GenePattern GeneSet Table Format
GenePattern GeneSet Table Format is an analytical tool and file format for the analysis of gene expression and network analysis provided by GenePattern.
Description
More detailed information about this field from each metasource.
GenePattern GeneSet Table Format is an analytical tool and file format for the analysis of gene expression and network analysis provided by GenePattern.
metasource: Fairsharing.orgversion: FAIRsharing.org: GenePattern GeneSet Table Format; GenePattern GeneSet Table Format; DOI: https://doi.org/10.25504/FAIRsharing.z057ar; Last edited: Jan. 8, 2019, 1:32 p.m.; Last accessed: Jan 03 2022 7:14 p.m.
Webpage:
http://software.broadinstitute.org/cancer/software/genepattern/file-formats-guideWebpage
More detailed information about this field from each metasource.
http://software.broadinstitute.org/cancer/software/genepattern/file-formats-guide
metasource: Fairsharing.orgversion: FAIRsharing.org: GenePattern GeneSet Table Format; GenePattern GeneSet Table Format; DOI: https://doi.org/10.25504/FAIRsharing.z057ar; Last edited: Jan. 8, 2019, 1:32 p.m.; Last accessed: Jan 03 2022 7:14 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
GenePattern 2.0
PMID: 16642009
metasource: Fairsharing.org
version: FAIRsharing.org: GenePattern GeneSet Table Format; GenePattern GeneSet Table Format; DOI: https://doi.org/10.25504/FAIRsharing.z057ar; Last edited: Jan. 8, 2019, 1:32 p.m.; Last accessed: Jan 03 2022 7:14 p.m.
Publications
More detailed information about this field from each metasource.
GenePattern 2.0
PMID: 16642009
metasource: Fairsharing.org
version: FAIRsharing.org: GenePattern GeneSet Table Format; GenePattern GeneSet Table Format; DOI: https://doi.org/10.25504/FAIRsharing.z057ar; Last edited: Jan. 8, 2019, 1:32 p.m.; Last accessed: Jan 03 2022 7:14 p.m.
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GenePattern 2.0
PubMed citations: 1069.
1069 articles citing: GenePattern 2.0
Protein kinase inhibitor responses in uveal melanoma reflects a diminished dependency on PKC-MAPK signaling. PMID:35352024
Establishing a Prognostic Model Based on Ulceration and Immune Related Genes in Melanoma Patients and Identification of EIF3B as a Therapeutic Target. PMID:35273605
Computing microRNA-gene interaction networks in pan-cancer using miRDriver. PMID:35260634
Identification and Comprehensive Analysis of FREM2 Mutation as a Potential Prognostic Biomarker in Colorectal Cancer. PMID:35252356
The Predictive Value of PAK7 Mutation for Immune Checkpoint Inhibitors Therapy in Non-Small Cell Cancer. PMID:35242138
Loss of function of BRCA1 promotes EMT in mammary tumors through activation of TGFβR2 signaling pathway. PMID:35236825
Alterations in blood proteins in the prodromal stage of bipolar II disorders. PMID:35210508
Elevated level of lysophosphatidic acid among patients with HNF1B mutations and its role in RCAD syndrome: a multiomic study. PMID:35179657
Data Integration Challenges for Machine Learning in Precision Medicine. PMID:35145977
A simple guide to de novo transcriptome assembly and annotation. PMID:35076693
High expression of Ran binding protein 1 predicts poor outcomes in hepatocellular carcinoma patients: a Cancer Genome Atlas database analysis. PMID:35070423
YAP1 and PRDM14 converge to promote cell survival and tumorigenesis. PMID:34990589
Co-existing TP53 and ARID1A mutations promote aggressive endometrial tumorigenesis. PMID:34941867
TP53 Mutation Infers a Poor Prognosis and Is Correlated to Immunocytes Infiltration in Breast Cancer. PMID:34917611
Uncovering drug repurposing candidates for head and neck cancers: insights from systematic pharmacogenomics data analysis. PMID:34907286
Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severity. PMID:34889978
Importance of Bile Composition for Diagnosis of Biliary Obstructions. PMID:34885858
Discovery proteomics defines androgen-regulated glycoprotein networks in prostate cancer cells, as well as putative biomarkers of prostatic diseases. PMID:34782677
Identification of Signaling Pathways for Early Embryonic Lethality and Developmental Retardation in Sephs1-/- Mice. PMID:34769078
Model-based assessment of mammalian cell metabolic functionalities using omics data. PMID:34761247
Heparan sulfate proteoglycans serve as alternative receptors for low affinity LCMV variants. PMID:34648606
Modelling the bioinformatics tertiary analysis research process. PMID:34592928
Prediction and identification of synergistic compound combinations against pancreatic cancer cells. PMID:34585118
A gene expression-based immune content predictor for survival and postoperative radiotherapy response in head and neck cancer. PMID:34553026
Paired comparisons of mutational profiles before and after brachytherapy in asian uveal melanoma patients. PMID:34545149
Signatures of Multi-Omics Reveal Distinct Tumor Immune Microenvironment Contributing to Immunotherapy in Lung Adenocarcinoma. PMID:34539658
A human liver cell-based system modeling a clinical prognostic liver signature for therapeutic discovery. PMID:34535664
Optogenetic modeling of human neuromuscular circuits in Duchenne muscular dystrophy with CRISPR and pharmacological corrections. PMID:34516770
CPT1A and fatty acid β-oxidation are essential for tumor cell growth and survival in hormone receptor-positive breast cancer. PMID:34514415
Transcriptomic analysis of elderly women with low muscle mass: association with immune system pathway. PMID:34493690
Exosomal miR-19a and IBSP cooperate to induce osteolytic bone metastasis of estrogen receptor-positive breast cancer. PMID:34465793
Recurrent Human Papillomavirus-Related Head and Neck Cancer Undergoes Metabolic Reprogramming and Is Driven by Oxidative Phosphorylation. PMID:34407971
Clinical Positioning of the IAP Antagonist Tolinapant (ASTX660) in Colorectal Cancer. PMID:34389694
Mutations in the transcription factor FOXO1 mimic positive selection signals to promote germinal center B cell expansion and lymphomagenesis. PMID:34380064
Predictive biomarkers for 5-fluorouracil and oxaliplatin-based chemotherapy in gastric cancers via profiling of patient-derived xenografts. PMID:34376661
Met and Cxcr4 cooperate to protect skeletal muscle stem cells against inflammation-induced damage during regeneration. PMID:34350830
Immune and stromal scoring system associated with tumor microenvironment and prognosis: a gene-based multi-cancer analysis. PMID:34344410
Identification and Validation of Immune Molecular Subtypes in Pancreatic Ductal Adenocarcinoma: Implications for Prognosis and Immunotherapy. PMID:34335594
Reprogramming mRNA Expression in Response to Defect in RNA Polymerase III Assembly in the Yeast Saccharomyces cerevisiae. PMID:34298922
SPTAN1 Expression Predicts Treatment and Survival Outcomes in Colorectal Cancer. PMID:34298848
An Immune-Gene-Based Classifier Predicts Prognosis in Patients With Cervical Squamous Cell Carcinoma. PMID:34291084
A network-biology approach for identification of key genes and pathways involved in malignant peritoneal mesothelioma. PMID:34261301
Integrative Transcriptomic Analysis Reveals Distinctive Molecular Traits and Novel Subtypes of Collecting Duct Carcinoma. PMID:34200770
SLX4IP promotes RAP1 SUMOylation by PIAS1 to coordinate telomere maintenance through NF-κB and Notch signaling. PMID:34187905
Catenin Alpha-2 Mutation Changes the Immune Microenvironment in Lung Adenocarcinoma Patients Receiving Immune Checkpoint Inhibitors. PMID:34163353
ULK1 inhibition overcomes compromised antigen presentation and restores antitumor immunity in LKB1 mutant lung cancer. PMID:34142094
Transcriptional drug repositioning and cheminformatics approach for differentiation therapy of leukaemia cells. PMID:34131166
Association Between FSIP2 Mutation and an Improved Efficacy of Immune Checkpoint Inhibitors in Patients With Skin Cutaneous Melanoma. PMID:34113648
Tumor metabolism and associated serum metabolites define prognostic subtypes of Asian hepatocellular carcinoma. PMID:34103600
Data-Driven Kidney Transplant Phenotyping as a Histology-Independent Framework for Biomarker Discovery. PMID:34078665
Melanoma Cell State-Specific Responses to TNFα. PMID:34073253
Spontaneous Cell Detachment and Reattachment in Cancer Cell Lines: An In Vitro Model of Metastasis and Malignancy. PMID:34066490
The PTEN and ATM axis controls the G1/S cell cycle checkpoint and tumorigenesis in HER2-positive breast cancer. PMID:34059798
Inferring and analyzing gene regulatory networks from multi-factorial expression data: a complete and interactive suite. PMID:34039282
Dynamic regulation of B cell complement signaling is integral to germinal center responses. PMID:34031614
driveR: a novel method for prioritizing cancer driver genes using somatic genomics data. PMID:34030627
SFRP2 induces a mesenchymal subtype transition by suppression of SOX2 in glioblastoma. PMID:34021259
Metastasis is altered through multiple processes regulated by the E2F1 transcription factor. PMID:33947907
Promotion of cholangiocarcinoma growth by diverse cancer-associated fibroblast subpopulations. PMID:33930309
LINC00460 Is a Dual Biomarker That Acts as a Predictor for Increased Prognosis in Basal-Like Breast Cancer and Potentially Regulates Immunogenic and Differentiation-Related Genes. PMID:33912452
Longitudinal transcriptomics define the stages of myeloid activation in the living human brain after intracerebral hemorrhage. PMID:33891558
Comprehensive omic characterization of breast cancer in Mexican-Hispanic women. PMID:33854067
A cell-to-patient machine learning transfer approach uncovers novel basal-like breast cancer prognostic markers amongst alternative splice variants. PMID:33845831
Functional annotation of lung cancer‒associated genetic variants by cell type‒specific epigenome and long-range chromatin interactome. PMID:33840167
Chemotherapy Induces Tumor-Associated Macrophages that Aid Adaptive Immune Responses in Ovarian Cancer. PMID:33839687
SOX4 and SMARCA4 cooperatively regulate PI3k signaling through transcriptional activation of TGFBR2. PMID:33837205
Hypoxia-inducible factor activity promotes antitumor effector function and tissue residency by CD8+ T cells. PMID:33792560
Cytoplasmic DNA accumulation preferentially triggers cell death of myeloid leukemia cells by interacting with intracellular DNA sensing pathway. PMID:33771977
Effect of NCOR1 Mutations on Immune Microenvironment and Efficacy of Immune Checkpoint Inhibitors in Patient with Bladder Cancer. PMID:33763074
Visibility graph based temporal community detection with applications in biological time series. PMID:33707481
The Multiomics Analyses of Fecal Matrix and Its Significance to Coeliac Disease Gut Profiling. PMID:33671197
Tumor immune microenvironment-based classifications of bladder cancer for enhancing the response rate of immunotherapy. PMID:33665361
Identification of Potential Driver Genes Based on Multi-Genomic Data in Cervical Cancer. PMID:33664766
Wnt-β-catenin activation epigenetically reprograms Treg cells in inflammatory bowel disease and dysplastic progression. PMID:33664518
Dissecting the impact of regional identity and the oncogenic role of human-specific NOTCH2NL in an hESC model of H3.3G34R-mutant glioma. PMID:33631117
Identification of MFGE8 and KLK5/7 as mediators of breast tumorigenesis and resistance to COX-2 inhibition. PMID:33588911
Clinically significant genomic alterations in the Chinese and Western patients with intrahepatic cholangiocarcinoma. PMID:33579226
The serine hydroxymethyltransferase-2 (SHMT2) initiates lymphoma development through epigenetic tumor suppressor silencing. PMID:33569544
GalaxyTrakr: a distributed analysis tool for public health whole genome sequence data accessible to non-bioinformaticians. PMID:33568057
Effect of the p53 P72R Polymorphism on Mutant TP53 Allele Selection in Human Cancer. PMID:33555293
Identification of Novel Serological Autoantibodies in Takayasu Arteritis Patients Using HuProt Arrays. PMID:33545363
CARD11 alteration as a candidate biomarker of skin cutaneous melanoma treated with immune checkpoint blockade. PMID:33527024
The chromosomal protein SMCHD1 regulates DNA methylation and the 2c-like state of embryonic stem cells by antagonizing TET proteins. PMID:33523915
MethCORR infers gene expression from DNA methylation and allows molecular analysis of ten common cancer types using fresh-frozen and formalin-fixed paraffin-embedded tumor samples. PMID:33509261
Cyclophilin D-dependent mitochondrial permeability transition amplifies inflammatory reprogramming in endotoxemia. PMID:33471430
A subset of liver resident natural killer cells is expanded in hepatitis C-infected patients with better liver function. PMID:33452360
Injection site vaccinology of a recombinant vaccinia-based vector reveals diverse innate immune signatures. PMID:33439897
Mexican Ganoderma Lucidum Extracts Decrease Lipogenesis Modulating Transcriptional Metabolic Networks and Gut Microbiota in C57BL/6 Mice Fed with a High-Cholesterol Diet. PMID:33374283
Alterations in TP53 Are a Potential Biomarker of Bladder Cancer Patients Who Benefit From Immune Checkpoint Inhibition. PMID:33356494
Immune response drives outcomes in prostate cancer: implications for immunotherapy. PMID:33338321
Transcriptomic and proteomic intra-tumor heterogeneity of colorectal cancer varies depending on tumor location within the colorectum. PMID:33332369
Prognostic Biomarker TP53 Mutations for Immune Checkpoint Blockade Therapy and Its Association With Tumor Microenvironment of Lung Adenocarcinoma. PMID:33330629
Enzalutamide response in a panel of prostate cancer cell lines reveals a role for glucocorticoid receptor in enzalutamide resistant disease. PMID:33303959
Transmembrane Prolyl 4-Hydroxylase is a Novel Regulator of Calcium Signaling in Astrocytes. PMID:33298456
A blood transcriptome-based analysis of disease progression, immune regulation, and symptoms in coronavirus-infected patients. PMID:33293514
Fifteen Years of Gene Set Analysis for High-Throughput Genomic Data: A Review of Statistical Approaches and Future Challenges. PMID:33286201
Differential immunomodulatory effect of PARP inhibition in BRCA1 deficient and competent tumor cells. PMID:33285109
Isabl Platform, a digital biobank for processing multimodal patient data. PMID:33256603
Application of the RBBP9 Serine Hydrolase Inhibitor, ML114, Decouples Human Pluripotent Stem Cell Proliferation and Differentiation. PMID:33256189
Role of LFA-1 integrin in the control of a lymphocytic choriomeningitis virus (LCMV) infection. PMID:33251934
An IL-27-Driven Transcriptional Network Identifies Regulators of IL-10 Expression across T Helper Cell Subsets. PMID:33238123
Embryonic periventricular endothelial cells demonstrate a unique pro-neurodevelopment and anti-inflammatory gene signature. PMID:33230288
Antagonistic Inflammatory Phenotypes Dictate Tumor Fate and Response to Immune Checkpoint Blockade. PMID:33220234
Bridging the Brain and Data Sciences. PMID:33211552
Aberrant expression of USF2 in refractory rheumatoid arthritis and its regulation of proinflammatory cytokines in Th17 cells. PMID:33203678
A Middle-Out Modeling Strategy to Extend a Colon Cancer Logical Model Improves Drug Synergy Predictions in Epithelial-Derived Cancer Cell Lines. PMID:33195403
Single-cell analyses identify dysfunctional CD16+ CD8 T cells in smokers. PMID:33163982
Serum lipoprotein-derived fatty acids regulate hypoxia-inducible factor. PMID:33109611
RNA sequencing of whole blood in dogs with primary immune-mediated hemolytic anemia (IMHA) reveals novel insights into disease pathogenesis. PMID:33091028
Involvement of a Transcription factor, Nfe2, in Breast Cancer Metastasis to Bone. PMID:33081224
SWI/SNF inactivation in the endometrial epithelium leads to loss of epithelial integrity. PMID:33075803
Phytotoxicity, Morphological, and Metabolic Effects of the Sesquiterpenoid Nerolidol on Arabidopsis thaliana Seedling Roots. PMID:33053766
Machine learning integration of scleroderma histology and gene expression identifies fibroblast polarisation as a hallmark of clinical severity and improvement. PMID:33028580
