PMID: 10802651DOI: 10.1038/75556May 10, 2000

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium

Nature Genetics
M AshburnerG Sherlock
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Abstract

No abstract listed.

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Evolutionary rate of human tissue-specific genes are related with transposable element insertions

Jan 23, 2013·Genetica·Ping JinFei Ma

Ontological evaluation of transcriptional differences between sperm of infertile males and fertile donors using microarray analysis

Feb 4, 2010·Journal of Assisted Reproduction and Genetics·Sandra García-HerreroMarcos Meseguer

Carboxylator: incorporating solvent-accessible surface area for identifying protein carboxylation sites

Nov 1, 2011·Journal of Computer-aided Molecular Design·Cheng-Tsung LuTzong-Yi Lee

eFindSite: improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands

Jul 11, 2013·Journal of Computer-aided Molecular Design·Michal Brylinski, Wei P Feinstein

Individual-based modelling: an essential tool for microbiology

Apr 1, 2008·Journal of Biological Physics·Jordi FerrerDaniel López

Amino acid biases in the N- and C-termini of proteins are evolutionarily conserved and are conserved between functionally related proteins

May 15, 2008·The Protein Journal·Peter M Palenchar

A new approach to assess and predict the functional roles of proteins across all known structures

Mar 30, 2011·Journal of Structural and Functional Genomics·Elchin S JulfayevWilliam A McLaughlin

The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods

Apr 8, 2011·Journal of Structural and Functional Genomics·Margaret J GabanyiHelen M Berman

KB-Rank: efficient protein structure and functional annotation identification via text query

Jan 25, 2012·Journal of Structural and Functional Genomics·Elchin S JulfayevWilliam A McLaughlin

Expression of copper-responsive genes in HepG2 cells

Nov 12, 2005·Molecular and Cellular Biochemistry·Min Ok Song, Jonathan H Freedman

MYBBP1A: a new Ipr1's binding protein in mice

Mar 12, 2010·Molecular Biology Reports·Lei CaiIgor Kramnik

Heterogeneity of breast cancer among patients and implications for patient selection for adjuvant chemotherapy

Aug 15, 2006·Pharmaceutical Research·Fabrice Andre, Lajos Pusztai

Functional genomics of cell elongation in developing cotton fibers

Dec 18, 2004·Plant Molecular Biology·A Bulak ArpatThea A Wilkins

Computational prediction and experimental verification of HVA1-like abscisic acid responsive promoters in rice (Oryza sativa)

Jul 18, 2006·Plant Molecular Biology·Christian Ross, Qingxi J Shen

Transcriptional changes in powdery mildew infected wheat and Arabidopsis leaves undergoing syringolin-triggered hypersensitive cell death at infection sites

Aug 31, 2006·Plant Molecular Biology·Kathrin MichelRobert Dudler

An in silico strategy identified the target gene candidates regulated by dehydration responsive element binding proteins (DREBs) in Arabidopsis genome

Oct 22, 2008·Plant Molecular Biology·Shichen WangDongyun Hao

Genome-wide targeted prediction of ABA responsive genes in rice based on over-represented cis-motif in co-expressed genes

Nov 11, 2008·Plant Molecular Biology·Sangram K LenkaKailash C Bansal

Genome-wide comparison of two poplar genotypes with different growth rates

May 27, 2011·Plant Molecular Biology·Shuang HaoWeilun Yin

miRDeepFinder: a miRNA analysis tool for deep sequencing of plant small RNAs

Feb 1, 2012·Plant Molecular Biology·Fuliang XieBaohong Zhang

High-throughput sequencing-based gene profiling on multi-staged fruit development of date palm (Phoenix dactylifera, L.)

Feb 22, 2012·Plant Molecular Biology·Yuxin YinJun Yu

Coexpression network analysis associated with call of rice seedlings for encountering heat stress

Aug 27, 2013·Plant Molecular Biology·Neelam K SarkarAnil Grover

De novo transcriptome analysis of an imminent biofuel crop, Camelina sativa L. using Illumina GAIIX sequencing platform and identification of SSR markers

Sep 5, 2013·Plant Molecular Biology·Shalini MudalkarAttipalli Ramachandra Reddy

Power training and postmenopausal hormone therapy affect transcriptional control of specific co-regulated gene clusters in skeletal muscle

Jul 20, 2010·Age·Eija PöllänenVuokko Kovanen

Widely predicting specific protein functions based on protein-protein interaction data and gene expression profile

Mar 30, 2007·Science in China. Series C, Life Sciences·Lei GaoShaoqi Rao

Mechanism of Roux-en-Y gastric bypass treatment for type 2 diabetes in rats

Apr 13, 2013·Journal of Gastrointestinal Surgery : Official Journal of the Society for Surgery of the Alimentary Tract·Hongwei YuZongming Zhang

Amyloid pathway-based candidate gene analysis of [(11)C]PiB-PET in the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort

Sep 9, 2011·Brain Imaging and Behavior·Shanker SwaminathanAlzheimer’s Disease Neuroimaging Initiative

Systems biology via redescription and ontologies (I): finding phase changes with applications to malaria temporal data

Nov 13, 2008·Systems and Synthetic Biology·Samantha KleinbergBud Mishra

Adipocyte accumulation of long-chain fatty acids in obesity is multifactorial, resulting from increased fatty acid uptake and decreased activity of genes involved in fat utilization

Oct 30, 2009·Obesity Surgery·José L WalewskiPaul D Berk

Candidate genes expressed in human islets and their role in the pathogenesis of type 1 diabetes

Aug 9, 2013·Current Diabetes Reports·Joachim Storling, Caroline Anna Brorsson

Differential DNA methylation status between human preadipocytes and mature adipocytes

Jan 25, 2012·Cell Biochemistry and Biophysics·Jin-Gai ZhuXi-Rong Guo

Altered miRNA expression is associated with differentiation, invasion, and metastasis of esophageal squamous cell carcinoma (ESCC) in patients from Huaian, China

Mar 22, 2013·Cell Biochemistry and Biophysics·Hai Long FuYa Ping Zhao

Microarray analysis of altered gene expression in ERbeta-overexpressing HEK293 cells

Aug 15, 2009·Endocrine·Chunyan ZhaoKarin Dahlman-Wright

Follicle-stimulating hormone regulation of microRNA expression on progesterone production in cultured rat granulosa cells

Aug 25, 2010·Endocrine·Nan YaoXu Ma

Domain-specific data sharing in neuroscience: what do we have to learn from each other?

May 14, 2008·Neuroinformatics·John Darrell Van Horn, C A Ball

Terminology for neuroscience data discovery: multi-tree syntax and investigator-derived semantics

Oct 30, 2008·Neuroinformatics·Daniel GardnerEsther P Gardner

Textpresso for neuroscience: searching the full text of thousands of neuroscience research papers

Oct 25, 2008·Neuroinformatics·Hans-Michael MüllerPaul W Sternberg

The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience

Nov 1, 2008·Neuroinformatics·William J BugMaryann E Martone

Genome-wide pathway analysis in major depressive disorder

Jun 25, 2013·Journal of Molecular Neuroscience : MN·Gwan Gyu SongYoung Ho Lee

Identification of candidate molecular markers of nasopharyngeal carcinoma by tissue microarray and in situ hybridization

Nov 9, 2010·Medical Oncology·Shilong XiongJunling Li

The genome browser at UCSC for locating genes, and much more!

Dec 7, 2007·Molecular Biotechnology·Minou Bina

MitoP2: an integrative tool for the analysis of the mitochondrial proteome

Sep 10, 2008·Molecular Biotechnology·Matthias ElstnerHolger Prokisch

Human protein reference database and human proteinpedia as discovery resources for molecular biotechnology

Oct 12, 2010·Molecular Biotechnology·Renu GoelT S Keshava Prasad

Identification of miRNAs and their target genes using deep sequencing and degradome analysis in trifoliate orange [Poncirus trifoliata L. Raf] [corrected

Jul 29, 2011·Molecular Biotechnology·Jin-Zhi ZhangChun-Gen Hu

Integration of MicroRNA databases to study MicroRNAs associated with multiple sclerosis

May 3, 2012·Molecular Neurobiology·Charlotte AngersteinUwe Klaus Zettl

Cytoview: development of a cell modelling framework

Oct 5, 2007·Journal of Biosciences·Prashant KhodadeNagasuma Chandra

A model-based strategy to investigate the role of microRNA regulation in cancer signalling networks

Sep 3, 2010·Theory in Biosciences = Theorie in Den Biowissenschaften·Svetoslav NikolovOlaf Wolkenhauer

Bioinformatics and cancer: an essential alliance

Jun 23, 2006·Clinical & Translational Oncology : Official Publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico·Joaquín Dopazo

Bioinformatics and cancer research: building bridges for translational research

Feb 9, 2008·Clinical & Translational Oncology : Official Publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico·Gonzalo Gómez-López, Alfonso Valencia

Transcriptional profiling of hematopoietic stem cells by high-throughput sequencing

Dec 4, 2008·International Journal of Hematology·Yoshimi YashiroHiromitsu Nakauchi

A microarray analysis of the effects of moderate hypothermia and rewarming on gene expression by human hepatocytes (HepG2)

Jun 8, 2010·Cell Stress & Chaperones·Larry A SonnaCraig M Lilly

Candidate agents for papillary thyroid cancer identified by gene expression analysis

