| Author | Journal | Year | Publication Title |
| 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 |
| Elkon R | PLoS Comput Biol | 2008 | Removal of AU bias from microarray mRNA expression data enhances computational identification of active microRNAs |
| 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 |
| Ouyang C | PLoS ONE | 2008 | Evolutionary signatures of common human cis-regulatory haplotypes |
| Janoueix-Lerosey I | Nature | 2008 | Somatic and germline activating mutations of the ALK kinase receptor in neuroblastoma |
| Sun Y | PLoS ONE | 2008 | Evolutionarily conserved transcriptional co-expression guiding embryonic stem cell differentiation |
| Liu J | BMC Cancer | 2008 | In silico analysis and verification of S100 gene expression in gastric cancer |
| Maurer J | PLoS ONE | 2008 | Contrasting expression of keratins in mouse and human embryonic stem cells |
| Venanzi ES | Proc Natl Acad Sci U S A | 2008 | The variable immunological self: genetic variation and nongenetic noise in Aire-regulated transcription |
| Crawford NP | Proc Natl Acad Sci U S A | 2008 | Bromodomain 4 activation predicts breast cancer survival |
| Chain FJ | PLoS ONE | 2008 | Single-species microarrays and comparative transcriptomics |
| Hsu SD | Nucleic Acids Res | 2008 | miRNAMap 20: genomic maps of microRNAs in metazoan genomes |
| 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 |
| Ertel A | BMC Genomics | 2008 | Switch-like genes populate cell communication pathways and are enriched for extracellular proteins |
| Solé X | BMC Genomics | 2008 | Genetic and genomic analysis modeling of germline c-MYC overexpression and cancer susceptibility |
| 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 |
| Moran LB | Neurogenetics | 2008 | Towards a pathway definition of Parkinson's disease: a complex disorder with links to cancer, diabetes and inflammation |
| Davids W | BMC Evol Biol | 2008 | The impact of horizontal gene transfer in shaping operons and protein interaction networks--direct evidence of preferential attachment |
| Giangreco A | Aging Cell | 2008 | Epidermal stem cells are retained in vivo throughout skin aging |
| Lee CK | Genome Biol | 2008 | Quantitative methods for genome-scale analysis of in situ hybridization and correlation with microarray data |
| 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 |
| Ye H | BMC Genomics | 2008 | Transcriptomic dissection of tongue squamous cell carcinoma |
| Pang H | BMC Bioinformatics | 2008 | Building pathway clusters from Random Forests classification using class votes |
| Cho H | Mol Cell Biol | 2008 | Rgs5 targeting leads to chronic low blood pressure and a lean body habitus |
| Tomlins SA | Neoplasia | 2008 | Role of the TMPRSS2-ERG gene fusion in prostate cancer |
| 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 |
| 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 |
| Creighton CJ. | PLoS ONE | 2008 | Multiple oncogenic pathway signatures show coordinate expression patterns in human prostate tumors |
| Thorrez L | PLoS ONE | 2008 | Using ribosomal protein genes as reference: a tale of caution |
| Astrand M | BMC Bioinformatics | 2008 | Empirical Bayes models for multiple probe type microarrays at the probe level |
| Rybaczyk LA | BMC Genomics | 2008 | An indicator of cancer: downregulation of monoamine oxidase-A in multiple organs and species |
| Greco D | PLoS ONE | 2008 | Physiology, pathology and relatedness of human tissues from gene expression meta-analysis |
| Xu B | Hum Reprod | 2008 | Myeloid ecotropic viral integration site 1 (MEIS) 1 involvement in embryonic implantation |
| Kim SY | BMC Genomics | 2008 | A gene sets approach for identifying prognostic gene signatures for outcome prediction |
| Cheng C | PLoS ONE | 2008 | Inferring microRNA activities by combining gene expression with microRNA target prediction |
| Oti M | BMC Bioinformatics | 2008 | Conserved co-expression for candidate disease gene prioritization |
| Li H | BMC Genomics | 2008 | A statistical framework for consolidating "sibling" probe sets for Affymetrix GeneChip data |
| Mosley JD | BMC Med Genomics | 2008 | Cell cycle correlated genes dictate the prognostic power of breast cancer gene lists |
| Kalathur RK | BMC Genomics | 2008 | RETINOBASE: a web database, data mining and analysis platform for gene expression data on retina |
| Ivliev AE | Nucleic Acids Res | 2008 | Microarray retriever: a web-based tool for searching and large scale retrieval of public microarray data |