NFIA differentially controls adipogenic and myogenic gene program through distinct pathways to ensure brown and beige adipocyte differentiation. PMID:32991581
Genome-wide CRISPR screens of oral squamous cell carcinoma reveal fitness genes in the Hippo pathway. PMID:32990596
Next-Generation Analytics for Omics Data. PMID:32976776
Machine learning predicts stem cell transplant response in severe scleroderma. PMID:32933919
ATM Mutations Benefit Bladder Cancer Patients Treated With Immune Checkpoint Inhibitors by Acting on the Tumor Immune Microenvironment. PMID:32922441
Prognosis of Lung Adenocarcinoma Patients With NTRK3 Mutations to Immune Checkpoint Inhibitors. PMID:32903385
Drug Vulnerabilities and Disease Prognosis Linked to the Stem Cell-Like Gene Expression Program Triggered by the RHO GTPase Activator VAV2 in Hyperplastic Keratinocytes and Head and Neck Cancer. PMID:32899210
Sphingosine kinase 2 restricts T cell immunopathology but permits viral persistence. PMID:32897877
Proteomics identifies EGF-like domain multiple 7 as a potential therapeutic target for epidermal growth factor receptor-positive glioma. PMID:32888253
Immune landscape, evolution, hypoxia-mediated viral mimicry pathways and therapeutic potential in molecular subtypes of pancreatic neuroendocrine tumours. PMID:32883872
The genomic landscape of Mongolian hepatocellular carcinoma. PMID:32873799
Age-induced accumulation of methylmalonic acid promotes tumour progression. PMID:32814897
Id Proteins Promote a Cancer Stem Cell Phenotype in Mouse Models of Triple Negative Breast Cancer via Negative Regulation of Robo1. PMID:32766238
EPHA5 mutation predicts the durable clinical benefit of immune checkpoint inhibitors in patients with lung adenocarcinoma. PMID:32759987
Context-Dependent IL-1 mRNA-Destabilization by TTP Prevents Dysregulation of Immune Homeostasis Under Steady State Conditions. PMID:32733464
The Meningioma Enhancer Landscape Delineates Novel Subgroups and Drives Druggable Dependencies. PMID:32703768
Pathogenic Autoimmunity in Atherosclerosis Evolves From Initially Protective Apolipoprotein B100-Reactive CD4+ T-Regulatory Cells. PMID:32703007
Tumor Fibroblast Growth Factor Receptor 4 Level Predicts the Efficacy of Lenvatinib in Patients With Advanced Hepatocellular Carcinoma. PMID:32677805
Checkpoint Receptor TIGIT Expressed on Tim-1+ B Cells Regulates Tissue Inflammation. PMID:32668241
Impact of processing method on donated human breast milk microRNA content. PMID:32667939
Classical monocyte transcriptomes reveal significant anti-inflammatory statin effect in women with chronic HIV. PMID:32658258
Effects of valproic acid on histone deacetylase inhibition in vitro and in glioblastoma patient samples. PMID:32642660
A frameshift variant in specificity protein 1 triggers superactivation of Sp1-mediated transcription in familial bone marrow failure. PMID:32636268
The environmental stress response causes ribosome loss in aneuploid yeast cells. PMID:32632008
A Geometric Clustering Tool (AGCT) to robustly unravel the inner cluster structures of time-series gene expressions. PMID:32628677
Glioma escape signature and clonal development under immune pressure. PMID:32603315
The integrated genomic and epigenomic landscape of brainstem glioma. PMID:32555164
Chemogenomic profiling of breast cancer patient-derived xenografts reveals targetable vulnerabilities for difficult-to-treat tumors. PMID:32546838
Differentiation of the human PAX7-positive myogenic precursors/satellite cell lineage in vitro. PMID:32541004
TP53-Deficient Angiosarcoma Expression Profiling in Rat Model. PMID:32532104
Stem Cell Determinant SOX9 Promotes Lineage Plasticity and Progression in Basal-like Breast Cancer. PMID:32521267
Omics Integration Analyses Reveal the Early Evolution of Malignancy in Breast Cancer. PMID:32512721
Selective Mediator dependence of cell-type-specifying transcription. PMID:32483291
CSI NGS Portal: An Online Platform for Automated NGS Data Analysis and Sharing. PMID:32481589
Sindbis Virus with Anti-OX40 Overcomes the Immunosuppressive Tumor Microenvironment of Low-Immunogenic Tumors. PMID:32478167
Frequent upregulation of G9a promotes RelB-dependent proliferation and survival in multiple myeloma. PMID:32477831
LGR5 controls extracellular matrix production by stem cells in the developing intestine. PMID:32468660
Tradeoff between metabolic i-proteasome addiction and immune evasion in triple-negative breast cancer. PMID:32423906
The Genomic Landscape of Intrinsic and Acquired Resistance to Cyclin-Dependent Kinase 4/6 Inhibitors in Patients with Hormone Receptor-Positive Metastatic Breast Cancer. PMID:32404308
BRAFV600E expression in neural progenitors results in a hyperexcitable phenotype in neocortical pyramidal neurons. PMID:32401131
Amyloid-beta peptide neurotoxicity in human neuronal cells is associated with modulation of insulin-like growth factor transport, lysosomal machinery and extracellular matrix receptor interactions. PMID:32394972
Genomic landscape of platinum resistant and sensitive testicular cancers. PMID:32366847
MethCORR modelling of methylomes from formalin-fixed paraffin-embedded tissue enables characterization and prognostication of colorectal cancer. PMID:32332866
Transcriptional downregulation of MHC class I and melanoma de- differentiation in resistance to PD-1 inhibition. PMID:32312968
DolphinNext: a distributed data processing platform for high throughput genomics. PMID:32306927
Transcriptome sequencing reveals dynamic changes in matrix metalloproteinases in facet joint osteoarthritis. PMID:32256724
Landscape of copy number aberrations in esophageal squamous cell carcinoma from a high endemic region of South Africa. PMID:32252688
Urinary detection of lung cancer in mice via noninvasive pulmonary protease profiling. PMID:32238573
Targeting clinical epigenetic reprogramming for chemoprevention of metabolic and viral hepatocellular carcinoma. PMID:32217639
HNF1A recruits KDM6A to activate differentiated acinar cell programs that suppress pancreatic cancer. PMID:32154941
A Systematic Analysis Revealed the Potential Gene Regulatory Processes of ATRA-Triggered Neuroblastoma Differentiation and Identified a Novel RA Response Sequence in the NTRK2 Gene. PMID:32149119
Targeting of inflammatory pathways with R2CHOP in high-risk DLBCL. PMID:32139889
Distinct cachexia profiles in response to human pancreatic tumours in mouse limb and respiratory muscle. PMID:32039571
Identification of cancer driver genes based on nucleotide context. PMID:32015527
Knowledge-guided analysis of "omics" data using the KnowEnG cloud platform. PMID:31971940
In Silico Analysis of the Age-Dependent Evolution of the Transcriptome of Mouse Skin Stem Cells. PMID:31936599
Diversity spectrum analysis identifies mutation-specific effects of cancer driver genes. PMID:31925297
Integration of IgA and IgG Autoantigens Improves Performance of Biomarker Panels for Early Diagnosis of Lung Cancer. PMID:31924693
Metabolomics: A Way Forward for Crop Improvement. PMID:31847393
Vertical and horizontal integration of multi-omics data with miodin. PMID:31823712
The MS-lincRNA landscape reveals a novel lincRNA BCLIN25 that contributes to tumorigenesis by upregulating ERBB2 expression via epigenetic modification and RNA-RNA interactions in breast cancer. PMID:31801944
Transcriptome changes in undifferentiated Caco-2 cells exposed to food-grade titanium dioxide (E171): contribution of the nano- and micro- sized particles. PMID:31797963
The notch target gene HEYL modulates metastasis forming capacity of colorectal cancer patient-derived spheroid cells in vivo. PMID:31796022
Humanized Stem Cell Models of Pediatric Medulloblastoma Reveal an Oct4/mTOR Axis that Promotes Malignancy. PMID:31786016
PyIOmica: longitudinal omics analysis and trend identification. PMID:31778155
DAPK1 loss triggers tumor invasion in colorectal tumor cells. PMID:31772156
CREB5 Promotes Resistance to Androgen-Receptor Antagonists and Androgen Deprivation in Prostate Cancer. PMID:31747605
A Potent and Selective Small-Molecule Degrader of STAT3 Achieves Complete Tumor Regression In Vivo. PMID:31715132
Comprehensive Outline of Whole Exome Sequencing Data Analysis Tools Available in Clinical Oncology. PMID:31690036
Comparative genome-scale analysis of Pichia pastoris variants informs selection of an optimal base strain. PMID:31654411
MPIC: Molecular Prognostic Indicators in Cirrhosis Database for Clinical Context-Specific in Silico Prognostic Biomarker Validation. PMID:31620162
Adverse prognosis of glioblastoma contacting the subventricular zone: Biological correlates. PMID:31603915
Migratory and Dancing Macrophage Subsets in Atherosclerotic Lesions. PMID:31594470
Mitochondrial Reprogramming Underlies Resistance to BCL-2 Inhibition in Lymphoid Malignancies. PMID:31543463
Transcriptional Responses to IFN-γ Require Mediator Kinase-Dependent Pause Release and Mechanistically Distinct CDK8 and CDK19 Functions. PMID:31495563
Genetic hallmarks of recurrent/metastatic adenoid cystic carcinoma. PMID:31483290
Cytoscape Automation: empowering workflow-based network analysis. PMID:31477170
Metabolic switches from quiescence to growth in synchronized Saccharomyces cerevisiae. PMID:31468142
Depletion of the Transcriptional Coactivator Amplified in Breast Cancer 1 (AIB1) Uncovers Functionally Distinct Subpopulations in Triple-Negative Breast Cancer. PMID:31437536
ADAMDEC1 Maintains a Growth Factor Signaling Loop in Cancer Stem Cells. PMID:31434712
PAK4 suppresses RELB to prevent senescence-like growth arrest in breast cancer. PMID:31399573
Heterocellular gene signatures reveal luminal-A breast cancer heterogeneity and differential therapeutic responses. PMID:31396557
Neuroinflammatory astrocytes generated from cord blood-derived human induced pluripotent stem cells. PMID:31395092
Toxoplasma gondii infection drives conversion of NK cells into ILC1-like cells. PMID:31393266
Connecting signaling and metabolic pathways in EGF receptor-mediated oncogenesis of glioblastoma. PMID:31386654
Insulin Enhances Migration and Invasion in Prostate Cancer Cells by Up-Regulation of FOXC2. PMID:31379747
Individual liver plasmacytoid dendritic cells are capable of producing IFNα and multiple additional cytokines during chronic HCV infection. PMID:31356648
Molecular Evolution and Functional Analysis of Rubredoxin-Like Proteins in Plants. PMID:31355252
An Immune Gene Expression Signature Associated With Development of Human Hepatocellular Carcinoma Identifies Mice That Respond to Chemopreventive Agents. PMID:31344396
Canine osteosarcoma genome sequencing identifies recurrent mutations in DMD and the histone methyltransferase gene SETD2. PMID:31341965
E2F1 Drives Breast Cancer Metastasis by Regulating the Target Gene FGF13 and Altering Cell Migration. PMID:31341204
Integrative Genomic Characterization Identifies Molecular Subtypes of Lung Carcinoids. PMID:31300474
Tumor‑infiltrating M2 macrophages driven by specific genomic alterations are associated with prognosis in bladder cancer. PMID:31233191
MetaGxData: Clinically Annotated Breast, Ovarian and Pancreatic Cancer Datasets and their Use in Generating a Multi-Cancer Gene Signature. PMID:31217513
Targetable genetic alterations of TCF4 (E2-2) drive immunoglobulin expression in diffuse large B cell lymphoma. PMID:31217338
TCF1 and LEF1 Control Treg Competitive Survival and Tfr Development to Prevent Autoimmune Diseases. PMID:31216480
Cloud bursting galaxy: federated identity and access management. PMID:31197310
GenPipes: an open-source framework for distributed and scalable genomic analyses. PMID:31185495
Non-oncogene Addiction to SIRT3 Plays a Critical Role in Lymphomagenesis. PMID:31185214
Total copy number variation as a prognostic factor in adult astrocytoma subtypes. PMID:31177992
Airway host-microbiome interactions in chronic obstructive pulmonary disease. PMID:31170986
Receptor tyrosine kinases (RTKs) consociate in regulatory clusters in Alzheimer's disease and type 2 diabetes. PMID:31154588
Software engineering for scientific big data analysis. PMID:31121028
Identification of portal vein tumor thrombus with an independent clonal origin in hepatocellular carcinoma via multi-omics data analysis. PMID:31119055
Mitohormesis Primes Tumor Invasion and Metastasis. PMID:31116976
An accessible GenePattern notebook for the copy number variation analysis of Illumina Infinium DNA methylation arrays. PMID:31105932
modEnrichr: a suite of gene set enrichment analysis tools for model organisms. PMID:31069376
Combined Analysis of Metabolomes, Proteomes, and Transcriptomes of Hepatitis C Virus-Infected Cells and Liver to Identify Pathways Associated With Disease Development. PMID:30978357
Lactic acidosis caused by repressed lactate dehydrogenase subunit B expression down-regulates mitochondrial oxidative phosphorylation via the pyruvate dehydrogenase (PDH)-PDH kinase axis. PMID:30923124
A Machine Learning Classifier for Assigning Individual Patients With Systemic Sclerosis to Intrinsic Molecular Subsets. PMID:30920766
Semantic workflows for benchmark challenges: Enhancing comparability, reusability and reproducibility. PMID:30864323
Molecular Mechanisms of Polybrominated Diphenyl Ethers (BDE-47, BDE-100, and BDE-153) in Human Breast Cancer Cells and Patient-Derived Xenografts. PMID:30796839
L1 drives IFN in senescent cells and promotes age-associated inflammation. PMID:30728521
Targeting NOTCH activation in small cell lung cancer through LSD1 inhibition. PMID:30723171
GeneLab Database Analyses Suggest Long-Term Impact of Space Radiation on the Cardiovascular System by the Activation of FYN Through Reactive Oxygen Species. PMID:30717456
Blockade of RGMb inhibits allergen-induced airways disease. PMID:30703386
Stems cells, big data and compendium-based analyses for identifying cell types, signalling pathways and gene regulatory networks. PMID:30684132
Hope4Genes: a Hopfield-like class prediction algorithm for transcriptomic data. PMID:30674955
Identification and Characterization of Oncogenic SOS1 Mutations in Lung Adenocarcinoma. PMID:30635434
Epilepsy Associates with Decreased HIF-1α/STAT5b Signaling in Glioblastoma. PMID:30621209
SIX2 Mediates Late-Stage Metastasis via Direct Regulation of SOX2 and Induction of a Cancer Stem Cell Program. PMID:30606720
Dermal Condensate Niche Fate Specification Occurs Prior to Formation and Is Placode Progenitor Dependent. PMID:30595537
Regulation of mycobacterial infection by macrophage Gch1 and tetrahydrobiopterin. PMID:30573728
iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data. PMID:30567491
A Curated Resource for Phosphosite-specific Signature Analysis. PMID:30563849
Immunological and classical subtypes of oral premalignant lesions. PMID:30524889
Sex separation induces differences in the olfactory sensory receptor repertoires of male and female mice. PMID:30514924
MTBseq: a comprehensive pipeline for whole genome sequence analysis of Mycobacterium tuberculosis complex isolates. PMID:30479891
Dissecting clinical outcome of porcine circovirus type 2 with in vivo derived transcriptomic signatures of host tissue responses. PMID:30458705
BioJupies: Automated Generation of Interactive Notebooks for RNA-Seq Data Analysis in the Cloud. PMID:30447998
Constitutive Activation of NF-κB Pathway in Hematopoietic Stem Cells Causes Loss of Quiescence and Deregulated Transcription Factor Networks. PMID:30425986
Characterization of Proteome Variation During Modern Maize Breeding. PMID:30409858
RIVET: comprehensive graphic user interface for analysis and exploration of genome-wide translatomics data. PMID:30409155
Deep Learning-Based Multi-Omics Data Integration Reveals Two Prognostic Subtypes in High-Risk Neuroblastoma. PMID:30405689
Single sample scoring of molecular phenotypes. PMID:30400809
N6-methyladenine DNA Modification in Glioblastoma. PMID:30392959
CamurWeb: a classification software and a large knowledge base for gene expression data of cancer. PMID:30367574
Distributed Bayesian networks reconstruction on the whole genome scale. PMID:30364537