Mar 23, 2013·Pathology Oncology Research : POR·Wei ZhuZhilong Ai

The effect of trans-10, cis-12 conjugated linoleic acid on gene expression profiles related to lipid metabolism in human intestinal-like Caco-2 cells

Mar 14, 2009·Genes & Nutrition·Eileen F MurphyKevin D Cashman

Mechanisms underlying the radioprotective properties of γ-tocotrienol: comparative gene expression profiling in tocol-treated endothelial cells

Apr 26, 2011·Genes & Nutrition·Maaike BerbéeMartin Hauer-Jensen

Evaluation of multiple variate selection methods from a biological perspective: a nutrigenomics case study

Mar 3, 2012·Genes & Nutrition·Henri S TappUwe Thissen

A pathway approach to investigate the function and regulation of SREBPs

Mar 22, 2013·Genes & Nutrition·Sabine DaemenChris T Evelo

Effect of the quality of the interaction data on predicting protein function from protein-protein interactions

Mar 1, 2009·Interdisciplinary Sciences, Computational Life Sciences·Qing-Shan NiYing-Jie Zhao

Predicting the impact of deleterious single point mutations in SMAD gene family using structural bioinformatics approach

Jul 31, 2012·Interdisciplinary Sciences, Computational Life Sciences·C George Priya DossHimani Tanwar

A serial analysis of gene expression profile of the Alzheimer's disease Tg2576 mouse model

Sep 18, 2009·Neurotoxicity Research·Amee J GeorgeQiao-Xin Li

Dual blockade of PKA and NF-κB inhibits H2 relaxin-mediated castrate-resistant growth of prostate cancer sublines and induces apoptosis

Jul 27, 2011·Hormones & Cancer·Ruth L VinallRalph W de Vere White

Genomic signatures of pregnancy-associated breast cancer epithelia and stroma and their regulation by estrogens and progesterone

Mar 13, 2013·Hormones & Cancer·Djuana M E HarvellKathryn B Horwitz

Staged-probability strategy of processing shotgun proteomic data to discover more functionally important proteins

Jan 10, 2012·Protein & Cell·Hong XuRongxiu Li

Mass spectrometry identification of granins and other proteins secreted by neuroblastoma cells

Mar 23, 2013·Tumour Biology : the Journal of the International Society for Oncodevelopmental Biology and Medicine·Wojciech RozekJan F Zmudzinski

Identification and characterization of seed-specific transcription factors regulating anthocyanin biosynthesis in black rice

Feb 3, 2011·Journal of Applied Genetics·C-K KimS-H Park

Using radial basis function on the general form of Chou's pseudo amino acid composition and PSSM to predict subcellular locations of proteins with both single and multiple sites

May 15, 2013·Bio Systems·Chao Huang, Jingqi Yuan

Effect of linoleic acid on proliferation and gene expression in the breast cancer cell line T47D

May 18, 2004·Cancer Letters·Niradiz ReyesJan Geliebter

A pleiotropically acting microRNA, miR-31, inhibits breast cancer metastasis

Jun 16, 2009·Cell·Scott ValastyanRobert A Weinberg

Computational identification of operon-like transcriptional loci in eukaryotes

May 15, 2013·Computers in Biology and Medicine·Kishore NannapaneniTodd E Scheetz

Multi-stage filtering for improving confidence level and determining dominant clusters in clustering algorithms of gene expression data

Aug 13, 2013·Computers in Biology and Medicine·Shahreen KasimRazib M Othman

Application of eVOC: controlled vocabularies for unifying gene expression data

Jan 28, 2004·Comptes rendus biologies·Winston HideJanet Kelso

Exploring the sialome of the blood-sucking bug Rhodnius prolixus

Feb 24, 2004·Insect Biochemistry and Molecular Biology·José M C RibeiroJesus G Valenzuela

Technological advances and genomics in metazoan parasites

Mar 24, 2004·International Journal for Parasitology·D P Knox

Protozoan genomes: gene identification and annotation

Apr 14, 2005·International Journal for Parasitology·E A Worthey, P J Myler

Screening and evaluation of traditional Chinese medicine by microarray expression analysis

Apr 6, 2013·Journal of Ethnopharmacology·Guixiang RenGuoan Luo

PABPN1 overexpression leads to upregulation of genes encoding nuclear proteins that are sequestered in oculopharyngeal muscular dystrophy nuclear inclusions

Mar 10, 2005·Neurobiology of Disease·Louis-Philippe Corbeil-GirardBernard Brais

Transcription factor gene expression profiling after acute intermittent nicotine treatment in the rat cerebral cortex

May 14, 2005·Neuroscience·N BelluardoK Fuxe

A two-sorted logic for structurally modeling systems

Apr 20, 2013·Progress in Biophysics and Molecular Biology·H T Goranson, Beth Cardier

A 7872 cDNA microarray and its use in bovine functional genomics

Apr 6, 2005·Veterinary Immunology and Immunopathology·Robin E EvertsHarris A Lewin

Crustacean oxi-reductases protein sequences derived from a functional genomic project potentially involved in ecdysteroid hormones metabolism - a starting point for function examination

Sep 24, 2013·General and Comparative Endocrinology·Moshe TomAlberto Pallavicini

Studying phospholipid metabolism using yeast systematic and chemical genetics

May 17, 2005·Methods : a Companion to Methods in Enzymology·Gregory D Fairn, Christopher R McMaster

BRIC-seq: a genome-wide approach for determining RNA stability in mammalian cells

Jul 23, 2013·Methods : a Companion to Methods in Enzymology·Naoto ImamachiNobuyoshi Akimitsu

AvGI, an index of genes transcribed in the salivary glands of the ixodid tick Amblyomma variegatum

Oct 24, 2002·International Journal for Parasitology·Vishvanath NeneRichard Bishop

Helminth vaccines: from mining genomic information for vaccine targets to systems used for protein expression

Jun 5, 2003·International Journal for Parasitology·John P DaltonAlex Loukas

Prediction of human protein function from post-translational modifications and localization features

Jun 25, 2002·Journal of Molecular Biology·L J JensenS Brunak

Model systems in drug discovery: chemical genetics meets genomics

Jul 31, 2003·Pharmacology & Therapeutics·Pamela M CarrollKevin FitzGerald

Characterization of the protein processing and secretion pathways in a comprehensive set of expressed sequence tags from Trichoderma reesei

Feb 6, 2004·FEMS Microbiology Letters·S E DienerR A Dean

Global functional profiling of gene expression

Mar 7, 2003·Genomics·Sorin DrăghiciStephen A Krawetz

Genome comparisons highlight similarity and diversity within the eukaryotic kingdoms

Feb 13, 2001·Current Opinion in Chemical Biology·C A Ball, J M Cherry

Molecular classification of renal tumors by gene expression profiling

Apr 29, 2005·The Journal of Molecular Diagnostics : JMD·Audrey N SchuetzAndrew N Young

The systemic paradigm and its relevance to the modelling of biological functions

Aug 7, 2002·Comptes rendus biologies·Magali Roux-Rouquié, Jean-Louis Le Moigne

Maternal protein restriction with or without folic acid supplementation during pregnancy alters the hepatic transcriptome in adult male rats

Mar 10, 2010·The British Journal of Nutrition·Karen A LillycropGraham C Burdge

Analysis of the workers head transcriptome of the Asian subterranean termite, Coptotermes gestroi

Jan 6, 2011·Bulletin of Entomological Research·F C LeonardoG A Pereira

Missense mutation in the MEN1 gene discovered through whole exome sequencing co-segregates with familial hyperparathyroidism

Oct 1, 2013·Genetics Research·Ofer IsakovEitan Friedman

Data mining parasite genomes

Feb 4, 2006·Parasitology·Matthew Berriman

A classification of tasks for the systematic study of immune response using functional genomics data

Feb 14, 2006·Parasitology·C HedelerK J Else

Transcriptional changes in Teladorsagia circumcincta upon encountering host tissue of differing immune status

Jan 6, 2012·Parasitology·Aileen M HallidayDave P Knox

Proteomic analysis of Plasmodium in the mosquito: progress and pitfalls

Feb 18, 2012·Parasitology·M N WassR E Sinden

An instant cell recognition system using a microfabricated coordinate standard chip useful for combinable cell observation with multiple microscopic apparatuses

Mar 4, 2008·Microscopy and Microanalysis : the Official Journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada·Yohei YamadaHideaki Matsuoka

Comparisons of mass spectrometry compatible surfactants for global analysis of the mammalian brain proteome

Oct 22, 2008·Analytical Chemistry·Emily I ChenJohn R Yates

Software tool for researching annotations of proteins: open-source protein annotation software with data visualization

Oct 21, 2009·Analytical Chemistry·Vivek N BhatiaMark McComb

Multisteric regulation by structural disorder in modular signaling proteins: an extension of the concept of allostery

Feb 19, 2014·Chemical Reviews·Peter Tompa

Responses of mouse liver to dechlorane plus exposure by integrative transcriptomic and metabonomic studies

Aug 24, 2012·Environmental Science & Technology·Bing WuShupei Cheng

Insight into the Sialome of the Bed Bug, Cimex lectularius

May 6, 2010·Journal of Proteome Research·Ivo M B FrancischettiJosé M C Ribeiro

Insight into the salivary transcriptome and proteome of Dipetalogaster maxima

Nov 10, 2010·Journal of Proteome Research·Teresa C F AssumpçãoJosé M C Ribeiro

Label-free proteomics and systems biology analysis of mycobacterial phagosomes in dendritic cells and macrophages

