Structure and biosynthesis of carotenoids produced by a novel Planococcus sp. isolated from South Africa.
PMID:35305628
Full-length transcriptome analysis of Adiantum flabellulatum gametophyte.
PMID:35287343
Comparative genomics and evolutionary analysis of Lactococcus garvieae isolated from human endocarditis.
PMID:35196218
Slipknot or Crystallographic Error: A Computational Analysis of the Plasmodium falciparum DHFR Structural Folds.
PMID:35163439
Computational analysis and prediction of PE_PGRS proteins using machine learning.
PMID:35140886
The highly continuous reference genome of a leaf-chimeric red pineapple (Ananas comosus var. bracteatus f. tricolor) provides insights into elaboration of leaf color.
PMID:35100332
CottonGen: The Community Database for Cotton Genomics, Genetics, and Breeding Research.
PMID:34961276
Exploration and augmentation of pharmacological space via adversarial auto-encoder model for facilitating kinase-centric drug development.
PMID:34872613
Daily rhythms in gene expression of the human parasite Schistosoma mansoni.
PMID:34852797
The carbohydrate-active enzyme database: functions and literature.
PMID:34850161
The CRISPR-associated Cas4 protein from Leptospira interrogans demonstrate versatile nuclease activity.
PMID:34841331
Phenotypic Screening of Molecular Docking Enriched Chemical Libraries from Targets Identified in Ischemic Stroke Genome Data by Network-Based Method.
PMID:34820079
A Superefficient Ochratoxin A Hydrolase with Promising Potential for Industrial Applications.
PMID:34788069
Chalcones identify cTXNPx as a potential antileishmanial drug target.
PMID:34780470
Transcriptomic and Metabolomic Analyses Reveals That Exogenous Methyl Jasmonate Regulates Galanthamine Biosynthesis in Lycoris longituba Seedlings.
PMID:34659286
Comprehensive annotation of the Chinese tree shrew genome by large-scale RNA sequencing and long-read isoform sequencing.
PMID:34581030
Effect of food source availability in the salivary gland transcriptome of the unique burying beetle Nicrophorus pustulatus (Coleoptera: Silphidae).
PMID:34555059
A deep-learning framework for multi-level peptide-protein interaction prediction.
PMID:34526500
Arabidopsis-Based Dual-Layered Biological Network Analysis Elucidates Fully Modulated Pathways Related to Sugarcane Resistance on Biotrophic Pathogen Infection.
PMID:34490009
On the Need to Tell Apart Fraternal Twins eEF1A1 and eEF1A2, and Their Respective Outfits.
PMID:34203525
Methanogenic archaea use a bacteria-like methyltransferase system to demethoxylate aromatic compounds.
PMID:34145392
Structure-based Method for Predicting Deleterious Missense SNPs.
PMID:34136829
Structure-based protein function prediction using graph convolutional networks.
PMID:34039967
digIS: towards detecting distant and putative novel insertion sequence elements in prokaryotic genomes.
PMID:34016050
bla OXA-48-like genome architecture among carbapenemase-producing Escherichia coli and Klebsiella pneumoniae in the Netherlands.
PMID:33961543
The language of proteins: NLP, machine learning & protein sequences.
PMID:33897979
Effects of Simulated Microgravity on the Proteome and Secretome of the Polyextremotolerant Black Fungus Knufia chersonesos.
PMID:33815472
Transcriptome analysis reveals major transcriptional changes during regrowth after mowing of red clover (Trifolium pratense).
PMID:33588756
Querying knowledge graphs in natural language.
PMID:33489717
Embeddings from deep learning transfer GO annotations beyond homology.
PMID:33441905
Reconstruction and analysis of a genome-scale metabolic model for Agrobacterium tumefaciens.
PMID:33433944
PTMsnp: A Web Server for the Identification of Driver Mutations That Affect Protein Post-translational Modification.
PMID:33240890
GasPhos: Protein Phosphorylation Site Prediction Using a New Feature Selection Approach with a GA-Aided Ant Colony System.
PMID:33114312
Side chain similarity comparisons for integrated drug repositioning and potential toxicity assessments in epidemic response scenarios: The case for COVID-19.
PMID:33101604
MolTrans: Molecular Interaction Transformer for drug-target interaction prediction.
PMID:33070179
IDPology of the living cell: intrinsic disorder in the subcellular compartments of the human cell.
PMID:32997198
Hidden dynamic signatures drive substrate selectivity in the disordered phosphoproteome.
PMID:32900925
High-Quality Assemblies for Three Invasive Social Wasps from the Vespula Genus.
