| Author | Journal | Year | Publication Title |
| Akerman M | Genome Biol | 2009 | A computational approach for genome-wide mapping of splicing factor binding sites |
| Bierie B | J Clin Invest | 2009 | Abrogation of TGF-beta signaling enhances chemokine production and correlates with prognosis in human breast cancer |
| Bisognin A | BMC Bioinformatics | 2009 | A-MADMAN: annotation-based microarray data meta-analysis tool |
| Cho SB | BMC Bioinformatics | 2009 | Identifying set-wise differential co-expression in gene expression microarray data |
| Danko CG | BMC Med Genomics | 2009 | Identification of gene co-regulatory modules and associated cis-elements involved in degenerative heart disease |
| Du Z | BMC Genomics | 2009 | plantsUPS: a database of plants' Ubiquitin Proteasome System |
| Ebhardt HA | Nucleic Acids Res | 2009 | Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications |
| Foat BC | Mol Syst Biol | 2009 | Discovering structural cis-regulatory elements by modeling the behaviors of mRNAs |
| Glover CN | Toxicol Sci | 2009 | Methylmercury speciation influences brain gene expression and behavior in gestationally-exposed mice pups |
| Godmann M | Mol Hum Reprod | 2009 | The pluripotency transcription factor Krüppel-like factor 4 is strongly expressed in intratubular germ cell neoplasia unclassified and seminoma |
| Gohlke JM | BMC Syst Biol | 2009 | Genetic and environmental pathways to complex diseases |
| Hackenberg M | Nucleic Acids Res | 2009 | miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments |
| Haldar M | Cancer Res | 2009 | A CreER-based random induction strategy for modeling translocation-associated sarcomas in mice |
| Israel A | PLoS One | 2009 | Increased microRNA activity in human cancers |
| Kauer M | PLoS One | 2009 | A molecular function map of Ewing's sarcoma |
| Kim SY | BMC Bioinformatics | 2009 | Effects of sample size on robustness and prediction accuracy of a prognostic gene signature |
| Ko Y | BMC Syst Biol | 2009 | Inference of gene pathways using mixture Bayesian networks |
| Lee YS | Nucleic Acids Res | 2009 | Microarray labeling extension values: laboratory signatures for Affymetrix GeneChips |
| Leimgruber E | Nucleic Acids Res | 2009 | Nucleosome eviction from MHC class II promoters controls positioning of the transcription start site |
| Lin X | BMC Bioinformatics | 2009 | Assessing reliability of protein-protein interactions by integrative analysis of data in model organisms |
| Mayburd AL | PLoS One | 2009 | Expression variation: its relevance to emergence of chronic disease and to therapy |
| Mizuno H | BMC Med Genomics | 2009 | PrognoScan: a new database for meta-analysis of the prognostic value of genes |
| Murph MM | PLoS One | 2009 | Lysophosphatidic acid-induced transcriptional profile represents serous epithelial ovarian carcinoma and worsened prognosis |
| Nitsch D | PLoS One | 2009 | Network analysis of differential expression for the identification of disease-causing genes |
| Rody A | Breast Cancer Res | 2009 | T-cell metagene predicts a favorable prognosis in estrogen receptor-negative and HER2-positive breast cancers |
| Seike M | Proc Natl Acad Sci U S A | 2009 | MiR-21 is an EGFR-regulated anti-apoptotic factor in lung cancer in never-smokers |
| Staub E | J Mol Med | 2009 | An expression module of WIPF1-coexpressed genes identifies patients with favorable prognosis in three tumor types |
| Tang B | Aging Cell | 2009 | Normal human aging and early-stage schizophrenia share common molecular profiles |
| Wan J | Bioinformatics | 2009 | Relating periodicity of nucleosome organization and gene regulation |
| Zhang J | PLoS One | 2009 | A systems biology-based gene expression classifier of glioblastoma predicts survival with solid tumors |
| Arya R | Cell Stress Chaperones | 2008 | Hsp60D is essential for caspase-mediated induced apoptosis in Drosophila melanogaster |
| Ivanov SV | Biochem Biophys Res Commun | 2008 | Two novel VHL targets, TGFBI (BIGH3) and its transactivator KLF10, are up-regulated in renal clear cell carcinoma and other tumors |