| Legewie S | Mol Syst Biol | 2008 | Recurrent design patterns in the feedback regulation of the mammalian signalling network |
| Okada K | BMC Genomics | 2008 | Expansion of signaling genes for adaptive immune system evolution in early vertebrates |
| Becker SA | PLoS Comput Biol | 2008 | Context-specific metabolic networks are consistent with experiments |
| Gotea V | Nucleic Acids Res | 2008 | DiRE: identifying distant regulatory elements of co-expressed genes |
| Vias M | BMC Med Genomics | 2008 | Pro-neural transcription factors as cancer markers |
| Sun W | BMC Genomics | 2008 | Trait-trait dynamic interaction: 2D-trait eQTL mapping for genetic variation study |
| Palmer RD | Cancer Res | 2008 | Pediatric malignant germ cell tumors show characteristic transcriptome profiles |
| Rakyan VK | Genome Res | 2008 | An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs) |
| Tempelman RJ. | Int J Plant Genomics | 2008 | Statistical analysis of efficient unbalanced factorial designs for two-color microarray experiments |
| Ho JW | Bioinformatics | 2008 | Differential variability analysis of gene expression and its application to human diseases |
| 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 |
| 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 |
| Traka M | PLoS ONE | 2008 | Broccoli consumption interacts with GSTM1 to perturb oncogenic signalling pathways in the prostate |
| Casellas J | BMC Genomics | 2008 | Between-groups within-gene heterogeneity of residual variances in microarray gene expression data |
| Chen X | BMC Genomics | 2008 | Meta-analysis of nasopharyngeal carcinoma microarray data explores mechanism of EBV-regulated neoplastic transformation |
| Hu J | Nucleic Acids Res | 2008 | MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs |
| Martínez O | Proc Natl Acad Sci U S A | 2008 | Defining diversity, specialization, and gene specificity in transcriptomes through information theory |
| Grosso AR | Nucleic Acids Res | 2008 | Tissue-specific splicing factor gene expression signatures |
| Simcox A | PLoS Genet | 2008 | Efficient genetic method for establishing Drosophila cell lines unlocks the potential to create lines of specific genotypes |
| Williams PD | Neoplasia | 2008 | Molecular credentialing of rodent bladder carcinogenesis models |
| Vinci G | PLoS ONE | 2008 | Preservation of genes involved in sterol metabolism in cholesterol auxotrophs: facts and hypotheses |
| van Vliet MH | BMC Genomics | 2008 | Pooling breast cancer datasets has a synergetic effect on classification performance and improves signature stability |
| Rehrauer H | Bioinformatics | 2008 | PhyloDetect: a likelihood-based strategy for detecting microorganisms with diagnostic 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 |
| Martin KJ | PLoS ONE | 2008 | Prognostic breast cancer signature identified from 3D culture model accurately predicts clinical outcome across independent datasets |
| Bonte D | Neoplasia | 2008 | Cdc7-Dbf4 kinase overexpression in multiple cancers and tumor cell lines is correlated with p53 inactivation |
| Tanner SW | BMC Bioinformatics | 2008 | Gene Vector Analysis (Geneva): a unified method to detect differentially-regulated gene sets and similar microarray experiments |
| Ptitsyn AA | BMC Bioinformatics | 2008 | Systems biology approach to identification of biomarkers for metastatic progression in cancer |
| Rouchka EC | Bioinformation | 2008 | Effect of single nucleotide polymorphisms on Affymetrix(R) match-mismatch probe pairs |
| Michael TP | PLoS Biol | 2008 | A Morning-Specific Phytohormone Gene Expression Program underlying Rhythmic Plant Growth |
| 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? |
| Sahni J | Biochem J | 2007 | SLC41A2 encodes a plasma-membrane Mg2+ transporter |
| Stalteri MA | BMC Bioinformatics | 2007 | Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips |
| 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 |
| Ergün A | Mol Syst Biol | 2007 | A network biology approach to prostate cancer |
| Truntzer C | BMC Bioinformatics | 2007 | Importance of data structure in comparing two dimension reduction methods for classification of microarray gene expression data |
| Al-Shahrour F | BMC Bioinformatics | 2007 | From genes to functional classes in the study of biological systems |
| Kapur K | Genome Biol | 2007 | Exon arrays provide accurate assessments of gene expression |
