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Citation listings: deposit and third-party usage

The following list represents third-party publications that cite GEO data as evidence to support or complement independent studies, or use GEO data as the basis of statistical/analytical hypotheses or tools. Please report omitted publications to geo@ncbi.nlm.nih.gov

Total number of citations: 1,211

  • Grills C, Jithesh PV, Blayney J, Zhang SD et al. Gene expression meta-analysis identifies VDAC1 as a predictor of poor outcome in early stage non-small cell lung cancer. PLoS One 2011 Jan 31;6(1):e14635. PMID: 21297950
  • Schulte A, Günther HS, Phillips HS, Kemming D et al. A distinct subset of glioma cell lines with stem cell-like properties reflects the transcriptional phenotype of glioblastomas and overexpresses CXCR4 as therapeutic target. Glia 2011 Apr;59(4):590-602. PMID: 21294158
  • Saintigny P, Zhang L, Fan YH, El-Naggar AK et al. Gene expression profiling predicts the development of oral cancer. Cancer Prev Res (Phila) 2011 Feb;4(2):218-29. PMID: 21292635
  • Wang G, Ye Y, Yang X, Liao H et al. Expression-based in silico screening of candidate therapeutic compounds for lung adenocarcinoma. PLoS One 2011 Jan 21;6(1):e14573. PMID: 21283735
  • Zhang B, Chen B, Wu T, Tan Y et al. Estimating the quality of reprogrammed cells using ES cell differentiation expression patterns. PLoS One 2011 Jan 11;6(1):e15336. PMID: 21283513
  • Zhou Y, Shi R, Bao Y, Li CZ et al. [Bioinformatic analysis of genes related to temporal epilepsy]. Nan Fang Yi Ke Da Xue Xue Bao 2011 Jan;31(1):180-3. PMID: 21269987
  • Diez-Roux G, Banfi S, Sultan M, Geffers L et al. A high-resolution anatomical atlas of the transcriptome in the mouse embryo. PLoS Biol 2011 Jan 18;9(1):e1000582. PMID: 21267068
  • Smith SC, Havaleshko DM, Moon K, Baras AS et al. Use of yeast chemigenomics and COXEN informatics in preclinical evaluation of anticancer agents. Neoplasia 2011 Jan;13(1):72-80. PMID: 21253455
  • Coutant C, Rouzier R, Qi Y, Lehmann-Che J et al. Distinct p53 gene signatures are needed to predict prognosis and response to chemotherapy in ER-positive and ER-negative breast cancers. Clin Cancer Res 2011 Apr 15;17(8):2591-601. PMID: 21248301
  • Liao Q, Liu C, Yuan X, Kang S et al. Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network. Nucleic Acids Res 2011 May;39(9):3864-78. PMID: 21247874
  • Mustafiz A, Singh AK, Pareek A, Sopory SK et al. Genome-wide analysis of rice and Arabidopsis identifies two glyoxalase genes that are highly expressed in abiotic stresses. Funct Integr Genomics 2011 Jun;11(2):293-305. PMID: 21213008
  • Gonzalez-Roca E, Garcia-Albéniz X, Rodriguez-Mulero S, Gomis RR et al. Accurate expression profiling of very small cell populations. PLoS One 2010 Dec 28;5(12):e14418. PMID: 21203435
  • Pedicini M, Barrenäs F, Clancy T, Castiglione F et al. Combining network modeling and gene expression microarray analysis to explore the dynamics of Th1 and Th2 cell regulation. PLoS Comput Biol 2010 Dec 16;6(12):e1001032. PMID: 21187905
  • Yang CH, Chuang LY, Shih TM, Chang HW. hSAGEing: an improved SAGE-based software for identification of human tissue-specific or common tumor markers and suppressors. PLoS One 2010 Dec 17;5(12):e14369. PMID: 21179408