Mar 19, 2011·Journal of Proteome Research·Qingbo LiChinnaswamy Jagannath

Correlation between protein function and ligand binding profiles

Mar 4, 2011·Journal of Proteome Research·Matthew D ShortridgeRobert Powers

Proteomic profiling of the influence of iron availability on Cryptococcus gattii

Oct 6, 2011·Journal of Proteome Research·Juliana CrestaniMarilene Henning Vainstein

Proteomic analysis of an immortalized mouse pancreatic stellate cell line identifies differentially-expressed proteins in activated vs nonproliferating cell states

Aug 16, 2011·Journal of Proteome Research·Joao A PauloHanno Steen

Vesicle and vesicle-free extracellular proteome of Paracoccidioides brasiliensis: comparative analysis with other pathogenic fungi

Feb 1, 2012·Journal of Proteome Research·Milene C VallejoRosana Puccia

Proteomic analysis (GeLC-MS/MS) of ePFT-collected pancreatic fluid in chronic pancreatitis

Jan 17, 2012·Journal of Proteome Research·Joao A PauloHanno Steen

Identification of prostate-enriched proteins by in-depth proteomic analyses of expressed prostatic secretions in urine

Feb 22, 2012·Journal of Proteome Research·Simona PrincipeJeffrey A Medin

Label-free quantitative LC-MS proteomics of Alzheimer's disease and normally aged human brains

May 9, 2012·Journal of Proteome Research·Victor P AndreevAmanda J Myers

Computational framework for analysis of prey-prey associations in interaction proteomics identifies novel human protein-protein interactions and networks

Aug 1, 2012·Journal of Proteome Research·Sudipto SahaRob M Ewing

Urinary proteome analysis of irritable bowel syndrome (IBS) symptom subgroups

Sep 25, 2012·Journal of Proteome Research·Young Ah GooMargaret Heitkemper

Extracellular matrix remodeling by bone marrow fibroblast-like cells correlates with disease progression in multiple myeloma

Nov 22, 2013·Journal of Proteome Research·Astrid SlanyJohannes Drach

Proteome response to the panneural expression of human wild-type alpha-synuclein: a Drosophila model of Parkinson's disease

Aug 8, 2008·Journal of Proteome Research·Zhiyin XunDavid E Clemmer

Large-scale analysis of thermostable, mammalian proteins provides insights into the intrinsically disordered proteome

Dec 11, 2008·Journal of Proteome Research·Charles A GaleaRichard W Kriwacki

Proteomic analysis of an alpha7 nicotinic acetylcholine receptor interactome

Aug 29, 2009·Journal of Proteome Research·Joao A PauloEdward Hawrot

Insight into the sialome of the Black Fly, Simulium vittatum

Jan 27, 2009·Journal of Proteome Research·John F AndersenJosé M C Ribeiro

Stable isotope labeling and label-free proteomics of Drosophila parkin null mutants

Aug 27, 2009·Journal of Proteome Research·Zhiyin XunDavid E Clemmer

Sequence tagging reveals unexpected modifications in toxicoproteomics

Jan 11, 2011·Chemical Research in Toxicology·Surendra DasariDavid L Tabb

Transcriptomic responses of cancerous and noncancerous human colon cells to sulforaphane and selenium

Jan 5, 2014·Chemical Research in Toxicology·Simona ConstantinescuNiko Beerenwinkel

Mutant p53(R175H) upregulates Twist1 expression and promotes epithelial-mesenchymal transition in immortalized prostate cells

Aug 7, 2010·Cell Death and Differentiation·I Kogan-SakinV Rotter

HDAC inhibitors induce tumor-cell-selective pro-apoptotic transcriptional responses

Mar 2, 2013·Cell Death & Disease·J E BoldenR W Johnstone

Variable set enrichment analysis in genome-wide association studies

Mar 24, 2011·European Journal of Human Genetics : EJHG·Wei YangC Charles Gu

Gene set analysis of SNP data: benefits, challenges, and future directions

Apr 14, 2011·European Journal of Human Genetics : EJHG·Brooke L Fridley, Joanna M Biernacka

Gene-ontology enrichment analysis in two independent family-based samples highlights biologically plausible processes for autism spectrum disorders

Apr 28, 2011·European Journal of Human Genetics : EJHG·Richard J L AnneyLouise Gallagher

Prioritising risk pathways of complex human diseases based on functional profiling

Oct 11, 2012·European Journal of Human Genetics : EJHG·Yan LiYixue Li

Informatics and clinical genome sequencing: opening the black box

Sep 15, 2012·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Sowmiya MoorthieCaroline F Wright

Retroviral vector integration in post-transplant hematopoiesis in mice conditioned with either submyeloablative or ablative irradiation

Aug 7, 2009·Gene Therapy·M A SadatM C Dinauer

All dosage compensation is local: gene-by-gene regulation of sex-biased expression on the chicken Z chromosome

Nov 6, 2008·Heredity·J E Mank, H Ellegren

Body size in Drosophila: genetic architecture, allometries and sexual dimorphism

Nov 20, 2008·Heredity·V P CarreiraJ J Fanara

Preadipocytes of type 2 diabetes subjects display an intrinsic gene expression profile of decreased differentiation capacity

Feb 18, 2011·International Journal of Obesity : Journal of the International Association for the Study of Obesity·F H J van TienenH J M Smeets

Bioinformatics advances in saliva diagnostics

Jun 16, 2012·International Journal of Oral Science·Ji-Ye AiDavid T W Wong

Biogeography and phylogenetic diversity of a cluster of exclusively marine myxobacteria

Dec 23, 2011·The ISME Journal·Thorsten BrinkhoffMeinhard Simon

Genome-wide pathway analysis implicates intracellular transmembrane protein transport in Alzheimer disease

Jul 30, 2010·Journal of Human Genetics·Mun-Gwan HongJonathan A Prince

Unexpected functional similarities between gatekeeper tumour suppressor genes and proto-oncogenes revealed by systems biology

Mar 4, 2011·Journal of Human Genetics·Yongzhong Zhao, Richard J Epstein

DBGSA: a novel method of distance-based gene set analysis

Jul 13, 2012·Journal of Human Genetics·Jin LiXia Li

Correlation analysis between genome-wide expression profiles and cytoarchitectural abnormalities in the prefrontal cortex of psychiatric disorders

Sep 3, 2008·Molecular Psychiatry·S Kim, Maree J Webster

SZGR: a comprehensive schizophrenia gene resource

Apr 29, 2010·Molecular Psychiatry·Peilin JiaZhongming Zhao

Gene Expression Profile Changes After Short-activating RNA-mediated Induction of Endogenous Pluripotency Factors in Human Mesenchymal Stem Cells

Jan 25, 2013·Molecular Therapy. Nucleic Acids·Jon VoutilaNoriyuki Kasahara

Sequence and analysis of chromosome 2 of Dictyostelium discoideum

Jul 5, 2002·Nature·Gernot GlöcknerDictyostelium Genome Sequencing Consortium

Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14

Oct 9, 2002·Nature·Malcolm J GardnerClaire M Fraser

Sequence of Plasmodium falciparum chromosomes 1, 3-9 and 13

Oct 9, 2002·Nature·Neil HallBart Barrell

Genome sequence of the human malaria parasite Plasmodium falciparum

Oct 9, 2002·Nature·Malcolm J GardnerBart Barrell

Sequence of Plasmodium falciparum chromosome 12

Oct 9, 2002·Nature·Richard W HymanRonald W Davis

From genomics to proteomics

Mar 14, 2003·Nature·Mike Tyers, Matthias Mann

Biomedical informatics for proteomics

Mar 14, 2003·Nature·Mark S Boguski, Martin W McIntosh

Evolutionary changes in cis and trans gene regulation

Jul 2, 2004·Nature·Patricia J WittkoppAndrew G Clark

Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs

Feb 3, 2005·Nature·Lee P LimJason M Johnson

Initial sequence of the chimpanzee genome and comparison with the human genome

Sep 2, 2005·Nature·Chimpanzee Sequencing and Analysis Consortium

The Plasmodium protein network diverges from those of other eukaryotes

Nov 4, 2005·Nature·Silpa SuthramTrey Ideker

A haplotype map of the human genome

Oct 29, 2005·Nature·International HapMap Consortium

A genomic code for nucleosome positioning

Jul 25, 2006·Nature·Eran SegalJonathan Widom

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

Nov 13, 2007·Nature·Alexander StarkManolis Kellis

The impact of microRNAs on protein output

Aug 1, 2008·Nature·Daehyun BaekDavid P Bartel

Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans

Jul 17, 2009·Nature·Johan MalmströmRuedi Aebersold

Remarkably ancient balanced polymorphisms in a multi-locus gene network

Feb 19, 2010·Nature·Chris Todd HittingerAntonis Rokas

Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis

Apr 16, 2010·Nature·Rajnish A GuptaHoward Y Chang

Genome-wide measurement of RNA secondary structure in yeast

Sep 3, 2010·Nature·Michael KerteszEran Segal

Comparative and demographic analysis of orang-utan genomes

Jan 29, 2011·Nature·Devin P LockeRichard K Wilson

Mapping and analysis of chromatin state dynamics in nine human cell types

Mar 29, 2011·Nature·Jason ErnstBradley E Bernstein

Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis

Aug 13, 2011·Nature·Stephen SawcerAlastair Compston

A framework for human microbiome research

Jun 16, 2012·Nature·Human Microbiome Project Consortium

Structure-based prediction of protein-protein interactions on a genome-wide scale