PMID:32859687
Chromosome-Level Assembly of the Common Lizard (Zootoca vivipara) Genome.
PMID:32835354
Recent advances of automated methods for searching and extracting genomic variant information from biomedical literature.
PMID:32770181
Hybrid phenotype mining method for investigating off-target protein and underlying side effects of anti-tumor immunotherapy.
PMID:32646421
Large Ankyrin repeat proteins are formed with similar and energetically favorable units.
PMID:32579546
Brain-related genes are specifically enriched with long phase 1 introns.
PMID:32470086
Three Novel Variants identified in FBN1 and TGFBR2 in seven Iranian families with suspected Marfan syndrome.
PMID:32431097
Independent evolution of ancestral and novel defenses in a genus of toxic plants (Erysimum, Brassicaceae).
PMID:32252891
The genome evolution and low-phosphorus adaptation in white lupin.
PMID:32103018
Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes.
PMID:32093654
Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff.
PMID:32060277
Isolation of an archaeon at the prokaryote-eukaryote interface.
PMID:31942073
Predicting and designing therapeutics against the Nipah virus.
PMID:31830030
Secretome analysis of patient-derived GBM tumor spheres identifies midkine as a potent therapeutic target.
PMID:31811117
Complete Genome Sequence of the Plant Growth-Promoting Bacterium Hartmannibacter diazotrophicus Strain E19T.
PMID:31583244
Reference gene and small RNA data from multiple tissues of Davidia involucrata Baill.
PMID:31551451
Adaptive Properties of the Genetically Encoded Amino Acid Alphabet Are Inherited from Its Subsets.
PMID:31462646
Using distant supervision to augment manually annotated data for relation extraction.
PMID:31361753
CyMIRA: The Cytonuclear Molecular Interactions Reference for Arabidopsis.
PMID:31282937
CELF2 suppresses non-small cell lung carcinoma growth by inhibiting the PREX2-PTEN interaction.
PMID:31241130
Proteomic Response of Three Marine Ammonia-Oxidizing Archaea to Hydrogen Peroxide and Their Metabolic Interactions with a Heterotrophic Alphaproteobacterium.
PMID:31239395
Structural, functional, and stability change predictions in human telomerase upon specific point mutations.
PMID:31213647
Time of day and network reprogramming during drought induced CAM photosynthesis in Sedum album.
PMID:31199791
VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations.
PMID:31192369
Hair Proteome Variation at Different Body Locations on Genetically Variant Peptide Detection for Protein-Based Human Identification.
PMID:31113963
Proteomic characterisation of leech microglia extracellular vesicles (EVs): comparison between differential ultracentrifugation and Optiprep™ density gradient isolation.
PMID:31069026
Cross-species alcohol dependence-associated gene networks: Co-analysis of mouse brain gene expression and human genome-wide association data.
PMID:31017905
Computational Prediction of MoRFs, Short Disorder-to-order Transitioning Protein Binding Regions.
PMID:31007871
Thermal selection as a driver of marine ecological speciation.
PMID:30963923
How to design potent and selective DYRK1B inhibitors? Molecular modeling study.
PMID:30673861
Draft Genome Sequence of an Onion Basal Rot Isolate of Fusarium proliferatum.
PMID:30637390
Recombination of ecologically and evolutionarily significant loci maintains genetic cohesion in the Pseudomonas syringae species complex.
PMID:30606234
Impact of Rearing Conditions on the Ambrosia Beetle's Microbiome.
PMID:30551580
Protein-protein interaction sites prediction by ensemble random forests with synthetic minority oversampling technique.
PMID:30520961
A differential k-mer analysis pipeline for comparing RNA-Seq transcriptome and meta-transcriptome datasets without a reference.
PMID:30483906
Interactive online application for the prediction, ranking and prioritisation of drug targets in Schistosoma haematobium.
PMID:30482220
WebNetCoffee: a web-based application to identify functionally conserved proteins from Multiple PPI networks.
PMID:30419809
Marginal protein stability drives subcellular proteome isoelectric point.
PMID:30385634
Desiccation Tolerance Evolved through Gene Duplication and Network Rewiring in Lindernia.
PMID:30361236
Leishmania donovani Parasites Are Inhibited by the Benzoxaborole AN2690 Targeting Leucyl-tRNA Synthetase.
PMID:29941647
Cross-species inference of long non-coding RNAs greatly expands the ruminant transcriptome.
PMID:29690875
Identification of Metabolites and Transcripts Involved in Salt Stress and Recovery in Peanut.