Genome-wide characterization of the NRAMP gene family in Phaseolus vulgaris provides insights into functional implications during common bean development. PMID:30334565
Cdh1 and Pik3ca Mutations Cooperate to Induce Immune-Related Invasive Lobular Carcinoma of the Breast. PMID:30332649
ATRX, DAXX or MEN1 mutant pancreatic neuroendocrine tumors are a distinct alpha-cell signature subgroup. PMID:30315258
Meta-analysis of data from spaceflight transcriptome experiments does not support the idea of a common bacterial "spaceflight response". PMID:30258082
Biologically anchored knowledge expansion approach uncovers KLF4 as a novel insulin signaling regulator. PMID:30240435
The Sjögren's syndrome-associated autoantigen Ro52/TRIM21 modulates follicular B cell homeostasis and immunoglobulin production. PMID:30178506
Systematic analysis reveals molecular characteristics of ERG-negative prostate cancer. PMID:30150711
Increased expression of the thyroid hormone nuclear receptor TRα1 characterizes intestinal tumors with high Wnt activity. PMID:30123421
Epithelial-to-mesenchymal transition signature assessment in colorectal cancer quantifies tumour stromal content rather than true transition. PMID:30105762
Vav proteins maintain epithelial traits in breast cancer cells using miR-200c-dependent and independent mechanisms. PMID:30087437
Selection of computational environments for PSP processing on scientific gateways. PMID:30073212
Acylsugar amount and fatty acid profile differentially suppress oviposition by western flower thrips, Frankliniella occidentalis, on tomato and interspecific hybrid flowers. PMID:30063755
An alternative splicing switch in FLNB promotes the mesenchymal cell state in human breast cancer. PMID:30059005
A microRNA signature and TGF-β1 response were identified as the key master regulators for spaceflight response. PMID:30044882
Thrombin and Plasmin Alter the Proteome of Neutrophil Extracellular Traps. PMID:30038618
Leukemogenic nucleophosmin mutation disrupts the transcription factor hub that regulates granulomonocytic fates. PMID:30015632
Immune signatures correlate with L1 retrotransposition in gastrointestinal cancers. PMID:29970450
Practical Computational Reproducibility in the Life Sciences. PMID:29953862
Transcriptomics analysis reveals new insights in E171-induced molecular alterations in a mouse model of colon cancer. PMID:29950665
Endogenous Protection from Ischemic Brain Injury by Preconditioned Monocytes. PMID:29946039
A recurrent point mutation in PRKCA is a hallmark of chordoid gliomas. PMID:29915258
Prioritizing predictive biomarkers for gene essentiality in cancer cells with mRNA expression data and DNA copy number profile. PMID:29912344
Induction and transcriptional regulation of the co-inhibitory gene module in T cells. PMID:29899446
SciApps: a cloud-based platform for reproducible bioinformatics workflows. PMID:29897418
Inhibition of Bacterial Gene Transcription with an RpoN-Based Stapled Peptide. PMID:29887265
Targeting of colony-stimulating factor 1 receptor (CSF1R) in the CLL microenvironment yields antineoplastic activity in primary patient samples. PMID:29872489
SV-BR-1-GM, a Clinically Effective GM-CSF-Secreting Breast Cancer Cell Line, Expresses an Immune Signature and Directly Activates CD4+ T Lymphocytes. PMID:29867922
The Immediate Early Gene Egr3 Is Required for Hippocampal Induction of Bdnf by Electroconvulsive Stimulation. PMID:29867393
Murine HPV16 E7-expressing transgenic skin effectively emulates the cellular and molecular features of human high-grade squamous intraepithelial lesions. PMID:29807614
Osteoglycin, a novel coordinator of bone and glucose homeostasis. PMID:29799418
Clinically Relevant Cytotoxic Immune Cell Signatures and Clonal Expansion of T-Cell Receptors in High-Risk MYCN-Not-Amplified Human Neuroblastoma. PMID:29784674
The transcriptomic and epigenetic map of vascular quiescence in the continuous lung endothelium. PMID:29749927
Genetic and Epigenetic Features of Rapidly Progressing IDH-Mutant Astrocytomas. PMID:29741737
Chronophin regulates active vitamin B6 levels and transcriptomic features of glioblastoma cell lines cultured under non-adherent, serum-free conditions. PMID:29724193
Analysis of the microRNA signature in left atrium from patients with valvular heart disease reveals their implications in atrial fibrillation. PMID:29723239
Multi-omics profiling of younger Asian breast cancers reveals distinctive molecular signatures. PMID:29713003
Loss of KLHL6 promotes diffuse large B-cell lymphoma growth and survival by stabilizing the mRNA decay factor roquin2. PMID:29695787
A systematic and prospectively validated approach for identifying synergistic drug combinations against malaria. PMID:29642892
Quantitative Proteomic Profiling of the Human Ovary from Early to Mid-Gestation Reveals Protein Expression Dynamics of Oogenesis and Folliculogenesis. PMID:29631484
Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas. PMID:29622466
A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers. PMID:29622464
Resveratrol Acts Anti-Inflammatory and Neuroprotective in an Infant Rat Model of Pneumococcal Meningitis by Modulating the Hippocampal miRNome. PMID:29611100
DNA Methylation variability among individuals is related to CpGs cluster density and evolutionary signatures. PMID:29606093
Functional genomics identifies specific vulnerabilities in PTEN-deficient breast cancer. PMID:29566768
New drug candidates for treatment of atypical meningiomas: An integrated approach using gene expression signatures for drug repurposing. PMID:29558515
Aqueous humor protein dysregulation in primary angle-closure glaucoma. PMID:29536409
Exploiting an Asp-Glu "switch" in glycogen synthase kinase 3 to design paralog-selective inhibitors for use in acute myeloid leukemia. PMID:29515000
Redirection to the bone marrow improves T cell persistence and antitumor functions. PMID:29485974
Regenerative proliferation of differentiated cells by mTORC1-dependent paligenosis. PMID:29467218
The SCN9A channel and plasma membrane depolarization promote cellular senescence through Rb pathway. PMID:29446526
Comprehensive characterisation of compartment-specific long non-coding RNAs associated with pancreatic ductal adenocarcinoma. PMID:29440233
Octopus-toolkit: a workflow to automate mining of public epigenomic and transcriptomic next-generation sequencing data. PMID:29420797
CancerDiscover: an integrative pipeline for cancer biomarker and cancer class prediction from high-throughput sequencing data. PMID:29416792
Integrated multi-omic analysis of host-microbiota interactions in acute oak decline. PMID:29378627
Large-scale copy number analysis reveals variations in genes not previously associated with malignant pleural mesothelioma. PMID:29371938
Respiromics - An integrative analysis linking mitochondrial bioenergetics to molecular signatures. PMID:29361498
qPortal: A platform for data-driven biomedical research. PMID:29352322
Histological subtypes of mouse mammary tumors reveal conserved relationships to human cancers. PMID:29346386
Human Placental-Derived Adherent Stromal Cells Co-Induced with TNF-α and IFN-γ Inhibit Triple-Negative Breast Cancer in Nude Mouse Xenograft Models. PMID:29330447
Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma. PMID:29301960
Scalable multi-sample single-cell data analysis by Partition-Assisted Clustering and Multiple Alignments of Networks. PMID:29281633
The impact on high-grade serous ovarian cancer of obesity and lipid metabolism-related gene expression patterns: the underestimated driving force affecting prognosis. PMID:29266765
GDC-0879, a BRAFV600E Inhibitor, Protects Kidney Podocytes from Death. PMID:29249695
Transcriptome-wide analysis of natural antisense transcripts shows their potential role in breast cancer. PMID:29234122
Pas de deux: An Intricate Dance of Anther Smut and Its Host. PMID:29196496
Mutant-IDH1-dependent chromatin state reprogramming, reversibility, and persistence. PMID:29180699
Challenges in the Setup of Large-scale Next-Generation Sequencing Analysis Workflows. PMID:29158876
Evaluation of two high-throughput proteomic technologies for plasma biomarker discovery in immunotherapy-treated melanoma patients. PMID:29152306
Transcriptional signature of human pro-inflammatory TH17 cells identifies reduced IL10 gene expression in multiple sclerosis. PMID:29150604
Multiplexed Biomarker Panels Discriminate Zika and Dengue Virus Infection in Humans. PMID:29141913
Genomic analysis of atypical fibroxanthoma. PMID:29141020
KLHL6 Is Preferentially Expressed in Germinal Center-Derived B-Cell Lymphomas. PMID:29140403
ω-3 polyunsaturated fatty acids direct differentiation of the membrane phenotype in mesenchymal stem cells to potentiate osteogenesis. PMID:29134198
PDGFR-modulated miR-23b cluster and miR-125a-5p suppress lung tumorigenesis by targeting multiple components of KRAS and NF-kB pathways. PMID:29133857
Novel lung imaging biomarkers and skin gene expression subsetting in dasatinib treatment of systemic sclerosis-associated interstitial lung disease. PMID:29121645
Tumor-adjacent tissue co-expression profile analysis reveals pro-oncogenic ribosomal gene signature for prognosis of resectable hepatocellular carcinoma. PMID:29117471
Belimumab for the Treatment of Early Diffuse Systemic Sclerosis: Results of a Randomized, Double-Blind, Placebo-Controlled, Pilot Trial. PMID:29073351
Identification of Serological Biomarkers for Early Diagnosis of Lung Cancer Using a Protein Array-Based Approach. PMID:29021294
Non-digestible oligosaccharides directly regulate host kinome to modulate host inflammatory responses without alterations in the gut microbiota. PMID:29017607
Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer. PMID:28988769
The lncRNA BORG Drives Breast Cancer Metastasis and Disease Recurrence. PMID:28983112
Isolation and detection of circulating tumour cells from metastatic melanoma patients using a slanted spiral microfluidic device. PMID:28978038
Role for ribosome-associated complex and stress-seventy subfamily B (RAC-Ssb) in integral membrane protein translation. PMID:28972146
In vitro toxicoproteomic analysis of A549 human lung epithelial cells exposed to urban air particulate matter and its water-soluble and insoluble fractions. PMID:28969663
Pathway-Enriched Gene Signature Associated with 53BP1 Response to PARP Inhibition in Triple-Negative Breast Cancer. PMID:28958991
Cellular heterogeneity contributes to subtype-specific expression of ZEB1 in human glioblastoma. PMID:28945795
Androgenic to oestrogenic switch in the human adult prostate gland is regulated by epigenetic silencing of steroid 5α-reductase 2. PMID:28940538
Integrated molecular analysis of Tamoxifen-resistant invasive lobular breast cancer cells identifies MAPK and GRM/mGluR signaling as therapeutic vulnerabilities. PMID:28935545
Targeted reconstruction of T cell receptor sequence from single cell RNA-seq links CDR3 length to T cell differentiation state. PMID:28934479
TGFbeta and miRNA regulation in familial and sporadic breast cancer. PMID:28881597
A 13-gene expression-based radioresistance score highlights the heterogeneity in the response to radiation therapy across HPV-negative HNSCC molecular subtypes. PMID:28859688
Stem Cell-Like Properties of CK2β-down Regulated Mammary Cells. PMID:28858215
PO and ID BCG vaccination in humans induce distinct mucosal and systemic immune responses and CD4+ T cell transcriptomal molecular signatures. PMID:28853442
Increased Effector Memory Insulin-Specific CD4+ T Cells Correlate With Insulin Autoantibodies in Patients With Recent-Onset Type 1 Diabetes. PMID:28842400
Asynchronous lineage priming determines commitment to T cell and B cell lineages in fetal liver. PMID:28825702
The GenePattern Notebook Environment. PMID:28822753
SG-ADVISER mtDNA: a web server for mitochondrial DNA annotation with data from 200 samples of a healthy aging cohort. PMID:28821228
NFIA co-localizes with PPARγ and transcriptionally controls the brown fat gene program. PMID:28812581
Genomic profiling of ER+ breast cancers after short-term estrogen suppression reveals alterations associated with endocrine resistance. PMID:28794284
GATA4 loss of function in liver cancer impedes precursor to hepatocyte transition. PMID:28758902
Induction of Sphk1 activity in obese adipose tissue macrophages promotes survival. PMID:28753653
Natural variation of macrophage activation as disease-relevant phenotype predictive of inflammation and cancer survival. PMID:28737175
Genomic landscape of high-grade meningiomas. PMID:28713588
Loss of DNA methylation in zebrafish embryos activates retrotransposons to trigger antiviral signaling. PMID:28698226
tsRNA signatures in cancer. PMID:28696308
CD40L and Its Receptors in Atherothrombosis-An Update. PMID:28676852
Limited cutaneous systemic sclerosis skin demonstrates distinct molecular subsets separated by a cardiovascular development gene expression signature. PMID:28676069
Paucimannose-Rich N-glycosylation of Spatiotemporally Regulated Human Neutrophil Elastase Modulates Its Immune Functions. PMID:28630087
Seed-effect modeling improves the consistency of genome-wide loss-of-function screens and identifies synthetic lethal vulnerabilities in cancer cells. PMID:28569207
Selective analysis of cancer-cell intrinsic transcriptional traits defines novel clinically relevant subtypes of colorectal cancer. PMID:28561063
Systematic discovery of mutation-specific synthetic lethals by mining pan-cancer human primary tumor data. PMID:28561042
Effects of genistein supplementation on genome‑wide DNA methylation and gene expression in patients with localized prostate cancer. PMID:28560383
Regulatory T Cells in Skin Facilitate Epithelial Stem Cell Differentiation. PMID:28552347
Host mediated inflammatory influence on glioblastoma multiforme recurrence following high-dose ionizing radiation. PMID:28542439
Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers. PMID:28542180
ASAP: a web-based platform for the analysis and interactive visualization of single-cell RNA-seq data. PMID:28541377
The microRNA miR-31 inhibits CD8+ T cell function in chronic viral infection. PMID:28530712
TWEAK mediates inflammation in experimental atopic dermatitis and psoriasis. PMID:28530223
GeMSTONE: orchestrated prioritization of human germline mutations in the cloud. PMID:28521008
Postzygotic single-nucleotide mosaicisms contribute to the etiology of autism spectrum disorder and autistic traits and the origin of mutations. PMID:28503910
shinyheatmap: Ultra fast low memory heatmap web interface for big data genomics. PMID:28493881
Integrative Analysis of MicroRNA-Mediated Gene Signatures and Pathways Modulating White Blood Cell Count in Childhood Acute Lymphoblastic Leukemia. PMID:28469402
An Integrative Genomics Approach for Associating Genome-Wide Association Studies Information With Localized and Metastatic Prostate Cancer Phenotypes. PMID:28469398
Conservation and innovation in the DUX4-family gene network. PMID:28459454
Neuroprotective effects of ellagic acid on cuprizone-induced acute demyelination through limitation of microgliosis, adjustment of CXCL12/IL-17/IL-11 axis and restriction of mature oligodendrocytes apoptosis. PMID:28447514
Tumour-associated changes in intestinal epithelial cells cause local accumulation of KLRG1+ GATA3+ regulatory T cells in mice. PMID:28437001
Extensive alterations of blood metabolites in pediatric cerebral malaria. PMID:28426698
A Kinase-Independent Role for Cyclin-Dependent Kinase 19 in p53 Response. PMID:28416637
GAD1 Upregulation Programs Aggressive Features of Cancer Cell Metabolism in the Brain Metastatic Microenvironment. PMID:28400476
eTumorType, An Algorithm of Discriminating Cancer Types for Circulating Tumor Cells or Cell-free DNAs in Blood. PMID:28389380
A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis. PMID:28330499
Comprehensive proteomic characterization of stem cell-derived extracellular matrices. PMID:28327460