  • Gentles AJ, Plevritis SK, Majeti R, Alizadeh AA. Association of a leukemic stem cell gene expression signature with clinical outcomes in acute myeloid leukemia. JAMA 2010 Dec 22;304(24):2706-15. PMID: 21177505
  • Xu H, Lemischka IR, Ma'ayan A. SVM classifier to predict genes important for self-renewal and pluripotency of mouse embryonic stem cells. BMC Syst Biol 2010 Dec 21;4:173. PMID: 21176149
  • Liu W, Li D, Liu Q, Zhu Y et al. A novel parametric approach to mine gene regulatory relationship from microarray datasets. BMC Bioinformatics 2010 Dec 14;11 Suppl 11:S15. PMID: 21172050
  • Xu T, Ping J, Yu Y, Yu F et al. Revealing parasite influence in metabolic pathways in Apicomplexa infected patients. BMC Bioinformatics 2010 Dec 14;11 Suppl 11:S13. PMID: 21172048
  • Yu Y, Xu T, Yu Y, Hao P et al. Association of tissue lineage and gene expression: conservatively and differentially expressed genes define common and special functions of tissues. BMC Bioinformatics 2010 Dec 14;11 Suppl 11:S1. PMID: 21172044
  • Engreitz JM, Morgan AA, Dudley JT, Chen R et al. Content-based microarray search using differential expression profiles. BMC Bioinformatics 2010 Dec 21;11:603. PMID: 21172034
  • Wang L, Guo K, Li Y, Tu Y et al. Expression profiling and integrative analysis of the CESA/CSL superfamily in rice. BMC Plant Biol 2010 Dec 20;10:282. PMID: 21167079
  • Klomp JA, Petillo D, Niemi NM, Dykema KJ et al. Birt-Hogg-Dubé renal tumors are genetically distinct from other renal neoplasias and are associated with up-regulation of mitochondrial gene expression. BMC Med Genomics 2010 Dec 16;3:59. PMID: 21162720
  • Tuna M, Smid M, Zhu D, Martens JW et al. Association between acquired uniparental disomy and homozygous mutations and HER2/ER/PR status in breast cancer. PLoS One 2010 Nov 30;5(11):e15094. PMID: 21152100
  • Kilpinen S, Ojala K, Kallioniemi O. Analysis of kinase gene expression patterns across 5681 human tissue samples reveals functional genomic taxonomy of the kinome. PLoS One 2010 Dec 3;5(12):e15068. PMID: 21151926
  • Tominaga D. Periodicity detection method for small-sample time series datasets. Bioinform Biol Insights 2010 Nov 22;4:127-36. PMID: 21151841
  • Maresh EL, Mah V, Alavi M, Horvath S et al. Differential expression of anterior gradient gene AGR2 in prostate cancer. BMC Cancer 2010 Dec 13;10:680. PMID: 21144054
  • Kim J, Ji M, DiDonato JA, Rackley RR et al. An hTERT-immortalized human urothelial cell line that responds to anti-proliferative factor. In Vitro Cell Dev Biol Anim 2011 Jan;47(1):2-9. PMID: 21136194
  • Saito M, Kumamoto K, Robles AI, Horikawa I et al. Targeted disruption of Ing2 results in defective spermatogenesis and development of soft-tissue sarcomas. PLoS One 2010 Nov 19;5(11):e15541. PMID: 21124965
  • Kerkel K, Schupf N, Hatta K, Pang D et al. Altered DNA methylation in leukocytes with trisomy 21. PLoS Genet 2010 Nov 18;6(11):e1001212. PMID: 21124956
  • Wang X, Björklund S, Wasik AM, Grandien A et al. Gene expression profiling and chromatin immunoprecipitation identify DBN1, SETMAR and HIG2 as direct targets of SOX11 in mantle cell lymphoma. PLoS One 2010 Nov 22;5(11):e14085. PMID: 21124928
  • Ye ZQ, Niu S, Yu Y, Yu H et al. Analyses of copy number variation of GK rat reveal new putative type 2 diabetes susceptibility loci. PLoS One 2010 Nov 23;5(11):e14077. PMID: 21124896
