experiment: a proposed reporting standard for spinal cord injury experiments. PMID:24870067
Vitamin D and the RNA transcriptome: more than mRNA regulation. PMID:24860511
Amniotic fluid RNA gene expression profiling provides insights into the phenotype of Turner syndrome. PMID:24850140
Os odontoideum in identical twins: Comparative gene expression analysis. PMID:24818044
Commentary on Shimoyama et al. (2012): three ontologies to define phenotype measurement data. PMID:24795755
Evaluation of gene expression classification studies: factors associated with classification performance. PMID:24770439
LMKB/MARF1 localizes to mRNA processing bodies, interacts with Ge-1, and regulates IFI44L gene expression. PMID:24755989
Acute exercise leads to regulation of telomere-associated genes and microRNA expression in immune cells. PMID:24752326
Application of transcriptomics in Chinese herbal medicine studies. PMID:24716122
ADAM9 up-regulates N-cadherin via miR-218 suppression in lung adenocarcinoma cells. PMID:24705471
Plant pathology 2.0. PMID:24698279
The mechanisms underlying α-amanitin resistance in Drosophila melanogaster: a microarray analysis. PMID:24695618
The eGenVar data management system--cataloguing and sharing sensitive data and metadata for the life sciences. PMID:24682735
T helper type 17 pathway suppression by appendicitis and appendectomy protects against colitis. PMID:24666024
Fish oil supplementation induces expression of genes related to cell cycle, endoplasmic reticulum stress and apoptosis in peripheral blood mononuclear cells: a transcriptomic approach. PMID:24641624
CCR+: Metadata Based Extended Personal Health Record Data Model Interoperable with the ASTM CCR Standard. PMID:24627817
Genome-wide transcriptomic analysis of response to low temperature reveals candidate genes determining divergent cold-sensitivity of maize inbred lines. PMID:24623520
Expressional regulation of genes linked to immunity & programmed development in human early placental villi. PMID:24604048
Gene expression analysis in RA: towards personalized medicine. PMID:24589910
Gene expression changes for antioxidants pathways in the mouse cochlea: relations to age-related hearing deficits. PMID:24587312
The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again. PMID:24564732
CorrelaGenes: a new tool for the interpretation of the human transcriptome. PMID:24564370
Guidelines for managing data and processes in bone and cartilage tissue engineering. PMID:24564199
Differentially expressed genes and signalling pathways are involved in mouse osteoblast-like MC3T3-E1 cells exposed to 17-β estradiol. PMID:24556956
Serum response factor: positive and negative regulation of an epithelial gene expression network in the destrin mutant cornea. PMID:24550211
The NRF2-KEAP1 pathway is an early responsive gene network in arsenic exposed lymphoblastoid cells. PMID:24516582
Fpk1/2 kinases regulate cellular sphingoid long-chain base abundance and alter cellular resistance to LCB elevation or depletion. PMID:24510621
HIV-1 Tat- and Vpr-responsive microRNAs of neuronal cells. PMID:24489003
Minimum information about a biofilm experiment (MIABiE): standards for reporting experiments and data on sessile microbial communities living at interfaces. PMID:24478124
A microarray for assessing transcription from pelagic marine microbial taxa. PMID:24477198
Toward more transparent and reproducible omics studies through a common metadata checklist and data publications. PMID:24456465
Systems toxicology: from basic research to risk assessment. PMID:24446777
Computational resources for high-dimensional immune analysis from the Human Immunology Project Consortium. PMID:24441472
Impact of acute metal stress in Saccharomyces cerevisiae. PMID:24416162
Increasing value and reducing waste in research design, conduct, and analysis. PMID:24411645
Effect of aerosol particles generated by ultrasonic humidifiers on the lung in mouse. PMID:24359587
Regulation of anergy-related ubiquitin E3 ligase, GRAIL, in murine models of colitis and patients with Crohn's disease. PMID:24356810
Alcohol-induced histone acetylation reveals a gene network involved in alcohol tolerance. PMID:24348266
Functional analyses of cotton (Gossypium hirsutum L.) immature fiber (im) mutant infer that fiber cell wall development is associated with stress responses. PMID:24341782
Differential response to abiraterone acetate and di-n-butyl phthalate in an androgen-sensitive human fetal testis xenograft bioassay. PMID:24284787
Ten simple rules for reproducible computational research. PMID:24204232
Gene expression studies for the analysis of domoic acid production in the marine diatom Pseudo-nitzschia multiseries. PMID:24180290
Toward an integrated software platform for systems pharmacology. PMID:24150748
Gene expression of bone morphogenic protein 8B in the primary site, peripheral blood and bone marrow of patients with gastric cancer. PMID:24137334
Function of dynamic models in systems biology: linking structure to behaviour. PMID:24103739
Biomarkers in autism spectrum disorder: the old and the new. PMID:24096533
Canonical Nlrp3 inflammasome links systemic low-grade inflammation to functional decline in aging. PMID:24093676
Influence of developmental stage and genotype on liver mRNA levels among wild, domesticated, and hybrid rainbow trout (Oncorhynchus mykiss). PMID:24088438
NR4A2 is regulated by gastrin and influences cellular responses of gastric adenocarcinoma cells. PMID:24086717
Guidelines for the design, analysis and interpretation of 'omics' data: focus on human endometrium. PMID:24082038
Custom microarray construction and analysis for determining potential biomarkers of subchronic androgen exposure in the Eastern Mosquitofish (Gambusia holbrooki). PMID:24074126
Metadata management and semantics in microarray repositories. PMID:24052712
Making open data work for plant scientists. PMID:24043847
Publishing 13C metabolic flux analysis studies: a review and future perspectives. PMID:24025367
Transcription of Tnfaip3 is regulated by NF-κB and p38 via C/EBPβ in activated macrophages. PMID:24023826
Standardization of sample collection, isolation and analysis methods in extracellular vesicle research. PMID:24009894
Deciphering the contribution of human meningothelial cells to the inflammatory and antimicrobial response at the meninges. PMID:24002066
Involvement of yeast HSP90 isoforms in response to stress and cell death induced by acetic acid. PMID:23967187
Assessment of fusion gene status in sarcomas using a custom made fusion gene microarray. PMID:23967081
Independent validation of a model using cell line chemosensitivity to predict response to therapy. PMID:23964133
Gene expression changes in the olfactory bulb of mice induced by exposure to diesel exhaust are dependent on animal rearing environment. PMID:23940539
Comparative antigen-induced gene expression profiles unveil novel aspects of susceptibility/resistance to adjuvant arthritis in rats. PMID:23911410
Analysis of the transcriptome in molecular epidemiology studies. PMID:23907930
MicroRNA regulate immune pathways in T-cells in multiple sclerosis (MS). PMID:23895517
MMP-9 and CXCL8/IL-8 are potential therapeutic targets in epidermolysis bullosa simplex. PMID:23894602
Gene set based integrated data analysis reveals phenotypic differences in a brain cancer model. PMID:23874576
Systematic dielectrophoretic analysis of the Ara-C-induced NB4 cell apoptosis combined with gene expression profiling. PMID:23847416
The duration of gastrin treatment affects global gene expression and molecular responses involved in ER stress and anti-apoptosis. PMID:23805861
Toward Reproducible Computational Research: An Empirical Analysis of Data and Code Policy Adoption by Journals. PMID:23805293
Systems biological approaches to measure and understand vaccine immunity in humans. PMID:23796714
Impact of bioinformatic procedures in the development and translation of high-throughput molecular classifiers in oncology. PMID:23780890
Transcript profiling by microarray and marker analysis of the short cotton (Gossypium hirsutum L.) fiber mutant Ligon lintless-1 (Li1). PMID:23767687
Exploration of sialic acid diversity and biology using sialoglycan microarrays. PMID:23765393
Effects of estradiol on transcriptional profiles in atherosclerotic iliac arteries in ovariectomized cynomolgus macaques. PMID:23760433
Differential network analysis for the identification of condition-specific pathway activity and regulation. PMID:23749957
Djeen (Database for Joomla!'s Extensible Engine): a research information management system for flexible multi-technology project administration. PMID:23742665
Early changes in gene expression induced by blue light irradiation of A2E-laden retinal pigment epithelial cells. PMID:23742627
Age-specific gene expression signatures for breast tumors and cross-species conserved potential cancer progression markers in young women. PMID:23704896
Attachment-regulated signaling networks in the fibroblast-populated 3D collagen matrix. PMID:23697962
A simple and reproducible breast cancer prognostic test. PMID:23682826
Deoxyribonucleic acid damage-associated biomarkers of ionising radiation: current status and future relevance for radiology and radiotherapy. PMID:23659923
Adaptation of the hydrocarbonoclastic bacterium Alcanivorax borkumensis SK2 to alkanes and toxic organic compounds: a physiological and transcriptomic approach. PMID:23645199
A metadata-aware application for remote scoring and exchange of tissue microarray images. PMID:23635078
Gene expression profiling and association studies implicate the neuregulin signaling pathway in Behçet's disease susceptibility. PMID:23625463
User-friendly solutions for microarray quality control and pre-processing on ArrayAnalysis.org. PMID:23620278
Genetic polymorphisms in LDLR, APOB, PCSK9 and other lipid related genes associated with familial hypercholesterolemia in Malaysia. PMID:23593297
Quantitative imaging biomarker ontology (QIBO) for knowledge representation of biomedical imaging biomarkers. PMID:23589184
Translational biomedical informatics in the cloud: present and future. PMID:23586054
IBC's 23rd Annual Antibody Engineering, 10th Annual Antibody Therapeutics international conferences and the 2012 Annual Meeting of The Antibody Society: December 3-6, 2012, San Diego, CA. PMID:23575266
CovR and VicRK regulate cell surface biogenesis genes required for biofilm formation in Streptococcus mutans. PMID:23554881
A novel knowledge representation framework for the statistical validation of quantitative imaging biomarkers. PMID:23546775
Changes in transcriptome of native nasal epithelium expressing F508del-CFTR and intersecting data from comparable studies. PMID:23537407
Muscle ring finger 1 and muscle ring finger 2 are necessary but functionally redundant during developmental cardiac growth and regulate E2F1-mediated gene expression in vivo. PMID:23512667
Estrogen signalling and the metabolic syndrome: targeting the hepatic estrogen receptor alpha action. PMID:23451233
Genetic and genomic analysis of Rhizoctonia solani interactions with Arabidopsis; evidence of resistance mediated through NADPH oxidases. PMID:23451091
Pathway-focused bioassays and transcriptome analysis contribute to a better activity monitoring of complex herbal remedies. PMID:23445205
crcTRP: a translational research platform for colorectal cancer. PMID:23431356
Transcriptional profiling of Zea mays roots reveals roles for jasmonic acid and terpenoids in resistance against Phytophthora cinnamomi. PMID:23430324
Globin gene expression in correlation with G protein-related genes during erythroid differentiation. PMID:23425329
The minimum information required for a glycomics experiment (MIRAGE) project: improving the standards for reporting mass-spectrometry-based glycoanalytic data. PMID:23378518
Development of a versatile TaqMan™ real-time quantitative PCR (RT-qPCR) compliant anchor sequence to quantify bacterial gene transcripts from RNA samples containing carryover genomic DNA. PMID:23369378
Data submission and quality in microarray-based microRNA profiling. PMID:23358751
Transcriptional programming during cell wall maturation in the expanding Arabidopsis stem. PMID:23350960
Expression analysis in multiple muscle groups and serum reveals complexity in the microRNA transcriptome of the mdx mouse with implications for therapy. PMID:23344181
Identification of biologically relevant enhancers in human erythroid cells. PMID:23341446
More data, please! PMID:23340443
Perspectives on validation of high-throughput assays supporting 21st century toxicity testing. PMID:23338806
XperimentR: painless annotation of a biological experiment for the laboratory scientist. PMID:23323856
ISA-TAB-Nano: a specification for sharing nanomaterial research data in spreadsheet-based format. PMID:23311978
Overview of DNA microarrays: types, applications, and their future. PMID:23288464
Evaluation of quality of DNA extracted from buccal swabs for microarray based genotyping. PMID:23277709
Evaluation of the effects of erythritol on gene expression in Brucella abortus. PMID:23272076
Reuse of public genome-wide gene expression data. PMID:23269463
Advancing the field of cancer immunotherapy: MIATA consensus guidelines become available to improve data reporting and interpretation for T-cell immune monitoring. PMID:23264891
Differences in metabolomic and transcriptomic profiles between responders and non-responders to an n-3 polyunsaturated fatty acids (PUFAs) supplementation. PMID:23250786
Analyzing illumina gene expression microarray data from different tissues: methodological aspects of data analysis in the metaxpress consortium. PMID:23236413
miRNA profiles of monocyte-lineage cells are consistent with complicated roles in HIV-1 restriction. PMID:23202444
Using genome-wide expression profiling to define gene networks relevant to the study of complex traits: from RNA integrity to network topology. PMID:23195313
ArrayExpress update--trends in database growth and links to data analysis tools. PMID:23193272
NCBI GEO: archive for functional genomics data sets--update. PMID:23193258
Comparability and reproducibility of biomedical data. PMID:23193203
Strategies for annotation and curation of translational databases: the eTUMOUR project. PMID:23180768
Subsequent gene expression pattern in dendritic cells following multiple trauma. PMID:23179318
InSilico DB genomic datasets hub: an efficient starting point for analyzing genome-wide studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor. PMID:23158523
Dynamics of membrane potential variation and gene expression induced by Spodoptera littoralis, Myzus persicae, and Pseudomonas syringae in Arabidopsis. PMID:23118859
Development, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L.) gene expression oligonucleotide microarray. PMID:23110046
Gene Fusion Markup Language: a prototype for exchanging gene fusion data. PMID:23072312
Prognostic value of blood mRNA expression signatures in castration-resistant prostate cancer: a prospective, two-stage study. PMID:23059046
Genome-wide screening of genes regulated by DNA methylation in colon cancer development. PMID:23049694
Data management strategies for multinational large-scale systems biology projects. PMID:23047157
Grape berry ripening delay induced by a pre-véraison NAA treatment is paralleled by a shift in the expression pattern of auxin- and ethylene-related genes. PMID:23046684
System wide analysis of the evolution of innate immunity in the nematode model species Caenorhabditis elegans and Pristionchus pacificus. PMID:23028509
Genome wide analysis of differentially expressed genes in HK-2 cells, a line of human kidney epithelial cells in response to oxalate. PMID:23028475
Stress associated gene expression in blood cells is related to outcome in radiotherapy treated head and neck cancer patients. PMID:23009663
Exposure to solute stress affects genome-wide expression but not the polycyclic aromatic hydrocarbon-degrading activity of Sphingomonas sp. strain LH128 in biofilms. PMID:23001650
Mining gene expression signature for the detection of pre-malignant melanocytes and early melanomas with risk for metastasis. PMID:22984562
Transcriptional signatures as a disease-specific and predictive inflammatory biomarker for type 1 diabetes. PMID:22972474
A Systems Biology Approach to Deciphering the Etiology of Steatosis Employing Patient-Derived Dermal Fibroblasts and iPS Cells. PMID:22969728
Effects of genotype and dietary fish oil replacement with vegetable oil on the intestinal transcriptome and proteome of Atlantic salmon (Salmo salar). PMID:22943471
Role of aldo-keto reductases and other doxorubicin pharmacokinetic genes in doxorubicin resistance, DNA binding, and subcellular localization. PMID:22938713
Identification of the Streptococcus mutans LytST two-component regulon reveals its contribution to oxidative stress tolerance. PMID:22937869
Host gene expression changes in cattle infected with Alcelaphine herpesvirus 1. PMID:22925730
Hepatic transcriptome analysis of inter-family variability in flesh n-3 long-chain polyunsaturated fatty acid content in Atlantic salmon. PMID:22905698
Regulation of gene expression with thyroid hormone in rats with myocardial infarction. PMID:22870193
Remarkable stability in patterns of blood-stage gene expression during episodes of non-lethal Plasmodium yoelii malaria. PMID:22866913
BioGPS and GXD: mouse gene expression data-the benefits and challenges of data integration. PMID:22847375
Reverse engineering biomolecular systems using -omic data: challenges, progress and opportunities. PMID:22833495
Integrative prescreening in analysis of multiple cancer genomic studies. PMID:22799431
Microarray-based identification of differentially expressed genes in families of turbot (Scophthalmus maximus) after infection with viral haemorrhagic septicaemia virus (VHSV). PMID:22790792
Transcriptomine, a web resource for nuclear receptor signaling transcriptomes. PMID:22786849
Genome-wide gene expression profiling of human narcolepsy. PMID:22783726
Transcriptional changes underlying elemental stoichiometry shifts in a marine heterotrophic bacterium. PMID:22783226
Topical delivery of siRNA-based spherical nucleic acid nanoparticle conjugates for gene regulation. PMID:22773805
The connexin43-dependent transcriptome during brain development: importance of genetic background. PMID:22771707
Microarray analyses of inflammation response of human dermal fibroblasts to different strains of Borrelia burgdorferi sensu stricto. PMID:22768217
BiofOmics: a Web platform for the systematic and standardized collection of high-throughput biofilm data. PMID:22768184
Transcriptome analysis during human trophectoderm specification suggests new roles of metabolic and epigenetic genes. PMID:22761758
Arabidopsis PYR/PYL/RCAR receptors play a major role in quantitative regulation of stomatal aperture and transcriptional response to abscisic acid. PMID:22739828
Perspectives on systems biology applications in diabetic kidney disease. PMID:22733404
MuteinDB: the mutein database linking substrates, products and enzymatic reactions directly with genetic variants of enzymes. PMID:22730453
The effect of iron limitation on the transcriptome and proteome of Pseudomonas fluorescens Pf-5. PMID:22723948
An unexpected role of semaphorin3a-neuropilin-1 signaling in lymphatic vessel maturation and valve formation. PMID:22723300