| Kennedy L | Biomark Insights | 2008 | Hematopoietic Lineage Transcriptome Stability and Representation in PAXgene Collected Peripheral Blood Utilising SPIA Single-Stranded cDNA Probes for Microarray |
| Kim WK | Exp Mol Med | 2008 | Glycoproteomic analysis of plasma from patients with atopic dermatitis: CD5L and ApoE as potential biomarkers |
| Lee BT | Biomark Insights | 2008 | Candidate List of yoUr Biomarker (CLUB): A Web-based Platform to Aid Cancer Biomarker Research |
| Preker P | Science | 2008 | RNA exosome depletion reveals transcription upstream of active human promoters |
| Swindell WR | Mech Ageing Dev | 2008 | Comparative analysis of microarray data identifies common responses to caloric restriction among mouse tissues |
| Tang H | Dev Biol | 2008 | Expression and functional analysis of Gm114, a putative mammalian ortholog of Drosophila bam |
| Holt JE | Curr Genomics | 2007 | Regulation of Nuclear Import During Differentiation; The IMP alpha Gene Family and Spermatogenesis |
| Platts AE | Genet Test | 2005 | LARaLink 2.0: a comprehensive aid to basic and clinical cytogenetic research |
| Bailey MJ | J Biol Chem | 2009 | Night/Day Changes in Pineal Expression of >600 Genes: CENTRAL ROLE OF ADRENERGIC/cAMP SIGNALING |
| Beltrame L | PLoS ONE | 2009 | Using pathway signatures as means of identifying similarities among microarray experiments |
| Blizard DA | Physiol Genomics | 2009 | Blood pressure and heart rate QTL in mice of the B6/D2 lineage: sex differences and environmental influences |
| Chandramohanadas R | Science | 2009 | Apicomplexan Parasites Co-Opt Host Calpains to Facilitate Their Escape from Infected Cells |
| Chien AJ | Proc Natl Acad Sci U S A | 2009 | Activated Wnt/beta-catenin signaling in melanoma is associated with decreased proliferation in patient tumors and a murine melanoma model |
| de Tayrac M | BMC Genomics | 2009 | Simultaneous analysis of distinct Omics data sets with integration of biological knowledge: Multiple Factor Analysis approach |
| Guillen N | Physiol Genomics | 2009 | Microarray Analysis of Hepatic Gene Expression Identifies New Genes Involved in Steatotic Liver |
| Hennah W | PLoS ONE | 2009 | The DISC1 pathway modulates expression of neurodevelopmental, synaptogenic and sensory perception genes |
| Howell KA | Plant Physiol | 2009 | Mapping metabolic and transcript temporal switches during germination in rice highlights specific transcription factors and the role of RNA instability in the germination process |
| Huang S | Plant Physiol | 2009 | Experimental analysis of the rice mitochondrial proteome, its biogenesis, and heterogeneity |
| Kolesnikova TV | Neoplasia | 2009 | Glioblastoma inhibition by cell surface immunoglobulin protein EWI-2, in vitro and in vivo |
| Le DT | J Biol Chem | 2009 | Functional analysis of free methionine-R-sulfoxide reductase from Saccharomyces cerevisiae |
| Leimgruber E | Nucleic Acids Res | 2009 | Nucleosome eviction from MHC class II promoters controls positioning of the transcription start site |
| Lito P | J Biol Chem | 2009 | Sprouty 2 regulates DNA damage-induced apoptosis in Ras-transformed human fibroblasts |
| Malhas AN | J Cell Biol | 2009 | Lamin B1 controls oxidative stress responses via Oct-1 |
| Miyagawa Y | PLoS ONE | 2009 | EWS/ETS regulates the expression of the Dickkopf family in Ewing family tumor cells |
| Morris KE | Am J Physiol Cell Physiol | 2009 | Autonomic nervous system regulates secretion of anti-inflammatory prohormone SMR1 from rat salivary glands |
| Murphy TM | PLoS ONE | 2009 | Requirement for abasic endonuclease gene homologues in Arabidopsis seed development |
| Nilsson R | BMC Bioinformatics | 2009 | On reliable discovery of molecular signatures |
| Parker BJ | BMC Bioinformatics | 2009 | Predicting microRNA targets in time-series microarray experiments via functional data analysis |
| Pei Y | Acta Biochim Biophys Sin (Shanghai) | 2009 | An overview of hepatocellular carcinoma study by omics-based methods |
| Pendino F | Blood | 2009 | Functional involvement of RINF, retinoid-inducible nuclear factor (CXXC5), in normal and tumoral human myelopoiesis |