| Warnat P | BMC Cancer | 2007 | Cross-study analysis of gene expression data for intermediate neuroblastoma identifies two biological subtypes |
| Shephard EA | Biochem J | 2007 | Alternative promoters and repetitive DNA elements define the species-dependent tissue-specific expression of the FMO1 genes of human and mouse |
| Yu H | BMC Bioinformatics | 2007 | Transcript-level annotation of Affymetrix probesets improves the interpretation of gene expression data |
| Harrison AP | BMC Bioinformatics | 2007 | Establishing a major cause of discrepancy in the calibration of Affymetrix GeneChips |
| Day A | Genome Biol | 2007 | Celsius: a community resource for Affymetrix microarray data |
| Sarangi A | Proc Natl Acad Sci U S A | 2007 | Identification of a retroviral receptor used by an envelope protein derived by peptide library screening |
| Holst CR | PLoS ONE | 2007 | Secreted sulfatases Sulf1 and Sulf2 have overlapping yet essential roles in mouse neonatal survival |
| Singh AV | Bioinformation | 2007 | Integrative analysis of the mouse embryonic transcriptome |
| Yap DY | BMC Genomics | 2007 | Using biomarker signature patterns for an mRNA molecular diagnostic of mouse embryonic stem cell differentiation state |
| McElwee JJ | Genome Biol | 2007 | Evolutionary conservation of regulated longevity assurance mechanisms |
| Scott MS | BMC Bioinformatics | 2007 | Probabilistic prediction and ranking of human protein-protein interactions |
| Fujibuchi W | BMC Bioinformatics | 2007 | Classification of heterogeneous microarray data by maximum entropy kernel |
| Tian F | BMC Bioinformatics | 2007 | miRAS: a data processing system for miRNA expression profiling study |
| Xie RL | Gene | 2007 | Transcriptional activation of the histone nuclear factor P (HiNF-P) gene by HiNF-P and its cyclin E/CDK2 responsive co-factor p220NPAT defines a novel autoregulatory loop at the G1/S phase transition |
| Li H | EURASIP J Bioinform Syst Biol | 2007 | Analysis of Gene Coexpression by B-Spline Based CoD Estimation |
| Zhang Z | BMC Genomics | 2007 | Integrated analysis of independent gene expression microarray datasets improves the predictability of breast cancer outcome |
| Yu JX | BMC Cancer | 2007 | Pathway analysis of gene signatures predicting metastasis of node-negative primary breast cancer |
| Costa IG | BMC Immunol | 2007 | Gene expression trees in lymphoid development |
| Chen J | BMC Bioinformatics | 2007 | Improved human disease candidate gene prioritization using mouse phenotype |
| Danko CG | BMC Bioinformatics | 2007 | Bioinformatic identification of novel putative photoreceptor specific cis-elements |
| Gormley M | BMC Bioinformatics | 2007 | Prediction potential of candidate biomarker sets identified and validated on gene expression data from multiple datasets |
| Caspi A | Proc Natl Acad Sci U S A | 2007 | Moderation of breastfeeding effects on the IQ by genetic variation in fatty acid metabolism |
| Sturgill D | Nature | 2007 | Demasculinization of X chromosomes in the Drosophila genus |
| Kim TM | BMC Bioinformatics | 2007 | Inferring biological functions and associated transcriptional regulators using gene set expression coherence analysis |
| Hoshida Y | PLoS ONE | 2007 | Subclass mapping: identifying common subtypes in independent disease data sets |
| Chng WJ | Best Pract Res Clin Haematol | 2007 | Genetic events in the pathogenesis of multiple myeloma |
| Febbo PG | BMC Genomics | 2007 | Literature Lab: a method of automated literature interrogation to infer biology from microarray analysis |
| Camargo A | PLoS ONE | 2007 | Linking gene expression and functional network data in human heart failure |
| Tuller T | PLoS Comput Biol | 2007 | Determinants of protein abundance and translation efficiency in S cerevisiae |
| Chen GK | BMC Proc | 2007 | An empirical evaluation of the common disease-common variant hypothesis |
| Lin YA | AMIA Annu Symp Proc | 2007 | Methodologies for extracting functional pharmacogenomic experiments from international repository |
| Price MN | BMC Bioinformatics | 2006 | OpWise: operons aid the identification of differentially expressed genes in bacterial microarray experiments |
| McClintick JN | BMC Bioinformatics | 2006 | Effects of filtering by Present call on analysis of microarray experiments |
| Borghei A | J Biol Chem | 2006 | Targeted disruption of tyrosylprotein sulfotransferase-2, an enzyme that catalyzes post-translational protein tyrosine O-sulfation, causes male infertility |