Sensitive detection of chromatin coassociations using enhanced chromosome conformation capture on chip. PMID:22722369
Divergent gene expression in the conserved dauer stage of the nematodes Pristionchus pacificus and Caenorhabditis elegans. PMID:22712530
Sertoli-cell-specific knockout of connexin 43 leads to multiple alterations in testicular gene expression in prepubertal mice. PMID:22699423
JAK-STAT and AKT pathway-coupled genes in erythroid progenitor cells through ontogeny. PMID:22676255
Multipurpose instantaneous microarray detection of acute encephalitis causing viruses and their expression profiles. PMID:22674173
Dynamic gene expression in the human cerebral cortex distinguishes children from adults. PMID:22666384
Microarray-based gene expression profiling reveals the mediators and pathways involved in the anti-arthritic activity of Celastrus-derived Celastrol. PMID:22664142
Behavioral barcoding in the cloud: embracing data-intensive digital phenotyping in neuropharmacology. PMID:22652049
Gene regulation by cytokinin in Arabidopsis. PMID:22639635
Plant cell biology: with grand challenges come great possibilities. PMID:22639571
Transcriptome-based identification of antioxidative gene expression after fish oil supplementation in normo- and dyslipidemic men. PMID:22621246
Identification of a gene expression signature common to distinct cancer pathways. PMID:22619501
Leukocyte CCR2 expression is associated with mini-mental state examination score in older adults. PMID:22607625
Identification of maize genes associated with host plant resistance or susceptibility to Aspergillus flavus infection and aflatoxin accumulation. PMID:22606305
MGEx-Udb: a mammalian uterus database for expression-based cataloguing of genes across conditions, including endometriosis and cervical cancer. PMID:22606288
Transcriptomic profiles of skeletal muscle tissue following an euglycemic-hyperinsulinemic clamp in insulin-resistant obese subjects. PMID:22566203
Cross-comparison of protein recognition of sialic acid diversity on two novel sialoglycan microarrays. PMID:22549775
Detecting phenotype-specific interactions between biological processes from microarray data and annotations. PMID:22547431
miR-125b promotes early germ layer specification through Lin28/let-7d and preferential differentiation of mesoderm in human embryonic stem cells. PMID:22545159
Research tools: A recipe for disaster. PMID:22538584
Chemocentric informatics approach to drug discovery: identification and experimental validation of selective estrogen receptor modulators as ligands of 5-hydroxytryptamine-6 receptors and as potential cognition enhancers. PMID:22537153
Data mining in networks of differentially expressed genes during sow pregnancy. PMID:22532788
Phenotypic diversification is associated with host-induced transposon derepression in the sudden oak death pathogen Phytophthora ramorum. PMID:22529930
Complement protein C1q directs macrophage polarization and limits inflammasome activity during the uptake of apoptotic cells. PMID:22523386
How can microarrays unlock asthma? PMID:22500180
Bcl11a is required for neuronal morphogenesis and sensory circuit formation in dorsal spinal cord development. PMID:22491945
Molecular characterisation of transport mechanisms at the developing mouse blood-CSF interface: a transcriptome approach. PMID:22457777
Pan-genomic analysis of bovine monocyte-derived macrophage gene expression in response to in vitro infection with Mycobacterium avium subspecies paratuberculosis. PMID:22455317
TTC7B emerges as a novel risk factor for ischemic stroke through the convergence of several genome-wide approaches. PMID:22453632
Differences in gene expression between first and third trimester human placenta: a microarray study. PMID:22442682
A prognostic gene expression profile that predicts circulating tumor cell presence in breast cancer patients. PMID:22384245
Global gene expression and systems biology analysis of bovine monocyte-derived macrophages in response to in vitro challenge with Mycobacterium bovis. PMID:22384131
Novel insights into the downstream pathways and targets controlled by transcription factors CREM in the testis. PMID:22384077
Ten years of pathway analysis: current approaches and outstanding challenges. PMID:22383865
Translating the brain transcriptome in neuroAIDS: from non-human primates to humans. PMID:22367717
Regulatory mechanisms in bone following mechanical loading. PMID:22346344
Overexpression of PFTK1 predicts resistance to chemotherapy in patients with oesophageal squamous cell carcinoma. PMID:22333595
When one and one gives more than two: challenges and opportunities of integrative omics. PMID:22303399
MicroRNA signatures in tumor tissue related to angiogenesis in non-small cell lung cancer. PMID:22295063
Data ontology and an information system realization for web-based management of image measurements. PMID:22275893
A semantic problem solving environment for integrative parasite research: identification of intervention targets for Trypanosoma cruzi. PMID:22272365
Toxicogenomic biomarkers for liver toxicity. PMID:22271975
Transcriptome and proteome research in veterinary science: what is possible and what questions can be asked? PMID:22262952
Host gene targets for novel influenza therapies elucidated by high-throughput RNA interference screens. PMID:22247330
Guidelines for information about therapy experiments: a proposal on best practice for recording experimental data on cancer therapy. PMID:22226027
Alterations in tumor necrosis factor signaling pathways are associated with cytotoxicity and resistance to taxanes: a study in isogenic resistant tumor cells. PMID:22225778
An integrated framework to model cellular phenotype as a component of biochemical networks. PMID:22190923
Genome-wide transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis reveals suppression of host immune genes. PMID:22182502
Minimum Information about a Genotyping Experiment (MIGEN). PMID:22180825
Solving the Problem: Genome Annotation Standards before the Data Deluge. PMID:22180819
Stability of double-stranded oligonucleotide DNA with a bulged loop: a microarray study. PMID:22166491
High-throughput processing and normalization of one-color microarrays for transcriptional meta-analyses. PMID:22166002
Uropathogenic E. coli induce different immune response in testicular and peritoneal macrophages: implications for testicular immune privilege. PMID:22164293
Database resources of the National Center for Biotechnology Information. PMID:22140104
The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments. PMID:22110025
eXframe: reusable framework for storage, analysis and visualization of genomics experiments. PMID:22103807
Transcriptome and membrane fatty acid analyses reveal different strategies for responding to permeating and non-permeating solutes in the bacterium Sphingomonas wittichii. PMID:22082453
modMine: flexible access to modENCODE data. PMID:22080565
Expression profiling of non-aflatoxigenic Aspergillus parasiticus mutants obtained by 5-azacytosine treatment or serial mycelial transfer. PMID:22069749
Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles). PMID:22053864
Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles). PMID:22052993
Software for systems biology: from tools to integrated platforms. PMID:22048662
Investigation of variation in gene expression profiling of human blood by extended principle component analysis. PMID:22046403
The effect of the CCR5-delta32 deletion on global gene expression considering immune response and inflammation. PMID:22029606
Benfotiamine increases glucose oxidation and downregulates NADPH oxidase 4 expression in cultured human myotubes exposed to both normal and high glucose concentrations. PMID:21984258
Curcumin is a potent modulator of microglial gene expression and migration. PMID:21958395
[DNA microarrays]. PMID:21956826
BμG@Sbase--a microbial gene expression and comparative genomic database. PMID:21948792
How yeast re-programmes its transcriptional profile in response to different nutrient impulses. PMID:21943358
Transcriptome profiling of immune responses to cardiomyopathy syndrome (CMS) in Atlantic salmon. PMID:21943289
Decreased expression of B cell related genes in leukocytes of women with Parkinson's disease. PMID:21943286
Patterns of histone H3 lysine 27 monomethylation and erythroid cell type-specific gene expression. PMID:21937433
The gene expression profile of preclinical autoimmune arthritis and its modulation by a tolerogenic disease-protective antigenic challenge. PMID:21914168
Increased endoplasmic reticulum stress in decidual tissue from pregnancies complicated by fetal growth restriction with and without pre-eclampsia. PMID:21907405
A combined functional and structural genomics approach identified an EST-SSR marker with complete linkage to the Ligon lintless-2 genetic locus in cotton (Gossypium hirsutum L.). PMID:21902843
2009 pandemic H1N1 influenza virus causes disease and upregulation of genes related to inflammatory and immune responses, cell death, and lipid metabolism in pigs. PMID:21900171
Minimum information about a bioactive entity (MIABE). PMID:21878981
Approaches for the study of cancer: towards the integration of genomics, proteomics and metabolomics. PMID:21865133
Rhythmic diel pattern of gene expression in juvenile maize leaf. PMID:21858187
The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details. PMID:21856757
A pilot study to evaluate the application of a generic protein standard panel for quality control of biomarker detection technologies. PMID:21834984
The clinical and functional relevance of microparticles induced by activated protein C treatment in sepsis. PMID:21834973
Identification of candidate genes linking systemic inflammation to atherosclerosis; results of a human in vivo LPS infusion study. PMID:21827714
Comparative gene expression profiling of placentas from patients with severe pre-eclampsia and unexplained fetal growth restriction. PMID:21810232
Combined analysis of transcriptome and metabolite data reveals extensive differences between black and brown nearly-isogenic soybean (Glycine max) seed coats enabling the identification of pigment isogenes. PMID:21801362
The two-component signal transduction system CopRS of Corynebacterium glutamicum is required for adaptation to copper-excess stress. PMID:21799779
Research and technology in neurocritical care. PMID:21796494
COLOMBOS: access port for cross-platform bacterial expression compendia. PMID:21779320
Retrieval, alignment, and clustering of computational models based on semantic annotations. PMID:21772260
Who shares? Who doesn't? Factors associated with openly archiving raw research data. PMID:21765886
Association of sirtuin 1 (SIRT1) gene SNPs and transcript expression levels with severe obesity. PMID:21760635
Minimum Information about a Cardiac Electrophysiology Experiment (MICEE): standardised reporting for model reproducibility, interoperability, and data sharing. PMID:21745496
Whole blood gene expression analyses in patients with single versus recurrent venous thromboembolism. PMID:21737128
Informatics and standards for nanomedicine technology. PMID:21721140
Protective pathways against colitis mediated by appendicitis and appendectomy. PMID:21707591
Gene expression analysis characterizes antemortem stress and has implications for establishing cause of death. PMID:21693618
Integrative computational biology for cancer research. PMID:21691773
Gene expression profiling of the brain: pondering facts and fiction. PMID:21689753
Repeated developmental exposure of mice to chlorpyrifos oxon is associated with paraoxonase 1 (PON1)-modulated effects on cerebellar gene expression. PMID:21673326
Functional and transcriptomic recovery of infarcted mouse myocardium treated with bone marrow mononuclear cells. PMID:21671060
Tracheal occlusion conditioning in conscious rats modulates gene expression profile of medial thalamus. PMID:21660287
Estrogens and selective estrogen receptor modulators regulate gene and protein expression in the mesenteric arteries. PMID:21658471
Genetic networks in the mouse retina: growth associated protein 43 and phosphatase tensin homolog network. PMID:21655357
Gene expression signatures differ with extent of atherosclerosis in monkey iliac artery. PMID:21646924
Channeling the data deluge. PMID:21623351
Gene expression differences between stroke-associated and asymptomatic carotid plaques. PMID:21607540
Using DNA microarrays to assay part function. PMID:21601083
Genotype-specific responses in Atlantic salmon (Salmo salar) subject to dietary fish oil replacement by vegetable oil: a liver transcriptomic analysis. PMID:21599965
The NS1 protein of influenza A virus suppresses interferon-regulated activation of antigen-presentation and immune-proteasome pathways. PMID:21593271
Recommendations from the iSBTc-SITC/FDA/NCI Workshop on Immunotherapy Biomarkers. PMID:21558394
Managing and querying gene expression data using Curray. PMID:21554758
PHENOPSIS DB: an information system for Arabidopsis thaliana phenotypic data in an environmental context. PMID:21554668
Significant alteration of gene expression in wood decay fungi Postia placenta and Phanerochaete chrysosporium by plant species. PMID:21551287
Canonical NF-kappaB activation is essential for Epstein-Barr virus latent membrane protein 1 TES2/CTAR2 gene regulation. PMID:21543491
Comparative gene expression profiles induced by PPARγ and PPARα/γ agonists in human hepatocytes. PMID:21533120
Ecological genetics and genomics of plant defenses: Evidence and approaches. PMID:21532968
Bacterial subfamily of LuxR regulators that respond to plant compounds. PMID:21531826
On the formalization and reuse of scientific research. PMID:21490004
An adaptable method using human mixed tissue ratiometric controls for benchmarking performance on gene expression microarrays in clinical laboratories. PMID:21486464
Statistical Test of Expression Pattern (STEPath): a new strategy to integrate gene expression data with genomic information in individual and meta-analysis studies. PMID:21481242
A 44K microarray dataset of the changing transcriptome in developing Atlantic salmon (Salmo salar L.). PMID:21447175
Regulation of chondrocyte gene expression by osteogenic protein-1. PMID:21447156
Systematic polymorphism discovery after genome-wide identification of potential susceptibility loci in a hereditary rodent model of human hypertension. PMID:21428728
Conceptual aspects of large meta-analyses with publicly available microarray data: a case study in oncology. PMID:21423405
Comparison of automated and human assignment of MeSH terms on publicly-available molecular datasets. PMID:21420508
Multiplex cDNA quantification method that facilitates the standardization of gene expression data. PMID:21415008
The impact of quantitative optimization of hybridization conditions on gene expression analysis. PMID:21401920
Gene expression in human sepsis: what have we learned? PMID:21392407
Type VIII collagen modulates TGF-β1-induced proliferation of mesangial cells. PMID:21372207
Data standards for Omics data: the basis of data sharing and reuse. PMID:21370078
Complement protein C1q-mediated neuroprotection is correlated with regulation of neuronal gene and microRNA expression. PMID:21368058
Improving bioscience research reporting: The ARRIVE guidelines for reporting animal research. PMID:21350617
Hot transcriptomics. PMID:21350598
Towards interoperable reporting standards for omics data: hopes and hurdles. PMID:21347181
Semantically enabled and statistically supported biological hypothesis testing with tissue microarray databases. PMID:21342584
Public sharing of research datasets: a pilot study of associations. PMID:21339841
A PXR-mediated negative feedback loop attenuates the expression of CYP3A in response to the PXR agonist pregnenalone-16α-carbonitrile. PMID:21311750
Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop. PMID:21304730
Obesity resistant mechanisms in the Lean polygenic mouse model as indicated by liver transcriptome and expression of selected genes in skeletal muscle. PMID:21291556
Methoxychlor affects multiple hormone signaling pathways in the largemouth bass (Micropterus salmoides) liver. PMID:21276474
Identification of radiation-induced expression changes in nonimmortalized human T cells. PMID:21268710
Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains. PMID:21266995
The 3 prime paradigm of the miR-200 family and other microRNAs. PMID:21242719
Control of heme homeostasis in Corynebacterium glutamicum by the two-component system HrrSA. PMID:21217007
Serum biomarkers for improved diagnostic of pancreatic cancer: a current overview. PMID:21193998
Genome-wide transcription profiling of human sepsis: a systematic review. PMID:21190579
General guidelines for authors for submission of manuscripts that contain molecular biological content. PMID:21184257
Epstein-Barr virus nuclear antigen 3C regulated genes in lymphoblastoid cell lines. PMID:21173222
Early response mechanisms of perennial ryegrass (Lolium perenne) to phosphorus deficiency. PMID:21148585
Habituation to thaxtomin A in hybrid poplar cell suspensions provides enhanced and durable resistance to inhibitors of cellulose synthesis. PMID:21143977
Advancing standards for bioinformatics activities: persistence, reproducibility, disambiguation and Minimum Information About a Bioinformatics investigation (MIABi). PMID:21143811
NCBI GEO: archive for functional genomics data sets--10 years on. PMID:21097893
Database resources of the National Center for Biotechnology Information. PMID:21097890
Members of the LATERAL ORGAN BOUNDARIES DOMAIN transcription factor family are involved in the regulation of secondary growth in Populus. PMID:21097711
Alternative splicing in bone following mechanical loading. PMID:21095247
Minimal information about T cell assays: the process of reaching the community of T cell immunologists in cancer and beyond. PMID:21080166
Early transcriptional events during osteogenic differentiation of human bone marrow stromal cells induced by Lim mineralization protein 3. PMID:21061915
Assessing the quality of annotations in asthma gene expression experiments. PMID:21044366
Signaling pathways mediating the induction of apple fruitlet abscission. PMID:21037112
BeadDataPackR: A Tool to Facilitate the Sharing of Raw Data from Illumina BeadArray Studies. PMID:20981138
Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics. PMID:20965973
Integrated database for identifying candidate genes for Aspergillus flavus resistance in maize. PMID:20946609
EuroDia: a beta-cell gene expression resource. PMID:20940178
Genomic profiling of tumor necrosis factor alpha (TNF-alpha) receptor and interleukin-1 receptor knockout mice reveals a link between TNF-alpha signaling and increased severity of 1918 pandemic influenza virus infection. PMID:20926563
Toward a complete in silico, multi-layered embryonic stem cell regulatory network. PMID:20890967
Distinct transcriptome expression of the temporal cortex of the primate Microcebus murinus during brain aging versus Alzheimer's disease-like pathology. PMID:20862281
Queen conch (Strombus gigas) testis regresses during the reproductive season at nearshore sites in the Florida Keys. PMID:20856805
In silico models of cancer. PMID:20836040
Using expression genetics to study the neurobiology of ethanol and alcoholism. PMID:20813241
A call for BMC Research Notes contributions promoting best practice in data standardization, sharing and publication. PMID:20813027