| Praz V | Nucleic Acids Res | 2009 | CleanEx: new data extraction and merging tools based on MeSH term annotation |
| Rauch TA | Proc Natl Acad Sci U S A | 2009 | A human B cell methylome at 100-base pair resolution |
| Sun Z | Bioinformatics | 2009 | Exploring phenotype-associated modules in an oral cavity tumor using an integrated framework |
| Sunagawa S | PLoS ONE | 2009 | Identification and gene expression analysis of a taxonomically restricted cysteine-rich protein family in reef-building corals |
| Taccioli C | Nucleic Acids Res | 2009 | UCbase & miRfunc: a database of ultraconserved sequences and microRNA function. |
| Tsuchihara K | Nucleic Acids Res | 2009 | Massive transcriptional start site analysis of human genes in hypoxia cells |
| Wang G | Cancer Res | 2009 | Osteoblast-Derived Factors Induce an Expression Signature that Identifies Prostate Cancer Metastasis and Hormonal Progression |
| Williams-DeVane CR | Bioinformatics | 2009 | DSSTox chemical-index files for exposure-related experiments in ArrayExpress and Gene Expression Omnibus: enabling toxico-chemogenomics data linkages |
| Williams-Devane CR | Toxicol Sci | 2009 | Towards a public toxicogenomics capability for supporting predictive toxicology: Survey of current resources and chemical indexing of experiments in GEO and ArrayExpress |
| Yang E | BMC Bioinformatics | 2009 | Assessing and selecting gene expression signals based upon the quality of the measured dynamics |
| Yang S | PLoS ONE | 2009 | Genomic landscape of a three-generation pedigree segregating affective disorder |
| Abu-Asab MS | OMICS | 2008 | Phylogenetic modeling of heterogeneous gene-expression microarray data from cancerous specimens |
| Alter MD | PLoS ONE | 2008 | Variation in the large-scale organization of gene expression levels in the hippocampus relates to stable epigenetic variability in behavior |
| Anas MK | Development | 2008 | SIT1 is a betaine/proline transporter that is activated in mouse eggs after fertilization and functions until the 2-cell stage |
| Astrand M | BMC Bioinformatics | 2008 | Empirical Bayes models for multiple probe type microarrays at the probe level |
| Bar-Joseph Z | Proc Natl Acad Sci U S A | 2008 | Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells |
| Becker SA | PLoS Comput Biol | 2008 | Context-specific metabolic networks are consistent with experiments |
| Bhattacharya A | Bioinformatics | 2008 | Divisive Correlation Clustering Algorithm (DCCA) for grouping of genes: detecting varying patterns in expression profiles |
| Bonte D | Neoplasia | 2008 | Cdc7-Dbf4 kinase overexpression in multiple cancers and tumor cell lines is correlated with p53 inactivation |
| Calabria AR | J Cereb Blood Flow Metab | 2008 | A genomic comparison of in vivo and in vitro brain microvascular endothelial cells |
| Camargo A | Source Code Biol Med | 2008 | Permutation - based statistical tests for multiple hypotheses |
| Casellas J | BMC Genomics | 2008 | Between-groups within-gene heterogeneity of residual variances in microarray gene expression data |
| Chain FJ | PLoS ONE | 2008 | Single-species microarrays and comparative transcriptomics |
| Chen R | BMC Bioinformatics | 2008 | GeneChaser: Identifying all biological and clinical conditions in which genes of interest are differentially expressed |
| Chen R | Genome Biol | 2008 | FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease |
| Chen X | BMC Genomics | 2008 | Meta-analysis of nasopharyngeal carcinoma microarray data explores mechanism of EBV-regulated neoplastic transformation |
| Cheng C | PLoS ONE | 2008 | Inferring microRNA activities by combining gene expression with microRNA target prediction |
| Chesi M | Cancer Cell | 2008 | AID-dependent activation of a MYC transgene induces multiple myeloma in a conditional mouse model of post-germinal center malignancies |
| Cho H | Mol Cell Biol | 2008 | Rgs5 targeting leads to chronic low blood pressure and a lean body habitus |
| Crawford NP | Proc Natl Acad Sci U S A. | 2008 | Bromodomain 4 activation predicts breast cancer survival |