PMID:29520289
Improving eukaryotic genome annotation using single molecule mRNA sequencing.
PMID:29495964
Genetic variation in P2RX7 and pain tolerance.
PMID:29470314
The Glaciozyma antarctica genome reveals an array of systems that provide sustained responses towards temperature variations in a persistently cold habitat.
PMID:29385175
Listeria monocytogenes Induces a Virulence-Dependent microRNA Signature That Regulates the Immune Response in Galleria mellonella.
PMID:29312175
Computational Studies of Snake Venom Toxins.
PMID:29271884
Continuous Elution Proteoform Identification of Myelin Basic Protein by Superficially Porous Reversed-Phase Liquid Chromatography and Fourier Transform Mass Spectrometry.
PMID:29016107
O2 sensing-associated glycosylation exposes the F-box-combining site of the Dictyostelium Skp1 subunit in E3 ubiquitin ligases.
PMID:28928219
The cacao Criollo genome v2.0: an improved version of the genome for genetic and functional genomic studies.
PMID:28915793
Genetic Validation of Leishmania donovani Lysyl-tRNA Synthetase Shows that It Is Indispensable for Parasite Growth and Infectivity.
PMID:28875178
Integration of quantitated expression estimates from polyA-selected and rRNA-depleted RNA-seq libraries.
PMID:28610557
The draft genome of Ruellia speciosa (Beautiful Wild Petunia: Acanthaceae).
PMID:28431014
Drug-drug interaction discovery and demystification using Semantic Web technologies.
PMID:28031284
Large-scale identification of human protein function using topological features of interaction network.
PMID:27849060
EphA2 proteomics in human keratinocytes reveals a novel association with afadin and epidermal tight junctions.
PMID:27815408
ASAP: a machine learning framework for local protein properties.
PMID:27694209
Evaluating the accuracy of protein design using native secondary sub-structures.
PMID:27597167
Hemi-methylated DNA regulates DNA methylation inheritance through allosteric activation of H3 ubiquitylation by UHRF1.
PMID:27595565
Prediction of redox-sensitive cysteines using sequential distance and other sequence-based features.
PMID:27553667
Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome.
PMID:27453469
A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies.
PMID:27363390
DrugE-Rank: improving drug-target interaction prediction of new candidate drugs or targets by ensemble learning to rank.
PMID:27307615
Comparative genomics explains the evolutionary success of reef-forming corals.
PMID:27218454
Hologenome analysis of two marine sponges with different microbiomes.
PMID:26926518
Hydrophobic Core Variations Provide a Structural Framework for Tyrosine Kinase Evolution and Functional Specialization.
PMID:26925779
Cytochrome P450 2C9 (CYP2C9) polymorphisms in Chinese Li population.
PMID:26885033
Defining the Schistosoma haematobium kinome enables the prediction of essential kinases as anti-schistosome drug targets.
PMID:26635209
sORFs.org: a repository of small ORFs identified by ribosome profiling.
PMID:26527729
Transcriptomic Changes in Coral Holobionts Provide Insights into Physiological Challenges of Future Climate and Ocean Change.
PMID:26510159
Prenatal notch1 receptor blockade by protein delta homolog 1 (DLK1) modulates adipocyte size in vivo.
PMID:26499442
Assessing the Pathogenicity of Insertion and Deletion Variants with the Variant Effect Scoring Tool (VEST-Indel).
PMID:26442818
reSpect: software for identification of high and low abundance ion species in chimeric tandem mass spectra.
PMID:26419769
Identification of Circulating Biomarker Candidates for Hepatocellular Carcinoma (HCC): An Integrated Prioritization Approach.
PMID:26414287
Molecular Simulations of Solved Co-crystallized X-Ray Structures Identify Action Mechanisms of PDEδ Inhibitors.
PMID:26340817
Data for comparative proteomics analysis of the antitumor effect of CIGB-552 peptide in HT-29 colon adenocarcinoma cells.
PMID:26306321
Maternal and zygotic transcriptomes in the appendicularian, Oikopleura dioica: novel protein-encoding genes, intra-species sequence variations, and trans-spliced RNA leader.
PMID:26032664
APPRIS WebServer and WebServices.
PMID:25990727
ChSeq: A database of chameleon sequences.
PMID:25970262
SUMOhunt: Combining Spatial Staging between Lysine and SUMO with Random Forests to Predict SUMOylation.
PMID:25937950
MitoFates: improved prediction of mitochondrial targeting sequences and their cleavage sites.