Analyzing schizophrenia by DNA microarrays. PMID:20801428
A standard variation file format for human genome sequences. PMID:20796305
Structured digital tables on the Semantic Web: toward a structured digital literature. PMID:20739925
Dynamic changes in gene expression during human early embryo development: from fundamental aspects to clinical applications. PMID:20716614
Gene expression profiling of mouse embryos with microarrays. PMID:20699157
A novel tissue-specific meta-analysis approach for gene expression predictions, initiated with a mammalian gene expression testis database. PMID:20699007
Microarray meta-analysis database (M(2)DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database. PMID:20698961
Research resource: genome-wide profiling of methylated promoters in endometriosis reveals a subtelomeric location of hypermethylation. PMID:20685852
A biopsy sample reduction approach to identify significant alterations of the testicular transcriptome in the presence of Y-chromosomal microdeletions that are independent of germ cell composition. PMID:20668881
Gene expression patterns in bone following mechanical loading. PMID:20658561
Transcritpional effects of S100B on neuroblastoma cells: perturbation of cholesterol homeostasis and interference on the cell cycle. PMID:20635576
Mouse Resource Browser--a database of mouse databases. PMID:20627861
Expression of the selenoprotein S (SELS) gene in subcutaneous adipose tissue and SELS genotype are associated with metabolic risk factors. PMID:20619427
Improving bioscience research reporting: the ARRIVE guidelines for reporting animal research. PMID:20613859
Starvation alters the liver transcriptome of the innate immune response in Atlantic salmon (Salmo salar). PMID:20602791
Reciprocal communication between endometrial stromal cells and macrophages. PMID:20601541
Evaluation of one- and two-color gene expression arrays for microbial comparative genome hybridization analyses in routine applications. PMID:20592156
Towards interoperable and reproducible QSAR analyses: Exchange of datasets. PMID:20591161
Expectations, validity, and reality in gene expression profiling. PMID:20579843
Fathead minnow steroidogenesis: in silico analyses reveals tradeoffs between nominal target efficacy and robustness to cross-talk. PMID:20579396
Toxicity testing in the 21st century: a vision and a strategy. PMID:20574894
The autocrine motility factor receptor is overexpressed on the surface of B cells in Binet C chronic lymphocytic leukemia. PMID:20574759
Transcriptional profile analysis of RPGRORF15 frameshift mutation identifies novel genes associated with retinal degeneration. PMID:20574030
The effects of aging vs. α7 nAChR subunit deficiency on the mouse brain transcriptome: aging beats the deficiency. PMID:20526689
High gene expression of inflammatory markers and IL-17A correlates with severity of injection site reactions of Atlantic salmon vaccinated with oil-adjuvanted vaccines. PMID:20507624
Generating hepatic cell lineages from pluripotent stem cells for drug toxicity screening. PMID:20483202
Consistent annotation of gene expression arrays. PMID:20459806
Substance P in polymicrobial sepsis: molecular fingerprint of lung injury in preprotachykinin-A-/- mice. PMID:20454520
Dealing with the unknown: metabolomics and metabolite atlases. PMID:20452782
Transcriptome analysis of the Brucella abortus BvrR/BvrS two-component regulatory system. PMID:20422049
Reconstruction of gene regulatory modules in cancer cell cycle by multi-source data integration. PMID:20422009
Downstream targets of methyl CpG binding protein 2 and their abnormal expression in the frontal cortex of the human Rett syndrome brain. PMID:20420693
BioTorrents: a file sharing service for scientific data. PMID:20418944
Comparative transcriptome and secretome analysis of wood decay fungi Postia placenta and Phanerochaete chrysosporium. PMID:20400566
Robin: an intuitive wizard application for R-based expression microarray quality assessment and analysis. PMID:20388663
Toxicogenomic profiling of chemically exposed humans in risk assessment. PMID:20382258
Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput "omics" Data. PMID:20369061
Gene profiling in experimental models of eye growth: clues to myopia pathogenesis. PMID:20363242
Standards affecting the consistency of gene expression arrays in clinical applications. PMID:20332273
Depletion of the non-coding regulatory 6S RNA in E. coli causes a surprising reduction in the expression of the translation machinery. PMID:20222947
Zsyntax: a formal language for molecular biology with projected applications in text mining and biological prediction. PMID:20209084
Semantic Web for data harmonization in Chinese medicine. PMID:20205772
Probing the reproducibility of leaf growth and molecular phenotypes: a comparison of three Arabidopsis accessions cultivated in ten laboratories. PMID:20200072
A primer on metagenomics. PMID:20195499
Biomedical informatics and translational medicine. PMID:20187952
Correcting for intra-experiment variation in Illumina BeadChip data is necessary to generate robust gene-expression profiles. PMID:20181233
'Desperate house genes': the dramatic example of hypoxia. PMID:20179706
Identifying genetic loci and spleen gene coexpression networks underlying immunophenotypes in BXD recombinant inbred mice. PMID:20179155
Automated microscopy for high-content RNAi screening. PMID:20176920
The transcriptional programme of human heart valves reveals the natural history of infective endocarditis. PMID:20126625
Seasonal changes in hepatic gene expression reveal modulation of multiple processes in rainbow smelt (Osmerus mordax). PMID:20107851
Molecular remodeling of ion channels, exchangers and pumps in atrial and ventricular myocytes in ischemic cardiomyopathy. PMID:20090424
miR-17, miR-19b, miR-20a, and miR-106a are down-regulated in human aging. PMID:20089119
Luteolin triggers global changes in the microglial transcriptome leading to a unique anti-inflammatory and neuroprotective phenotype. PMID:20074346
Disease gene characterization through large-scale co-expression analysis. PMID:20046828
Sources of bias in specimens for research about molecular markers for cancer. PMID:20038718
Cardiac resynchronization therapy corrects dyssynchrony-induced regional gene expression changes on a genomic level. PMID:20031609
The filamentous fungal gene expression database (FFGED). PMID:20025988
Genomic markers for decision making: what is preventing us from using markers? PMID:20010899
Quantitative comparison of microarray experiments with published leukemia related gene expression signatures. PMID:20003504
The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources. PMID:19965766
Mining for coexpression across hundreds of datasets using novel rank aggregation and visualization methods. PMID:19961599
Evaluating annotations of an Agilent expression chip suggests that many features cannot be interpreted. PMID:19948035
iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis. PMID:19941647
TrichOME: a comparative omics database for plant trichomes. PMID:19939948
Data reporting standards: making the things we use better. PMID:19939294
Construction of a robust microarray from a non-model species (largemouth bass) using pyrosequencing technology. PMID:19936325
The European Bioinformatics Institute's data resources. PMID:19934258
Database resources of the National Center for Biotechnology Information. PMID:19910364
Gene expression atlas at the European bioinformatics institute. PMID:19906730
Anti-schistosomal intervention targets identified by lifecycle transcriptomic analyses. PMID:19885392
Quality control in microarray assessment of gene expression in human airway epithelium. PMID:19852842
Assessment of tumour hypoxia for prediction of response to therapy and cancer prognosis. PMID:19840191
Subgingival bacterial colonization profiles correlate with gingival tissue gene expression. PMID:19835625
Trends in modeling Biomedical Complex Systems. PMID:19828068
More than a decade of developmental gene expression atlases: where are we now? PMID:19822576
BASE--2nd generation software for microarray data management and analysis. PMID:19822003
Site-specific impacts on gene expression and behavior in fathead minnows (Pimephales promelas) exposed in situ to streams adjacent to sewage treatment plants. PMID:19811676
Francisella tularensis novicida proteomic and transcriptomic data integration and annotation based on semantic web technologies. PMID:19796400
Class prediction models of thrombocytosis using genetic biomarkers. PMID:19773543
Gene expression profiling in the aging ovary. PMID:19763498
Global analysis of extracytoplasmic stress signaling in Escherichia coli. PMID:19763168
Towards large-scale sample annotation in gene expression repositories. PMID:19761579
EDGE(3): a web-based solution for management and analysis of Agilent two color microarray experiments. PMID:19732451
The NS1 protein of the 1918 pandemic influenza virus blocks host interferon and lipid metabolism pathways. PMID:19706713
Gene expression profiles of HIV-1-infected glia and brain: toward better understanding of the role of astrocytes in HIV-1-associated neurocognitive disorders. PMID:19697136
A single-amino-acid substitution in a polymerase protein of an H5N1 influenza virus is associated with systemic infection and impaired T-cell activation in mice. PMID:19692471
Biomarker discovery in animal health and disease: the application of post-genomic technologies. PMID:19662203
Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks. PMID:19654116
Information management for high content live cell imaging. PMID:19622144
WebArrayDB: cross-platform microarray data analysis and public data repository. PMID:19602526
Genome wide analysis of human genes transcriptionally and post-transcriptionally regulated by the HTLV-I protein p30. PMID:19602286
Genome-wide transcription analysis of histidine-related cataract in Atlantic salmon (Salmo salar L). PMID:19597568
Differential gene expression during smoltification of Atlantic salmon (Salmo salar L.): a first large-scale microarray study. PMID:19585168
Comparative expression profiling of Leishmania: modulation in gene expression between species and in different host genetic backgrounds. PMID:19582145
Virus-host interactions: from systems biology to translational research. PMID:19576841
Characterization of conserved and nonconserved imprinted genes in swine. PMID:19571260
Translational bioinformatics applications in genome medicine. PMID:19566916
Novel regulators of Fgf23 expression and mineralization in Hyp bone. PMID:19556340
HPV16 E7 oncogene expression in normal human epithelial cells causes molecular changes indicative of an epithelial to mesenchymal transition. PMID:19552933
Generating 'omic knowledge': the role of informatics in high content screening. PMID:19531005
Meta Analysis of Gene Expression Data within and Across Species. PMID:19516959
eIF2alpha kinases GCN2 and PERK modulate transcription and translation of distinct sets of mRNAs in mouse liver. PMID:19509078
Importing ArrayExpress datasets into R/Bioconductor. PMID:19505942
Caenorhabditis elegans genomic response to soil bacteria predicts environment-specific genetic effects on life history traits. PMID:19503598
Coastal strains of marine Synechococcus species exhibit increased tolerance to copper shock and a distinctive transcriptional response relative to those of open-ocean strains. PMID:19502430
VisHiC--hierarchical functional enrichment analysis of microarray data. PMID:19483095
Transcriptome analysis of a bacterially induced basal and hypersensitive response of Medicago truncatula. PMID:19466566
A novel information retrieval model for high-throughput molecular medicine modalities. PMID:19458790
Challenges in the analysis of mass-throughput data: a technical commentary from the statistical machine learning perspective. PMID:19458765
Triple loss of function of protein phosphatases type 2C leads to partial constitutive response to endogenous abscisic acid. PMID:19458118
Apoptosis gene profiling reveals spatio-temporal regulated expression of the p53/Mdm2 pathway during lens development. PMID:19450442
MIMAS 3.0 is a Multiomics Information Management and Annotation System. PMID:19450266
Derivation of a novel undifferentiated human foetal phenotype in serum-free cultures with BMP-2. PMID:19438813
SDRF2GRAPH: a visualization tool of a spreadsheet-based description of experimental processes. PMID:19422683
Early upregulation of acute respiratory distress syndrome-associated cytokines promotes lethal disease in an aged-mouse model of severe acute respiratory syndrome coronavirus infection. PMID:19420084
Convergence of biomarkers, bioinformatics and nanotechnology for individualized cancer treatment. PMID:19409634
Web-queryable large-scale data sets for hypothesis generation in plant biology. PMID:19401381
New microbicidal functions of tracheal glands: defective anti-infectious response to Pseudomonas aeruginosa in cystic fibrosis. PMID:19399182
Transcriptome and secretome analyses of Phanerochaete chrysosporium reveal complex patterns of gene expression. PMID:19376920
Citrate utilization by Corynebacterium glutamicum is controlled by the CitAB two-component system through positive regulation of the citrate transport genes citH and tctCBA. PMID:19376865
Molecular and phenotypic characterisation of paediatric glioma cell lines as models for preclinical drug development. PMID:19365568
Gene expression profiling and the use of genome-scale in silico models of Escherichia coli for analysis: providing context for content. PMID:19363119
Characterisation of the fibroblast growth factor dependent transcriptome in early development. PMID:19333377
A national clinical decision support infrastructure to enable the widespread and consistent practice of genomic and personalized medicine. PMID:19309514
Bias, randomization, and ovarian proteomic data: a reply to "producers and consumers". PMID:19305627
STrengthening the REporting of Genetic Association studies (STREGA)--an extension of the STROBE statement. PMID:19297801
Towards agreement on best practice for publishing raw clinical trial data. PMID:19296844
Discovery of novel hypermethylated genes in prostate cancer using genomic CpG island microarrays. PMID:19283074
ebTrack: an environmental bioinformatics system built upon ArrayTrack. PMID:19278561
ALK7 expression is specific for adipose tissue, reduced in obesity and correlates to factors implicated in metabolic disease. PMID:19275893
Cerebrospinal fluid biomarkers in Guillain-Barré syndrome--where do we stand? PMID:19267167
Adaptable data management for systems biology investigations. PMID:19265554
A functional and regulatory network associated with PIP expression in human breast cancer. PMID:19262752
Analysis of variance components reveals the contribution of sample processing to transcript variation. PMID:19233957
Transcription profiling of rheumatic diseases. PMID:19232067
How to improve postgenomic knowledge discovery using imputation. PMID:19223972
RDML: structured language and reporting guidelines for real-time quantitative PCR data. PMID:19223324
Transcriptional profiling in pathogenic and non-pathogenic SIV infections reveals significant distinctions in kinetics and tissue compartmentalization. PMID:19214219
TRUNCATULIX--a data warehouse for the legume community. PMID:19210766
Gene expression patterns in hypoxic and post-hypoxic adult rat retina with special reference to the NMDA receptor and its interactome. PMID:19204789
EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data. PMID:19200358
STrengthening the REporting of Genetic Association Studies (STREGA): an extension of the STROBE statement. PMID:19192942
Strengthening the reporting of genetic association studies (STREGA): an extension of the STROBE statement. PMID:19189221
Strengthening the reporting of genetic association studies (STREGA): an extension of the STROBE Statement. PMID:19184668
Repeatability of published microarray gene expression analyses. PMID:19174838
An open access database of genome-wide association results. PMID:19161620
A universal assay for detection of oncogenic fusion transcripts by oligo microarray analysis. PMID:19152679
Genomic analysis reveals a potential role for cell cycle perturbation in HCV-mediated apoptosis of cultured hepatocytes. PMID:19148281
Using metabolomics to estimate unintended effects in transgenic crop plants: problems, promises, and opportunities. PMID:19137102
Gene expression profiles during early differentiation of mouse embryonic stem cells. PMID:19134196
Oligonucleotide microarray technology and its application to Mycobacterium avium subsp. paratuberculosis research: a review. PMID:19130317
A description of the origins, design and performance of the TRAITS-SGP Atlantic salmon Salmo salar L. cDNA microarray. PMID:19125201
Using pathway signatures as means of identifying similarities among microarray experiments. PMID:19125200
An integrated genomics approach to define niche establishment by Rhodococcus fascians. PMID:19118125
Nocturnal hemodialysis improves erythropoietin responsiveness and growth of hematopoietic stem cells. PMID:19092123
Expansion and diversification of the Populus R2R3-MYB family of transcription factors. PMID:19091872
A novel approach for reliable microarray analysis of microdissected tumor cells from formalin-fixed and paraffin-embedded colorectal cancer resection specimens. PMID:19066834
A cross-species transcriptomics approach to identify genes involved in leaf development. PMID:19061504
MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB. PMID:19038988
Much room for improvement in deposition rates of expression microarray datasets. PMID:19034265
Insulin-like growth factor-1 coordinately induces the expression of fatty acid and cholesterol biosynthetic genes in murine C2C12 myoblasts. PMID:19014463
iPad: Semantic annotation and markup of radiological images. PMID:18999144
Transcriptomes in healthy and diseased gingival tissues. PMID:18980520
Alteration of transcriptomic networks in adoptive-transfer experimental autoimmune encephalomyelitis. PMID:18958238
Nutritional genomics, polyphenols, diets, and their impact on dietetics. PMID:18954579
Implementation of GenePattern within the Stanford Microarray Database. PMID:18953035
Use of genomic DNA as an indirect reference for identifying gender-associated transcripts in morphologically identical, but chromosomally distinct, Schistosoma mansoni cercariae. PMID:18941520
Database resources of the National Center for Biotechnology Information. PMID:18940862
NCBI GEO: archive for high-throughput functional genomic data. PMID:18940857
Disturbances in metabolic, transport and structural genes in experimental colonic inflammation in the rat: a longitudinal genomic analysis. PMID:18928539
GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus. PMID:18842599
Identification of novel neuroendocrine-specific tumour genes. PMID:18827820
Virogenomics: the virus-host interaction revisited. PMID:18822388
Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues. PMID:18803840
MiMiR--an integrated platform for microarray data sharing, mining and analysis. PMID:18801157
Genome-wide transcriptional response of primary alveolar macrophages following infection with porcine reproductive and respiratory syndrome virus. PMID:18796724
Big data: The future of biocuration. PMID:18769432