The duplication mutation of Quebec platelet disorder dysregulates PLAU, but not C10orf55, selectively increasing production of normal PLAU transcripts by megakaryocytes but not granulocytes. PMID:28301587
The Shc1 adaptor simultaneously balances Stat1 and Stat3 activity to promote breast cancer immune suppression. PMID:28276425
Genome-wide transcriptomics of aging in the rotifer Brachionus manjavacas, an emerging model system. PMID:28249563
Mining Cancer Transcriptomes: Bioinformatic Tools and the Remaining Challenges. PMID:28229366
Identification of microRNAs associated with invasive and aggressive phenotype in cutaneous melanoma by next-generation sequencing. PMID:28218741
repo: an R package for data-centered management of bioinformatic pipelines. PMID:28209127
Module Anchored Network Inference: A Sequential Module-Based Approach to Novel Gene Network Construction from Genomic Expression Data on Human Disease Mechanism. PMID:28197408
The creatine kinase pathway is a metabolic vulnerability in EVI1-positive acute myeloid leukemia. PMID:28191887
Amplification of SOX4 promotes PI3K/Akt signaling in human breast cancer. PMID:28176176
Epigenome-Wide DNA Methylation Profiling Identifies Differential Methylation Biomarkers in High-Grade Bladder Cancer. PMID:28167242
miR-135a-5p-mediated downregulation of protein tyrosine phosphatase receptor delta is a candidate driver of HCV-associated hepatocarcinogenesis. PMID:28159835
MEDICI: Mining Essentiality Data to Identify Critical Interactions for Cancer Drug Target Discovery and Development. PMID:28118365
Tumor aneuploidy correlates with markers of immune evasion and with reduced response to immunotherapy. PMID:28104840
Clinical targeted exome-based sequencing in combination with genome-wide copy number profiling: precision medicine analysis of 203 pediatric brain tumors. PMID:28104717
Enrichment of putative PAX8 target genes at serous epithelial ovarian cancer susceptibility loci. PMID:28103614
Transcriptional analysis of mating and pre-infection stages of the anther smut, Microbotryum lychnidis-dioicae. PMID:28100297
Neuron-enriched RNA-binding Proteins Regulate Pancreatic Beta Cell Function and Survival. PMID:28077579
The CREBBP Acetyltransferase Is a Haploinsufficient Tumor Suppressor in B-cell Lymphoma. PMID:28069569
The primacy of NF1 loss as the driver of tumorigenesis in neurofibromatosis type 1-associated plexiform neurofibromas. PMID:28068329
GenomeCAT: a versatile tool for the analysis and integrative visualization of DNA copy number variants. PMID:28061750
DEIVA: a web application for interactive visual analysis of differential gene expression profiles. PMID:28061742
Planning bioinformatics workflows using an expert system. PMID:28052928
A Functional Genomic Meta-Analysis of Clinical Trials in Systemic Sclerosis: Toward Precision Medicine and Combination Therapy. PMID:28011145
Flexible model-based clustering of mixed binary and continuous data: application to genetic regulation and cancer. PMID:27994031
The Chromatin-Associated Phf12 Protein Maintains Nucleolar Integrity and Prevents Premature Cellular Senescence. PMID:27956701
Rare and common epilepsies converge on a shared gene regulatory network providing opportunities for novel antiepileptic drug discovery. PMID:27955713
Casitas B-cell lymphoma (Cbl) proteins protect mammary epithelial cells from proteotoxicity of active c-Src accumulation. PMID:27930322
Bone morphogenetic protein-2-mediated pain and inflammation in a rat model of posterolateral arthrodesis. PMID:27905881
Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform. PMID:27899609
The AP-1 transcription factor JunB is essential for multiple myeloma cell proliferation and drug resistance in the bone marrow microenvironment. PMID:27890927
MathIOmica: An Integrative Platform for Dynamic Omics. PMID:27883025
Conservation of immune gene signatures in solid tumors and prognostic implications. PMID:27871313
Reprogramming mouse fibroblasts into engraftable myeloerythroid and lymphoid progenitors. PMID:27869129
Transcriptome Dynamics and Potential Roles of Sox6 in the Postnatal Heart. PMID:27832192
Identification of Novel Biomarkers for Behcet Disease Diagnosis Using Human Proteome Microarray Approach. PMID:27777341
Landscape of Genomic Alterations in Pituitary Adenomas. PMID:27707790
The similar and different evolutionary trends of MATE family occurred between rice and Arabidopsis thaliana. PMID:27669820
OSAnalyzer: A Bioinformatics Tool for the Analysis of Gene Polymorphisms Enriched with Clinical Outcomes. PMID:27669316
MicroScope: ChIP-seq and RNA-seq software analysis suite for gene expression heatmaps. PMID:27659774
FBW7 suppression leads to SOX9 stabilization and increased malignancy in medulloblastoma. PMID:27625374
Timing of CSF-1/CSF-1R signaling blockade is critical to improving responses to CTLA-4 based immunotherapy. PMID:27622016
A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells. PMID:27610572
Multi-omics analysis of primary glioblastoma cell lines shows recapitulation of pivotal molecular features of parental tumors. PMID:27571888
Cell cycle arrest caused by MEK/ERK signaling is a mechanism for suppressing growth of antigen-hyperstimulated effector T cells. PMID:27543653
Selective single cell isolation for genomics using microraft arrays. PMID:27530426
A single nucleotide polymorphism genotyping platform for the authentication of patient derived xenografts. PMID:27528024
Prognostic relevance of molecular subtypes and master regulators in pancreatic ductal adenocarcinoma. PMID:27520560
Development of an integrated approach for comparison of in vitro and in vivo responses to particulate matter. PMID:27520027
A VEGF-dependent gene signature enriched in mesenchymal ovarian cancer predicts patient prognosis. PMID:27498762
Glutathione Transferases Superfamily: Cold-Inducible Expression of Distinct GST Genes in Brassica oleracea. PMID:27472324
Context Specific and Differential Gene Co-expression Networks via Bayesian Biclustering. PMID:27467526
The impact of tumor profiling approaches and genomic data strategies for cancer precision medicine. PMID:27460824
Underexpression of HOXA11 Is Associated with Treatment Resistance and Poor Prognosis in Glioblastoma. PMID:27456940
Control of the Inflammatory Macrophage Transcriptional Signature by miR-155. PMID:27447824
Crowdsourcing biomedical research: leveraging communities as innovation engines. PMID:27418159
IgG subclass switching and clonal expansion in cutaneous melanoma and normal skin. PMID:27411958
Transcriptional profiling reveals intrinsic mRNA alterations in multipotent mesenchymal stromal cells isolated from bone marrow of newly-diagnosed type 1 diabetes patients. PMID:27406064
Tools and techniques for computational reproducibility. PMID:27401684
Defining the Clinical Value of a Genomic Diagnosis in the Era of Next-Generation Sequencing. PMID:27362341
HDAC6 Deacetylates HMGN2 to Regulate Stat5a Activity and Breast Cancer Growth. PMID:27358110
Regulation of fetal liver growth in a model of diet restriction in the pregnant rat. PMID:27357801
Targeting MTHFD2 in acute myeloid leukemia. PMID:27325891
A crowdsourcing approach for reusing and meta-analyzing gene expression data. PMID:27323300
Computational flow cytometry: helping to make sense of high-dimensional immunology data. PMID:27320317
Maintenance-energy requirements and robustness of Saccharomyces cerevisiae at aerobic near-zero specific growth rates. PMID:27317316
Serum molecular signature for proliferative diabetic retinopathy in Saudi patients with type 2 diabetes. PMID:27307695
Calcineurin complex isolated from T-cell acute lymphoblastic leukemia (T-ALL) cells identifies new signaling pathways including mTOR/AKT/S6K whose inhibition synergize with calcineurin inhibition to promote T-ALL cell death. PMID:27304189
Motility and stem cell properties induced by the epithelial-mesenchymal transition require destabilization of lipid rafts. PMID:27303921
Presence of TMPRSS2-ERG is associated with alterations of the metabolic profile in human prostate cancer. PMID:27276682
SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis. PMID:27255077
Proteomic analysis of Plasmodium falciparum parasites from patients with cerebral and uncomplicated malaria. PMID:27245217
Transcription factor TLX1 controls retinoic acid signaling to ensure spleen development. PMID:27214556
Heatmapper: web-enabled heat mapping for all. PMID:27190236
Interleukin-15 receptor α on hepatic stellate cells regulates hepatic fibrogenesis in mice. PMID:27154062
Transcriptomic responses of mixed cultures of ascomycete fungi to lignocellulose using dual RNA-seq reveal inter-species antagonism and limited beneficial effects on CAZyme expression. PMID:27150814
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. PMID:27137889
Differential expression of major histocompatibility complex class I in subtypes of breast cancer is associated with estrogen receptor and interferon signaling. PMID:27121061
CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing. PMID:27100738
The cohesin-associated protein Wapal is required for proper Polycomb-mediated gene silencing. PMID:27087855
Factors affecting the persistence of drug-induced reprogramming of the cancer methylome. PMID:27082926
Interfacial geometry dictates cancer cell tumorigenicity. PMID:27043781
MicroRNA-375/SEC23A as biomarkers of the in vitro efficacy of vandetanib. PMID:27036030
Newborn Cystic Fibrosis Pigs Have a Blunted Early Response to an Inflammatory Stimulus. PMID:27027566
The dynamics of gene expression changes in a mouse model of oral tumorigenesis may help refine prevention and treatment strategies in patients with oral cancer. PMID:27027432
Molecular Analysis of Central Nervous System Disease Spectrum in Childhood Acute Lymphoblastic Leukemia. PMID:26997880
flowClean: Automated identification and removal of fluorescence anomalies in flow cytometry data. PMID:26990501
Identification of genes responsible for RelA-dependent proliferation arrest in human mammary epithelial cells conditionally expressing RelA. PMID:26981373
microRNA Profiles in Parkinson's Disease Prefrontal Cortex. PMID:26973511
LIN28B is over-expressed in specific subtypes of pediatric leukemia and regulates lncRNA H19. PMID:26969084
TIM3 Mediates T Cell Exhaustion during Mycobacterium tuberculosis Infection. PMID:26967901
Pathway Implications of Aberrant Global Methylation in Adrenocortical Cancer. PMID:26963385
Gene regulatory mechanisms underpinning prostate cancer susceptibility. PMID:26950096
Identification of STOML2 as a putative novel asthma risk gene associated with IL6R. PMID:26932604
Persistent effect of mTOR inhibition on preneoplastic foci progression and gene expression in a rat model of hepatocellular carcinoma. PMID:26905589
Autonomous Extracellular Matrix Remodeling Controls a Progressive Adaptation in Muscle Stem Cell Regenerative Capacity during Development. PMID:26904948
Activated Neutrophils Are Associated with Pediatric Cerebral Malaria Vasculopathy in Malawian Children. PMID:26884431
Pinin interacts with C-terminal binding proteins for RNA alternative splicing and epithelial cell identity of human ovarian cancer cells. PMID:26871283
Gene regulatory network inference using fused LASSO on multiple data sets. PMID:26864687
Netter: re-ranking gene network inference predictions using structural network properties. PMID:26862054
Metabolic stress is a barrier to Epstein-Barr virus-mediated B-cell immortalization. PMID:26802124
Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation. PMID:26795250
Autonomous beating rate adaptation in human stem cell-derived cardiomyocytes. PMID:26785135
Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace. PMID:26780094
Farewell to GBM-O: Genomic and transcriptomic profiling of glioblastoma with oligodendroglioma component reveals distinct molecular subgroups. PMID:26757882
Targeting polo-like kinase 1, a regulator of p53, in the treatment of adrenocortical carcinoma. PMID:26754547
Expression Characterization of Stress Genes Under High and Low Temperature Stresses in the Pacific Oyster, Crassostrea gigas. PMID:26746430
Tolerance is established in polyclonal CD4(+) T cells by distinct mechanisms, according to self-peptide expression patterns. PMID:26726812
Snord116 is critical in the regulation of food intake and body weight. PMID:26726071
Genetic alterations in fatty acid transport and metabolism genes are associated with metastatic progression and poor prognosis of human cancers. PMID:26725848
ELF5 Drives Lung Metastasis in Luminal Breast Cancer through Recruitment of Gr1+ CD11b+ Myeloid-Derived Suppressor Cells. PMID:26717410
A subset of myofibroblastic cancer-associated fibroblasts regulate collagen fiber elongation, which is prognostic in multiple cancers. PMID:26716418
NTRK1 fusions for the therapeutic intervention of Korean patients with colon cancer. PMID:26716414
The Macrophage Inhibitor CNI-1493 Blocks Metastasis in a Mouse Model of Ewing Sarcoma through Inhibition of Extravasation. PMID:26709919
SOX4 Is Essential for Prostate Tumorigenesis Initiated by PTEN Ablation. PMID:26701805
Novel Markers to Delineate Murine M1 and M2 Macrophages. PMID:26699615
Dintor: functional annotation of genomic and proteomic data. PMID:26691694
Cohort Profile: The MD Anderson Cancer Patients and Survivors Cohort (MDA-CPSC). PMID:26686840
Systematic identification and annotation of human methylation marks based on bisulfite sequencing methylomes reveals distinct roles of cell type-specific hypomethylation in the regulation of cell identity genes. PMID:26635396
Osteoclasts control reactivation of dormant myeloma cells by remodelling the endosteal niche. PMID:26632274
Drug Signature-based Finding of Additional Clinical Use of LC28-0126 for Neutrophilic Bronchial Asthma. PMID:26626943
ALK inhibitor resistance in ALK(F1174L)-driven neuroblastoma is associated with AXL activation and induction of EMT. PMID:26616860
A 4-gene expression score associated with high levels of Wilms Tumor-1 (WT1) expression is an adverse prognostic factor in acute myeloid leukaemia. PMID:26597595
Similar Squamous Cell Carcinoma Epithelium microRNA Expression in Never Smokers and Ever Smokers. PMID:26544609
Stroma-associated master regulators of molecular subtypes predict patient prognosis in ovarian cancer. PMID:26530441
Gender-specific differences in diabetic neuropathy in BTBR ob/ob mice. PMID:26525588
Changes in correlation between promoter methylation and gene expression in cancer. PMID:26510534
Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud. PMID:26501966
Thyroid Hormone Regulates the mRNA Expression of Small Heterodimer Partner through Liver Receptor Homolog-1. PMID:26485468
miRNA expression profiling of formalin-fixed paraffin-embedded (FFPE) hereditary breast tumors. PMID:26484152
Gene expression profiling to define the cell intrinsic role of the SKI proto-oncogene in hematopoiesis and myeloid neoplasms. PMID:26484093
RelA-Induced Interferon Response Negatively Regulates Proliferation. PMID:26460486
Hepatic Long Intergenic Noncoding RNAs: High Promoter Conservation and Dynamic, Sex-Dependent Transcriptional Regulation by Growth Hormone. PMID:26459762
Competitive SWIFT cluster templates enhance detection of aging changes. PMID:26441030
A Gene Expression Signature That Correlates with CD8+ T Cell Expansion in Acute EBV Infection. PMID:26416268
Repression by RB1 characterizes genes involved in the penultimate stage of erythroid development. PMID:26397180
SeqMule: automated pipeline for analysis of human exome/genome sequencing data. PMID:26381817
Preclinical Childhood Sarcoma Models: Drug Efficacy Biomarker Identification and Validation. PMID:26380223
Disruption of KMT2D perturbs germinal center B cell development and promotes lymphomagenesis. PMID:26366712
A systematic analysis reveals heterogeneous changes in the endocytic activities of cancer cells. PMID:26359453
Clustering of Expression Data in Chronic Lymphocytic Leukemia Reveals New Molecular Subdivisions. PMID:26355846
Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future. PMID:26309733