PMID:25670805
Draft Genome Sequence of a Xylanase-Producing Bacterial Strain, Cellvibrio mixtus J3-8.
PMID:25502674
Early transcriptional changes in the reef-building coral Acropora aspera in response to thermal and nutrient stress.
PMID:25467196
Life-cycle modification in open oceans accounts for genome variability in a cosmopolitan phytoplankton.
PMID:25461969
A new multi-label classifier in identifying the functional types of human membrane proteins.
PMID:25433431
FRET detection of lymphocyte function-associated antigen-1 conformational extension.
PMID:25378583
Identifying common components across biological network graphs using a bipartite data model.
PMID:25374613
Draft Genome Sequence of the Iron-Oxidizing, Acidophilic, and Halotolerant "Thiobacillus prosperus" Type Strain DSM 5130.
PMID:25342676
Caspase cleavage sites in the human proteome: CaspDB, a database of predicted substrates.
PMID:25330111
nDNA-Prot: identification of DNA-binding proteins based on unbalanced classification.
PMID:25196432
FSim: a novel functional similarity search algorithm and tool for discovering functionally related gene products.
PMID:25184141
Compositions of fungal secretomes indicate a greater impact of phylogenetic history than lifestyle adaptation.
PMID:25159997
Functional annotation of human cytomegalovirus gene products: an update.
PMID:24904534
NeuroPID: a classifier of neuropeptide precursors.
PMID:24792159
qcML: an exchange format for quality control metrics from mass spectrometry experiments.
PMID:24760958
A comprehensive study of small non-frameshift insertions/deletions in proteins and prediction of their phenotypic effects by a machine learning method (KD4i).
PMID:24742296
Computational redesign of bacterial biotin carboxylase inhibitors using structure-based virtual screening of combinatorial libraries.
PMID:24699146
Herceptin resistance database for understanding mechanism of resistance in breast cancer patients.
PMID:24670875
Antimicrobial peptides in the centipede Scolopendra subspinipes mutilans.
PMID:24652097
Plus ça change - evolutionary sequence divergence predicts protein subcellular localization signals.
PMID:24438075
SIDD: a semantically integrated database towards a global view of human disease.
PMID:24146757
In silico approach for predicting toxicity of peptides and proteins.
PMID:24058508
eVolver: an optimization engine for evolving protein sequences to stabilize the respective structures.
PMID:23902875
Short toxin-like proteins attack the defense line of innate immunity.
PMID:23881252
Mining Proteins with Non-Experimental Annotations Based on an Active Sample Selection Strategy for Predicting Protein Subcellular Localization.
PMID:23840667
Insight into pleiotropic drug resistance ATP-binding cassette pump drug transport through mutagenesis of Cdr1p transmembrane domains.
PMID:23824183
A study on the distribution of 37 well conserved families of C2H2 zinc finger genes in eukaryotes.
PMID:23800006
NRF2-ome: an integrated web resource to discover protein interaction and regulatory networks of NRF2.
PMID:23710289
Large-scale global identification of protein lysine methylation in vivo.
PMID:23644510
Characterizing the state of the art in the computational assignment of gene function: lessons from the first critical assessment of functional annotation (CAFA).
PMID:23630983
Network characteristic analysis of ADR-related proteins and identification of ADR-ADR associations.
PMID:23625301
Draft genome sequence of the rubber tree Hevea brasiliensis.
PMID:23375136
Chapter 3: Small molecules and disease.
PMID:23300405
The state of the human proteome in 2012 as viewed through PeptideAtlas.
PMID:23215161
Short toxin-like proteins abound in Cnidaria genomes.
PMID:23202321
PMRD: a curated database for genes and mutants involved in plant male reproduction.
PMID:23153247
Microbial virus genome annotation-mustering the troops to fight the sequence onslaught.
PMID:23084289
Draft genome sequence of butanol-acetone-producing Clostridium beijerinckii strain G117.
PMID:22965093
Genetic characterization of Erve virus, a European Nairovirus distantly related to Crimean-Congo hemorrhagic fever virus.
PMID:22864548
Getting personalized cancer genome analysis into the clinic: the challenges in bioinformatics.
PMID:22839973
In silico prediction and analysis of Caenorhabditis EF-hand containing proteins.
PMID:22701514
Linking proteins to signaling pathways for experiment design and evaluation.
PMID:22558382
Iron sulfur cluster proteins and microbial regulation: implications for understanding tuberculosis.
PMID:22483328
Pleiotropic roles of a ribosomal protein in Dictyostelium discoideum.