Key issues in conducting a meta-analysis of gene expression microarray datasets. PMID:18767902
Translational bioinformatics: coming of age. PMID:18755990
MIFlowCyt: the minimum information about a Flow Cytometry Experiment. PMID:18752282
Analysis of gene expression patterns by microarray hybridization in blood mononuclear cells of SLA-DRB1 defined Canadian Yorkshire pigs. PMID:18710484
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. PMID:18688244
Performing statistical analyses on quantitative data in Taverna workflows: an example using R and maxdBrowse to identify differentially-expressed genes from microarray data. PMID:18687127
Similar transcriptomic alterations in Cx43 knockdown and knockout astrocytes. PMID:18649190
Minimal information: an urgent need to assess the functional reliability of recombinant proteins used in biological experiments. PMID:18647423
Regulation of human aldoketoreductase 1C3 (AKR1C3) gene expression in the adipose tissue. PMID:18641923
Transcript profiling in Vitis riparia during chilling requirement fulfillment reveals coordination of gene expression patterns with optimized bud break. PMID:18633655
Genomic analysis reveals age-dependent innate immune responses to severe acute respiratory syndrome coronavirus. PMID:18632870
BmuG@Sbase--a microarray database and analysis tool. PMID:18629280
Standards and ontologies for functional genomics 2. PMID:18629185
Standardization Initiatives in the (eco)toxicogenomics domain: a review. PMID:18629184
MAGIC database and interfaces: an integrated package for gene discovery and expression. PMID:18629159
Navigating public microarray databases. PMID:18629145
On the MIAME Standards and Central Repositories of Microarray Data. PMID:18629115
The MGED ontology: a framework for describing functional genomics experiments. PMID:18629093
Standards and ontologies for functional genomics: towards unified ontologies for biology and biomedicine. PMID:18629091
From genotype to phenotype: linking bioinformatics and medical informatics ontologies. PMID:18629054
From gene regulation to gene function: regulatory networks in bacillus subtilis. PMID:18628883
Proposal for a standard representation of two-dimensional gel electrophoresis data. PMID:18628860
Website review: how to get the best from fission yeast genome data. PMID:18628858
Meeting review: plant bioinformatics at the NSF and NPGI (PAMGX satellite) meetings. PMID:18628836
Short time-series microarray analysis: methods and challenges. PMID:18605994
The EXACT description of biomedical protocols. PMID:18586727
Identification of JAK/STAT pathway regulators--insights from RNAi screens. PMID:18586112
Electroacupuncture induced spinal plasticity is linked to multiple gene expressions in dorsal root deafferented rats. PMID:18581269
Guidelines for reporting health research: the EQUATOR network's survey of guideline authors. PMID:18578566
Functional genomics reveals increases in cholesterol biosynthetic genes and highly unsaturated fatty acid biosynthesis after dietary substitution of fish oil with vegetable oils in Atlantic salmon (Salmo salar). PMID:18577222
In praise of arrays. PMID:18568367
The incredible shrinking world of DNA microarrays. PMID:18563246
Venezuelan equine encephalitis virus infection causes modulation of inflammatory and immune response genes in mouse brain. PMID:18558011
Helping editors, peer reviewers and authors improve the clarity, completeness and transparency of reporting health research. PMID:18558004
Cadmium toxicity in glutathione mutants of Escherichia coli. PMID:18539742
A plant resource and experiment management system based on the Golm Plant Database as a basic tool for omics research. PMID:18495032
A comprehensive analysis of the combined effects of high light and high temperature stresses on gene expression in sunflower. PMID:18477560
The gene expression profiles of medulloblastoma cell lines resistant to preactivated cyclophosphamide. PMID:18473730
Domain-specific data sharing in neuroscience: what do we have to learn from each other? PMID:18473189
Surveying expression level polymorphism and single-feature polymorphism in near-isogenic wheat lines differing for the Yr5 stripe rust resistance locus. PMID:18470504
RETINOBASE: a web database, data mining and analysis platform for gene expression data on retina. PMID:18457592
Making a new technology work: the standardization and regulation of microarrays. PMID:18449388
Data capture in bioinformatics: requirements and experiences with Pedro. PMID:18402673
A software framework for microarray and gene expression object model (MAGE-OM) array design annotation. PMID:18366695
Annotating genes of known and unknown function by large-scale coexpression analysis. PMID:18354039
Pioglitazone administration alters ovarian gene expression in aging obese lethal yellow mice. PMID:18348723
Transcriptomic analyses reveal novel genes with sexually dimorphic expression in the zebrafish gonad and brain. PMID:18335061
Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). PMID:18327244
Gene expression profiling in human skeletal muscle during recovery from eccentric exercise. PMID:18321953
Beyond good and evil in the oral cavity: insights into host-microbe relationships derived from transcriptional profiling of gingival cells. PMID:18296603
Validation of virulence and epidemiology DNA microarray for identification and characterization of Staphylococcus aureus isolates. PMID:18287310
Molecular networks discriminating mouse bladder responses to intravesical bacillus Calmette-Guerin (BCG), LPS, and TNF-alpha. PMID:18267009
Bioinformatics and cancer research: building bridges for translational research. PMID:18258507
Tomato transcriptional changes in response to Clavibacter michiganensis subsp. michiganensis reveal a role for ethylene in disease development. PMID:18245454
A set of activators and repressors control peripheral glucose pathways in Pseudomonas putida to yield a common central intermediate. PMID:18245293
Genome-wide analysis of aging and learning-related genes in the hippocampal dentate gyrus. PMID:18234529
GSE: a comprehensive database system for the representation, retrieval, and analysis of microarray data. PMID:18229714
SGDI: system for genomic data integration. PMID:18229682
Development of a human mitochondrial oligonucleotide microarray (h-MitoArray) and gene expression analysis of fibroblast cell lines from 13 patients with isolated F1Fo ATP synthase deficiency. PMID:18221507
Transcriptome analyses of amoebic gill disease-affected Atlantic salmon (Salmo salar) tissues reveal localized host gene suppression. PMID:18219527
EzArray: a web-based highly automated Affymetrix expression array data management and analysis system. PMID:18218103
Protease nexin-1, tPA, and PAI-1 are upregulated in cryoglobulinemic membranoproliferative glomerulonephritis. PMID:18199802
Guidelines for reporting an fMRI study. PMID:18191585
Overview of microarray analysis of gene expression and its applications to cervical cancer investigation. PMID:18182341
Model-based variance-stabilizing transformation for Illumina microarray data. PMID:18178591
Validation and quality control of protein microarray-based analytical methods. PMID:18095188
Computational prediction of protein-protein interactions. PMID:18095187
The first trimester human trophoblast cell line ACH-3P: a novel tool to study autocrine/paracrine regulatory loops of human trophoblast subpopulations--TNF-alpha stimulates MMP15 expression. PMID:18093301
The development of an Arabidopsis model system for genome-wide analysis of polyploidy effects. PMID:18079994
Regulator of G-protein signalling 2 mRNA is differentially expressed in mammary epithelial subpopulations and over-expressed in the majority of breast cancers. PMID:18067675
Co-ordinated regulation of gluconate catabolism and glucose uptake in Corynebacterium glutamicum by two functionally equivalent transcriptional regulators, GntR1 and GntR2. PMID:18047570
Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database. PMID:18039715
In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation. PMID:18039370
JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. PMID:18006571
The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. PMID:17989687
Establishment and maintenance of the innate antiviral response to West Nile Virus involves both RIG-I and MDA5 signaling through IPS-1. PMID:17977974
CEBS--Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data. PMID:17962311
Optimization of cDNA microarrays procedures using criteria that do not rely on external standards. PMID:17949480
Distinct RIG-I and MDA5 signaling by RNA viruses in innate immunity. PMID:17942531
CATdb: a public access to Arabidopsis transcriptome data from the URGV-CATMA platform. PMID:17940091
CanGEM: mining gene copy number changes in cancer. PMID:17932056
Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata. PMID:17932051
Software development vis à vis collaboration in interdisciplinary research. PMID:17917128
Sharing and reusing gene expression profiling data in neuroscience. PMID:17917127
Molecular targets of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) within the zebrafish ovary: insights into TCDD-induced endocrine disruption and reproductive toxicity. PMID:17884332
Membrane-active compounds activate the transcription factors Pdr1 and Pdr3 connecting pleiotropic drug resistance and membrane lipid homeostasis in saccharomyces cerevisiae. PMID:17881724
Osteopenia in Sparc (osteonectin)-deficient mice: characterization of phenotypic determinants of femoral strength and changes in gene expression. PMID:17878319
YPED: a web-accessible database system for protein expression analysis. PMID:17867667
JAK2V617F-negative ET patients do not display constitutively active JAK/STAT signaling. PMID:17764814
Transcriptional profiling of chickpea genes differentially regulated in response to high-salinity, cold and drought. PMID:17764573
Design and evaluation of Actichip, a thematic microarray for the study of the actin cytoskeleton. PMID:17727702
Utrophin up-regulation by an artificial transcription factor in transgenic mice. PMID:17712422
Molecular portrait of cisplatin induced response in human testis cancer cell lines based on gene expression profiles. PMID:17711579
Transcription factor network downstream of protease activated receptors (PARs) modulating mouse bladder inflammation. PMID:17705868
Functional genomics highlights differential induction of antiviral pathways in the lungs of SARS-CoV-infected macaques. PMID:17696609
Video in science. Protocol videos: the implications for research and society. PMID:17667999
Gap junction and purinergic P2 receptor proteins as a functional unit: insights from transcriptomics. PMID:17665085
DNA microarrays: a powerful genomic tool for biomedical and clinical research. PMID:17660860
The effects of estrogen and testosterone on gene expression in the rat mesenteric arteries. PMID:17652031
Meta-analysis of microarray results: challenges, opportunities, and recommendations for standardization. PMID:17651921
Arabidopsis Gene Family Profiler (aGFP)--user-oriented transcriptomic database with easy-to-use graphic interface. PMID:17645793
Attributing effects of aqueous C60 nano-aggregates to tetrahydrofuran decomposition products in larval zebrafish by assessment of gene expression. PMID:17637923
Strategy for encoding and comparison of gene expression signatures. PMID:17612401
Integrated olfactory receptor and microarray gene expression databases. PMID:17603910
Challenges and standards in integrating surveys of structural variation. PMID:17597783
Transcriptional analysis of the tomato resistance response triggered by recognition of the Xanthomonas type III effector AvrXv3. PMID:17582538
HMGB1 and LPS induce distinct patterns of gene expression and activation in neutrophils from patients with sepsis-induced acute lung injury. PMID:17581740
Microarray analysis of gene expression induced by sexual contact in Schistosoma mansoni. PMID:17578584
Molecular determinants of caste differentiation in the highly eusocial honeybee Apis mellifera. PMID:17577409
RNA profiling in host-pathogen interactions. PMID:17574903
Celsius: a community resource for Affymetrix microarray data. PMID:17570842
MASPECTRAS: a platform for management and analysis of proteomics LC-MS/MS data. PMID:17567892
Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates. PMID:17555589
Comparative temporal and dose-dependent morphological and transcriptional uterine effects elicited by tamoxifen and ethynylestradiol in immature, ovariectomized mice. PMID:17555576
Directional responses following recombinant cytokine stimulation of rainbow trout (Oncorhynchus mykiss) RTS-11 macrophage cells as revealed by transcriptome profiling. PMID:17555569
PrestOMIC, an open source application for dissemination of proteomic datasets by individual laboratories. PMID:17553161
Potential of gene expression profiling in the management of childhood acute lymphoblastic leukemia. PMID:17523695
Bladder inflammatory transcriptome in response to tachykinins: neurokinin 1 receptor-dependent genes and transcription regulatory elements. PMID:17519035
Functional genomics analyses of differential macaque peripheral blood mononuclear cell infections by human immunodeficiency virus-1 and simian immunodeficiency virus. PMID:17507074
An annotation infrastructure for the analysis and interpretation of Affymetrix exon array data. PMID:17498294
Convergent peripheral pathways catalyze initial glucose catabolism in Pseudomonas putida: genomic and flux analysis. PMID:17483213
Molecular profiling of experimental endometriosis identified gene expression patterns in common with human disease. PMID:17478174
Use of consomic rats for genomic insights into ventilator-associated lung injury. PMID:17468131
Solid type clear cell carcinoma of the pancreas: differential diagnosis of an unusual case and review of the literature. PMID:17453235
Neonatal dopamine depletion induces changes in morphogenesis and gene expression in the developing cortex. PMID:17449454
Mouse Phenotype Database Integration Consortium: integration [corrected] of mouse phenome data resources. PMID:17436037
The positive role of the ecological community in the genomic revolution. PMID:17436031
The genopolis microarray database. PMID:17430566
Transcript profiling of poplar leaves upon infection with compatible and incompatible strains of the foliar rust Melampsora larici-populina. PMID:17400708
Regulatory network of inflammation downstream of proteinase-activated receptors. PMID:17397547
The use of transcriptomic biomarkers for personalized medicine. PMID:17393305
Longitudinal analysis of gene expression in porcine skeletal muscle after post-injection local injury. PMID:17380264
Sharing detailed research data is associated with increased citation rate. PMID:17375194
Review of the literature examining the correlation among DNA microarray technologies. PMID:17370338
TAMEE: data management and analysis for tissue microarrays. PMID:17343750
Target genes of myostatin loss-of-function in muscles of late bovine fetuses. PMID:17331240
PASSIM--an open source software system for managing information in biomedical studies. PMID:17291344
Androgen responsive intronic non-coding RNAs. PMID:17263875
Biology by design: reduction and synthesis of cellular components and behaviour. PMID:17251159
High-density rhesus macaque oligonucleotide microarray design using early-stage rhesus genome sequence information and human genome annotations. PMID:17244361
A specific gene-expression signature quantifies the degree of hepatic fibrosis in patients with chronic liver disease. PMID:17230606
Transcriptional profiling of wheat caryopsis development using cDNA microarrays. PMID:17211515
Cross-talk between singlet oxygen- and hydrogen peroxide-dependent signaling of stress responses in Arabidopsis thaliana. PMID:17197417
The Stanford Microarray Database: implementation of new analysis tools and open source release of software. PMID:17182626
DNA microarrays in herbal drug research. PMID:17173108
Transcriptome and proteome profiling to understanding the biology of high productivity CHO cells. PMID:17172658
NCBI GEO standards and services for microarray data. PMID:17160034
ArrayExpress--a public database of microarray experiments and gene expression profiles. PMID:17132828
The transcription factor Gcr1 stimulates cell growth by participating in nutrient-responsive gene expression on a global level. PMID:17124610
Distinct cellular responses differentiating alcohol- and hepatitis C virus-induced liver cirrhosis. PMID:17121680
NCBI GEO: mining tens of millions of expression profiles--database and tools update. PMID:17099226
Dynamics of 17alpha-ethynylestradiol exposure in rainbow trout (Oncorhynchus mykiss): absorption, tissue distribution, and hepatic gene expression pattern. PMID:17089724
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. PMID:17087822
Identification of differentially expressed genes in HPV-positive and HPV-negative oropharyngeal squamous cell carcinomas. PMID:17079134
Mining housekeeping genes with a Naive Bayes classifier. PMID:17074078
The RpoT regulon of Pseudomonas putida DOT-T1E and its role in stress endurance against solvents. PMID:17071759
EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes. PMID:17071715
Evaluating different methods of microarray data normalization. PMID:17059609
A Fisheye Viewer for microarray-based gene expression data. PMID:17038193
Genomic analysis of increased host immune and cell death responses induced by 1918 influenza virus. PMID:17006449
Suppression of proinflammatory signal transduction and gene expression by the dual nucleic acid binding domains of the vaccinia virus E3L proteins. PMID:17005686
MicroArray Facility: a laboratory information management system with extended support for Nylon based technologies. PMID:16987406
Short-term arginine deprivation results in large-scale modulation of hepatic gene expression in both normal and tumor cells: microarray bioinformatic analysis. PMID:16961918
Major differences observed in transcript profiles of blueberry during cold acclimation under field and cold room conditions. PMID:16953429
Gene expression omnibus: microarray data storage, submission, retrieval, and analysis. PMID:16939800
Integrated molecular signature of disease: analysis of influenza virus-infected macaques through functional genomics and proteomics. PMID:16928763
Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). PMID:16901231
Data standards for flow cytometry. PMID:16901228
Tools for knowledge acquisition within the NeuroScholar system and their application to anatomical tract-tracing data. PMID:16895608
The end of the microarray Tower of Babel: will universal standards lead the way? PMID:16870711
Analysis of cell-based RNAi screens. PMID:16869968
Genome-wide approaches for identification of nuclear receptor target genes. PMID:16862224
Toxicogenomics in drug discovery and drug development: potential applications and future challenges. PMID:16858654
Toxicogenomics in regulatory ecotoxicology. PMID:16856717
An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes. PMID:16855282
The microarray data analysis process: from raw data to biological significance. PMID:16815220
Web-based analysis of the mouse transcriptome using Genevestigator. PMID:16790046
Host-specific response to HCV infection in the chimeric SCID-beige/Alb-uPA mouse model: role of the innate antiviral immune response. PMID:16789836
SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. PMID:16756676
MeMo: a hybrid SQL/XML approach to metabolomic data management for functional genomics. PMID:16753052
Expression profiling of the mouse early embryo: reflections and perspectives. PMID:16739220
Standardizing the standards. PMID:16738556
Personalized medicine and development of targeted therapies: The upcoming challenge for diagnostic molecular pathology. A review. PMID:16736190
Functional Annotation: extracting functional and regulatory order from microarrays. PMID:16729044
Extracellular phosphate alters cementoblast gene expression. PMID:16723645
Functional genomics of stress response in Pseudomonas putida KT2440. PMID:16707699
SARS-CoV virus-host interactions and comparative etiologies of acute respiratory distress syndrome as determined by transcriptional and cytokine profiling of formalin-fixed paraffin-embedded tissues. PMID:16689659
Early days: genomics and human responses to infection. PMID:16679048
Novel susceptibility genes in inflammatory bowel disease. PMID:16610046
MIMAS: an innovative tool for network-based high density oligonucleotide microarray data management and annotation. PMID:16597336
DNA microarray and proteomic analyses of the RpoS regulon in Geobacter sulfurreducens. PMID:16585740
Workgroup report: Review of genomics data based on experience with mock submissions--view of the CDER Pharmacology Toxicology Nonclinical Pharmacogenomics Subcommittee. PMID:16581548
Time course of microbiologic outcome and gene expression in Candida albicans during and following in vitro and in vivo exposure to fluconazole. PMID:16569846
Neutral and adaptive variation in gene expression. PMID:16567645
The Cinderella story of metabolic profiling: does metabolomics get to go to the functional genomics ball? PMID:16553314
An atlas of gene expression from seed to seed through barley development. PMID:16547597
GOurmet: a tool for quantitative comparison and visualization of gene expression profiles based on gene ontology (GO) distributions. PMID:16545118
Deciphering cellular states of innate tumor drug responses. PMID:16542501
From genomes to systems: the path with yeast. PMID:16524836
Meeting report: Validation of toxicogenomics-based test systems: ECVAM-ICCVAM/NICEATM considerations for regulatory use. PMID:16507466
Targeting of GFP to newborn rods by Nrl promoter and temporal expression profiling of flow-sorted photoreceptors. PMID:16505381
Global suppression of the host antiviral response by Ebola- and Marburgviruses: increased antagonism of the type I interferon response is associated with enhanced virulence. PMID:16501110
Human lung project: evaluating variance of gene expression in the human lung. PMID:16498083
Gene expression patterns in rainbow trout, Oncorhynchus mykiss, exposed to a suite of model toxicants. PMID:16488489
Stem cell factor receptor induces progenitor and natural killer cell-mediated cardiac survival and repair after myocardial infarction. PMID:16467148
Whole genome microarray analysis of growth hormone-induced gene expression in bone: T-box3, a novel transcription factor, regulates osteoblast proliferation. PMID:16464905
Gene expression profiles in developing nephrons using Lim1 metanephric mesenchyme-specific conditional mutant mice. PMID:16464245
Dirigent proteins in conifer defense: gene discovery, phylogeny, and differential wound- and insect-induced expression of a family of DIR and DIR-like genes in spruce (Picea spp.). PMID:16463097
Sustained trophism of the mammary gland is sufficient to accelerate and synchronize development of ErbB2/Neu-induced tumors. PMID:16434967
Understanding genomics: implications for the emergency medicine physician and the treatment of asthma. PMID:16418618
Creation and implications of a phenome-genome network. PMID:16404398
MIAME/Plant - adding value to plant microarrray experiments. PMID:16401339
Recent applications of DNA microarray technology to toxicology and ecotoxicology. PMID:16393650
Tomato Expression Database (TED): a suite of data presentation and analysis tools. PMID:16381976
ITTACA: a new database for integrated tumor transcriptome array and clinical data analysis. PMID:16381943
Nuclear Receptor Signaling Atlas (www.nursa.org): hyperlinking the nuclear receptor signaling community. PMID:16381851
Recent advances of protein microarrays. PMID:16376134
MicroGen: a MIAME compliant web system for microarray experiment information and workflow management. PMID:16351755
Insulin control of placental gene expression shifts from mother to foetus over the course of pregnancy. PMID:16344925
GPX-Macrophage Expression Atlas: a database for expression profiles of macrophages challenged with a variety of pro-inflammatory, anti-inflammatory, benign and pathogen insults. PMID:16343346
Platelet genomics and proteomics in human health and disease. PMID:16322782
Transcriptome profiling of bacterial responses to root exudates identifies genes involved in microbe-plant interactions. PMID:16301542
Analysis of microarray studies performed in the neurosciences. PMID:16280595
MiMiR: a comprehensive solution for storage, annotation and exchange of microarray data. PMID:16280078
Cross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes. PMID:16271137
maxdLoad2 and maxdBrowse: standards-compliant tools for microarray experimental annotation, data management and dissemination. PMID:16269077
The influence of muscle type and dystrophin deficiency on murine expression profiles. PMID:16261416
Cytoskeletal rearrangements in synovial fibroblasts as a novel pathophysiological determinant of modeled rheumatoid arthritis. PMID:16254600
Genomic analysis of anti-hepatitis B virus (HBV) activity by small interfering RNA and lamivudine in stable HBV-producing cells. PMID:16254373
Distinctions in the specificity of E2F function revealed by gene expression signatures. PMID:16249342
Global gene expression profiling reveals widespread yet distinctive translational responses to different eukaryotic translation initiation factor 2B-targeting stress pathways. PMID:16227585
Plant-based microarray data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a submission tool for Arabidopsis gene expression data to ArrayExpress. PMID:16219923
Comparison of the gene expression profile of undifferentiated human embryonic stem cell lines and differentiating embryoid bodies. PMID:16207381
No common denominator for breast cancer lymph node metastasis. PMID:16189523
Microarray methods in Drosophila neurobiology. PMID:16180035
L2L: a simple tool for discovering the hidden significance in microarray expression data. PMID:16168088
Fish and chips: various methodologies demonstrate utility of a 16,006-gene salmonid microarray. PMID:16164747
Sorghum bicolor's transcriptome response to dehydration, high salinity and ABA. PMID:16158244
TmaDB: a repository for tissue microarray data. PMID:16137321
Genome-wide identification of potential plant E2F target genes. PMID:16126853
Responses of genes involved in cell cycle control to diverse DNA damaging chemicals in human lung adenocarcinoma A549 cells. PMID:16120219
High-resolution mapping of genomic imbalance and identification of gene expression profiles associated with differential chemotherapy response in serous epithelial ovarian cancer. PMID:16036111
Adult mouse brain gene expression patterns bear an embryologic imprint. PMID:16002470
Temporal evolution of the Arabidopsis oxidative stress response. PMID:15988565
Storage and retrieval of microarray data and open source microarray database software. PMID:15988049
Microarrays and breast cancer clinical studies: forgetting what we have not yet learnt. PMID:15987437
How to improve quality assurance in fluorometry: fluorescence-inherent sources of error and suited fluorescence standards. PMID:15986157
The bioinformatics resource for oral pathogens. PMID:15980574
Profile and analysis of gene expression changes during early development in germinating spores of Ceratopteris richardii. PMID:15965014
Immunopurification of polyribosomal complexes of Arabidopsis for global analysis of gene expression. PMID:15955926
Exploring hepatic hormone actions using a compilation of gene expression profiles. PMID:15953391
TAp63alpha induces apoptosis by activating signaling via death receptors and mitochondria. PMID:15944736
A transcriptome map of cellular transformation by the fos oncogene. PMID:15918904
arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays. PMID:15910681
Gene expression profiling of cancer progression reveals intrinsic regulation of transforming growth factor-beta signaling in ErbB2/Neu-induced tumors from transgenic mice. PMID:15897883
The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging. PMID:15892875
Toward supportive data collection tools for plant metabolomics. PMID:15888680
DNA microarrays--techniques and applications in microbial systems. PMID:15881400
DNA microarray analysis of nitrogen fixation and Fe(III) reduction in Geobacter sulfurreducens. PMID:15870343
Methods for genome-wide analysis of gene expression changes in polyploids. PMID:15865985
Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR -- how well do they correlate? PMID:15854232
MARS: microarray analysis, retrieval, and storage system. PMID:15836795
Transcript AA454543 is a novel prognostic marker for hepatocellular carcinoma after curative partial hepatectomy. PMID:15810144
CGHPRO -- a comprehensive data analysis tool for array CGH. PMID:15807904
Analysis of target genes induced by IL-13 cytotoxin in human glioblastoma cells. PMID:15803373
Towards standardization of RNA quality assessment using user-independent classifiers of microcapillary electrophoresis traces. PMID:15800207
Role of the extracytoplasmic function protein family sigma factor RpoE in metal resistance of Escherichia coli. PMID:15774872
Marine genomics: a clearing-house for genomic and transcriptomic data of marine organisms. PMID:15760464
Global transcription profiling reveals comprehensive insights into hypoxic response in Arabidopsis. PMID:15734912
Presenilin-1-dependent transcriptome changes. PMID:15703411
Microarray analysis of pediatric ependymoma identifies a cluster of 112 candidate genes including four transcripts at 22q12.1-q13.3. PMID:15701279
Variation in tissue-specific gene expression among natural populations. PMID:15693942
Long oligonucleotide microarrays in wheat: evaluation of hybridization signal amplification and an oligonucleotide-design computer script. PMID:15682265
Evaluating concentration estimation errors in ELISA microarray experiments. PMID:15673468
Microarray analysis confirms the specificity of a Chlamydomonas reinhardtii chloroplast RNA stability mutant. PMID:15665248
BarleyBase--an expression profiling database for plant genomics. PMID:15608273
The Stanford Microarray Database accommodates additional microarray platforms and data formats. PMID:15608265
SIEGE: Smoking Induced Epithelial Gene Expression Database. PMID:15608264
NCBI GEO: mining millions of expression profiles--database and tools. PMID:15608262
ArrayExpress--a public repository for microarray gene expression data at the EBI. PMID:15608260
The European Bioinformatics Institute's data resources: towards systems biology. PMID:15608238
Spatial and temporal analysis of the local response to wounding in Arabidopsis leaves. PMID:15604673
Genomic and proteomic approaches for studying human cancer: prospects for true patient-tailored therapy. PMID:15601541
Application of microarrays in high-throughput enzymatic profiling. PMID:15542923
Characterization of antirrhinum petal development and identification of target genes of the class B MADS box gene DEFICIENS. PMID:15539471
Tocotrienol-rich fraction from palm oil affects gene expression in tumors resulting from MCF-7 cell inoculation in athymic mice. PMID:15506241
From ORFeome to biology: a functional genomics pipeline. PMID:15489336
A dynamic, web-accessible resource to process raw microarray scan data into consolidated gene expression values: importance of replication. PMID:15475389
Accelerating drug discovery. PMID:15470377
In control: systematic assessment of microarray performance. PMID:15459748
LIMaS: the JAVA-based application and database for microarray experiment tracking. PMID:15389322
GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. PMID:15375207
Standards for microarray data: an open letter. PMID:15345376
Performance evaluation of commercial short-oligonucleotide microarrays and the impact of noise in making cross-platform correlations. PMID:15345031
Submission of microarray data to public repositories. PMID:15340489
Interaction-dependent gene expression in Mla-specified response to barley powdery mildew. PMID:15319481
Global host immune response: pathogenesis and transcriptional profiling of type A influenza viruses expressing the hemagglutinin and neuraminidase genes from the 1918 pandemic virus. PMID:15308742
The use of MPSS for whole-genome transcriptional analysis in Arabidopsis. PMID:15289482
POSaM: a fast, flexible, open-source, inkjet oligonucleotide synthesizer and microarrayer. PMID:15287980
Transcriptional programs of early reproductive stages in Arabidopsis. PMID:15247381
Global survey of chromatin accessibility using DNA microarrays. PMID:15231753
Feature extraction and signal processing for nylon DNA microarrays. PMID:15222896
The host response to West Nile Virus infection limits viral spread through the activation of the interferon regulatory factor 3 pathway. PMID:15220448
A microarray screen for novel candidate genes in coeliac disease pathogenesis. PMID:15194641
Methodological considerations regarding single-cell gene expression profiling for brain injury. PMID:15176468
Methods for transcriptional profiling in plants. Be fruitful and replicate. PMID:15173570
[Microarrays]. PMID:15138693
Resolution of large and small differences in gene expression using models for the Bayesian analysis of gene expression levels and spotted DNA microarrays. PMID:15128431
Gene expression profiling: from microarrays to medicine. PMID:15114052
From microarray data to results. Workshop on genomic approaches to microarray data analysis. PMID:15105828
Charting gene regulatory networks: strategies, challenges and perspectives. PMID:15080794
ONCOMINE: a cancer microarray database and integrated data-mining platform. PMID:15068665
Exploring the portability of informatics capabilities from a clinical application to a bioscience application. PMID:15064294
Escalator-driven research. PMID:15060783
MiCoViTo: a tool for gene-centric comparison and visualization of yeast transcriptome states. PMID:15053844
Impact of human cytomegalovirus latent infection on myeloid progenitor cell gene expression. PMID:15047822
A guide to building image-centric databases. PMID:15043221
Database development in toxicogenomics: issues and efforts. PMID:15033600
Toxicogenomics in risk assessment: an overview of an HESI collaborative research program. PMID:15033589
Microarray segmentation methods significantly influence data precision. PMID:15028803
Microcystic tubulopapillary carcinoma of the pancreas: a new tumor entity? PMID:15014986
Genetic regulation of fruit development and ripening. PMID:15010516
Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics. PMID:14962987
Expression array annotation using the BioMediator biological data integration system and the BioConductor analytic platform. PMID:14728212
Scratching the (T cell) surface. PMID:14709166
NASCArrays: a repository for microarray data generated by NASC's transcriptomics service. PMID:14681484
SGMD: the Soybean Genomics and Microarray Database. PMID:14681442
Gene expression profiles of primary breast tumors maintained in distant metastases. PMID:14665696
ArrayTrack--supporting toxicogenomic research at the U.S. Food and Drug Administration National Center for Toxicological Research. PMID:14630514
Amplified RNA degradation in T7-amplification methods results in biased microarray hybridizations. PMID:14606961
Microarray analysis of gene expression during the cell cycle. PMID:14577836
New methods for finding disease-susceptibility genes: impact and potential. PMID:14519189
The Longhorn Array Database (LAD): an open-source, MIAME compliant implementation of the Stanford Microarray Database (SMD). PMID:12930545
Mechanisms of benzene-induced hematotoxicity and leukemogenicity: cDNA microarray analyses using mouse bone marrow tissue. PMID:12928149
Overexpression of the disease resistance gene Pto in tomato induces gene expression changes similar to immune responses in human and fruitfly. PMID:12913147
Gene expression profiling in response to ultraviolet radiation in maize genotypes with varying flavonoid content. PMID:12913132
Impact of surface chemistry and blocking strategies on DNA microarrays. PMID:12907739
Cell cycle arrest and apoptosis provoked by UV radiation-induced DNA damage are transcriptionally highly divergent responses. PMID:12907719
Statistical issues and methods for meta-analysis of microarray data: a case study in prostate cancer. PMID:12884057
Gene expression profiling of endocrine tumors using DNA microarrays: progress and promise. PMID:12858000
Mutual interference of adenovirus infection and myc expression. PMID:12829833
REDUCE: An online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data. PMID:12824350
GenePublisher: Automated analysis of DNA microarray data. PMID:12824347
The tissue microarray data exchange specification: a community-based, open source tool for sharing tissue microarray data. PMID:12769826
Genome informatics: current status and future prospects. PMID:12750305
Gene expression profiling of the cellular transcriptional network regulated by alpha/beta interferon and its partial attenuation by the hepatitis C virus nonstructural 5A protein. PMID:12743294
Monitoring global messenger RNA changes in externally controlled microarray experiments. PMID:12671682
Absolute mRNA concentrations from sequence-specific calibration of oligonucleotide arrays. PMID:12655013
Towards reconstruction of gene networks from expression data by supervised learning. PMID:12540298
The Stanford Microarray Database: data access and quality assessment tools. PMID:12519956
ArrayExpress--a public repository for microarray gene expression data at the EBI. PMID:12519949
The European Bioinformatics Institute's data resources. PMID:12519944
YMD: a microarray database for large-scale gene expression analysis. PMID:12463803
Gene expression profiling with DNA microarrays: advancing our understanding of psychiatric disorders. PMID:12462404
Optimizing gene expression analysis in archival brain tissue. PMID:12462400
Design and implementation of microarray gene expression markup language (MAGE-ML). PMID:12225585
BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data. PMID:12186655
NotI subtraction and NotI-specific microarrays to detect copy number and methylation changes in whole genomes. PMID:12149436
Cellular transcriptional profiling in influenza A virus-infected lung epithelial cells: the role of the nonstructural NS1 protein in the evasion of the host innate defense and its potential contribution to pandemic influenza. PMID:12149435
Optimization of oligonucleotide-based DNA microarrays. PMID:12034852
Search and retrieve. Large-scale data generation is becoming increasingly important in biological research. But how good are the tools to make sense of the data? PMID:11991940
Minimum Information About a Microarray Experiment (MIAME)--successes, failures, challenges PubMed citations: 86.