| Creighton CJ | PLoS ONE | 2008 | Multiple oncogenic pathway signatures show coordinate expression patterns in human prostate tumors |
| Davids W | BMC Evol Biol | 2008 | The impact of horizontal gene transfer in shaping operons and protein interaction networks--direct evidence of preferential attachment |
| Demetris AJ | J Hepatol | 2008 | Small proline-rich proteins (SPRR) function as SH3 domain ligands, increase resistance to injury and are associated with epithelial-mesenchymal transition (EMT) in cholangiocytes |
| Dudley J | Pac Symp Biocomput | 2008 | Enabling integrative genomic analysis of high-impact human diseases through text mining |
| Elkon R | PLoS Comput Biol | 2008 | Removal of AU bias from microarray mRNA expression data enhances computational identification of active microRNAs |
| Ertel A | BMC Genomics | 2008 | Switch-like genes populate cell communication pathways and are enriched for extracellular proteins |
| Ertel A | BMC Genomics | 2008 | Human and mouse switch-like genes share common transcriptional regulatory mechanisms for bimodality |
| Ferguson BJ | J Biol Chem | 2008 | AIRE's CARD Revealed, a New Structure for Central Tolerance Provokes Transcriptional Plasticity |
| Fukushima A | DNA Res | 2008 | SVD-based anatomy of gene expressions for correlation analysis in Arabidopsis thaliana |
| Fulp CT | Hum Mol Genet | 2008 | Identification of Arx transcriptional targets in the developing basal forebrain |
| Gallegos Ruiz MI | PLoS ONE | 2008 | Integration of gene dosage and gene expression in non-small cell lung cancer, identification of HSP90 as potential target |
| Garman KS | Proc Natl Acad Sci U S A | 2008 | A genomic approach to colon cancer risk stratification yields biologic insights into therapeutic opportunities |
| Ghosh D | Proc Natl Acad Sci U S A | 2008 | A link between SIN1 (MAPKAP1) and poly(rC) binding protein 2 (PCBP2) in counteracting environmental stress |
| Giangreco A | Aging Cell | 2008 | Epidermal stem cells are retained in vivo throughout skin aging |
| Gotea V | Nucleic Acids Res | 2008 | DiRE: identifying distant regulatory elements of co-expressed genes |
| Greco D | PLoS ONE | 2008 | Physiology, pathology and relatedness of human tissues from gene expression meta-analysis |
| Grosso AR | Nucleic Acids Res | 2008 | Tissue-specific splicing factor gene expression signatures |
| Grundberg E | Physiol Genomics | 2008 | Systematic Assessment of the Human Osteoblast Transcriptome in Resting and Induced Primary Cells |
| Gur-Dedeoglu B | BMC Cancer | 2008 | A resampling-based meta-analysis for detection of differential gene expression in breast cancer |
| Haibe-Kains B | Bioinformatics | 2008 | A comparative study of survival models for breast cancer prognostication based on microarray data: does a single gene beat them all? |
| Hassane DC | Blood | 2008 | Discovery of agents that eradicate leukemia stem cells using an in silico screen of public gene expression data |
| He F | BMC Genomics | 2008 | The prediction of protein-protein interaction networks in rice blast fungus |
| Hishiki T | AMIA Annu Symp Proc | 2008 | Gene-L'EXPO: a tool to extract knowledge From transcriptomes and find 'Literature-Sparse' relationships between genes and tissues |
| Ho JW | Bioinformatics | 2008 | Differential variability analysis of gene expression and its application to human diseases |
| Hsu SD | Nucleic Acids Res | 2008 | miRNAMap 20: genomic maps of microRNAs in metazoan genomes |
| Hu J | Nucleic Acids Res | 2008 | MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs |
| Iakoubova O | J Am Coll Cardiol | 2008 | Association of the 719Arg variant of KIF6 with both increased risk of coronary events and with greater response to statin therapy |
| Ivliev AE | Nucleic Acids Res | 2008 | Microarray retriever: a web-based tool for searching and large scale retrieval of public microarray data |
| Janoueix-Lerosey I | Nature | 2008 | Somatic and germline activating mutations of the ALK kinase receptor in neuroblastoma |
| Kalathur RK | BMC Genomics | 2008 | RETINOBASE: a web database, data mining and analysis platform for gene expression data on retina |