PMID:22363460
Exploiting gene families for phylogenomic analysis of myzostomid transcriptome data.
PMID:22276131
EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data.
PMID:22267905
The relationship between proteome size, structural disorder and organism complexity.
PMID:22182830
Bioinformatic analysis and post-translational modification crosstalk prediction of lysine acetylation.
PMID:22164248
Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis.
PMID:22139938
Insulin-like growth factor-I receptor (IGF-IR) translocates to nucleus and autoregulates IGF-IR gene expression in breast cancer cells.
PMID:22128190
The energy landscape analysis of cancer mutations in protein kinases.
PMID:21998754
Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop.
PMID:21994619
VPDB: Viral Protein Structural Database.
PMID:21769196
Immunogenicity of autoantigens.
PMID:21726451
A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas.
PMID:21632744
BioProfiling.de: analytical web portal for high-throughput cell biology.
PMID:21609949
Structural determinants of the alpha2 adrenoceptor subtype selectivity.
PMID:21602069
Insights of interaction between small and large subunits of ADP-glucose pyrophosphorylase from bread wheat (Triticum aestivum L.).
PMID:21572880
Signalogs: orthology-based identification of novel signaling pathway components in three metazoans.
PMID:21559328
Cost-effective cloud computing: a case study using the comparative genomics tool, roundup.
PMID:21258651
OrthoInspector: comprehensive orthology analysis and visual exploration.
PMID:21219603
Predicting DNA-binding specificities of eukaryotic transcription factors.
PMID:21152420
Arabidopsis lox3 lox4 double mutants are male sterile and defective in global proliferative arrest.
PMID:21052784
VnD: a structure-centric database of disease-related SNPs and drugs.
PMID:21051351
ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing.
PMID:21051348
RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans.
PMID:21037261
Verification of alternative splicing variants based on domain integrity, truncation length and intrinsic protein disorder.
PMID:20972208
Microarray-based analysis of cell-cycle gene expression during spermatogenesis in the mouse.
PMID:20631398
R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases.
PMID:20519200
ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids.
PMID:20478830
Bioinformatics and molecular modeling in glycobiology.
PMID:20364395
Mutation@A Glance: an integrative web application for analysing mutations from human genetic diseases.
PMID:20360267
Word add-in for ontology recognition: semantic enrichment of scientific literature.
PMID:20181245
Large-scale analyses of glycosylation in cellulases.
PMID:20172492
Identification of novel aspartic proteases from Strongyloides ratti and characterisation of their evolutionary relationships, stage-specific expression and molecular structure.
PMID:20015380
The association of virulence factors with genomic islands.
PMID:19956607
Novel protein-protein interactions inferred from literature context.
PMID:19924298
The Negatome database: a reference set of non-interacting protein pairs.
PMID:19920129
Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences.
PMID:19888206
Predicting meiotic pathways in human fetal oogenesis.
PMID:19846598
Sequence and structure signatures of cancer mutation hotspots in protein kinases.
PMID:19834613
Correlating protein function and stability through the analysis of single amino acid substitutions.
PMID:19758472
ZifBASE: a database of zinc finger proteins and associated resources.
PMID:19737425
Allergen databases: current status and perspectives.
PMID:19671381
Text-mining of PubMed abstracts by natural language processing to create a public knowledge base on molecular mechanisms of bacterial enteropathogens.
PMID:19515247
Structural features of mammalian histidine decarboxylase reveal the basis for specific inhibition.
PMID:19413567
FMM: a web server for metabolic pathway reconstruction and comparative analysis.
PMID:19401437
Sequence-based prediction of type III secreted proteins.
PMID:19390696
ANNIE: integrated de novo protein sequence annotation.
PMID:19389726
The Human Gene Mutation Database: 2008 update.
PMID:19348700
Global networks of functional coupling in eukaryotes from comprehensive data integration.
PMID:19246318
An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases.
PMID:19091018
Genome-scale models of bacterial metabolism: reconstruction and applications.
PMID:19067749
Bionemo: molecular information on biodegradation metabolism.
PMID:18986994
ExDom: an integrated database for comparative analysis of the exon-intron structures of protein domains in eukaryotes.
PMID:18984624
BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009.
PMID:18984617
The GOA database in 2009--an integrated Gene Ontology Annotation resource.
PMID:18957448
FlyBase: enhancing Drosophila Gene Ontology annotations.
PMID:18948289
MDPD: an integrated genetic information resource for Parkinson's disease.
PMID:18948286
The SWISS-MODEL Repository and associated resources.
PMID:18931379