86 articles citing: Minimum Information About a Microarray Experiment (MIAME)--successes, failures, challenges

Identification of Crucial Genes and Key Functions in Type 2 Diabetic Hearts by Bioinformatic Analysis. PMID:35242109
Data Integration Challenges for Machine Learning in Precision Medicine. PMID:35145977
Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications. PMID:34862503
Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model. PMID:34862501
BioSamples database: FAIRer samples metadata to accelerate research data management. PMID:34747489
Precision omics data integration and analysis with interoperable ontologies and their application for COVID-19 research. PMID:34159360
Increasing metadata coverage of SRA BioSample entries using deep learning-based named entity recognition. PMID:33914028
A Minimal Information Model for Potential Drug-Drug Interactions. PMID:33762928
seqQscorer: automated quality control of next-generation sequencing data using machine learning. PMID:33673854
A Meta-Analysis of the Effects of High-LET Ionizing Radiations in Human Gene Expression. PMID:33546472
Method comparison studies of telomere length measurement using qPCR approaches: A critical appraisal of the literature. PMID:33471860
Expanding and Remixing the Metadata Landscape. PMID:33229213
Available Software for Meta-analyses of Genome-wide Expression Studies. PMID:32476989
Normal myeloid progenitor cell subset-associated gene signatures for acute myeloid leukaemia subtyping with prognostic impact. PMID:32324791
A Systematic Bioinformatics Workflow With Meta-Analytics Identified Potential Pathogenic Factors of Alzheimer's Disease. PMID:32231518
Genes expression profiling of alveolar macrophages exposed to non-functionalized, anionic and cationic multi-walled carbon nanotubes shows three different mechanisms of toxicity. PMID:32093716
A systems approach to infectious disease. PMID:32060427
Current RNA-seq methodology reporting limits reproducibility. PMID:31813948
A cross-sector call to improve carcinogenicity risk assessment through use of genomic methodologies. PMID:31726190
Implementing the FAIR Data Principles in precision oncology: review of supporting initiatives. PMID:31263868
Cyberbiosecurity Challenges of Pathogen Genome Databases. PMID:31157218
The Potential Mechanism of Bufadienolide-Like Chemicals on Breast Cancer via Bioinformatics Analysis. PMID:30646630
A minimum information standard for reproducing bench-scale bacterial cell growth and productivity. PMID:30534611
Kinomics toolbox-A web platform for analysis and viewing of kinomic peptide array data. PMID:30130366
The Role of Specific Chemokines in the Amelioration of Colitis by Appendicitis and Appendectomy. PMID:30037025
CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata. PMID:30012108
Fast and Accurate Metadata Authoring Using Ontology-Based Recommendations. PMID:29854196
Transcriptomic Studies of Malaria: a Paradigm for Investigation of Systemic Host-Pathogen Interactions. PMID:29695497
A FAIR guide for data providers to maximise sharing of human genomic data. PMID:29543799
Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data. PMID:29144493
Predicting structured metadata from unstructured metadata. PMID:28637268
Transcriptomics technologies. PMID:28545146
Propelling the paradigm shift from reductionism to systems nutrition. PMID:28138347
Antiproliferative and Pro-Apoptotic Effects of MiR-4286 Inhibition in Melanoma Cells. PMID:28005927
The minimum information required for a glycomics experiment (MIRAGE) project: improving the standards for reporting glycan microarray-based data. PMID:27993942
Towards an open grapevine information system. PMID:27917288
Somatic cancer variant curation and harmonization through consensus minimum variant level data. PMID:27814769
Key Challenges and Opportunities Associated with the Use of In Vitro Models to Detect Human DILI: Integrated Risk Assessment and Mitigation Plans. PMID:27689095
NeuroRDF: semantic integration of highly curated data to prioritize biomarker candidates in Alzheimer's disease. PMID:27392431
Gene expression changes in the retina following subretinal injection of human neural progenitor cells into a rodent model for retinal degeneration. PMID:27217715
How should the completeness and quality of curated nanomaterial data be evaluated? PMID:27143028
From raw data to data-analysis for magnetic resonance spectroscopy--the missing link: jMRUI2XML. PMID:26552737
Non-Target Effects of Green Fluorescent Protein (GFP)-Derived Double-Stranded RNA (dsRNA-GFP) Used in Honey Bee RNA Interference (RNAi) Assays. PMID:26466797
Systems Medicine: The Application of Systems Biology Approaches for Modern Medical Research and Drug Development. PMID:26357572
The Global Alzheimer's Association Interactive Network. PMID:26318022
RIPOSTE: a framework for improving the design and analysis of laboratory-based research. PMID:25951517
A prophage-encoded actin-like protein required for efficient viral DNA replication in bacteria. PMID:25916847
Gene expression changes during retinal development and rod specification. PMID:25678762
Gene expression profiling studies in regenerating nerves in a mouse model for CMT1X: uninjured Cx32-knockout peripheral nerves display expression profile of injured wild type nerves. PMID:25447941
Current advances in systems and integrative biology. PMID:25379142
Endothelin and vascular remodelling in colitis pathogenesis--appendicitis and appendectomy limit colitis by suppressing endothelin pathways. PMID:25085204
Genome scale modeling in systems biology: algorithms and resources. PMID:24822031
Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data. PMID:24723752
T helper type 17 pathway suppression by appendicitis and appendectomy protects against colitis. PMID:24666024
Subtilase SprP exerts pleiotropic effects in Pseudomonas aeruginosa. PMID:24376018
Coregulation of HIV-1 dependency factors in individuals heterozygous to the CCR5-delta32 deletion. PMID:24245779
Differences in visceral fat and fat bacterial colonization between ulcerative colitis and Crohn's disease. An in vivo and in vitro study. PMID:24205244
Publishing 13C metabolic flux analysis studies: a review and future perspectives. PMID:24025367
Standardization of sample collection, isolation and analysis methods in extracellular vesicle research. PMID:24009894
Genome-wide transcriptional profiling of the purple sulfur bacterium Allochromatium vinosum DSM 180T during growth on different reduced sulfur compounds. PMID:23873913
Nutritionally driven differential gene expression leads to heterochronic brain development in honeybee castes. PMID:23738002
Hierarchical approaches for systems modeling in cardiac development. PMID:23463736
Data submission and quality in microarray-based microRNA profiling. PMID:23358751
Multiscale integration of -omic, imaging, and clinical data in biomedical informatics. PMID:23231990
Strategies for annotation and curation of translational databases: the eTUMOUR project. PMID:23180768
Hox gene expression leads to differential hind leg development between honeybee castes. PMID:22848371
DIPSBC--data integration platform for systems biology collaborations. PMID:22568834
How can microarrays unlock asthma? PMID:22500180
Host gene targets for novel influenza therapies elucidated by high-throughput RNA interference screens. PMID:22247330
Guidelines for information about therapy experiments: a proposal on best practice for recording experimental data on cancer therapy. PMID:22226027
The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons. PMID:22121217
The effect of the CCR5-delta32 deletion on global gene expression considering immune response and inflammation. PMID:22029606
COLOMBOS: access port for cross-platform bacterial expression compendia. PMID:21779320
Minimum Information about a Cardiac Electrophysiology Experiment (MICEE): standardised reporting for model reproducibility, interoperability, and data sharing. PMID:21745496
Expression profiles of differentially regulated genes during the early stages of apple flower infection with Erwinia amylovora. PMID:21725032
Protective pathways against colitis mediated by appendicitis and appendectomy. PMID:21707591
Combining DNA-microarray data in systemic lupus erythematosus. PMID:21639954
Conceptual aspects of large meta-analyses with publicly available microarray data: a case study in oncology. PMID:21423405
Web-enabled and improved software tools and data are needed to measure nutrient intakes and physical activity for personalized health research. PMID:20980656
Analysis of microarray data from the macaque corpus luteum; the search for common themes in primate luteal regression. PMID:20855453
Analyzing schizophrenia by DNA microarrays. PMID:20801428
A standard variation file format for human genome sequences. PMID:20796305
Generating hepatic cell lineages from pluripotent stem cells for drug toxicity screening. PMID:20483202
Development and validation of a resistance and virulence gene microarray targeting Escherichia coli and Salmonella enterica. PMID:20362014
miR-17, miR-19b, miR-20a, and miR-106a are down-regulated in human aging. PMID:20089119
CORNET: a user-friendly tool for data mining and integration. PMID:20053712