| Inaoka H | BMC Bioinformatics | 2006 | Lower expression of genes near microRNA in C elegans germline |
| van Haaften RI | BMC Bioinformatics | 2006 | Biologically relevant effects of mRNA amplification on gene expression profiles |
| Albers CJ | BMC Bioinformatics | 2006 | SIMAGE: simulation of DNA-microarray gene expression data |
| Khan RL | BMC Genomics | 2006 | A universal reference sample derived from clone vector for improved detection of differential gene expression |
| Elbez Y | BMC Genomics | 2006 | An analysis of intra array repeats: the good, the bad and the non informative |
| Yin H | BMC Cancer | 2006 | Down regulation of PSA by C/EBPalpha is associated with loss of AR expression and inhibition of PSA promoter activity in the LNCaP cell line |
| Kim SY | BMC Bioinformatics | 2006 | Genome-wide prediction of transcriptional regulatory elements of human promoters using gene expression and promoter analysis data |
| Paananen J | BMC Bioinformatics | 2006 | CROPPER: a metagene creator resource for cross-platform and cross-species compendium studies |
| Wormald S | BMC Genomics | 2006 | Proximal genomic localization of STAT1 binding and regulated transcriptional activity |
| Levine DM | Genome Biol | 2006 | Pathway and gene-set activation measurement from mRNA expression data: the tissue distribution of human pathways |
| Cheung TH | Genome Biol | 2006 | Unraveling transcriptional control and cis-regulatory codes using the software suite GeneACT |
| Farkas IJ | BMC Bioinformatics | 2006 | Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae |
| Campagne F | BMC Bioinformatics | 2006 | Mining expressed sequence tags identifies cancer markers of clinical interest |
| Romualdi C | BMC Genomics | 2006 | Defining the gene expression signature of rhabdomyosarcoma by meta-analysis |
| Balko JM | BMC Genomics | 2006 | Gene expression patterns that predict sensitivity to epidermal growth factor receptor tyrosine kinase inhibitors in lung cancer cell lines and human lung tumors |
| Kel A | BMC Bioinformatics | 2006 | Beyond microarrays: Finding key transcription factors controlling signal transduction pathways |
| Zapala MA | Proc Natl Acad Sci U S A | 2006 | Multivariate regression analysis of distance matrices for testing associations between gene expression patterns and related variables |
| Chari R | BMC Genomics | 2006 | SIGMA: a system for integrative genomic microarray analysis of cancer genomes |
| Lu T | BMC Bioinformatics | 2005 | Can Zipf's law be adapted to normalize microarrays? |
| Mercer SE | J Biol Chem | 2005 | Mirk/Dyrk1B mediates survival during the differentiation of C2C12 myoblasts |
| Wang H | BMC Genomics | 2005 | A study of inter-lab and inter-platform agreement of DNA microarray data |
| Larsson O | BMC Bioinformatics | 2005 | Considerations when using the significance analysis of microarrays (SAM) algorithm |
| Jiang T | BMC Bioinformatics | 2005 | AVID: an integrative framework for discovering functional relationships among proteins |
| Garge NR | BMC Bioinformatics | 2005 | Reproducible clusters from microarray research: whither? |
| Dawson K | BMC Bioinformatics | 2005 | Sample phenotype clusters in high-density oligonucleotide microarray data sets are revealed using Isomap, a nonlinear algorithm |
| Sczyrba A | BMC Genomics | 2005 | XenDB: full length cDNA prediction and cross species mapping in Xenopus laevis |
| Hughes AL. | Immunogenetics | 2005 | Consistent across-tissue signatures of differential gene expression in Crohn's disease |
| Oeder S | BMC Genomics | 2007 | Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets |
| Lu Y | PLoS ONE | 2007 | Common human cancer genes discovered by integrated gene-expression analysis |
| Davis FP | Protein Sci | 2007 | Host–pathogen protein interactions predicted by comparative modeling |
| Arteaga-Salas JM | Brief Bioinform | 2007 | An overview of image-processing methods for Affymetrix GeneChips |
| Gosink MM | Bioinformatics | 2007 | Electronically subtracting expression patterns from a mixed cell population |
| Masotti D | Bioinformatics | 2008 | TOM: enhancement and extension of a tool suite for in silico approaches to multigenic hereditary disorders |
| Dudley J | Pac Symp Biocomput | 2008 | Enabling integrative genomic analysis of high-impact human diseases through text mining |
| Zhu Y | BMC Bioinformatics | 2008 | EzArray: a web-based highly automated Affymetrix expression array data management and analysis system |