A Digital Repository and Execution Platform for Interactive Scholarly Publications in Neuroscience. PMID:26306864
Uterine activin receptor-like kinase 5 is crucial for blastocyst implantation and placental development. PMID:26305969
Identification of a Novel Coregulator, SH3YL1, That Interacts With the Androgen Receptor N-Terminus. PMID:26305679
Use of semantic workflows to enhance transparency and reproducibility in clinical omics. PMID:26289940
Nilotinib (Tasigna™) in the treatment of early diffuse systemic sclerosis: an open-label, pilot clinical trial. PMID:26283632
MUCOSAL IMMUNOLOGY. Individual intestinal symbionts induce a distinct population of RORγ⁺ regulatory T cells. PMID:26272906
Differentiation of pluripotent stem cells to muscle fiber to model Duchenne muscular dystrophy. PMID:26237517
Molecular characterization of systemic sclerosis esophageal pathology identifies inflammatory and proliferative signatures. PMID:26220546
QuickNGS elevates Next-Generation Sequencing data analysis to a new level of automation. PMID:26126663
Suppression of PGC-1α Is Critical for Reprogramming Oxidative Metabolism in Renal Cell Carcinoma. PMID:26119730
DNA copy number analysis of Grade II-III and Grade IV gliomas reveals differences in molecular ontogeny including chromothripsis associated with IDH mutation status. PMID:26091668
Neoplastic human embryonic stem cells as a model of radiation resistance of human cancer stem cells. PMID:26082437
Gene expression changes reflect clinical response in a placebo-controlled randomized trial of abatacept in patients with diffuse cutaneous systemic sclerosis. PMID:26071192
Strand-specific RNA sequencing in Plasmodium falciparum malaria identifies developmentally regulated long non-coding RNA and circular RNA. PMID:26070627
PADPIN: protein-protein interaction networks of angiogenesis, arteriogenesis, and inflammation in peripheral arterial disease. PMID:26058837
The DIONESUS algorithm provides scalable and accurate reconstruction of dynamic phosphoproteomic networks to reveal new drug targets. PMID:26057728
Transcriptome Analysis of Minimal Residual Disease in Subtypes of Pediatric B Cell Acute Lymphoblastic Leukemia. PMID:26056509
A hepatic stellate cell gene expression signature associated with outcomes in hepatitis C cirrhosis and hepatocellular carcinoma after curative resection. PMID:26045137
Unique somatic and malignant expression patterns implicate PIWI-interacting RNAs in cancer-type specific biology. PMID:26013764
An overhang-based DNA block shuffling method for creating a customized random library. PMID:26010273
Mechanism for enhanced 5-aminolevulinic acid fluorescence in isocitrate dehydrogenase 1 mutant malignant gliomas. PMID:26008980
Adaptation of HepG2 cells to a steady-state reduction in the content of protein phosphatase 6 (PP6) catalytic subunit. PMID:25999147
A comprehensive collection of systems biology data characterizing the host response to viral infection. PMID:25977790
Spinal Myxopapillary Ependymomas Demonstrate a Warburg Phenotype. PMID:25957288
NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data. PMID:25950236
A method for generating new datasets based on copy number for cancer analysis. PMID:25949998
Wnt/β-catenin controls follistatin signalling to regulate satellite cell myogenic potential. PMID:25949788
Profiling of the fetal and adult rat liver transcriptome and translatome reveals discordant regulation by the mechanistic target of rapamycin (mTOR). PMID:25924882
Antiviral Innate Immune Activation in HIV-Infected Adults Negatively Affects H1/IC31-Induced Vaccine-Specific Memory CD4+ T Cells. PMID:25924764
Proteomics-level analysis of myelin formation and regeneration in a mouse model for Vanishing White Matter disease. PMID:25920008
Loss of Wave1 gene defines a subtype of lethal prostate cancer. PMID:25906751
Subcutaneous fat transplantation alleviates diet-induced glucose intolerance and inflammation in mice. PMID:25899451
Unique patterns of transcript and miRNA expression in the South American strong voltage electric eel (Electrophorus electricus). PMID:25887781
Age and sun exposure-related widespread genomic blocks of hypomethylation in nonmalignant skin. PMID:25886480
Tumor evolution and intratumor heterogeneity of an epithelial ovarian cancer investigated using next-generation sequencing. PMID:25881093
Transcript profiles in cortical cells of maize primary root during ethylene-induced lysigenous aerenchyma formation under aerobic conditions. PMID:25858325
Flavin-containing monooxygenase 3 as a potential player in diabetes-associated atherosclerosis. PMID:25849138
NexGenEx-Tom: a gene expression platform to investigate the functionalities of the tomato genome. PMID:25849067
An epigenetically distinct breast cancer cell subpopulation promotes collective invasion. PMID:25844900
Expression profiles of 151 pediatric low-grade gliomas reveal molecular differences associated with location and histological subtype. PMID:25825052
Murine norovirus replication induces G0/G1 cell cycle arrest in asynchronously growing cells. PMID:25810556
Personal genomes, quantitative dynamic omics and personalized medicine. PMID:25798291
IL-4Rα-dependent alternative activation of macrophages is not decisive for Mycobacterium tuberculosis pathology and bacterial burden in mice. PMID:25790379
An atlas of gastric PIWI-interacting RNA transcriptomes and their utility for identifying signatures of gastric cancer recurrence. PMID:25779424
PATZ1 Is a DNA Damage-Responsive Transcription Factor That Inhibits p53 Function. PMID:25755280
Activation of muscular TrkB by its small molecular agonist 7,8-dihydroxyflavone sex-dependently regulates energy metabolism in diet-induced obese mice. PMID:25754472
A melanoma subtype with intrinsic resistance to BRAF inhibition identified by receptor tyrosine kinases gene-driven classification. PMID:25742786
Transcriptional profiling defines dynamics of parasite tissue sequestration during malaria infection. PMID:25722744
miR-27b synergizes with anticancer drugs via p53 activation and CYP1B1 suppression. PMID:25698578
Mycoplasma CG- and GATC-specific DNA methyltransferases selectively and efficiently methylate the host genome and alter the epigenetic landscape in human cells. PMID:25695131
Restricted dendritic cell and monocyte progenitors in human cord blood and bone marrow. PMID:25687283
β-PDGF receptor expressed by hepatic stellate cells regulates fibrosis in murine liver injury, but not carcinogenesis. PMID:25678385
EWI-2 negatively regulates TGF-β signaling leading to altered melanoma growth and metastasis. PMID:25656846
The evolution of drug resistance in clinical isolates of Candida albicans. PMID:25646566
ID helix-loop-helix proteins as determinants of cell survival in B-cell chronic lymphocytic leukemia cells in vitro. PMID:25644253
Transcriptional programs define molecular characteristics of innate lymphoid cell classes and subsets. PMID:25621825
Applying the logic of genetic interaction to discover small molecules that functionally interact with human disease alleles. PMID:25618333
Open pipelines for integrated tumor genome profiles reveal differences between pancreatic cancer tumors and cell lines. PMID:25594743
Effective targeting of the P53-MDM2 axis in preclinical models of infant MLL-rearranged acute lymphoblastic leukemia. PMID:25573381
Prevalent polymorphism in thyroid hormone-activating enzyme leaves a genetic fingerprint that underlies associated clinical syndromes. PMID:25569702
DNA hypomethylation induces a DNA replication-associated cell cycle arrest to block hepatic outgrowth in uhrf1 mutant zebrafish embryos. PMID:25564650
Identifying molecular subtypes related to clinicopathologic factors in pancreatic cancer. PMID:25560450
Unique genomic profile of fibrolamellar hepatocellular carcinoma. PMID:25557953
HeatmapGenerator: high performance RNAseq and microarray visualization software suite to examine differential gene expression levels using an R and C++ hybrid computational pipeline. PMID:25550709
CT perfusion as an imaging biomarker in monitoring response to neoadjuvant bevacizumab and radiation in soft-tissue sarcomas: comparison with tumor morphology, circulating and tumor biomarkers, and gene expression. PMID:25539263
Comparative transcriptome analyses reveal core parasitism genes and suggest gene duplication and repurposing as sources of structural novelty. PMID:25534030
A novel patient-derived tumorgraft model with TRAF1-ALK anaplastic large-cell lymphoma translocation. PMID:25533804
Molecular characterization of an intact p53 pathway subtype in high-grade serous ovarian cancer. PMID:25460179
Prostaglandin D2 and leukotriene E4 synergize to stimulate diverse TH2 functions and TH2 cell/neutrophil crosstalk. PMID:25441644
High dimensional biological data retrieval optimization with NoSQL technology. PMID:25435347
Survival analysis tools in genomics research. PMID:25421963
Next-generation sequencing of acute myeloid leukemia identifies the significance of TP53, U2AF1, ASXL1, and TET2 mutations. PMID:25412851
Epigenetic modulation of type-1 diabetes via a dual effect on pancreatic macrophages and β cells. PMID:25407682
Combined microRNA and ER expression: a new classifier for familial and sporadic breast cancer patients. PMID:25406994
Matrix metalloproteinase 9 production by monocytes is enhanced by TNF and participates in the pathology of human cutaneous Leishmaniasis. PMID:25393535
MicroRNA expression profiling in male and female familial breast cancer. PMID:25393370
Calcifying vascular smooth muscle cells and osteoblasts: independent cell types exhibiting extracellular matrix and biomineralization-related mimicries. PMID:25380738
High-resolution transcript profiling of the atypical biotrophic interaction between Theobroma cacao and the fungal pathogen Moniliophthora perniciosa. PMID:25371547
Prognostic biomarkers for HNSCC using quantitative real-time PCR and microarray analysis: β-tubulin isotypes and the p53 interactome. PMID:25355403
Hmga2 regulates self-renewal of retinal progenitors. PMID:25336737
Visualization of the entire differentiation process of murine M cells: suppression of their maturation in cecal patches. PMID:25336168
Angiogenesis interactome and time course microarray data reveal the distinct activation patterns in endothelial cells. PMID:25329517
GHK and DNA: resetting the human genome to health. PMID:25302294
Multiple Components of the VHL Tumor Suppressor Complex Are Frequently Affected by DNA Copy Number Loss in Pheochromocytoma. PMID:25298778
Genome-wide scan identifies a copy number variable region at 3p21.1 that influences the TLR9 expression levels in IgA nephropathy patients. PMID:25293716
Urine, peritoneal fluid and omental fat proteomes of reproductive age women: Endometriosis-related changes and associations with endocrine disrupting chemicals. PMID:25284053
A non-parametric Bayesian model for joint cell clustering and cluster matching: identification of anomalous sample phenotypes with random effects. PMID:25248977
Genomic analyses and transcriptional profiles of the glycoside hydrolase family 18 genes of the entomopathogenic fungus Metarhizium anisopliae. PMID:25232743
Molecular rationale for the use of PI3K/AKT/mTOR pathway inhibitors in combination with crizotinib in ALK-mutated neuroblastoma. PMID:25228590
Dysfunction of dendritic cells in aged C57BL/6 mice leads to failure of natural killer cell activation and of tumor eradication. PMID:25225399
Accelerating translational research by clinically driven development of an informatics platform--a case study. PMID:25203647
An integrated genomics approach identifies drivers of proliferation in luminal-subtype human breast cancer. PMID:25151356
Bioinformatic analysis reveals a pattern of STAT3-associated gene expression specific to basal-like breast cancers in human tumors. PMID:25139989
Unique pattern of component gene disruption in the NRF2 inhibitor KEAP1/CUL3/RBX1 E3-ubiquitin ligase complex in serous ovarian cancer. PMID:25114896
Bioinformatic approaches to augment study of epithelial-to-mesenchymal transition in lung cancer. PMID:25096367
SOX2 is a cancer-specific regulator of tumour initiating potential in cutaneous squamous cell carcinoma. PMID:25077433
Integrative genomic analysis for the discovery of biomarkers in prostate cancer. PMID:25057237
Insm1 promotes endocrine cell differentiation by modulating the expression of a network of genes that includes Neurog3 and Ripply3. PMID:25053427
Mutant IDH inhibits HNF-4α to block hepatocyte differentiation and promote biliary cancer. PMID:25043045
Post-transcriptional regulation of BCL2 mRNA by the RNA-binding protein ZFP36L1 in malignant B cells. PMID:25014217
Obatoclax overcomes resistance to cell death in aggressive thyroid carcinomas by countering Bcl2a1 and Mcl1 overexpression. PMID:25012986
The SMRT coregulator enhances growth of estrogen receptor-α-positive breast cancer cells by promotion of cell cycle progression and inhibition of apoptosis. PMID:24971610
Gene Set Enrichment Analysis (GSEA) of Toxoplasma gondii expression datasets links cell cycle progression and the bradyzoite developmental program. PMID:24962434
dbCerEx: a web-based database for the analysis of cervical cancer transcriptomes. PMID:24918550
Integrative analysis of transcriptional regulatory network and copy number variation in intrahepatic cholangiocarcinoma. PMID:24897108
The expression pattern of 19 genes predicts the histology of endometrial carcinoma. PMID:24894155
Transient expression of Bcl6 is sufficient for oncogenic function and induction of mature B-cell lymphoma. PMID:24887457
Exome sequencing identifies somatic gain-of-function PPM1D mutations in brainstem gliomas. PMID:24880341
A glimpse into the interactions of cells in a microenvironment: the modulation of T cells by mesenchymal stem cells. PMID:24872708
Identification of the RNA recognition element of the RBPMS family of RNA-binding proteins and their transcriptome-wide mRNA targets. PMID:24860013
Glucocorticoid-induced reversal of interleukin-1β-stimulated inflammatory gene expression in human oviductal cells. PMID:24848801
Bystander chronic infection negatively impacts development of CD8(+) T cell memory. PMID:24837104
Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine. PMID:24836576
Integrating omics technologies to study pulmonary physiology and pathology at the systems level. PMID:24802001
The role of carbon starvation in the induction of enzymes that degrade plant-derived carbohydrates in Aspergillus niger. PMID:24792495
Fluoxetine prevents dystrophic changes in a zebrafish model of Duchenne muscular dystrophy. PMID:24760771
Quantitative-proteomic comparison of alpha and Beta cells to uncover novel targets for lineage reprogramming. PMID:24759943
Triplication of a 21q22 region contributes to B cell transformation through HMGN1 overexpression and loss of histone H3 Lys27 trimethylation. PMID:24747640
Art27 interacts with GATA4, FOG2 and NKX2.5 and is a novel co-repressor of cardiac genes. PMID:24743694
Integrated genomic analysis illustrates the central role of JAK-STAT pathway activation in myeloproliferative neoplasm pathogenesis. PMID:24740812
Mesenchymal phenotype of CTC-enriched blood fraction and lymph node metastasis formation potential. PMID:24709997
Epidermal Wnt/β-catenin signaling regulates adipocyte differentiation via secretion of adipogenic factors. PMID:24706781
Targeted sequencing for gene discovery and quantification using RNA CaptureSeq. PMID:24705597
illuminaio: An open source IDAT parsing tool for Illumina microarrays. PMID:24701342
Tumor associated seizures in glioblastomas are influenced by survival gene expression in a region-specific manner: a gene expression imaging study. PMID:24690158
Serological screening of the Schistosoma mansoni adult worm proteome. PMID:24651847
Transcript analysis reveals a specific HOX signature associated with positional identity of human endothelial cells. PMID:24651450
Immunomic, genomic and transcriptomic characterization of CT26 colorectal carcinoma. PMID:24621249