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dna microarray
metasource: Fairsharing.org
version: FAIRsharing.org: MIAME; Minimum Information About a Microarray Experiment; DOI: https://doi.org/10.25504/FAIRsharing.32b10v; Last edited: Feb. 7, 2021, 7:56 p.m.; Last accessed: Jan 03 2022 7:11 p.m.

deoxyribonucleic acid
metasource: Fairsharing.org
version: FAIRsharing.org: MIAME; Minimum Information About a Microarray Experiment; DOI: https://doi.org/10.25504/FAIRsharing.32b10v; Last edited: Feb. 7, 2021, 7:56 p.m.; Last accessed: Jan 03 2022 7:11 p.m.

experimental measurement
metasource: Fairsharing.org
version: FAIRsharing.org: MIAME; Minimum Information About a Microarray Experiment; DOI: https://doi.org/10.25504/FAIRsharing.32b10v; Last edited: Feb. 7, 2021, 7:56 p.m.; Last accessed: Jan 03 2022 7:11 p.m.

experimentally determined
metasource: Fairsharing.org
version: FAIRsharing.org: MIAME; Minimum Information About a Microarray Experiment; DOI: https://doi.org/10.25504/FAIRsharing.32b10v; Last edited: Feb. 7, 2021, 7:56 p.m.; Last accessed: Jan 03 2022 7:11 p.m.