| Tchagang AB | Mol Cancer Ther | 2008 | Early detection of ovarian cancer using group biomarkers |
| Seo DC | Mol Cancer | 2007 | Gene expression profiling of cancer stem cell in human lung adenocarcinoma A549 cells |
| Riz I | Oncogene | 2007 | TLX1/HOX11-induced hematopoietic differentiation blockade |
| Chen M | Genetics | 2007 | A statistical framework for expression quantitative trait loci mapping |
| Crawford NP | Proc Natl Acad Sci U S A. | 2008 | Bromodomain 4 activation predicts breast cancer survival |
| Zhao XM | Nucleic Acids Res | 2008 | Uncovering signal transduction networks from high-throughput data by integer linear programming |
| Pavelka N | Mol Cell Proteomics | 2008 | Statistical similarities between transcriptomics and quantitative shotgun proteomics data |
| Sharma M | Am J Respir Crit Care Med | 2008 | A genetic variation in inositol polyphosphate 4 phosphatase a enhances susceptibility to asthma |
| Hassane DC | Blood | 2008 | Discovery of agents that eradicate leukemia stem cells using an in silico screen of public gene expression data |
| Grundberg E | Physiol Genomics | 2008 | Systematic Assessment of the Human Osteoblast Transcriptome in Resting and Induced Primary Cells |
| Lin SL | Carcinogenesis | 2008 | Androgen receptor regulates CD168 expression and signaling in prostate cancer |
| Hibbs MA | Bioinformatics | 2007 | Exploring the functional landscape of gene expression: directed search of large microarray compendia |
| Zilliox MJ | Nat Methods | 2007 | A gene expression bar code for microarray data |
| Stirewalt DL | Genes Chromosomes Cancer | 2007 | Identification of genes with abnormal expression changes in acute myeloid leukemia |
| Geerts D | Clin Cancer Res | 2007 | Expression of Prenylated Rab Acceptor 1 Domain Family, Member 2 (PRAF2) in Neuroblastoma: Correlation with Clinical Features, Cellular Localization, and Cerulenin-Mediated Apoptosis Regulation |
| Thompson DM | Mol Cell Biol | 2007 | Cytoplasmic decay of intergenic transcripts in Saccharomyces cerevisiae |
| Bosco EE | J Clin Invest | 2007 | The retinoblastoma tumor suppressor modifies the therapeutic response of breast cancer |
| Ramsey VG | Development | 2007 | The maturation of mucus-secreting gastric epithelial progenitors into digestive-enzyme secreting zymogenic cells requires Mist1 |
| Hurt EM | Blood | 2007 | Integrated molecular profiling of SOD2 expression in multiple myeloma |
| Brass DM | Proc Am Thorac Soc | 2007 | Using mouse genomics to understand idiopathic interstitial fibrosis |
| Turley RS | Cancer Res | 2007 | The type III transforming growth factor-beta receptor as a novel tumor suppressor gene in prostate cancer |
| Murray DB | Proc Natl Acad Sci U S A | 2007 | Regulation of yeast oscillatory dynamics |
| Buckanovich RJ | J Clin Oncol | 2007 | Tumor vascular proteins as biomarkers in ovarian cancer |
| Jia Z | Genetics | 2007 | Mapping quantitative trait loci for expression abundance |
| Arredouani MS | J Immunol | 2007 | Scavenger Receptors SR-AI/II and MARCO limit pulmonary dendritic cell migration and allergic airway inflammation |
| Sukhdeo K | Proc Natl Acad Sci U S A | 2007 | Targeting the beta-catenin/TCF transcriptional complex in the treatment of multiple myeloma |
| Hertzberg L | Bioinformatics | 2007 | STOP: searching for transcription factor motifs using gene expression |
| Lu ZH | Am J Pathol | 2007 | Hypoxia-inducible factor-1 facilitates cervical cancer progression in human papillomavirus type 16 transgenic mice |
| Jenner MW | Blood | 2007 | Gene mapping and expression analysis of 16q loss of heterozygosity identifies WWOX and CYLD as being important in determining clinical outcome in multiple myeloma |
| Paulson KE | Cancer Res | 2007 | Alterations of the HBP1 transcriptional repressor are associated with invasive breast cancer |
| Wu M | Cancer Res | 2007 | Repression of BCL2 by the tumor suppressor activity of the lysyl oxidase propeptide inhibits transformed phenotype of lung and pancreatic cancer cells |
| Lim WK | Bioinformatics | 2007 | Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks |
| Axelsen JB | Proc Natl Acad Sci U S A | 2007 | Genes overexpressed in different human solid cancers exhibit different tissue-specific expression profiles |
| Clement TM | Reproduction | 2007 | Regulation of the gonadal transcriptome during sex determination and testis morphogenesis: comparative candidate genes |