| Keller A | BMC Bioinformatics | 2008 | GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments. |
| Kim SY | BMC Genomics | 2008 | A gene sets approach for identifying prognostic gene signatures for outcome prediction |
| Konishi T | PLoS ONE | 2008 | Coincidence between transcriptome analyses on different microarray platforms using a parametric framework |
| Konishi T | Stat Appl Genet Mol Biol | 2008 | Data distribution of short oligonucleotide expression arrays and its application to the construction of a generalized intellectual framework |
| Lalancette C | Biol Reprod | 2008 | Transcriptome Analysis of Bull Semen with Extreme Nonreturn Rate: Use of Suppression-Subtractive Hybridization to Identify Functional Markers for Fertility |
| Lee CK | Genome Biol | 2008 | Quantitative methods for genome-scale analysis of in situ hybridization and correlation with microarray data |
| Legewie S | Mol Syst Biol | 2008 | Recurrent design patterns in the feedback regulation of the mammalian signalling network |
| Li H | BMC Genomics | 2008 | A statistical framework for consolidating "sibling" probe sets for Affymetrix GeneChip data |
| Li Y | Nucleic Acids Res | 2008 | Gene expression module-based chemical function similarity search |
| Liang Y | BMC Med Genomics | 2008 | An expression meta-analysis of predicted microRNA targets identifies a diagnostic signature for lung cancer |
| Lin SL | Carcinogenesis | 2008 | Androgen receptor regulates CD168 expression and signaling in prostate cancer |
| Lippman ME | Trans Am Clin Climatol Assoc | 2008 | An Expression Signature Of Estrogen-Regulated Genes Predicts Disease-Free Survival In Tamoxifen-Treated Patients Better Than Progesterone Receptor Status |
| Liu B | J Child Neurol | 2008 | Association of the Dusp6 (Mkp3) Gene With Mouse Brain Weight and Forebrain Structure |
| Liu H | AMIA Annu Symp Proc | 2008 | Annotating breast cancer microarray samples using ontologies |
| Liu J | BMC Cancer | 2008 | In silico analysis and verification of S100 gene expression in gastric cancer |
| Lopez F | PLoS ONE | 2008 | TranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database |
| Macartney-Coxson DP | BMC Cancer | 2008 | Metastatic susceptibility locus, an 8p hot-spot for tumour progression disrupted in colorectal liver metastases: 13 candidate genes examined at the DNA, mRNA and protein level |
| Malaspina A | BMC Genomics | 2008 | Comparative analysis of the time-dependent functional and molecular changes in spinal cord degeneration induced by the G93A SOD1 gene mutation and by mechanical compression |
| Martin KJ | PLoS ONE | 2008 | Prognostic breast cancer signature identified from 3D culture model accurately predicts clinical outcome across independent datasets |
| Martínez O | Proc Natl Acad Sci U S A | 2008 | Defining diversity, specialization, and gene specificity in transcriptomes through information theory |
| Masotti D | Bioinformatics | 2008 | TOM: enhancement and extension of a tool suite for in silico approaches to multigenic hereditary disorders |
| Maurer J | PLoS ONE | 2008 | Contrasting expression of keratins in mouse and human embryonic stem cells |
| McPartland JM | J Bodyw Mov Ther | 2008 | Expression of the endocannabinoid system in fibroblasts and myofascial tissues |
| Michael TP | PLoS Biol | 2008 | A Morning-Specific Phytohormone Gene Expression Program underlying Rhythmic Plant Growth |
| Moran LB | Neurogenetics | 2008 | Towards a pathway definition of Parkinson's disease: a complex disorder with links to cancer, diabetes and inflammation |
| Mosley JD | BMC Med Genomics | 2008 | Cell cycle correlated genes dictate the prognostic power of breast cancer gene lists |
| Nam S | Nucleic Acids Res | 2008 | miRGator: an integrated system for functional annotation of microRNAs |
| Neptune ER | J Biol Chem | 2008 | Targeted disruption of NeuroD, a proneural basic helix-loop-helix factor, impairs distal lung formation and neuroendocrine morphology in the neonatal lung |
| Novershtern N | Am J Respir Cell Mol Biol | 2008 | A Functional and Regulatory Map of Asthma |