  • Nodine MD, Bartel DP. MicroRNAs prevent precocious gene expression and enable pattern formation during plant embryogenesis. Genes Dev 2010 Dec 1;24(23):2678-92. PMID: 21123653
  • Maess MB, Sendelbach S, Lorkowski S. Selection of reliable reference genes during THP-1 monocyte differentiation into macrophages. BMC Mol Biol 2010 Dec 1;11:90. PMID: 21122122
  • Daniels JP, Gull K, Wickstead B. Cell biology of the trypanosome genome. Microbiol Mol Biol Rev 2010 Dec;74(4):552-69. PMID: 21119017
  • Warsow G, Greber B, Falk SS, Harder C et al. ExprEssence--revealing the essence of differential experimental data in the context of an interaction/regulation net-work. BMC Syst Biol 2010 Nov 30;4:164. PMID: 21118483
  • Wu FL, Jin WB, Li JH, Guo AG. Targets for human encoded microRNAs in HBV genes. Virus Genes 2011 Apr;42(2):157-61. PMID: 21113793
  • Anton MA, Aramburu A, Rubio A. Improvements to previous algorithms to predict gene structure and isoform concentrations using Affymetrix Exon arrays. BMC Bioinformatics 2010 Nov 26;11:578. PMID: 21110835
  • Rödelsperger C, Guo G, Kolanczyk M, Pletschacher A et al. Integrative analysis of genomic, functional and protein interaction data predicts long-range enhancer-target gene interactions. Nucleic Acids Res 2011 Apr;39(7):2492-502. PMID: 21109530
  • Narsai R, Castleden I, Whelan J. Common and distinct organ and stress responsive transcriptomic patterns in Oryza sativa and Arabidopsis thaliana. BMC Plant Biol 2010 Nov 24;10:262. PMID: 21106056
  • Xiong Y, Chen X, Chen Z, Wang X et al. RNA sequencing shows no dosage compensation of the active X-chromosome. Nat Genet 2010 Dec;42(12):1043-7. PMID: 21102464
  • Gupta R, Bhattacharyya A, Agosto-Perez FJ, Wickramasinghe P et al. MPromDb update 2010: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-seq experimental data. Nucleic Acids Res 2011 Jan;39(Database issue):D92-7. PMID: 21097880
  • Thomas R, de la Torre L, Chang X, Mehrotra S. Validation and characterization of DNA microarray gene expression data distribution and associated moments. BMC Bioinformatics 2010 Nov 24;11:576. PMID: 21092329
  • Thorrez L, Laudadio I, Van Deun K, Quintens R et al. Tissue-specific disallowance of housekeeping genes: the other face of cell differentiation. Genome Res 2011 Jan;21(1):95-105. PMID: 21088282
  • Merico D, Isserlin R, Stueker O, Emili A et al. Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PLoS One 2010 Nov 15;5(11):e13984. PMID: 21085593
  • Folsom JP, Richards L, Pitts B, Roe F et al. Physiology of Pseudomonas aeruginosa in biofilms as revealed by transcriptome analysis. BMC Microbiol 2010 Nov 17;10:294. PMID: 21083928
  • Cahan P, Graubert TA. Integrated genomics of susceptibility to alkylator-induced leukemia in mice. BMC Genomics 2010 Nov 17;11:638. PMID: 21080971
  • Verzi MP, Shin H, He HH, Sulahian R et al. Differentiation-specific histone modifications reveal dynamic chromatin interactions and partners for the intestinal transcription factor CDX2. Dev Cell 2010 Nov 16;19(5):713-26. PMID: 21074721
  • Komurov K, Ram PT. Patterns of human gene expression variance show strong associations with signaling network hierarchy. BMC Syst Biol 2010 Nov 12;4:154. PMID: 21073694
  • Uckun FM, Pitt J, Qazi S. JAK3 pathway is constitutively active in B-lineage acute lymphoblastic leukemia. Expert Rev Anticancer Ther 2011 Jan;11(1):37-48. PMID: 21070101