Genotoxic changes to rodent cells exposed in vitro to tungsten, nickel, cobalt and iron. PMID:24619124
Molecular subtypes of glioblastoma are relevant to lower grade glioma. PMID:24614622
Translational research platforms integrating clinical and omics data: a review of publicly available solutions. PMID:24608524
An epigenetic mechanism of resistance to targeted therapy in T cell acute lymphoblastic leukemia. PMID:24584072
Gap junction modulation and its implications for heart function. PMID:24578694
Traumatic injury, early gene expression, and gram-negative bacteremia. PMID:24561564
Molecular profiling of Mycobacterium tuberculosis identifies tuberculosinyl nucleoside products of the virulence-associated enzyme Rv3378c. PMID:24516143
Ectopic expression of HOXC6 blocks myeloid differentiation and predisposes to malignant transformation. PMID:24513167
Transcriptome profiling of archived sectioned formalin-fixed paraffin-embedded (AS-FFPE) tissue for disease classification. PMID:24498002
geneCommittee: a web-based tool for extensively testing the discriminatory power of biologically relevant gene sets in microarray data classification. PMID:24475928
Unifying immunology with informatics and multiscale biology. PMID:24448569
A T cell gene expression panel for the diagnosis and monitoring of disease activity in patients with systemic lupus erythematosus. PMID:24434273
Comparing the biological impact of glatiramer acetate with the biological impact of a generic. PMID:24421904
Human classical monocytes control the intracellular stage of Leishmania braziliensis by reactive oxygen species. PMID:24403561
Pten loss in Olig2 expressing neural progenitor cells and oligodendrocytes leads to interneuron dysplasia and leukodystrophy. PMID:24395742
Lipocalin-2 (Lcn2) expression is mediated by maternal nutrition during the development of the fetal liver. PMID:24382649
Flow cytometry bioinformatics. PMID:24363631
Inferring developmental stage composition from gene expression in human malaria. PMID:24348235
Mesenchymal-transitioned cancer cells instigate the invasion of epithelial cancer cells through secretion of WNT3 and WNT5B. PMID:24344732
A flexible statistical model for alignment of label-free proteomics data--incorporating ion mobility and product ion information. PMID:24341404
Metatranscriptomic and functional metagenomic analysis of methylphosphonate utilization by marine bacteria. PMID:24324460
Array data extractor (ADE): a LabVIEW program to extract and merge gene array data. PMID:24289243
Differential response to abiraterone acetate and di-n-butyl phthalate in an androgen-sensitive human fetal testis xenograft bioassay. PMID:24284787
Constitutive function of the Ikaros transcription factor in primary leukemia cells from pediatric newly diagnosed high-risk and relapsed B-precursor ALL patients. PMID:24278314
Changes in transcript abundance for cuticular proteins and other genes three hours after a blood meal in Anopheles gambiae. PMID:24269292
Transcriptome analysis of Salicornia europaea under saline conditions revealed the adaptive primary metabolic pathways as early events to facilitate salt adaptation. PMID:24265831
Altered gene expression in dry age-related macular degeneration suggests early loss of choroidal endothelial cells. PMID:24265543
Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia. PMID:24265505
The genetic landscape of clinical resistance to RAF inhibition in metastatic melanoma. PMID:24265153
Deciphering genomic alterations in colorectal cancer through transcriptional subtype-based network analysis. PMID:24260186
Identification of a neuronal transcription factor network involved in medulloblastoma development. PMID:24252690
Metabolic stress-induced microRNA and mRNA expression profiles of human fibroblasts. PMID:24246224
Cross-platform prediction of gene expression signatures. PMID:24244455
PTTG1 overexpression in adrenocortical cancer is associated with poor survival and represents a potential therapeutic target. PMID:24238056
Ten simple rules for reproducible computational research. PMID:24204232
Recurrence patterns across medulloblastoma subgroups: an integrated clinical and molecular analysis. PMID:24140199
Gene signatures related to B-cell proliferation predict influenza vaccine-induced antibody response. PMID:24136404
The CF-modifying gene EHF promotes p.Phe508del-CFTR residual function by altering protein glycosylation and trafficking in epithelial cells. PMID:24105369
MicroRNA-based molecular classification of non-BRCA1/2 hereditary breast tumours. PMID:24104964
Guide: a desktop application for analysing gene expression data. PMID:24093424
Transcriptional changes and developmental abnormalities in a zebrafish model of myotonic dystrophy type 1. PMID:24092878
Gfi1 and gfi1b repress rag transcription in plasmacytoid dendritic cells in vitro. PMID:24086657
INVEX--a web-based tool for integrative visualization of expression data. PMID:24078684
Pathway-based outlier method reveals heterogeneous genomic structure of autism in blood transcriptome. PMID:24063311
Methylation profiling and evaluation of demethylating therapy in renal cell carcinoma. PMID:24034811
Analysis of Patterns of Gene Expression Variation within and between Ethnic Populations in Pediatric B-ALL. PMID:24023509
Tissue-specific profiling reveals transcriptome alterations in Arabidopsis mutants lacking morphological phenotypes. PMID:24014549
BET inhibition silences expression of MYCN and BCL2 and induces cytotoxicity in neuroblastoma tumor models. PMID:24009722
Genome-wide investigation of the role of the tRNA nuclear-cytoplasmic trafficking pathway in regulation of the yeast Saccharomyces cerevisiae transcriptome and proteome. PMID:23979602
Large scale comparison of gene expression levels by microarrays and RNAseq using TCGA data. PMID:23977046
Microbial colonization influences early B-lineage development in the gut lamina propria. PMID:23965619
Tetraspanin TSPAN12 regulates tumor growth and metastasis and inhibits β-catenin degradation. PMID:23955570
GobyWeb: simplified management and analysis of gene expression and DNA methylation sequencing data. PMID:23936070
Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data. PMID:23895370
MYBL2 is a sub-haploinsufficient tumor suppressor gene in myeloid malignancy. PMID:23878725
Cytotoxic T cells mediate pathology and metastasis in cutaneous leishmaniasis. PMID:23874205
Correlation analysis connects cancer subtypes. PMID:23861980
The role of oxidative stress in nervous system aging. PMID:23844146
GenePattern flow cytometry suite. PMID:23822732
Glioma microvesicles carry selectively packaged coding and non-coding RNAs which alter gene expression in recipient cells. PMID:23807490
Histone demethylase Lsd1 represses hematopoietic stem and progenitor cell signatures during blood cell maturation. PMID:23795291
The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability. PMID:23793381
Neuron enriched nuclear proteome isolated from human brain. PMID:23768213
Maternal obesity and diabetes induces latent metabolic defects and widespread epigenetic changes in isogenic mice. PMID:23764993
Novel Integrative Genomics Approach for Associating GWAS Information with Intrinsic Subtypes of Breast Cancer. PMID:23761956
Gene expression profiling identifies different sub-types of retinoblastoma. PMID:23756868
CD33 Alzheimer's disease locus: altered monocyte function and amyloid biology. PMID:23708142
An aberrant transcription factor network essential for Wnt signaling and stem cell maintenance in glioblastoma. PMID:23707066
Stat and interferon genes identified by network analysis differentially regulate primitive and definitive erythropoiesis. PMID:23675896
Functional genomics identifies five distinct molecular subtypes with clinical relevance and pathways for growth control in epithelial ovarian cancer. PMID:23666744
Degree of focal immunoglobulin heavy chain locus deletion as a measure of B-cell tumor purity. PMID:23644420
Peripheral blood gene expression signature differentiates children with autism from unaffected siblings. PMID:23625158
Genetic evidence for p75NTR-dependent tetraploidy in cortical projection neurons from adult mice. PMID:23616554
Anatomical localization, gene expression profiling and functional characterization of adult human neck brown fat. PMID:23603815
The microRNA miR-155 controls CD8(+) T cell responses by regulating interferon signaling. PMID:23603793
Computational solutions for omics data. PMID:23594911
Identification of nine genomic regions of amplification in urothelial carcinoma, correlation with stage, and potential prognostic and therapeutic value. PMID:23593348
Defining the transcriptional and cellular landscape of type 1 diabetes in the NOD mouse. PMID:23555752
Physiological and transcriptional responses of Saccharomyces cerevisiae to d-limonene show changes to the cell wall but not to the plasma membrane. PMID:23542628
Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity. PMID:23525077
Where in the genome are we? A cautionary tale of database use in genomics research. PMID:23519237
The landscape of host transcriptional response programs commonly perturbed by bacterial pathogens: towards host-oriented broad-spectrum drug targets. PMID:23516507
ETV1 directs androgen metabolism and confers aggressive prostate cancer in targeted mice and patients. PMID:23512661
Functional genomic and phenotypic responses to desiccation in natural populations of a desert drosophilid. PMID:23505972
GATA factors efficiently direct cardiac fate from embryonic stem cells. PMID:23487308
Depletion of Jak2V617F myeloproliferative neoplasm-propagating stem cells by interferon-α in a murine model of polycythemia vera. PMID:23487027
An integrative genomic and transcriptomic analysis reveals potential targets associated with cell proliferation in uterine leiomyomas. PMID:23483937
Sodium chloride drives autoimmune disease by the induction of pathogenic TH17 cells. PMID:23467095
Dynamic regulatory network controlling TH17 cell differentiation. PMID:23467089
Induction of pathogenic TH17 cells by inducible salt-sensing kinase SGK1. PMID:23467085
In silico estimation of translation efficiency in human cell lines: potential evidence for widespread translational control. PMID:23460887
Differential effects of drug interventions and dietary lifestyle in developing type 2 diabetes and complications: a systems biology analysis in LDLr-/- mice. PMID:23457508
Signaling between transforming growth factor β (TGF-β) and transcription factor SNAI2 represses expression of microRNA miR-203 to promote epithelial-mesenchymal transition and tumor metastasis. PMID:23447531
Targeting MYCN in neuroblastoma by BET bromodomain inhibition. PMID:23430699
DOT1L-mediated H3K79 methylation in chromatin is dispensable for Wnt pathway-specific and other intestinal epithelial functions. PMID:23428873
The anti-CD19 antibody-drug conjugate SAR3419 prevents hematolymphoid relapse postinduction therapy in preclinical models of pediatric acute lymphoblastic leukemia. PMID:23426279
An Integrative Genomics Approach for Associating GWAS Information with Triple-Negative Breast Cancer. PMID:23423317
Nozzle: a report generation toolkit for data analysis pipelines. PMID:23419376
Concise review: new paradigms for Down syndrome research using induced pluripotent stem cells: tackling complex human genetic disease. PMID:23413375
Genome-wide identification and analysis of the B3 superfamily of transcription factors in Brassicaceae and major crop plants. PMID:23377560
Visualizing multidimensional cancer genomics data. PMID:23363777
Leukemic transformation by the MLL-AF6 fusion oncogene requires the H3K79 methyltransferase Dot1l. PMID:23361907
Next-generation text-mining mediated generation of chemical response-specific gene sets for interpretation of gene expression data. PMID:23356878
MicroRNA miR-308 regulates dMyc through a negative feedback loop in Drosophila. PMID:23336071
Genomic sequencing of meningiomas identifies oncogenic SMO and AKT1 mutations. PMID:23334667
Prognostic gene expression signature for patients with hepatitis C-related early-stage cirrhosis. PMID:23333348
Angiotensin II drives the production of tumor-promoting macrophages. PMID:23333075
ISA-TAB-Nano: a specification for sharing nanomaterial research data in spreadsheet-based format. PMID:23311978
Oxidative damage in clinical ischemia/reperfusion injury: a reappraisal. PMID:23305329
Identification of epigenetically altered genes in sporadic amyotrophic lateral sclerosis. PMID:23300739
Identification of accessory genome regions in poultry Clostridium perfringens isolates carrying the netB plasmid. PMID:23292780
Research resource: nuclear receptors as transcriptome: discriminant and prognostic value in breast cancer. PMID:23292282
ZFP36L1 negatively regulates plasmacytoid differentiation of BCL1 cells by targeting BLIMP1 mRNA. PMID:23284928
Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package. PMID:23281941
ATARiS: computational quantification of gene suppression phenotypes from multisample RNAi screens. PMID:23269662
Architecture for interoperable software in biology. PMID:23235920
Loss of anterior gradient 2 (Agr2) expression results in hyperplasia and defective lineage maturation in the murine stomach. PMID:23209296
ArrayExpress update--trends in database growth and links to data analysis tools. PMID:23193272
Comparability and reproducibility of biomedical data. PMID:23193203
A metabolic signature for long life in the Caenorhabditis elegans Mit mutants. PMID:23173729
5-aza-2'-deoxycytidine has minor effects on differentiation in human thyroid cancer cell lines, but modulates genes that are involved in adaptation in vitro. PMID:23167291
Network analysis reveals centrally connected genes and pathways involved in CD8+ T cell exhaustion versus memory. PMID:23159438
InSilico DB genomic datasets hub: an efficient starting point for analyzing genome-wide studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor. PMID:23158523
A toolkit for bulk PCR-based marker design from next-generation sequence data: application for development of a framework linkage map in bulb onion (Allium cepa L.). PMID:23157543
The miR-290-295 cluster suppresses autophagic cell death of melanoma cells. PMID:23150779
CDX2 is an amplified lineage-survival oncogene in colorectal cancer. PMID:23112155
Subnuclear cyclin D3 compartments and the coordinated regulation of proliferation and immunoglobulin variable gene repression. PMID:23109711
Automatic assignment of prokaryotic genes to functional categories using literature profiling. PMID:23077617
Combining multiple hypothesis testing and affinity propagation clustering leads to accurate, robust and sample size independent classification on gene expression data. PMID:23075381
Dual specificity phosphatase 4 mediates cardiomyopathy caused by lamin A/C (LMNA) gene mutation. PMID:23048029
Precise probes of type II interferon activity define the origin of interferon signatures in target tissues in rheumatic diseases. PMID:23045702
Cross-presenting CD103+ dendritic cells are protected from influenza virus infection. PMID:23041628
Profiling the anaerobic response of C. elegans using GC-MS. PMID:23029411
Astrogliosis during acute and chronic cuprizone demyelination and implications for remyelination. PMID:23025787
Influenza enhances caspase-1 in bronchial epithelial cells from asthmatic volunteers and is associated with pathogenesis. PMID:23021143
An RNA profile identifies two subsets of multiple sclerosis patients differing in disease activity. PMID:23019656
The cytokines interleukin 27 and interferon-γ promote distinct Treg cell populations required to limit infection-induced pathology. PMID:22981537
Notch signaling is activated in human hepatocellular carcinoma and induces tumor formation in mice. PMID:22974708
A novel imaging system permits real-time in vivo tumor bed assessment after resection of naturally occurring sarcomas in dogs. PMID:22972654
Transcriptome classification reveals molecular subtypes in psoriasis. PMID:22971201