| Obayashi T | Nucleic Acids Res | 2008 | COXPRESdb: a database of coexpressed gene networks in mammals |
| Okada K | BMC Genomics | 2008 | Expansion of signaling genes for adaptive immune system evolution in early vertebrates |
| Oti M | BMC Bioinformatics | 2008 | Conserved co-expression for candidate disease gene prioritization |
| Ouyang C | PLoS ONE | 2008 | Evolutionary signatures of common human cis-regulatory haplotypes |
| Palmer RD | Cancer Res | 2008 | Pediatric malignant germ cell tumors show characteristic transcriptome profiles |
| Pang H | BMC Bioinformatics | 2008 | Building pathway clusters from Random Forests classification using class votes |
| Park KW | Mol Endocrinol | 2008 | Inhibitor of DNA binding 2 is a small molecule-inducible modulator of peroxisome proliferator-activated receptor-gamma expression and adipocyte differentiation |
| Pavelka N | Mol Cell Proteomics | 2008 | Statistical similarities between transcriptomics and quantitative shotgun proteomics data |
| Pi M | PLoS ONE | 2008 | GPRC6A null mice exhibit osteopenia, feminization and metabolic syndrome |
| Pichler K | Retrovirology | 2008 | MicroRNA miR-146a and further oncogenesis-related cellular microRNAs are dysregulated in HTLV-1-transformed T lymphocytes |
| Ptitsyn AA | BMC Bioinformatics | 2008 | Systems biology approach to identification of biomarkers for metastatic progression in cancer |
| Rakyan VK | Genome Res | 2008 | An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs) |
| Rehrauer H | Bioinformatics | 2008 | PhyloDetect: a likelihood-based strategy for detecting microorganisms with diagnostic microarrays |
| Reid RW | BMC Bioinformatics | 2008 | Determining gene expression on a single pair of microarrays |
| Ronchetti D | BMC Med Genomics | 2008 | An integrative genomic approach reveals coordinated expression of intronic miR-335, miR-342, and miR-561 with deregulated host genes in multiple myeloma |
| Rondaij MG | Blood | 2008 | Guanine exchange factor RalGDS mediates exocytosis of Weibel-Palade bodies from endothelial cells |
| Rouchka EC | Bioinformation | 2008 | Effect of single nucleotide polymorphisms on Affymetrix(R) match-mismatch probe pairs |
| Rouf R | Circ Res | 2008 | Increased FOG-2 in failing myocardium disrupts thyroid hormone-dependent SERCA2 gene transcription |
| Rybaczyk LA | BMC Genomics | 2008 | An indicator of cancer: downregulation of monoamine oxidase-A in multiple organs and species |
| Sakai Y | Cancer Res | 2008 | Common transcriptional signature of tumor-infiltrating mononuclear inflammatory cells and peripheral blood mononuclear cells in hepatocellular carcinoma patients |
| Schnackenbergs LK | Toxicol Appl Pharmacol | 2008 | Evaluations of the trans-sulfuration pathway in multiple liver toxicity studies |
| Schnütgen F | Nucleic Acids Res | 2008 | Enhanced gene trapping in mouse embryonic stem cells |
| Sharma M | Am J Respir Crit Care Med | 2008 | A genetic variation in inositol polyphosphate 4 phosphatase a enhances susceptibility to asthma |
| Simcox A | PLoS Genet | 2008 | Efficient genetic method for establishing Drosophila cell lines unlocks the potential to create lines of specific genotypes |
| Sims AH | BMC Med Genomics | 2008 | The removal of multiplicative, systematic bias allows integration of breast cancer gene expression datasets - improving meta-analysis and prediction of prognosis |
| Solé X | BMC Genomics | 2008 | Genetic and genomic analysis modeling of germline c-MYC overexpression and cancer susceptibility |
| Soong TT | Bioinformatics | 2008 | Physical protein-protein interactions predicted from microarrays |
| Straub T | PLoS Genet | 2008 | The chromosomal high-affinity binding sites for the Drosophila dosage compensation complex |
| Sun W | BMC Genomics | 2008 | Trait-trait dynamic interaction: 2D-trait eQTL mapping for genetic variation study |
| Sun Y | PLoS ONE | 2008 | Evolutionarily conserved transcriptional co-expression guiding embryonic stem cell differentiation |
| Tanner SW | BMC Bioinformatics | 2008 | Gene Vector Analysis (Geneva): a unified method to detect differentially-regulated gene sets and similar microarray experiments |