| Ottolenghi C | Hum Mol Genet | 2007 | Loss of Wnt4 and Foxl2 leads to female-to-male sex reversal extending to germ cells |
| Alberstein M | RNA | 2007 | Regulation of transcription of the RNA splicing factor hSlu7 by Elk-1 and Sp1 affects alternative splicing |
| Jarboe JS | Cancer Res | 2007 | Expression of interleukin-13 receptor alpha2 in glioblastoma multiforme: implications for targeted therapies |
| Gary-Gouy H | J Immunol | 2007 | Natural phosphorylation of CD5 in chronic lymphocytic leukemia B cells and analysis of CD5-regulated genes in a B cell line suggest a role for CD5 in malignant phenotype |
| Gamberoni G | Bioinformatics | 2007 | Fun&Co: identification of key functional differences in transcriptomes |
| Novershtern N | Am J Respir Cell Mol Biol | 2007 | A Functional and Regulatory Map of Asthma |
| Foat BC | Nucleic Acids Res | 2007 | TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors |
| Strand AD | J Neurosci | 2007 | Expression profiling of Huntington's disease models suggests that brain-derived neurotrophic factor depletion plays a major role in striatal degeneration |
| Meir T | Invest Ophthalmol Vis Sci | 2007 | Molecular characteristics of liver metastases from uveal melanoma |
| Tsang J | Mol Cell | 2007 | MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals |
| Hipp J | BJU Int | 2007 | Microarray analysis of exstrophic human bladder smooth muscle |
| Chen R | Nat Methods | 2007 | AILUN: reannotating gene expression data automatically |
| Agarwal S | Proc Natl Acad Sci U S A | 2006 | Isolation, characterization, and genetic complementation of a cellular mutant resistant to retroviral infection |
| Barth AS | J Am Coll Cardiol | 2006 | Identification of a common gene expression signature in dilated cardiomyopathy across independent microarray studies |
| Liu F | Cancer Res | 2006 | A genome-wide screen reveals functional gene clusters in the cancer genome and identifies EphA2 as a mitogen in glioblastoma |
| DeVoss J | J Exp Med | 2006 | Spontaneous autoimmunity prevented by thymic expression of a single self-antigen |
| Sternlicht MD | Cancer Epidemiol Biomarkers Prev | 2006 | Prognostic value of PAI1 in invasive breast cancer: evidence that tumor-specific factors are more important than genetic variation in regulating PAI1 expression |
| Nguyen LN | Clin Cancer Res | 2006 | Sorting nexin 1 down-regulation promotes colon tumorigenesis |
| Kim YC | FEBS Lett | 2006 | Pan-genome isolation of low abundance transcripts using SAGE tag |
| Dolan ME | BMC Bioinformatics | 2006 | Genomes as geography: using GIS technology to build interactive genome feature maps |
| Kliman RM | Gene | 2005 | Unusual usage of AGG and TTG codons in humans and their viruses |
| Kim SY | BMC Bioinformatics | 2005 | PAGE: parametric analysis of gene set enrichment |
| Gorlov IP | Cancer Res | 2007 | Seizure 6-Like (SEZ6L) Gene and Risk for Lung Cancer |
| Ucar D | Bioinformatics | 2007 | Construction of a Reference Gene Association Networkf rom Multiple Profling Data: Application to Data Analysis |
| Chandramouli A | Carcinogenesis | 2007 | Haploinsufficiency of the cdc2l gene contributes to skin cancer development in mice |
| Fujibuchi W | Bioinformatics | 2007 | CellMontage: Similar Expression Profile Search Server |
| Obayashi T | Nucleic Acids Res | 2008 | COXPRESdb: a database of coexpressed gene networks in mammals |
| Nam S | Nucleic Acids Res | 2008 | miRGator: an integrated system for functional annotation of microRNAs |
| 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 |
| Kim B | Cancer Res | 2007 | Clinical Validity of the Lung Cancer Biomarkers Identified by Bioinformatics Analysis of Public Expression Data |
| Green ML | Bioinformatics | 2007 | Using genome-context data to identify specific types of functional associations in pathway/genome databases |
| Dyer MD | Bioinformatics | 2007 | Computational prediction of host-pathogen protein–protein interactions |
| Huang Y | Bioinformatics | 2007 | Systematic discovery of functional modules and context-specific functional annotation of human genome |
| Shiga M | Bioinformatics | 2007 | Annotating gene function by combining expression data with a modular gene network |
| Talavera D | PLoS Comput Biol | 2007 | The (In)dependence of Alternative Splicing and Gene Duplication |
| Dybbs M | PLoS Genet | 2005 | Using Microarrays to Facilitate Positional Cloning: Identification of Tomosyn as an Inhibitor of Neurosecretion |