Oct 2, 2012·Nature·Qiangfeng Cliff ZhangBarry Honig

Genome-wide signatures of convergent evolution in echolocating mammals

Sep 6, 2013·Nature·Joe ParkerStephen J Rossiter

Dynamic modularity in protein interaction networks predicts breast cancer outcome

Feb 3, 2009·Nature Biotechnology·Ian W TaylorJeffrey L Wrana

How to visually interpret biological data using networks

Oct 10, 2009·Nature Biotechnology·Daniele MericoGary D Bader

GREAT improves functional interpretation of cis-regulatory regions

May 4, 2010·Nature Biotechnology·Cory Y McLeanGill Bejerano

Genome sequence of the model mushroom Schizophyllum commune

Jul 14, 2010·Nature Biotechnology·Robin A OhmHan A B Wösten

Chemical genetics screen for enhancers of rapamycin identifies a specific inhibitor of an SCF family E3 ubiquitin ligase

Jun 29, 2010·Nature Biotechnology·Mariam AghajanJing Huang

The BioPAX community standard for pathway data sharing

Sep 11, 2010·Nature Biotechnology·Emek DemirGary D Bader

Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers

Nov 8, 2011·Nature Biotechnology·Rajeev K VarshneyScott A Jackson

Three-dimensional reconstruction of protein networks provides insight into human genetic disease

Jan 19, 2012·Nature Biotechnology·Xiujuan WangHaiyuan Yu

Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential

May 15, 2012·Nature Biotechnology·Gengyun ZhangJian Wang

A gene ontology inferred from molecular networks

Dec 18, 2012·Nature Biotechnology·Janusz DutkowskiTrey Ideker

Automating the construction of gene ontologies

Jan 11, 2013·Nature Biotechnology·K Dolinski, D Botstein

Human Proteinpedia enables sharing of human protein data

Feb 9, 2008·Nature Biotechnology·Suresh MathivananAkhilesh Pandey

Ontology engineering

Feb 9, 2010·Nature Biotechnology·Gil AlterovitzMarco F Ramoni

Protein annotation by EBIMed

Aug 11, 2006·Nature Biotechnology·Dietrich Rebholz-SchuhmannPeter Stoehr

Functional annotation and network reconstruction through cross-platform integration of microarray data

Jan 18, 2005·Nature Biotechnology·Xianghong Jasmine ZhouWing Hung Wong

Are we stuck in the standards?

Nov 10, 2006·Nature Biotechnology·C A Ball

Creation and implications of a phenome-genome network

Jan 13, 2006·Nature Biotechnology·Atul J Butte, Isaac S Kohane

Minimum information requested in the annotation of biochemical models (MIRIAM)

Dec 8, 2005·Nature Biotechnology·Nicolas Le NovèreBarry L Wanner

The art of gene function prediction

Dec 13, 2006·Nature Biotechnology·T M MuraliSimon Kasif

Hematopoietic stem cell gene transfer in a tumor-prone mouse model uncovers low genotoxicity of lentiviral vector integration

May 30, 2006·Nature Biotechnology·Eugenio MontiniLuigi Naldini

ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe

Jul 11, 2006·Nature Biotechnology·Akihisa MatsuyamaMinoru Yoshida

Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis

Mar 6, 2007·Nature Biotechnology·Thomas W JeffriesPaul Richardson

Towards zoomable multidimensional maps of the cell

May 8, 2007·Nature Biotechnology·Zhenjun HuCharles DeLisi

Decoding global gene expression programs in liver cancer by noninvasive imaging

May 23, 2007·Nature Biotechnology·Eran SegalMichael D Kuo

A modular approach for integrative analysis of large-scale gene-expression and drug-response data

May 10, 2008·Nature Biotechnology·Zoltán KutalikSven Bergmann

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

May 6, 2008·Nature Biotechnology·Diego MartinezThomas S Brettin

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

Oct 11, 2008·Nature Biotechnology·Markus J HerrgårdDouglas B Kell

An integrated functional genomics screening program reveals a role for BMP-9 in glucose homeostasis

Feb 25, 2003·Nature Biotechnology·Cecil ChenCharles E Birse

Modelling data across labs, genomes, space and time

Oct 25, 2006·Nature Cell Biology·Jason R SwedlowIlya G Goldberg

TFEB controls cellular lipid metabolism through a starvation-induced autoregulatory loop

Apr 23, 2013·Nature Cell Biology·Carmine SettembreAndrea Ballabio

Automatic policing of biochemical annotations using genomic correlations

Nov 26, 2009·Nature Chemical Biology·Tzu-Lin HsiaoDennis Vitkup

Gene expression signatures and small-molecule compounds link a protein kinase to Plasmodium falciparum motility

May 6, 2008·Nature Chemical Biology·Nobutaka KatoElizabeth A Winzeler

Missing in action: enzyme functional annotations in biological databases

Jul 22, 2009·Nature Chemical Biology·Nicholas FurnhamJanet M Thornton

Ectopic expression of the histone methyltransferase Ezh2 in haematopoietic stem cells causes myeloproliferative disease

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Whole-genome sequencing reveals untapped genetic potential in Africa's indigenous cereal crop sorghum

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Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia

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Many sequence variants affecting diversity of adult human height

Apr 9, 2008·Nature Genetics·Daniel F GudbjartssonKari Stefansson

RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo

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Apr 3, 2012·Nature Genetics·Lei SunLisa J Strug

The yak genome and adaptation to life at high altitude

Jul 4, 2012·Nature Genetics·Qiang QiuJianquan Liu

Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle

Mar 26, 2013·Nature Genetics·Xiangjiang ZhanMichael W Bruford

The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan

Apr 30, 2013·Nature Genetics·Zhuo WangNaoki Irie

The mutational landscape of adenoid cystic carcinoma

May 21, 2013·Nature Genetics·Allen S HoTimothy A Chan

Genome-wide inference of natural selection on human transcription factor binding sites

Jun 12, 2013·Nature Genetics·Leonardo ArbizaAdam Siepel

An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

Jul 3, 2013·Nature Genetics·Annabelle HaudryMathieu Blanchette

Discovery and refinement of loci associated with lipid levels

Oct 8, 2013·Nature Genetics·Cristen J WillerGlobal Lipids Genetics Consortium

Minke whale genome and aquatic adaptation in cetaceans

Nov 26, 2013·Nature Genetics·Hyung-Soon YimJung-Hyun Lee

Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization

Mar 3, 2009·Nature Genetics·Yair FieldEran Segal

Validation of candidate causal genes for obesity that affect shared metabolic pathways and networks

Mar 10, 2009·Nature Genetics·Xia YangThomas A Drake

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Aug 24, 2010·Nature Genetics·Matthew J BlowLen A Pennacchio

Whole-genome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing

Oct 26, 2010·Nature Genetics·Akihiro FujimotoTatsuhiko Tsunoda

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Apr 12, 2011·Nature Genetics·Qiye HeJulia Zeitlinger

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Apr 29, 2005·Nature Genetics·Greg Gibson

What everybody should know about the rat genome and its online resources

Apr 30, 2008·Nature Genetics·Simon N TwiggerHoward J Jacob

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May 29, 2004·Nature Genetics·Andrew G Fraser, Edward M Marcotte

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Feb 16, 2005·Nature Genetics·Elissa J CheslerRobert W Williams

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Apr 27, 2005·Nature Genetics·Dee R DenverW Kelley Thomas

Genetic regulators of large-scale transcriptional signatures in cancer

Mar 7, 2006·Nature Genetics·Adam S AdlerHoward Y Chang

Genome variation and evolution of the malaria parasite Plasmodium falciparum

Dec 13, 2006·Nature Genetics·Daniel C JeffaresMatthew Berriman

Systematic pathway analysis using high-resolution fitness profiling of combinatorial gene deletions

Jan 9, 2007·Nature Genetics·Robert P St OngeGuri Giaever

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Sep 18, 2007·Nature Genetics·Barbara E StrangerEmmanouil T Dermitzakis

A function for interleukin 2 in Foxp3-expressing regulatory T cells

Oct 18, 2005·Nature Immunology·Jason D FontenotAlexander Y Rudensky

A critical developmental switch defines the kinetics of kidney cyst formation after loss of Pkd1

Oct 30, 2007·Nature Medicine·Klaus PiontekGregory G Germino

Stromal gene expression predicts clinical outcome in breast cancer

Apr 29, 2008·Nature Medicine·Greg FinakMorag Park

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May 31, 2011·Nature Methods·Jason R SwedlowChristoph Best

Proteomic and phosphoproteomic comparison of human ES and iPS cells

Oct 11, 2011·Nature Methods·Douglas H PhanstielJoshua J Coon

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A pharmacological organization of G protein-coupled receptors

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Jan 29, 2013·Nature Methods·Predrag RadivojacIddo Friedberg

DGIdb: mining the druggable genome

Oct 15, 2013·Nature Methods·Malachi GriffithRichard K Wilson

RNAiCut: automated detection of significant genes from functional genomic screens

Jul 1, 2009·Nature Methods·Irene M KaplowBonnie Berger

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Mar 14, 2007·Nature Methods·Ralf KittlerFrank Buchholz

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Oct 14, 2008·Nature Neuroscience·Michael C OldhamDaniel H Geschwind

The neuron-specific chromatin regulatory subunit BAF53b is necessary for synaptic plasticity and memory