gene expression data
metasource: Fairsharing.org
version: FAIRsharing.org: MIAME; Minimum Information About a Microarray Experiment; DOI: https://doi.org/10.25504/FAIRsharing.32b10v; Last edited: Feb. 7, 2021, 7:56 p.m.; Last accessed: Jan 03 2022 7:11 p.m.

genome
metasource: Fairsharing.org
version: FAIRsharing.org: MIAME; Minimum Information About a Microarray Experiment; DOI: https://doi.org/10.25504/FAIRsharing.32b10v; Last edited: Feb. 7, 2021, 7:56 p.m.; Last accessed: Jan 03 2022 7:11 p.m.

nucleic acid hybridization
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version: FAIRsharing.org: MIAME; Minimum Information About a Microarray Experiment; DOI: https://doi.org/10.25504/FAIRsharing.32b10v; Last edited: Feb. 7, 2021, 7:56 p.m.; Last accessed: Jan 03 2022 7:11 p.m.

ribonucleic acid
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version: FAIRsharing.org: MIAME; Minimum Information About a Microarray Experiment; DOI: https://doi.org/10.25504/FAIRsharing.32b10v; Last edited: Feb. 7, 2021, 7:56 p.m.; Last accessed: Jan 03 2022 7:11 p.m.

study design
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version: FAIRsharing.org: MIAME; Minimum Information About a Microarray Experiment; DOI: https://doi.org/10.25504/FAIRsharing.32b10v; Last edited: Feb. 7, 2021, 7:56 p.m.; Last accessed: Jan 03 2022 7:11 p.m.

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Minimum Information About a Microarray Experiment involving Plants

Minimum Information about an ENVironmental transcriptomic experiment

Minimum Information About a Proteomics Experiment

Minimal Information about a high throughput SEQuencing Experiment

Minimum Information About a RNAi Experiment

MIAME Notation in Markup Language

Minimum Information About Cell Migration Experiment

Minimum Information About a Genotyping Experiment

Minimum Information about a Molecular Interaction Experiment

Minimum Information About a Spinal Cord Injury experiment

Minimum Information about a Cardiac Electrophysiology Experiment

Minimum Information About an RNAi Experiment Tabular

MicroArray Gene Expression Tabular Format

ArrayExpress

Microarray and Gene Expression Data Ontology

Minimum Information About a Peptide Array Experiment

Minimum Information About a Biofilm Experiment

Minimum Information Required for A Glycomics Experiment - Glycan Microarray Analysis

Minimum Information about Flow Cytometry

Nucleic Acids Database