| Frith MC | PLoS Genet | 2006 | The Abundance of Short Proteins in the Mammalian Proteome |
| Elnitski LL | Genome Res | 2007 | The ENCODEdb portal: Simplified access to ENCODE Consortium data |
| Hanada K | Genome Res | 2007 | A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection |
| Sun M | Genome Res | 2006 | Evidence for variation in abundance of antisense transcripts between multicellular animals but no relationship between antisense transcription and organismic complexity |
| Hong SE | Bioinformatics | 2006 | HCNet: a database of heart and calcium functional network |
| Xiong H | Bioinformatics | 2006 | Non-linear tests for identifying differentially expressed genes or genetic networks |
| Seo J | Bioinformatics | 2006 | An interactive power analysis tool for microarray hypothesis testing and generation |
| Gao G | Bioinformatics | 2006 | DRTF: a database of rice transcription factors |
| Li H | Bioinformatics | 2006 | Systematic intervention of transcription for identifying network response to disease and cellular phenotypes |
| Liu D | Nucleic Acids Res | 2007 | Systematic variation in mRNA 3'-processing signals during mouse spermatogenesis |
| Knowles DG | Mol Biol Evol | 2006 | High Rate of Recent Intron Gain and Loss in Simultaneously Duplicated Arabidopsis Genes |
| Rossi S | Nucleic Acids Res | 2006 | TOM: a web-based integrated approach for identification of candidate disease genes |
| Wang X | Nucleic Acids Res | 2006 | HPtaa database-potential target genes for clinical diagnosis and immunotherapy of human carcinoma |
| Song L | Bioinformatics | 2007 | Gene selection via the BAHSIC family of algorithms |
| Wei Z | Bioinformatics | 2007 | A Markov random field model for network-based analysis of genomic data |
| Shi Y | Bioinformatics | 2007 | Inferring pairwise regulatory relationships from multiple time series datasets |
| Carey VJ | Bioinformatics | 2007 | GGtools: analysis of genetics of gene expression in bioconductor |
| McRae AF | Hum Mol Genet | 2007 | Replicated effects of sex and genotype on gene expression in human lymphoblastoid cell lines |
| Pan F | Nucleic Acids Res | 2007 | Gene Aging Nexus: a web database and data mining platform for microarray data on aging |
| Hung MS | Hum Mol Genet | 2006 | Identification of the transcription factor ARNTL2 as a candidate gene for the type 1 diabetes locus Idd6 |
| Nilsson B | Genome Biol | 2007 | Threshold-free high-power methods for the ontological analysis of genome-wide gene expression studies |
| Herschkowitz JI | Genome Biol | 2007 | Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors |
| Irizarry RA | Genome Biol | 2006 | Feature-level exploration of a published Affymetrix GeneChip control dataset |
| Hu Z | Nucleic Acids Res | 2007 | VisANT 3.0: new modules for pathway visualization, editing, prediction and construction |
| Smith SC | Clin Cancer Res | 2007 | Expression of Ral GTPases, Their Effectors, and Activators in Human Bladder Cancer |
| Yi Y | Genome Biol | 2007 | Strategy for encoding and comparison of gene expression signatures |
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Proc Natl Acad Sci U S A |
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The conserved transcriptome in human and rodent male gametogenesis |
| Davis S |
Bioinformatics |
2007 |
GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor |
| Hardie WD |
Am J Respir Cell Mol Biol |
2007 |
Genomic Profile of Matrix and Vasculature Remodeling in TGF {alpha}-induced Pulmonary Fibrosis |
| Montano M |
J Clin Endocrinol Metab |
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Transcriptional Profiling Of Testosterone-Regulated Genes In The Skeletal Muscle Of Hiv-Infected Men Experiencing Weight Loss |
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Nucleic Acids Res |
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g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments |
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Plant Physiol |
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Distinct Expression Patterns of Natural Antisense Transcripts in Arabidopsis |
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Biostatistics |
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Group additive regression models for genomic data analysis |
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Nucleic Acids Res |
2007 |