Mar 26, 2013·Nature Neuroscience·Annie Vogel-CierniaMarcelo A Wood

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Apr 5, 2007·Nature Protocols·Adam A MargolinAndrea Califano

Integration of biological networks and gene expression data using Cytoscape

Oct 20, 2007·Nature Protocols·Melissa S ClineGary D Bader

Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms

Feb 16, 2008·Nature Protocols·Kuo-Chen Chou, Hong-Bin Shen

Network Analysis Tools: from biological networks to clusters and pathways

Sep 20, 2008·Nature Protocols·Sylvain BrohéeJacques van Helden

A protocol for generating a high-quality genome-scale metabolic reconstruction

Jan 9, 2010·Nature Protocols·Ines Thiele, Bernhard Ø Palsson

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Feb 6, 2010·Nature Protocols·Igor UlitskyRon Shamir

A general pipeline for quality and statistical assessment of protein interaction data using R and Bioconductor

Mar 28, 2009·Nature Protocols·Tony Chiang, Denise Scholtens

A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics

Apr 18, 2009·Nature Protocols·Jürgen CoxMatthias Mann

I-TASSER: a unified platform for automated protein structure and function prediction

Apr 3, 2010·Nature Protocols·Ambrish RoyYang Zhang

Gene function analysis in complex data sets using ErmineJ

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Assembling global maps of cellular function through integrative analysis of physical and genetic networks

Sep 3, 2011·Nature Protocols·Rohith SrivasTrey Ideker

Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network

Sep 3, 2011·Nature Protocols·Sohyun HwangInsuk Lee

A computational pipeline for comparative ChIP-seq analyses

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Integrated global profiling of cancer

Aug 3, 2004·Nature Reviews. Cancer·Samir Hanash

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Apr 25, 2008·Nature Reviews. Cancer·Debra M KrupkeJanan T Eppig

Polycomb group proteins: navigators of lineage pathways led astray in cancer

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The use and analysis of microarray data

Dec 4, 2002·Nature Reviews. Drug Discovery·Atul Butte

Chemogenomics: an emerging strategy for rapid target and drug discovery

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Standards for systems biology

Jul 19, 2006·Nature Reviews. Genetics·Alvis BrazmaUgis Sarkans

ChIP-seq: advantages and challenges of a maturing technology

Sep 9, 2009·Nature Reviews. Genetics·Peter J Park

Next-generation genomics: an integrative approach

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Statistical analysis strategies for association studies involving rare variants

Oct 14, 2010·Nature Reviews. Genetics·Vikas BansalNicholas J Schork

Computational tools for prioritizing candidate genes: boosting disease gene discovery

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Cancer pharmacogenomics: strategies and challenges

Nov 28, 2012·Nature Reviews. Genetics·Heather E WheelerMark J Ratain

Predicting protein function from sequence and structure

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Decoding signalling networks by mass spectrometry-based proteomics

May 13, 2010·Nature Reviews. Molecular Cell Biology·Chunaram Choudhary, Matthias Mann

Genetics and epigenetics of rheumatoid arthritis

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A conserved activation element in BMP signaling during Drosophila development

Dec 17, 2009·Nature Structural & Molecular Biology·Alexander WeissMarkus Affolter

Systematic identification of fragile sites via genome-wide location analysis of gamma-H2AX

Feb 9, 2010·Nature Structural & Molecular Biology·Rachel K SzilardDaniel Durocher

Exploring functional relationships between components of the gene expression machinery

Feb 11, 2005·Nature Structural & Molecular Biology·Todd BurckinManuel Ares

MicroRNA-21 promotes cell transformation by targeting the programmed cell death 4 gene

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Individualized therapy in non-small-cell lung cancer: future versus current clinical practice

Aug 15, 2009·Oncogene·R Pérez-Soler

Protooncogene TCL1b functions as an Akt kinase co-activator that exhibits oncogenic potency in vivo

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Gene expression in archived newborn blood spots distinguishes infants who will later develop cerebral palsy from matched controls

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The involvement of XPC protein in the cisplatin DNA damaging treatment-mediated cellular response

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Identification of key genes responsible for cytokine-induced erythroid and myeloid differentiation and switching of hematopoietic stem cells by RAGE

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A text-mining analysis of the human phenome

Feb 24, 2006·European Journal of Human Genetics : EJHG·Marc A van DrielJack A M Leunissen

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Haplotype patterns in cancer-related genes with long-range linkage disequilibrium: no evidence of association with breast cancer or positive selection

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Deregulated stress system in non-obese diabetic lymphocyte

May 13, 2006·Genes and Immunity·Z Liu, Thomas M Aune

Bayesian mapping of genotype x expression interactions in quantitative and qualitative traits

May 4, 2006·Heredity·F Hoti, M J Sillanpää

Deregulated expression of fat and muscle genes in B-cell chronic lymphocytic leukemia with high lipoprotein lipase expression

Apr 18, 2006·Leukemia·M BilbanGerman CLL Study Group

Targeting lipid metabolism by the lipoprotein lipase inhibitor orlistat results in apoptosis of B-cell chronic lymphocytic leukemia cells

Dec 15, 2007·Leukemia·C P PallaschC-M Wendtner

Disrupted in Schizophrenia 1 Interactome: evidence for the close connectivity of risk genes and a potential synaptic basis for schizophrenia

Oct 18, 2006·Molecular Psychiatry·L M CamargoN J Brandon

Lack of serotonin1B receptor expression leads to age-related motor dysfunction, early onset of brain molecular aging and reduced longevity

Apr 11, 2007·Molecular Psychiatry·E SibilleC Belzung

Gender-specific gene expression in post-mortem human brain: localization to sex chromosomes

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Neurotoxic consequences of chronic alcohol withdrawal: expression profiling reveals importance of gender over withdrawal severity

Jun 28, 2007·Neuropsychopharmacology : Official Publication of the American College of Neuropsychopharmacology·Joel G Hashimoto, Kristine M Wiren

G1/S transcriptional networks modulated by the HOX11/TLX1 oncogene of T-cell acute lymphoblastic leukemia

May 18, 2005·Oncogene·Irene Riz, Robert G Hawley

7q deletion mapping and expression profiling in uterine fibroids

Jun 9, 2005·Oncogene·Sakari VanharantaLauri A Aaltonen

Two subclasses of lung squamous cell carcinoma with different gene expression profiles and prognosis identified by hierarchical clustering and non-negative matrix factorization

Jul 12, 2005·Oncogene·Kentaro InamuraYuichi Ishikawa

Gene expression profiling identifies molecular subgroups among nodal peripheral T-cell lymphomas

Nov 17, 2005·Oncogene·B BallesterL Xerri

Parallel induction of ATM-dependent pro- and antiapoptotic signals in response to ionizing radiation in murine lymphoid tissue

Nov 30, 2005·Oncogene·S Rashi-ElkelesY Shiloh

Molecular signatures of metaplastic carcinoma of the breast by large-scale transcriptional profiling: identification of genes potentially related to epithelial-mesenchymal transition

Jul 3, 2007·Oncogene·H C LienF J Hsieh

High expression of DNA repair pathways is associated with metastasis in melanoma patients

Sep 25, 2007·Oncogene·A KauffmannA Sarasin

Genes involved in cell adhesion, cell motility and mitogenic signaling are altered due to HPV 16 E5 protein expression

Nov 6, 2007·Oncogene·N KiviE Auvinen

The use of animal models in expression pharmacogenomic analyses

Mar 27, 2002·The Pharmacogenomics Journal·B E Rothberg

Mining the bibliome

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Development of a human mitochondria-focused cDNA microarray (hMitChip) and validation in skeletal muscle cells: implications for pharmaco- and mitogenomics

Mar 15, 2006·The Pharmacogenomics Journal·S AlesciG P Chrousos

Multi-locus genome-wide association analysis supports the role of glutamatergic synaptic transmission in the etiology of major depressive disorder

Nov 15, 2012·Translational Psychiatry·Phil H LeeJ W Smoller

The brain expression of genes involved in inflammatory response, the ribosome, and learning and memory is altered by centrally injected lipopolysaccharide in mice

Oct 30, 2008·The Pharmacogenomics Journal·R H BonowF Bosetti

Functional analysis of multiple genomic signatures demonstrates that classification algorithms choose phenotype-related genes

Aug 3, 2010·The Pharmacogenomics Journal·W ShiY Nikolsky

DEFOG: discrete enrichment of functionally organized genes

Jun 19, 2012·Integrative Biology : Quantitative Biosciences From Nano to Macro·Tobias WittkopSean D Mooney

The need for a standard nomenclature for gene classification (a Nucleotide Function Code) and an automated data-based tool to assist in understanding the molecular associations in cell signalling in plant-pathogen interactions

Mar 1, 2002·Molecular Plant Pathology·Gary D LyonBruce Marshall

Scalable learning of large networks

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Network integration and graph analysis in mammalian molecular systems biology

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Reduced-order modelling of biochemical networks: application to the GTPase-cycle signalling module

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Functional evolution of the p53 regulatory network through its target response elements

Jan 12, 2008·Proceedings of the National Academy of Sciences of the United States of America·Anil G JeggaMichael A Resnick

A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation

Jan 1, 2008·Proceedings of the National Academy of Sciences of the United States of America·Michal Brylinski, Jeffrey Skolnick

Modularity of stress response evolution

May 23, 2008·Proceedings of the National Academy of Sciences of the United States of America·Amoolya H SinghAdam P Arkin