| Tchagang AB | Mol Cancer Ther | 2008 | Early detection of ovarian cancer using group biomarkers |
| Tempelman RJ | Int J Plant Genomics | 2008 | Statistical analysis of efficient unbalanced factorial designs for two-color microarray experiments |
| Tenenbaum JD | BMC Med Genomics | 2008 | Expression-based Pathway Signature Analysis (EPSA): Mining publicly available microarray data for insight into human disease |
| Thorrez L | PLoS ONE | 2008 | Using ribosomal protein genes as reference: a tale of caution |
| Tomlins SA | Neoplasia | 2008 | Role of the TMPRSS2-ERG gene fusion in prostate cancer |
| Traka M | PLoS ONE | 2008 | Broccoli consumption interacts with GSTM1 to perturb oncogenic signalling pathways in the prostate |
| Tuller T | Genome Biol | 2008 | Evolutionary rate and gene expression across different brain regions |
| Upton GJ | BMC Genomics | 2008 | G-spots cause incorrect expression measurement in Affymetrix microarrays |
| van Dongen S | Nat Methods | 2008 | Detecting microRNA binding and siRNA off-target effects from expression data |
| van Vliet MH | BMC Genomics | 2008 | Pooling breast cancer datasets has a synergetic effect on classification performance and improves signature stability |
| Vazquez F | Nucleic Acids Res | 2008 | Evolution of Arabidopsis MIR genes generates novel microRNA classes |
| Venanzi ES | Proc Natl Acad Sci U S A | 2008 | The variable immunological self: genetic variation and nongenetic noise in Aire-regulated transcription |
| Vias M | BMC Med Genomics | 2008 | Pro-neural transcription factors as cancer markers |
| Vinci G | PLoS ONE | 2008 | Preservation of genes involved in sterol metabolism in cholesterol auxotrophs: facts and hypotheses |
| Waardenberg AJ | BMC Syst Biol | 2008 | Using a 3D virtual muscle model to link gene expression changes during myogenesis to protein spatial location in muscle |
| Wang G | Cancer Res | 2008 | Crosstalk between the androgen receptor and beta-catenin in castrate-resistant prostate cancer |
| Wang Z | Cancer Res | 2008 | The adenocarcinoma-associated antigen, AGR2, promotes tumor growth, cell migration, and cellular transformation |
| Wang-Sattler R | PLoS ONE | 2008 | Metabolic profiling reveals distinct variations linked to nicotine consumption in humans--first results from the KORA study |
| Williams PD | Neoplasia | 2008 | Molecular credentialing of rodent bladder carcinogenesis models |
| Wirapati P | Breast Cancer Res | 2008 | Meta-analysis of gene expression profiles in breast cancer: toward a unified understanding of breast cancer subtyping and prognosis signatures |
| Xu B | Hum Reprod | 2008 | Myeloid ecotropic viral integration site 1 (MEIS) 1 involvement in embryonic implantation |
| Yagi T | Proc Natl Acad Sci U S A | 2008 | Defective signal transduction in B lymphocytes lacking presenilin proteins |
| Yang PH | J Biol Chem | 2008 | Makorin-2 is a neurogenesis inhibitor downstream of phosphatidylinositol 3-kinase/Akt (PI3K/Akt) signal |
| Yau C | Breast Cancer Res | 2008 | Genes responsive to both oxidant stress and loss of estrogen receptor function identify a poor prognosis group of estrogen receptor positive primary breast cancers |
| Ye H | BMC Genomics | 2008 | Transcriptomic dissection of tongue squamous cell carcinoma |
| Yellaboina S | BMC Genomics | 2008 | Prediction of evolutionarily conserved interologs in Mus musculus |
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| Zhao Y | Cancer Inform | 2008 | BRB-ArrayTools Data Archive for Human Cancer Gene Expression: A Unique and Efficient Data Sharing Resource |
| Zheng G | Bioinformatics | 2008 | ITFP: an integrated platform of mammalian transcription factors |
| Zhu Y | BMC Bioinformatics | 2008 | EzArray: a web-based highly automated Affymetrix expression array data management and analysis system |
| Zhu Y | Bioinformatics | 2008 | GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus |
| Alberstein M | RNA | 2007 | Regulation of transcription of the RNA splicing factor hSlu7 by Elk-1 and Sp1 affects alternative splicing |