MADAP a flexible clustering tool for the interpretation of one-dimensional genome annotation data |
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Endocrinology |
2007 |
Altered expression of genes involved in regulation of vitamin a metabolism solute transportation and cytoskeletal function in the androgen-insensitive tfm mouse testis |
| Graham RR |
Proc Natl Acad Sci U S A |
2007 |
Three functional variants of IFN regulatory factor 5 (IRF5) define risk and protective haplotypes for human lupus |
| Choi JK |
Genetics |
2007 |
Environmental effects on gene expression phenotype have regional biases in the human genome |
| Simmen FA |
Am J Physiol Gastrointest Liver Physiol |
2007 |
Dysregulation of intestinal crypt cell proliferation and villus cell migration in mice lacking Kruppel-like factor 9 (Klf9) |
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Biol Reprod |
2007 |
Quantitative cellular and molecular analysis of the effect of progesterone withdrawal in a murine model of decidualization |
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Identification of Candidate Disease Genes by EST Alignments Synteny and Expression and Verification of Ensembl Genes on Rat Chromosome 1q43-54 |
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AtDGK2 a Novel Diacylglycerol Kinase from Arabidopsis thaliana Phosphorylates 1-Stearoyl-2-arachidonoyl-sn-glycerol and 12-Dioleoyl-sn-glycerol and Exhibits Cold-inducible Gene Expression |
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Genome-Wide Analyses of Avian Sarcoma Virus Integration Sites |
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Mol Biol Evol |
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Mol Cell Biol |
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Glucose Utilization Is Essential for Hypoxia-Inducible Factor 1{alpha}-Dependent Phosphorylation of c-Jun |
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Mol Cell Biol |
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The Mouse Genomic Instability Mutation chaos1 Is an Allele of Polq That Exhibits Genetic Interaction with Atm |
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The RAB25 small GTPase determines aggressiveness of ovarian and breast cancers |
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Evaluation of the host transcriptional response to human cytomegalovirus infection |
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Plant Physiol |
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Maximizing the Efficacy of SAGE Analysis Identifies Novel Transcripts in Arabidopsis |
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PLoS Biol |
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A transcriptional profile of aging in the human kidney |
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Mapping of sudden infant death with dysgenesis of the testes syndrome (SIDDT) by a SNP genome scan and identification of TSPYL loss of function |
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Proc Natl Acad Sci U S A |
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NF-{kappa}B-mediated repression of growth arrest- and DNA-damage-inducible proteins 45{alpha} and {gamma} is essential for cancer cell survival |
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Stem Cells |
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Comparison of Gene Expression of Umbilical Cord Vein and Bone Marrow-Derived Mesenchymal Stem Cells |
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Appl Bioinformatics |
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Cancer Res |
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Identification of Genes Expressed in Malignant Cells That Promote Invasion |
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Hum Mol Genet |
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Genomic convergence: identifying candidate genes for Parkinson's disease by combining serial analysis of gene expression and genetic linkage |
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Nucleic Acids Res |
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Amplification of repeat-containing transcribed sequences (ARTS): a transcriptome fingerprinting strategy to detect functionally relevant microsatellite mutations in cancer |
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Science |
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Transcription Start Regions in the Human Genome Are Favored Targets for MLV Integration |