Defining genetic interaction

Feb 29, 2008·Proceedings of the National Academy of Sciences of the United States of America·Ramamurthy ManiFrederick P Roth

Global gene expression profiles for life stages of the deadly amphibian pathogen Batrachochytrium dendrobatidis

Oct 15, 2008·Proceedings of the National Academy of Sciences of the United States of America·Erica Bree RosenblumMichael B Eisen

A quantitative atlas of mitotic phosphorylation

Aug 2, 2008·Proceedings of the National Academy of Sciences of the United States of America·Noah DephoureSteven P Gygi

ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes

Jan 2, 2009·Proceedings of the National Academy of Sciences of the United States of America·Adam A MargolinGustavo Stolovitzky

Annotating proteins with generalized functional linkages

Nov 14, 2008·Proceedings of the National Academy of Sciences of the United States of America·Richard Llewellyn, David S Eisenberg

Long-lived Indy induces reduced mitochondrial reactive oxygen species production and oxidative damage

Jan 24, 2009·Proceedings of the National Academy of Sciences of the United States of America·Nicola NerettiStephen L Helfand

DNA methylation is widespread and associated with differential gene expression in castes of the honeybee, Apis mellifera

Jun 27, 2009·Proceedings of the National Academy of Sciences of the United States of America·Navin ElangoSoojin V Yi

Transcriptional neoteny in the human brain

Mar 25, 2009·Proceedings of the National Academy of Sciences of the United States of America·Mehmet SomelPhilipp Khaitovich

Impaired tumor growth, metastasis, angiogenesis and wound healing in annexin A1-null mice

Oct 7, 2009·Proceedings of the National Academy of Sciences of the United States of America·Ming Yi, Jan E Schnitzer

A transcriptomic analysis of superhybrid rice LYP9 and its parents

Apr 18, 2009·Proceedings of the National Academy of Sciences of the United States of America·Gang WeiLihuang Zhu

The transcriptome of human CD34+ hematopoietic stem-progenitor cells

May 7, 2009·Proceedings of the National Academy of Sciences of the United States of America·Yeong C KimSan Ming Wang

Changes in transcript abundance relating to colony collapse disorder in honey bees (Apis mellifera)

Aug 27, 2009·Proceedings of the National Academy of Sciences of the United States of America·Reed M JohnsonMay R Berenbaum

Triplet repeat length bias and variation in the human transcriptome

Oct 7, 2009·Proceedings of the National Academy of Sciences of the United States of America·Michael MollaSimon Kasif

Toward a quantitative theory of intrinsically disordered proteins and their function

Nov 12, 2009·Proceedings of the National Academy of Sciences of the United States of America·Jintao LiuCarlos J Camacho

Dual coding in alternative reading frames correlates with intrinsic protein disorder

Mar 10, 2010·Proceedings of the National Academy of Sciences of the United States of America·Erika KovacsLajos Kalmar

Posttranslational regulation impacts the fate of duplicated genes

Jan 19, 2010·Proceedings of the National Academy of Sciences of the United States of America·Grigoris D AmoutziasYves Van de Peer

Transcriptional response in the peripheral blood of patients infected with Salmonella enterica serovar Typhi

Dec 19, 2009·Proceedings of the National Academy of Sciences of the United States of America·Lucinda J ThompsonStanley Falkow

Polygenic and directional regulatory evolution across pathways in Saccharomyces

Mar 3, 2010·Proceedings of the National Academy of Sciences of the United States of America·James H BullardRachel B Brem

MiDReG: a method of mining developmentally regulated genes using Boolean implications

Mar 17, 2010·Proceedings of the National Academy of Sciences of the United States of America·Debashis SahooDavid L Dill

Diversification in the genetic architecture of gene expression and transcriptional networks in organ differentiation of Populus

Apr 21, 2010·Proceedings of the National Academy of Sciences of the United States of America·Derek R DrostMatias Kirst

Role of microRNA-23b in flow-regulation of Rb phosphorylation and endothelial cell growth

Feb 6, 2010·Proceedings of the National Academy of Sciences of the United States of America·Kuei-Chun WangShu Chien

Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function

Sep 21, 2010·Proceedings of the National Academy of Sciences of the United States of America·James A Cotton, James O McInerney

Developmental regulation and individual differences of neuronal H3K4me3 epigenomes in the prefrontal cortex

Apr 28, 2010·Proceedings of the National Academy of Sciences of the United States of America·Iris CheungSchahram Akbarian

Longitudinal shift in diabetic wound microbiota correlates with prolonged skin defense response

Jul 30, 2010·Proceedings of the National Academy of Sciences of the United States of America·Elizabeth A GriceJulia A Segre

Tracking, tuning, and terminating microbial physiology using synthetic riboregulators

Aug 18, 2010·Proceedings of the National Academy of Sciences of the United States of America·Jarred M CalluraJames J Collins

Prognostic gene-expression signature of carcinoma-associated fibroblasts in non-small cell lung cancer

Apr 9, 2011·Proceedings of the National Academy of Sciences of the United States of America·Roya NavabMing-Sound Tsao

Regulation of hematopoietic stem cells by their mature progeny

Dec 1, 2010·Proceedings of the National Academy of Sciences of the United States of America·Carolyn A de GraafDouglas J Hilton

Antennal transcriptome of Manduca sexta

Apr 19, 2011·Proceedings of the National Academy of Sciences of the United States of America·Ewald Grosse-WildeBill S Hansson

Network-based prediction for sources of transcriptional dysregulation using latent pathway identification analysis

Jul 27, 2011·Proceedings of the National Academy of Sciences of the United States of America·Lisa PhamEric D Kolaczyk

Measuring the evolutionary rate of protein-protein interaction

May 11, 2011·Proceedings of the National Academy of Sciences of the United States of America·Wenfeng QianJianzhi Zhang

ATM kinase inhibition in glial cells activates the innate immune response and causes neurodegeneration in Drosophila

Feb 23, 2012·Proceedings of the National Academy of Sciences of the United States of America·Andrew J PetersenDavid A Wassarman

Protein misinteraction avoidance causes highly expressed proteins to evolve slowly

Mar 15, 2012·Proceedings of the National Academy of Sciences of the United States of America·Jian-Rong YangJianzhi Zhang

Branching process deconvolution algorithm reveals a detailed cell-cycle transcription program

Feb 8, 2013·Proceedings of the National Academy of Sciences of the United States of America·Xin GuoAlexander J Hartemink

Congenital diaphragmatic hernia candidate genes derived from embryonic transcriptomes

Feb 9, 2012·Proceedings of the National Academy of Sciences of the United States of America·Meaghan K RussellPatricia K Donahoe

Computational design of genomic transcriptional networks with adaptation to varying environments

Aug 29, 2012·Proceedings of the National Academy of Sciences of the United States of America·Javier CarreraAlfonso Jaramillo

Genetic heterogeneity of diffuse large B-cell lymphoma

Jan 8, 2013·Proceedings of the National Academy of Sciences of the United States of America·Jenny ZhangSandeep S Dave

Dinoflagellate tandem array gene transcripts are highly conserved and not polycistronic

Sep 29, 2012·Proceedings of the National Academy of Sciences of the United States of America·Mathieu BeaucheminDavid Morse

Recombination is associated with the evolution of genome structure and worker behavior in honey bees

Oct 17, 2012·Proceedings of the National Academy of Sciences of the United States of America·Clement F KentAmro Zayed

Bioinformatic identification of genes suppressing genome instability

Nov 7, 2012·Proceedings of the National Academy of Sciences of the United States of America·Christopher D PutnamRichard D Kolodner

The human gene connectome as a map of short cuts for morbid allele discovery

Mar 20, 2013·Proceedings of the National Academy of Sciences of the United States of America·Yuval ItanJean-Laurent Casanova

Physical and genetic-interaction density reveals functional organization and informs significance cutoffs in genome-wide screens

Apr 17, 2013·Proceedings of the National Academy of Sciences of the United States of America·John C DittmarRobert J D Reid

Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants

Feb 6, 2013·Proceedings of the National Academy of Sciences of the United States of America·Riet De SmetYves Van de Peer

Genetic circuitry of Survival motor neuron, the gene underlying spinal muscular atrophy

Jun 13, 2013·Proceedings of the National Academy of Sciences of the United States of America·Anindya SenSpyros Artavanis-Tsakonas

The first draft of the endostatin interaction network

Jun 23, 2009·The Journal of Biological Chemistry·Clément FayeSylvie Ricard-Blum

Growth factor regulation of prostaglandin-endoperoxide synthase 2 (Ptgs2) expression in colonic mesenchymal stem cells

Dec 19, 2009·The Journal of Biological Chemistry·Monica R WalkerThaddeus S Stappenbeck

An integrated approach for experimental target identification of hypoxia-induced miR-210

Oct 15, 2009·The Journal of Biological Chemistry·Pasquale FasanaroFabio Martelli

Purification of nuclear poly(A)-binding protein Nab2 reveals association with the yeast transcriptome and a messenger ribonucleoprotein core structure

Oct 21, 2009·The Journal of Biological Chemistry·Julien BatisseEd Hurt

A protein involved in the assembly of an extracellular calcium storage matrix

Feb 13, 2010·The Journal of Biological Chemistry·Lilah GlazerAmir Sagi

Integration of general amino acid control and target of rapamycin (TOR) regulatory pathways in nitrogen assimilation in yeast