| Alberts R | BMC Bioinformatics | 2007 | A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, human and rat |
| Al-Shahrour F | BMC Bioinformatics | 2007 | From genes to functional classes in the study of biological systems |
| Arredouani MS | J Immunol | 2007 | Scavenger Receptors SR-AI/II and MARCO limit pulmonary dendritic cell migration and allergic airway inflammation |
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| Axelsen JB | Proc Natl Acad Sci U S A | 2007 | Genes overexpressed in different human solid cancers exhibit different tissue-specific expression profiles |
| Bianchetti L | Nucleic Acids Res | 2007 | SAGETTARIUS: a program to reduce the number of tags mapped to multiple transcripts and to plan SAGE sequencing stages |
| Bonig H | Exp Hematol | 2007 | Hematopoietic progenitor cells (HPC) from mobilized peripheral blood display enhanced migration and marrow homing compared to steady-state bone marrow HPC |
| Bosco EE | J Clin Invest | 2007 | The retinoblastoma tumor suppressor modifies the therapeutic response of breast cancer |
| Brass DM | Proc Am Thorac Soc | 2007 | Using mouse genomics to understand idiopathic interstitial fibrosis |
| Buckanovich RJ | J Clin Oncol | 2007 | Tumor vascular proteins as biomarkers in ovarian cancer |
| Camargo A | PLoS ONE | 2007 | Linking gene expression and functional network data in human heart failure |
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| Caspi A | Proc Natl Acad Sci U S A | 2007 | Moderation of breastfeeding effects on the IQ by genetic variation in fatty acid metabolism |
| Chalmel F | Proc Natl Acad Sci U S A. | 2007 | The conserved transcriptome in human and rodent male gametogenesis |
| Chandramouli A | Carcinogenesis | 2007 | Haploinsufficiency of the cdc2l gene contributes to skin cancer development in mice |
| Chen GK | BMC Proc | 2007 | An empirical evaluation of the common disease-common variant hypothesis |
| Chen J | BMC Bioinformatics | 2007 | Improved human disease candidate gene prioritization using mouse phenotype |
| Chen M | Genetics | 2007 | A statistical framework for expression quantitative trait loci mapping |
| Chen R | Nat Methods | 2007 | AILUN: reannotating gene expression data automatically |
| Cheng CW | Biol Reprod. | 2007 | Quantitative cellular and molecular analysis of the effect of progesterone withdrawal in a murine model of decidualization |
| Chng WJ | Best Pract Res Clin Haematol | 2007 | Genetic events in the pathogenesis of multiple myeloma |
| Choi JK | Genetics. | 2007 | Environmental effects on gene expression phenotype have regional biases in the human genome |
| Clement TM | Reproduction | 2007 | Regulation of the gonadal transcriptome during sex determination and testis morphogenesis: comparative candidate genes |
| Costa IG | BMC Immunol | 2007 | Gene expression trees in lymphoid development |
| Crasto CJ | J Am Med Inform Assoc. | 2007 | NeuroExtract: facilitating neuroscience-oriented retrieval from broadly-focused bioscience databases using text-based query mediation |
| Danko CG | BMC Bioinformatics | 2007 | Bioinformatic identification of novel putative photoreceptor specific cis-elements |
| Davis FP | Protein Sci | 2007 | Hostpathogen protein interactions predicted by comparative modeling |
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| Day A | Genome Biol | 2007 | Celsius: a community resource for Affymetrix microarray data |
| Duarte NC | Proc Natl Acad Sci U S A. | 2007 | Global reconstruction of the human metabolic network based on genomic and bibliomic data |
| Dyer MD | Bioinformatics | 2007 | Computational prediction of host-pathogen proteinprotein interactions |
| Elnitski LL | Genome Res | 2007 | The ENCODEdb portal: Simplified access to ENCODE Consortium data |
| Ergün A | Mol Syst Biol | 2007 | A network biology approach to prostate cancer |
| Febbo PG | BMC Genomics | 2007 | Literature Lab: a method of automated literature interrogation to infer biology from microarray analysis |
| Foat BC | Nucleic Acids Res | 2007 | TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors |
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