A multiply redundant genetic switch 'locks in' the transcriptional signature of regulatory T cells. PMID:22961053
Induction and molecular signature of pathogenic TH17 cells. PMID:22961052
Expression of human paraoxonase 1 decreases superoxide levels and alters bacterial colonization in the gut of Drosophila melanogaster. PMID:22952763
Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling. PMID:22913808
Small-molecule inhibition of BRDT for male contraception. PMID:22901802
Imp2 controls oxidative phosphorylation and is crucial for preserving glioblastoma cancer stem cells. PMID:22899010
Next-generation sequencing data interpretation: enhancing reproducibility and accessibility. PMID:22898652
O6-Methylguanine DNA lesions induce an intra-S-phase arrest from which cells exit into apoptosis governed by early and late multi-pathway signaling network activation. PMID:22892544
Cloudgene: a graphical execution platform for MapReduce programs on private and public clouds. PMID:22888776
Analysis of Epstein-Barr virus-regulated host gene expression changes through primary B-cell outgrowth reveals delayed kinetics of latent membrane protein 1-mediated NF-κB activation. PMID:22855490
An integrated functional genomics approach identifies the regulatory network directed by brachyury (T) in chordoma. PMID:22847733
Global expression profiling of globose basal cells and neurogenic progression within the olfactory epithelium. PMID:22847514
A phase I trial of dasatinib, an SRC-family kinase inhibitor, in combination with paclitaxel and carboplatin in patients with advanced or recurrent ovarian cancer. PMID:22837181
Inhibition of phosphodiesterase-4 (PDE4) activity triggers luminal apoptosis and AKT dephosphorylation in a 3-D colonic-crypt model. PMID:22830422
A gene expression signature distinguishes normal tissues of sporadic and radiation-induced papillary thyroid carcinomas. PMID:22828612
Copy number aberrations of BCL2 and CDKN2A/B identified by array-CGH in thymic epithelial tumors. PMID:22825469
Transcriptional profiling of Plasmodium falciparum parasites from patients with severe malaria identifies distinct low vs. high parasitemic clusters. PMID:22815802
Reduced retinal microvascular density, improved forepaw reach, comparative microarray and gene set enrichment analysis with c-jun targeting DNA enzyme. PMID:22815700
Wnt-pathway activation in two molecular classes of hepatocellular carcinoma and experimental modulation by sorafenib. PMID:22811581
Recurrent transcriptional clusters in the genome of mouse pluripotent stem cells. PMID:22798478
Deciphering the transcriptional network of the dendritic cell lineage. PMID:22797772
Wisdom of crowds for robust gene network inference. PMID:22796662
Identification of human germinal center light and dark zone cells and their relationship to human B-cell lymphomas. PMID:22740445
Diverse epigenetic strategies interact to control epidermal differentiation. PMID:22729083
Stimulation of host immune defenses by a small molecule protects C. elegans from bacterial infection. PMID:22719261
Computational analysis of high-throughput flow cytometry data. PMID:22708834
Systematic single-cell analysis of Pichia pastoris reveals secretory capacity limits productivity. PMID:22685548
RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. PMID:22684630
Tyrosine kinase pathways modulate tumor susceptibility to natural killer cells. PMID:22684105
Pancreatic damage in fetal and newborn cystic fibrosis pigs involves the activation of inflammatory and remodeling pathways. PMID:22683312
Polar opposites: Erk direction of CD4 T cell subsets. PMID:22675204
Comprehensive microarray-based analysis for stage-specific larval camouflage pattern-associated genes in the swallowtail butterfly, Papilio xuthus. PMID:22651552
METAGENassist: a comprehensive web server for comparative metagenomics. PMID:22645318
Integrative genomic analysis implicates gain of PIK3CA at 3q26 and MYC at 8q24 in chronic lymphocytic leukemia. PMID:22623730
HOTAIR is a negative prognostic factor and exhibits pro-oncogenic activity in pancreatic cancer. PMID:22614017
Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. PMID:22610119
Central nervous system endoplasmic reticulum stress in a murine model of type 2 diabetes. PMID:22581041
Tavaxy: integrating Taverna and Galaxy workflows with cloud computing support. PMID:22559942
MetaboAnalyst 2.0--a comprehensive server for metabolomic data analysis. PMID:22553367
From sequence to molecular pathology, and a mechanism driving the neuroendocrine phenotype in prostate cancer. PMID:22553170
Non-overlapping progesterone receptor cistromes contribute to cell-specific transcriptional outcomes. PMID:22545144
RNA-SeQC: RNA-seq metrics for quality control and process optimization. PMID:22539670
Epigenetic silencing of the circadian clock gene CRY1 is associated with an indolent clinical course in chronic lymphocytic leukemia. PMID:22470559
Transcriptional profiling of stroma from inflamed and resting lymph nodes defines immunological hallmarks. PMID:22466668
Quantitative assessment of chromatin immunoprecipitation grade antibodies directed against histone modifications reveals patterns of co-occurring marks on histone protein molecules. PMID:22442256
Chromatin-targeting small molecules cause class-specific transcriptional changes in pancreatic endocrine cells. PMID:22434908
Genome-wide dynamic transcriptional profiling in Clostridium beijerinckii NCIMB 8052 using single-nucleotide resolution RNA-Seq. PMID:22433311
Oxidative stress and successful antioxidant treatment in models of RYR1-related myopathy. PMID:22418739
Integrative Analysis of Response to Tamoxifen Treatment in ER-Positive Breast Cancer Using GWAS Information and Transcription Profiling. PMID:22399860
iCanPlot: visual exploration of high-throughput omics data using interactive Canvas plotting. PMID:22393367
JunB contributes to Id2 repression and the epithelial-mesenchymal transition in response to transforming growth factor-β. PMID:22391036
Early window of diabetes determinism in NOD mice, dependent on the complement receptor CRIg, identified by noninvasive imaging. PMID:22366893
Systems-level analysis of age-related macular degeneration reveals global biomarkers and phenotype-specific functional networks. PMID:22364233
The metabolic footprint of aging in mice. PMID:22355651
Quantitative secretomic analysis of Trichoderma reesei strains reveals enzymatic composition for lignocellulosic biomass degradation. PMID:22355001
IDH1 mutation is sufficient to establish the glioma hypermethylator phenotype. PMID:22343889
Thymic negative selection is functional in NOD mice. PMID:22329992
Transcriptional response of the sulfur chemolithoautotroph Thiomicrospira crunogena to dissolved inorganic carbon limitation. PMID:22328671
Interleukin-1β modulates smooth muscle cell phenotype to a distinct inflammatory state relative to PDGF-DD via NF-κB-dependent mechanisms. PMID:22318995
Genetic mapping of habitual substance use, obesity-related traits, responses to mental and physical stress, and heart rate and blood pressure measurements reveals shared genes that are overrepresented in the neural synapse. PMID:22297481
Impact of caBIG on the European cancer community. PMID:22276064
Genetic resistance to JAK2 enzymatic inhibitors is overcome by HSP90 inhibition. PMID:22271575
Kinome expression profiling identifies IKBKE as a predictor of overall survival in clear cell renal cell carcinoma patients. PMID:22266464
Early alterations of the immune transcriptome in cultured progenitor cells from obese African-American women. PMID:22262158
A gene regulatory network for root epidermis cell differentiation in Arabidopsis. PMID:22253603
Defective CD8 T cell responses in aged mice are due to quantitative and qualitative changes in virus-specific precursors. PMID:22246631
Innate response activator B cells protect against microbial sepsis. PMID:22245738
A mathematical methodology for determining the temporal order of pathway alterations arising during gliomagenesis. PMID:22241976
Convergent structural alterations define SWItch/Sucrose NonFermentable (SWI/SNF) chromatin remodeler as a central tumor suppressive complex in pancreatic cancer. PMID:22233809
Mild Plasmodium falciparum malaria following an episode of severe malaria is associated with induction of the interferon pathway in Malawian children. PMID:22232187
Phagocytosis of bacterial pathogens. PMID:22223092
A complex genomic rearrangement involving the endothelin 3 locus causes dermal hyperpigmentation in the chicken. PMID:22216010
Mutant p53 uses p63 as a molecular chaperone to alter gene expression and induce a pro-invasive secretome. PMID:22203497
Gene network inference and visualization tools for biologists: application to new human transcriptome datasets. PMID:22121215
Evaluating genetic markers and neurobiochemical analytes for fluoxetine response using a panel of mouse inbred strains. PMID:22113448
Potential responders to FOLFOX therapy for colorectal cancer by Random Forests analysis. PMID:22095227
Integrative genomic analyses of sporadic clear cell renal cell carcinoma define disease subtypes and potential new therapeutic targets. PMID:22094876
Using systems and structure biology tools to dissect cellular phenotypes. PMID:22081223
SIGNATURE: a workbench for gene expression signature analysis. PMID:22078435
Determination of the human cardiomyocyte mRNA and miRNA differentiation network by fine-scale profiling. PMID:22050602
A microRNA gene expression signature predicts response to erlotinib in epithelial cancer cell lines and targets EMT. PMID:22045191
Pattern specification and immune response transcriptional signatures of pericardial and subcutaneous adipose tissue. PMID:22022522
Screening and identification of seed-specific genes using digital differential display tools combined with microarray data from common wheat. PMID:22003838
Chipster: user-friendly analysis software for microarray and other high-throughput data. PMID:21999641
A high-throughput single-cell analysis of human CD8⁺ T cell functions reveals discordance for cytokine secretion and cytolysis. PMID:21965332
Innate lymphoid cells promote lung-tissue homeostasis after infection with influenza virus. PMID:21946417
Cellular model of Warburg effect identifies tumor promoting function of UCP2 in breast cancer and its suppression by genipin. PMID:21935467
TCR-dependent transformation of mature memory phenotype T cells in mice. PMID:21926465
The identification of gene expression profiles associated with progression of human diabetic neuropathy. PMID:21926103
Microarray expression profiling in 6-hydroxydopamine-induced dopaminergic neuronal cell death. PMID:21904894
Inactivation of a single copy of Crebbp selectively alters pre-mRNA processing in mouse hematopoietic stem cells. PMID:21901164
Characterization of the DNA copy-number genome in the blood of cutaneous T-cell lymphoma patients. PMID:21881587
Tissue-specific gene expression templates for accurate molecular characterization of the normal physiological states of multiple human tissues with implication in development and cancer studies. PMID:21880155
CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing. PMID:21878105
An integrative genomics approach to biomarker discovery in breast cancer. PMID:21869864
Fibroblast growth factor 1 (FGFR1) modulation regulates repair capacity of oligodendrocyte progenitor cells following chronic demyelination. PMID:21854849
Delineation of two clinically and molecularly distinct subgroups of posterior fossa ependymoma. PMID:21840481
RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukaemia. PMID:21814200
Measuring cell identity in noisy biological systems. PMID:21803789
The mutational landscape of head and neck squamous cell carcinoma. PMID:21798893
ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data. PMID:21797991
Waves of early transcriptional activation and pluripotency program initiation during human preimplantation development. PMID:21775417
A cross-species analysis of a mouse model of breast cancer-specific osteolysis and human bone metastases using gene expression profiling. PMID:21774828
Retrieval, alignment, and clustering of computational models based on semantic annotations. PMID:21772260
MLL-rearranged leukemia is dependent on aberrant H3K79 methylation by DOT1L. PMID:21741597
Genomic imbalances in esophageal carcinoma cell lines involve Wnt pathway genes. PMID:21734802
Directional RNA deep sequencing sheds new light on the transcriptional response of Anabaena sp. strain PCC 7120 to combined-nitrogen deprivation. PMID:21711558
Protective effect of the apoptosis-sensing nanoparticle AnxCLIO-Cy5.5. PMID:21704591
Gene-expression signature of vascular invasion in hepatocellular carcinoma. PMID:21703203
Gene expression analysis characterizes antemortem stress and has implications for establishing cause of death. PMID:21693618
Intrinsic subtypes of gastric cancer, based on gene expression pattern, predict survival and respond differently to chemotherapy. PMID:21684283
GLI1 confers profound phenotypic changes upon LNCaP prostate cancer cells that include the acquisition of a hormone independent state. PMID:21633508
Transcriptional profiling of diabetic neuropathy in the BKS db/db mouse: a model of type 2 diabetes. PMID:21617178
Gitools: analysis and visualisation of genomic data using interactive heat-maps. PMID:21602921
Using DNA microarrays to assay part function. PMID:21601083
Extracellular matrix composition and remodeling in human abdominal aortic aneurysms: a proteomics approach. PMID:21593211
Associating GWAS Information with the Notch Signaling Pathway Using Transcription Profiling. PMID:21584266
P. falciparum modulates erythroblast cell gene expression in signaling and erythrocyte production pathways. PMID:21573240
The BioExtract Server: a web-based bioinformatic workflow platform. PMID:21546552
Light-induced transcriptional responses associated with proteorhodopsin-enhanced growth in a marine flavobacterium. PMID:21472017
Mapping and analysis of chromatin state dynamics in nine human cell types. PMID:21441907
Breast cancer methylomes establish an epigenomic foundation for metastasis. PMID:21430268
Making sense of cancer genomic data. PMID:21406553
LabKey Server: an open source platform for scientific data integration, analysis and collaboration. PMID:21385461
Connectedness of PPI network neighborhoods identifies regulatory hub proteins. PMID:21367871
Toward the commoditization of translational genomic research: Design and implementation features of the Galaxy genomic workbench. PMID:21347127
MicroRNA-based classification of hepatocellular carcinoma and oncogenic role of miR-517a. PMID:21324318
Transcriptomes of the B and T lineages compared by multiplatform microarray profiling. PMID:21307297
Two unique human decidual macrophage populations. PMID:21257965
Amplification of the ch19p13.2 NACC1 locus in ovarian high-grade serous carcinoma. PMID:21240255
SIDEKICK: Genomic data driven analysis and decision-making framework. PMID:21192813
BiologicalNetworks 2.0--an integrative view of genome biology data. PMID:21190573
Disease allele-dependent small-molecule sensitivities in blood cells from monogenic diabetes. PMID:21183721
Enabling Data Analysis on High-Throughput Data in Large Data Depository Using Web-Based Analysis Platform - A Case Study on Integrating QUEST with GenePattern in Epigenetics Research. PMID:21151835
Epigenetic changes induced by air toxics: formaldehyde exposure alters miRNA expression profiles in human lung cells. PMID:21147603
MULTIPRED2: a computational system for large-scale identification of peptides predicted to bind to HLA supertypes and alleles. PMID:21130094
Nearest template prediction: a single-sample-based flexible class prediction with confidence assessment. PMID:21124904
The Mycobacterium tuberculosis drugome and its polypharmacological implications. PMID:21079673
Haploinsufficiency for ribosomal protein genes causes selective activation of p53 in human erythroid progenitor cells. PMID:21068437
Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells. PMID:21057500
In silico research in the era of cloud computing. PMID:21057489
Challenges of molecular nutrition research 6: the nutritional phenotype database to store, share and evaluate nutritional systems biology studies. PMID:21052526
The TLX1 oncogene drives aneuploidy in T cell transformation. PMID:20972433
The air-liquid interface and use of primary cell cultures are important to recapitulate the transcriptional profile of in vivo airway epithelia. PMID:20971803
Epigenetic antagonism between polycomb and SWI/SNF complexes during oncogenic transformation. PMID:20951942
Unbiased, genome-wide in vivo mapping of transcriptional regulatory elements reveals sex differences in chromatin structure associated with sex-specific liver gene expression. PMID:20876297
Computational ecosystems for data-driven medical genomics. PMID:20854645
The proneural molecular signature is enriched in oligodendrogliomas and predicts improved survival among diffuse gliomas. PMID:20838435
The Neural/Immune Gene Ontology: clipping the Gene Ontology for neurological and immunological systems. PMID:20831831
Next generation tools for genomic data generation, distribution, and visualization. PMID:20828407
Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme. PMID:20822536
*omeSOM: a software for clustering and visualization of transcriptional and metabolite data mined from interspecific crosses of crop plants. PMID:20796314
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. PMID:20738864
Molecular diagnostics in transplantation. PMID:20736923
Long-lived mitochondrial (Mit) mutants of Caenorhabditis elegans utilize a novel metabolism. PMID:20732954
Smad proteins bind a conserved RNA sequence to promote microRNA maturation by Drosha. PMID:20705240
Mass spectrometry protein expression profiles in colorectal cancer tissue associated with clinico-pathological features of disease. PMID:20691062
The histone demethylase JMJD2B is regulated by estrogen receptor alpha and hypoxia, and is a key mediator of estrogen induced growth. PMID:20682797
Tissue type-specific expression of the dsRNA-binding protein 76 and genome-wide elucidation of its target mRNAs. PMID:20668518
Effective knowledge management in translational medicine. PMID:20642836
GliomaPredict: a clinically useful tool for assigning glioma patients to specific molecular subtypes. PMID:20633285
Human Wharton's jelly stem cells have unique transcriptome profiles compared to human embryonic stem cells and other mesenchymal stem cells. PMID:20602182
Subtype-specific genomic alterations define new targets for soft-tissue sarcoma therapy. PMID:20601955
Wilms tumor chromatin profiles highlight stem cell properties and a renal developmental network. PMID:20569696
Integrative genomic and proteomic analyses identify targets for Lkb1-deficient metastatic lung tumors. PMID:20541700
What do I want from the publisher of the future? PMID:20523744
geWorkbench: an open source platform for integrative genomics. PMID:20511363
Fenofibrate increases very low density lipoprotein triglyceride production despite reducing plasma triglyceride levels in APOE*3-Leiden.CETP mice. PMID:20501652
Expression of miR-196b is not exclusively MLL-driven but is especially linked to activation of HOXA genes in pediatric acute lymphoblastic leukemia. PMID:20494936
BioCatalogue: a universal catalogue of web services for the life sciences. PMID:20484378
ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems. PMID:20484371
Altered expression of genes involved in inflammation and apoptosis in frontal cortex in major depression. PMID:20479761
Molecular mechanisms mediating the effect of mono-(2-ethylhexyl) phthalate on hormone-stimulated steroidogenesis in MA-10 mouse tumor Leydig cells. PMID:20463053
A defective Il15 allele underlies the deficiency in natural killer cell activity in nonobese diabetic mice. PMID:20439722
Evidence for Alteration of Gene Regulatory Networks through MicroRNAs of the HIV-infected brain: novel analysis of retrospective cases. PMID:20436668
ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking. PMID:20427518
Analysis of post-operative changes in serum protein expression profiles from colorectal cancer patients by MALDI-TOF mass spectrometry: a pilot methodological study. PMID:20420661
Microarray-based transcriptional and epigenetic profiling of matrix metalloproteinases, collagens, and related genes in cancer. PMID:20404328
Preclinical model of organotypic culture for pharmacodynamic profiling of human tumors. PMID:20404174
CNAReporter: a GenePattern pipeline for the generation of clinical reports of genomic alterations. PMID:20380730
Coregulation mapping based on individual phenotypic variation in response to virus infection. PMID:20298589
Genomic definition of multiple ex vivo regulatory T cell subphenotypes. PMID:20231436
Functional analysis of the Cdk7.cyclin H.Mat1 complex in mouse embryonic stem cells and embryos. PMID:20231280
A systems biology approach to understanding atherosclerosis. PMID:20201031
Visualization of omics data for systems biology. PMID:20195258
Intrinsic sex differences in the early growth hormone responsiveness of sex-specific genes in mouse liver. PMID:20150183
Inactivation of LEF1 in T-cell acute lymphoblastic leukemia. PMID:20124220
Computer science. Accessible reproducible research. PMID:20093459
Jumonji modulates polycomb activity and self-renewal versus differentiation of stem cells. PMID:20064376
Mass-spectrometry-based metabolomics: limitations and recommendations for future progress with particular focus on nutrition research. PMID:20046865
A gene expression signature of invasive potential in metastatic melanoma cells. PMID:20041153
DR-Integrator: a new analytic tool for integrating DNA copy number and gene expression data. PMID:20031972
Unbiased discovery of in vivo imaging probes through in vitro profiling of nanoparticle libraries. PMID:20023731
Neuropeptide Y functions as a facilitator of GDNF-induced budding of the Wolffian duct. PMID:19934016
Differential effects of cytokines and corticosteroids on toll-like receptor 2 expression and activity in human airway epithelia. PMID:19835594
Generation of functional ventricular heart muscle from mouse ventricular progenitor cells. PMID:19833966
BASE--2nd generation software for microarray data management and analysis. PMID:19822003
How punctual ablation of regulatory T cells unleashes an autoimmune lesion within the pancreatic islets. PMID:19818653
Comparing gene annotation enrichment tools for functional modeling of agricultural microarray data. PMID:19811693
Semantic web data warehousing for caGrid. PMID:19796399
Annotation and analysis of low-complexity protein families of Anopheles gambiae that are associated with cuticle. PMID:19754739
Thyroid hormone receptor mutants implicated in human hepatocellular carcinoma display an altered target gene repertoire. PMID:19749797
Gene expression meta-analysis supports existence of molecular apocrine breast cancer with a role for androgen receptor and implies interactions with ErbB family. PMID:19747394
Mobyle: a new full web bioinformatics framework. PMID:19689959
Genome-wide mRNA expression analysis of hepatic adaptation to high-fat diets reveals switch from an inflammatory to steatotic transcriptional program. PMID:19680557
Gene expression profiles of tumor biology provide a novel approach to prognosis and may guide the selection of therapeutic targets in multiple myeloma. PMID:19636021
Lean, but not obese, fat is enriched for a unique population of regulatory T cells that affect metabolic parameters. PMID:19633656
A System for Information Management in BioMedical Studies--SIMBioMS. PMID:19633095
Isoform-specific transcriptional activity of overlapping target genes that respond to thyroid hormone receptors alpha1 and beta1. PMID:19628582
Tubulin polymerization-promoting protein (TPPP/p25) is critical for oligodendrocyte differentiation. PMID:19606501
A-MADMAN: annotation-based microarray data meta-analysis tool. PMID:19563634
A novel and universal method for microRNA RT-qPCR data normalization. PMID:19531210
Gene and protein expression profiles in the foetal liver of the pregnant rat fed a low protein diet. PMID:19484284
Data perturbation independent diagnosis and validation of breast cancer subtypes using clustering and patterns. PMID:19458770
Public databases and software for the pathway analysis of cancer genomes. PMID:19455256
Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions. PMID:19451690
Convergence of biomarkers, bioinformatics and nanotechnology for individualized cancer treatment. PMID:19409634
Owner controlled data exchange in nutrigenomic collaborations: the NuGO information network. PMID:19408032
Effect of body fat distribution on the transcription response to dietary fat interventions. PMID:19404697
Chronic lymphocytic leukemia and B and T cells differ in their response to cyclic nucleotide phosphodiesterase inhibitors. PMID:19380787
Gene expression profiling of leukemia stem cells. PMID:19277590
Adaptable data management for systems biology investigations. PMID:19265554
Elevated expression of protein biosynthesis genes in liver and muscle of hibernating black bears (Ursus americanus). PMID:19240299
Rembrandt: helping personalized medicine become a reality through integrative translational research. PMID:19208739
Genetic mechanisms in Apc-mediated mammary tumorigenesis. PMID:19197353
The cancer translational research informatics platform. PMID:19108734
PGC-1alpha and ERRalpha target gene downregulation is a signature of the failing human heart. PMID:19061896
HIF-alpha effects on c-Myc distinguish two subtypes of sporadic VHL-deficient clear cell renal carcinoma. PMID:19061835
HOXA9 is required for survival in human MLL-rearranged acute leukemias. PMID:19056693
High-resolution mapping of copy-number alterations with massively parallel sequencing. PMID:19043412
NuGO contributions to GenePattern. PMID:19034553
EMAAS: an extensible grid-based rich internet application for microarray data analysis and management. PMID:19032776
Retinoic acid enhances Foxp3 induction indirectly by relieving inhibition from CD4+CD44hi Cells. PMID:19006694
Identification of dynamically regulated microRNA and mRNA networks in developing oligodendrocytes. PMID:18987208
Ott1 (Rbm15) is essential for placental vascular branching morphogenesis and embryonic development of the heart and spleen. PMID:18981216
Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PMID:18974828
Molecular consequences of altered neuronal cholesterol biosynthesis. PMID:18951487
Pivotal role of mTOR signaling in hepatocellular carcinoma. PMID:18929564
Gene expression in fixed tissues and outcome in hepatocellular carcinoma. PMID:18923165
The variable immunological self: genetic variation and nongenetic noise in Aire-regulated transcription. PMID:18838677
TB database: an integrated platform for tuberculosis research. PMID:18835847
Quantitative transcriptional neuroanatomy of the rat hippocampus: evidence for wide-ranging, pathway-specific heterogeneity among three principal cell layers. PMID:18830999
Transcriptional impact of Aire varies with cell type. PMID:18780794
Translational bioinformatics: coming of age. PMID:18755990
Focal gains of VEGFA and molecular classification of hepatocellular carcinoma. PMID:18701503
A review of imaging techniques for systems biology. PMID:18700030
Molecular subsets in the gene expression signatures of scleroderma skin. PMID:18648520
Systems biology driven software design for the research enterprise. PMID:18578887
Cytometric profiling in multiple sclerosis uncovers patient population structure and a reduction of CD8low cells. PMID:18567923
Using GenePattern for gene expression analysis. PMID:18551415
MicroRNA-mediated control of cell fate in megakaryocyte-erythrocyte progenitors. PMID:18539114
Bioinformatic tools for inferring functional information from plant microarray data: tools for the first steps. PMID:18528524
Carcinoma-associated fibroblast-like differentiation of human mesenchymal stem cells. PMID:18519693
Gene expression changes in an animal melanoma model correlate with aggressiveness of human melanoma metastases. PMID:18505921
Perturbational profiling of nanomaterial biologic activity. PMID:18492802
Developmental expression patterns of cuticular protein genes with the R&R Consensus from Anopheles gambiae. PMID:18405829
An integrated approach to the prediction of chemotherapeutic response in patients with breast cancer. PMID:18382681
The AKT-mTOR axis regulates de novo differentiation of CD4+Foxp3+ cells. PMID:18283119
An erythroid differentiation signature predicts response to lenalidomide in myelodysplastic syndrome. PMID:18271621
GSE: a comprehensive database system for the representation, retrieval, and analysis of microarray data. PMID:18229714
Signature Evaluation Tool (SET): a Java-based tool to evaluate and visualize the sample discrimination abilities of gene expression signatures. PMID:18221568
SNPExpress: integrated visualization of genome-wide genotypes, copy numbers and gene expression levels. PMID:18221515
SignS: a parallelized, open-source, freely available, web-based tool for gene selection and molecular signatures for survival and censored data. PMID:18208605
Sequential and concerted gene expression changes in a chronic in vitro model of parkinsonism. PMID:18191903
A viral microRNA functions as an orthologue of cellular miR-155. PMID:18075594
DNA methylation signatures within the human brain. PMID:17999367
Characterizing the cancer genome in lung adenocarcinoma. PMID:17982442
Identification of prostate cancer modifier pathways using parental strain expression mapping. PMID:17978178
Reversible and permanent effects of tobacco smoke exposure on airway epithelial gene expression. PMID:17894889
Assessing the significance of conserved genomic aberrations using high resolution genomic microarrays. PMID:17722985
Epigenetic specificity of loss of imprinting of the IGF2 gene in Wilms tumors. PMID:17686827
Protein 4.1B suppresses prostate cancer progression and metastasis. PMID:17640904
Lesional gene expression profiling in cutaneous T-cell lymphoma reveals natural clusters associated with disease outcome. PMID:17638852
MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals. PMID:17560377
Evidence that p53-mediated cell-cycle-arrest inhibits chemotherapeutic treatment of ovarian carcinomas. PMID:17505532
Accelerating medical research using the swift workflow system. PMID:17476063
bioNMF: a versatile tool for non-negative matrix factorization in biology. PMID:16875499
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differential gene expression analysis
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gene expression data
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version: FAIRsharing.org: GenePattern GeneSet Table Format; GenePattern GeneSet Table Format; DOI: https://doi.org/10.25504/FAIRsharing.z057ar; Last edited: Jan. 8, 2019, 1:32 p.m.; Last accessed: Jan 03 2022 7:14 p.m.
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version: FAIRsharing.org: GenePattern GeneSet Table Format; GenePattern GeneSet Table Format; DOI: https://doi.org/10.25504/FAIRsharing.z057ar; Last edited: Jan. 8, 2019, 1:32 p.m.; Last accessed: Jan 03 2022 7:14 p.m.
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differential gene expression analysis
metasource: Fairsharing.orgversion: FAIRsharing.org: GenePattern GeneSet Table Format; GenePattern GeneSet Table Format; DOI: https://doi.org/10.25504/FAIRsharing.z057ar; Last edited: Jan. 8, 2019, 1:32 p.m.; Last accessed: Jan 03 2022 7:14 p.m.
gene expression data
metasource: Fairsharing.orgversion: FAIRsharing.org: GenePattern GeneSet Table Format; GenePattern GeneSet Table Format; DOI: https://doi.org/10.25504/FAIRsharing.z057ar; Last edited: Jan. 8, 2019, 1:32 p.m.; Last accessed: Jan 03 2022 7:14 p.m.
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differential gene expression analysis gene expression rna
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