Mar 18, 2010·The Journal of Biological Chemistry·Kirk A StaschkeRonald C Wek

Negative regulation of meiotic gene expression by the nuclear poly(a)-binding protein in fission yeast

Jul 14, 2010·The Journal of Biological Chemistry·Olivier St-AndréFrançois Bachand

Integrated quantitative analysis of the phosphoproteome and transcriptome in tamoxifen-resistant breast cancer

Nov 4, 2010·The Journal of Biological Chemistry·Masaaki OyamaMariko Okada-Hatakeyama

Endothelin-1 increases collagen accumulation in renal mesangial cells by stimulating a chemokine and cytokine autocrine signaling loop

Dec 21, 2010·The Journal of Biological Chemistry·Michael S Simonson, Faramarz Ismail-Beigi

Interorgan coordination of the murine adaptive response to fasting

Mar 12, 2011·The Journal of Biological Chemistry·Theodorus B M HakvoortMilka Sokolović

A systems biology approach for the investigation of the heparin/heparan sulfate interactome

Apr 2, 2011·The Journal of Biological Chemistry·Alessandro OriDavid G Fernig

DLK1-DIO3 genomic imprinted microRNA cluster at 14q32.2 defines a stemlike subtype of hepatocellular carcinoma associated with poor survival

Jul 9, 2011·The Journal of Biological Chemistry·John M LukMao Mao

Aberrant epigenetic and genetic marks are seen in myelodysplastic leukocytes and reveal Dock4 as a candidate pathogenic gene on chromosome 7q

May 3, 2011·The Journal of Biological Chemistry·Li ZhouAmit Verma

Secretoglobin 3A2 suppresses bleomycin-induced pulmonary fibrosis by transforming growth factor beta signaling down-regulation

Apr 12, 2011·The Journal of Biological Chemistry·Reiko KurotaniShioko Kimura

Identification and characterization of novel immunomodulatory bursal-derived pentapeptide-II (BPP-II)

Dec 21, 2011·The Journal of Biological Chemistry·Xiu-Li FengPu-Yan Chen

Caenorhabditis elegans RNA-processing protein TDP-1 regulates protein homeostasis and life span

Jan 11, 2012·The Journal of Biological Chemistry·Tao ZhangJiou Wang

Coordination of growth and endoplasmic reticulum stress signaling by regulator of calcineurin 1 (RCAN1), a novel ATF6-inducible gene

Mar 6, 2008·The Journal of Biological Chemistry·Peter J BelmontChristopher C Glembotski

A chemical genomics study identifies Snf1 as a repressor of GCN4 translation

Oct 29, 2008·The Journal of Biological Chemistry·Margaret K ShirraKaren M Arndt

The unfolded protein response is necessary but not sufficient to compensate for defects in disulfide isomerization

Feb 24, 2009·The Journal of Biological Chemistry·Jai-Hyun KimHiram F Gilbert

Comprehensive proteomic analysis of membrane proteins in Toxoplasma gondii

Oct 12, 2010·Molecular & Cellular Proteomics : MCP·Fa-Yun CheLouis M Weiss

PTMScout, a Web resource for analysis of high throughput post-translational proteomics studies

Jul 16, 2010·Molecular & Cellular Proteomics : MCP·Kristen M NaegleForest M White

Quantitative proteomics discloses MET expression in mitochondria as a direct target of MET kinase inhibitor in cancer cells

Aug 18, 2010·Molecular & Cellular Proteomics : MCP·Tiannan GuoSiu Kwan Sze

Dynamics of the skeletal muscle secretome during myoblast differentiation

Jul 16, 2010·Molecular & Cellular Proteomics : MCP·Jeanette HenningsenIrina Kratchmarova

The protein interaction network of the human transcription machinery reveals a role for the conserved GTPase RPAP4/GPN1 and microtubule assembly in nuclear import and biogenesis of RNA polymerase II

Sep 22, 2010·Molecular & Cellular Proteomics : MCP·Diane ForgetBenoit Coulombe

Comprehensive analysis of yeast surface displayed cDNA library selection outputs by exon microarray to identify novel protein-ligand interactions

Dec 4, 2010·Molecular & Cellular Proteomics : MCP·Scott BidlingmaierBin Liu

Proteomic and metabolomic profiling of a trait anxiety mouse model implicate affected pathways

Aug 25, 2011·Molecular & Cellular Proteomics : MCP·Yaoyang ZhangChristoph W Turck

Quantitative phospho-proteomics to investigate the polo-like kinase 1-dependent phospho-proteome

Aug 23, 2011·Molecular & Cellular Proteomics : MCP·Karin Grosstessner-HainKarl Mechtler

Independent analysis of the flagellum surface and matrix proteomes provides insight into flagellum signaling in mammalian-infectious Trypanosoma brucei

Jun 21, 2011·Molecular & Cellular Proteomics : MCP·Michael OberholzerKent L Hill

Chitinase-like proteins are candidate biomarkers for sepsis-induced acute kidney injury

Jan 12, 2012·Molecular & Cellular Proteomics : MCP·B MaddensE Meyer

Identification of autophagosome-associated proteins and regulators by quantitative proteomic analysis and genetic screens

Feb 9, 2012·Molecular & Cellular Proteomics : MCP·Jörn DengjelJens S Andersen

Proteomic profiling of the planarian Schmidtea mediterranea and its mucous reveals similarities with human secretions and those predicted for parasitic flatworms

Jun 2, 2012·Molecular & Cellular Proteomics : MCP·Donald G BocchinfusoMichael F Moran

A deep exploration of the transcriptome and "excretory/secretory" proteome of adult Fascioloides magna

Aug 18, 2012·Molecular & Cellular Proteomics : MCP·Cinzia CantacessiRobin B Gasser

Phosphoproteome of Pristionchus pacificus provides insights into architecture of signaling networks in nematode models

Aug 28, 2012·Molecular & Cellular Proteomics : MCP·Nadine BorchertBoris Macek

Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples

Oct 24, 2012·Molecular & Cellular Proteomics : MCP·Paul J BoersemaMatthias Mann

Monosodium urate activates Src/Pyk2/PI3 kinase and cathepsin dependent unconventional protein secretion from human primary macrophages

Jan 8, 2013·Molecular & Cellular Proteomics : MCP·Elina VälimäkiTuula A Nyman

Analysis of the zebrafish proteome during embryonic development

Jan 24, 2008·Molecular & Cellular Proteomics : MCP·Margaret B LucittTilo Grosser

Quantitative proteomics of a presymptomatic A53T alpha-synuclein Drosophila model of Parkinson disease

Mar 21, 2008·Molecular & Cellular Proteomics : MCP·Zhiyin XunDavid E Clemmer

Comparative proteomic phenotyping of cell lines and primary cells to assess preservation of cell type-specific functions

Oct 28, 2008·Molecular & Cellular Proteomics : MCP·Cuiping PanMatthias Mann

Stable isotope labeling by amino acids in cell culture (SILAC) and quantitative comparison of the membrane proteomes of self-renewing and differentiating human embryonic stem cells

Jan 20, 2009·Molecular & Cellular Proteomics : MCP·Tatyana A ProkhorovaBlagoy Blagoev

Proteome-wide prediction of signal flow direction in protein interaction networks based on interacting domains

Jun 9, 2009·Molecular & Cellular Proteomics : MCP·Wei LiuFuchu He

MitoMiner, an integrated database for the storage and analysis of mitochondrial proteomics data

Feb 12, 2009·Molecular & Cellular Proteomics : MCP·Anthony C Smith, Alan J Robinson

Proteomics analysis of epithelial cells reprogrammed in cell-free extract

Mar 3, 2009·Molecular & Cellular Proteomics : MCP·Emma PewseyAlireza Fazeli

A complex-based reconstruction of the Saccharomyces cerevisiae interactome

Jan 30, 2009·Molecular & Cellular Proteomics : MCP·Haidong WangDaphne Koller

Novel proteomics strategy brings insight into the prevalence of SUMO-2 target sites

Feb 26, 2009·Molecular & Cellular Proteomics : MCP·Henri A BlomsterLea Sistonen

SysPTM: a systematic resource for proteomic research on post-translational modifications

Apr 16, 2009·Molecular & Cellular Proteomics : MCP·Hong LiYixue Li

Proteomic analysis of microtubule-associated proteins during macrophage activation

Aug 5, 2009·Molecular & Cellular Proteomics : MCP·Prerna C PatelRene E Harrison

Network-based Identification of novel cancer genes

Dec 5, 2009·Molecular & Cellular Proteomics : MCP·Gabriel OstlundErik L L Sonnhammer

In-depth qualitative and quantitative profiling of tyrosine phosphorylation using a combination of phosphopeptide immunoaffinity purification and stable isotope dimethyl labeling

Sep 23, 2009·Molecular & Cellular Proteomics : MCP·Paul J BoersemaAlbert J R Heck

Site-specific phosphorylation dynamics of the nuclear proteome during the DNA damage response

Feb 19, 2010·Molecular & Cellular Proteomics : MCP·Martin V BennetzenJens S Andersen

GProX, a user-friendly platform for bioinformatics analysis and visualization of quantitative proteomics data

May 24, 2011·Molecular & Cellular Proteomics : MCP·Kristoffer T G RigboltBlagoy Blagoev

Proteome-wide detection of Abl1 SH3-binding peptides by integrating computational prediction and peptide microarray

Oct 26, 2011·Molecular & Cellular Proteomics : MCP·Zheng XuWei Wang

Combination of chemical genetics and phosphoproteomics for kinase signaling analysis enables confident identification of cellular downstream targets

Dec 27, 2011·Molecular & Cellular Proteomics : MCP·Felix S OppermannHenrik Daub

E3Net: a system for exploring E3-mediated regulatory networks of cellular functions

Dec 27, 2011·Molecular & Cellular Proteomics : MCP·Youngwoong HanGwan-Su Yi

A mass spectrometry proteomics data management platform

May 23, 2012·Molecular & Cellular Proteomics : MCP·Vagisha SharmaMichael Riffle

Popular computational methods to assess multiprotein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments

Oct 17, 2012·Molecular & Cellular Proteomics : MCP·Irina M ArmeanMatthew W B Trotter

Human Proteinpedia as a resource for clinical proteomics

Jun 25, 2008·Molecular & Cellular Proteomics : MCP·Suresh Mathivanan, Akhilesh Pandey

Identification of potential target genes of butyrate in dimethylhydrazine-induced colorectal cancer in mice

Oct 9, 2013·Nutrition and Cancer·Hui-Min ChenJing-Yuan Fang

The effects of two different ganoderma species (Lingzhi) on gene expression in human monocytic THP-1 cells

Jun 25, 2010·Nutrition and Cancer·Chun-Huai ChengChin-Fu Chen

Antiproliferative mechanisms of the flavonoids 2,2'-dihydroxychalcone and fisetin in human prostate cancer cells

Jun 25, 2010·Nutrition and Cancer·Ahmed Q HaddadLaurence Klotz

Functional ontologies for cognition: The systematic definition of structure and function

May 1, 2005·Cognitive Neuropsychology·Cathy J Price, Karl J Friston

iSMART: an integrated cloud computing web server for traditional Chinese medicine for online virtual screening, de novo evolution and drug design

Jun 24, 2011·Journal of Biomolecular Structure & Dynamics·Kai-Wei ChangCalvin Yu-Chian Chen

A survey of mRNA sequences with a non-AUG start codon in RefSeq database

Jun 20, 2006·Journal of Biomolecular Structure & Dynamics·Suhas Tikole, Ramasubbu Sankararamakrishnan

Predicting protein N-glycosylation by combining functional domain and secretion information

Aug 7, 2007·Journal of Biomolecular Structure & Dynamics·Sujun LiYixue Li

Virus-mPLoc: a fusion classifier for viral protein subcellular location prediction by incorporating multiple sites

Jul 22, 2010·Journal of Biomolecular Structure & Dynamics·Hong-Bin Shen, Kuo-Chen Chou

Generation and analysis of ESTs from the grass carp, Ctenopharyngodon idellus

Oct 23, 2010·Animal Biotechnology·Bing XuZhanjiang Liu

BAFF controls B cell metabolic fitness through a PKC beta- and Akt-dependent mechanism

Oct 25, 2006·The Journal of Experimental Medicine·Alina PatkeAlexander Tarakhovsky

Microarray analysis of a Chlamydia pneumoniae-infected human epithelial cell line by use of gene ontology hierarchy

Jan 4, 2008·The Journal of Infectious Diseases·Joni AlvesaloPetri Auvinen

Processes of fungal proteome evolution and gain of function: gene duplication and domain rearrangement

May 17, 2011·Physical Biology·Inbar Cohen-GihonRuth Nussinov

Mining the biomedical literature in the genomic era: an overview

Feb 26, 2004·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Hagit Shatkay, Ronen Feldman

Methods in comparative genomics: genome correspondence, gene identification and regulatory motif discovery

Aug 3, 2004·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Manolis KellisEric S Lander

Whither biological database research?

Jul 2, 2003·Omics : a Journal of Integrative Biology·Toni KazicChi-Ren Shyu

Common objects: think global, act local

Jul 2, 2003·Omics : a Journal of Integrative Biology·Christian J Stoeckert

PAINT: a promoter analysis and interaction network generation tool for gene regulatory network identification

Oct 30, 2003·Omics : a Journal of Integrative Biology·Rajanikanth VadigepalliGregory E Gonye

The digital human: towards a unified ontology

Dec 20, 2003·Omics : a Journal of Integrative Biology·Stephanie LorangerHenry Kelly

Integrated analysis of microarray data and gene function information

Jul 23, 2004·Omics : a Journal of Integrative Biology·Yan CuiWing Hung Wong

Integrative biological analysis of the APOE*3-leiden transgenic mouse

Apr 27, 2004·Omics : a Journal of Integrative Biology·Clary B ClishStephen Naylor

PRIMOS: an integrated database of reassessed protein-protein interactions providing web-based access to in silico validation of experimentally derived data

Jun 19, 2013·Assay and Drug Development Technologies·Raphaela RidKamil Önder

Human T lymphotropic virus type 1 accessory protein p12I modulates calcium-mediated cellular gene expression and enhances p300 expression in T lymphocytes

Jun 10, 2005·AIDS Research and Human Retroviruses·Amrithraj NairMichael Lairmore

Cataloguing the HIV type 1 human protein interaction network

Nov 26, 2008·AIDS Research and Human Retroviruses·Roger G PtakCarl W Dieffenbach

Regulation of SIRT1 by oxidative stress-responsive miRNAs and a systematic approach to identify its role in the endothelium

Mar 13, 2013·Antioxidants & Redox Signaling·Zhen ChenJohn Y-J Shyy

A discriminative model for identifying spatial cis-regulatory modules

Aug 20, 2005·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Eran Segal, Roded Sharan

Probabilistic discovery of overlapping cellular processes and their regulation

Oct 6, 2005·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Alexis BattleDaphne Koller

Correcting BLAST e-values for low-complexity segments

Oct 6, 2005·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Itai SharonGolan Yona

Efficient algorithms for detecting signaling pathways in protein interaction networks

Apr 7, 2006·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Jacob ScottRoded Sharan

On methods for gene function scoring as a means of facilitating the interpretation of microarray results

May 19, 2006·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·N RaghavanM McMillian

Comparing protein interaction networks via a graph match-and-split algorithm

Sep 7, 2007·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Manikandan Narayanan, Richard M Karp

The chronic fatigue syndrome: a comparative pathway analysis

Sep 7, 2007·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Frank Emmert-Streib

Predicting and annotating catalytic residues: an information theoretic approach

Sep 25, 2007·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Beckett SternerBonnie Berger

Network legos: building blocks of cellular wiring diagrams

Aug 19, 2008·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·T M Murali, Corban G Rivera

QNet: a tool for querying protein interaction networks

Aug 19, 2008·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Banu DostRoded Sharan

Domain architecture comparison for multidomain homology identification

Jun 19, 2007·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·N SongD Durand

Assessing significance of connectivity and conservation in protein interaction networks

Aug 19, 2007·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Mehmet KoyutürkAnanth Grama

A model-based approach to gene clustering with missing observation reconstruction in a Markov random field framework

Mar 4, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Juliette Blanchet, Matthieu Vignes

Analysis of gene sets based on the underlying regulatory network

Mar 4, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Ali Shojaie, George Michailidis

Revealing biological modules via graph summarization

Feb 3, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Saket NavlakhaCarl Kingsford

Integrating biological knowledge with gene expression profiles for survival prediction of cancer

Feb 3, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Xi Chen, Lily Wang

Higher-order genomic organization of cellular functions in yeast

Feb 6, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Tamir TullerMartin Kupiec

Bootstrapping the interactome: unsupervised identification of protein complexes in yeast

Jul 28, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Caroline C FriedelRalf Zimmer

Towards improved assessment of functional similarity in large-scale screens: a study on indel length

Jan 19, 2010·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Alexander SchönhuthS Cenk Sahinalp

Automatic parameter learning for multiple local network alignment

Aug 4, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Jason FlannickSerafim Batzoglou

Fast and accurate alignment of multiple protein networks

Jul 25, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Maxim KalaevRoded Sharan

Detection of locally over-represented GO terms in protein-protein interaction networks

Apr 10, 2010·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Mathieu Lavallée-AdamMathieu Blanchette

Topology-free querying of protein interaction networks

Apr 10, 2010·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Sharon BrucknerRoded Sharan

Exploratory factor analysis of pathway copy number data with an application towards the integration with gene expression data

May 11, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Wessel N van Wieringen, Mark A van de Wiel

Introducing knowledge into differential expression analysis

Aug 24, 2010·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Ewa SzczurekMartin Vingron

Combining drug and gene similarity measures for drug-target elucidation

Feb 15, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Liat PerlmanRoded Sharan

Information flow in interaction networks II: channels, path lengths, and potentials

Mar 14, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Aleksandar Stojmirović, Yi-Kuo Yu

Hierarchical generative biclustering for microRNA expression analysis

Mar 10, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·José Caldas, Samuel Kaski

Extracting between-pathway models from E-MAP interactions using expected graph compression

Mar 10, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·David R Kelley, Carl Kingsford

A topology-based score for pathway enrichment

Apr 4, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Maysson Al-Haj IbrahimKenneth Langlands

Algorithm to identify frequent coupled modules from two-layered network series: application to study transcription and splicing coupling

Jun 16, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Wenyuan LiXianghong Jasmine Zhou

Network-induced classification kernels for gene expression profile analysis

Jun 16, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Ofer LaviRon Shamir

Simultaneously learning DNA motif along with its position and sequence rank preferences through expectation maximization algorithm

Mar 7, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·ZhiZhuo Zhang