  • Gonçalves A, Finetti P, Sabatier R, Gilabert M et al. Poly(ADP-ribose) polymerase-1 mRNA expression in human breast cancer: a meta-analysis. Breast Cancer Res Treat 2011 May;127(1):273-81. PMID: 21069454
  • Cho S, Jun Y, Lee S, Choi HS et al. miRGator v2.0: an integrated system for functional investigation of microRNAs. Nucleic Acids Res 2011 Jan;39(Database issue):D158-62. PMID: 21062822
  • Censi F, Calcagnini G, Bartolini P, Giuliani A. A systems biology strategy on differential gene expression data discloses some biological features of atrial fibrillation. PLoS One 2010 Oct 29;5(10):e13668. PMID: 21060823
  • Jones L, Wei G, Sevcikova S, Phan V et al. Gain of MYC underlies recurrent trisomy of the MYC chromosome in acute promyelocytic leukemia. J Exp Med 2010 Nov 22;207(12):2581-94. PMID: 21059853
  • Wang L, Srivastava AK, Schwartz CE. Microarray data integration for genome-wide analysis of human tissue-selective gene expression. BMC Genomics 2010 Nov 2;11 Suppl 2:S15. PMID: 21047382
  • Mercer TR, Dinger ME, Bracken CP, Kolle G et al. Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome. Genome Res 2010 Dec;20(12):1639-50. PMID: 21045082
  • Garg R, Jhanwar S, Tyagi AK, Jain M. Genome-wide survey and expression analysis suggest diverse roles of glutaredoxin gene family members during development and response to various stimuli in rice. DNA Res 2010 Dec;17(6):353-67. PMID: 21044985
  • Lacson R, Mbagwu M, Yousif H, Ohno-Machado L. Assessing the quality of annotations in asthma gene expression experiments. BMC Bioinformatics 2010 Oct 28;11 Suppl 9:S8. PMID: 21044366
  • Morgan AA, Khatri P, Jones RH, Sarwal MM et al. Comparison of multiplex meta analysis techniques for understanding the acute rejection of solid organ transplants. BMC Bioinformatics 2010 Oct 28;11 Suppl 9:S6. PMID: 21044364
  • Zhang J, Xiang Y, Ding L, Keen-Circle K et al. Using gene co-expression network analysis to predict biomarkers for chronic lymphocytic leukemia. BMC Bioinformatics 2010 Oct 28;11 Suppl 9:S5. PMID: 21044363
  • Payne PR, Huang K, Keen-Circle K, Kundu A et al. Multi-dimensional discovery of biomarker and phenotype complexes. BMC Bioinformatics 2010 Oct 28;11 Suppl 9:S3. PMID: 21044361
  • Chang HH, McGeachie M, Alterovitz G, Ramoni MF. Mapping transcription mechanisms from multimodal genomic data. BMC Bioinformatics 2010 Oct 28;11 Suppl 9:S2. PMID: 21044360
  • Yang X, Lee Y, Huang Y, Chen JL et al. Stromal microenvironment processes unveiled by biological component analysis of gene expression in xenograft tumor models. BMC Bioinformatics 2010 Oct 28;11 Suppl 9:S11. PMID: 21044358
  • Gorlov IP, Sircar K, Zhao H, Maity SN et al. Prioritizing genes associated with prostate cancer development. BMC Cancer 2010 Nov 2;10:599. PMID: 21044312
  • Langdon WB, Upton GJ, da Silva Camargo R, Harrison AP. A survey of spatial defects in Homo Sapiens Affymetrix GeneChips. IEEE/ACM Trans Comput Biol Bioinform 2010 Oct-Dec;7(4):647-53. PMID: 21030732
  • Suo C, Salim A, Chia KS, Pawitan Y et al. Modified least-variant set normalization for miRNA microarray. RNA 2010 Dec;16(12):2293-303. PMID: 20980676
  • Li J, Lenferink AE, Deng Y, Collins C et al. Identification of high-quality cancer prognostic markers and metastasis network modules. Nat Commun 2010 Jul 13;1:34. PMID: 20975711
  • Bareke E, Pierre M, Gaigneaux A, De Meulder B et al. PathEx: a novel multi factors based datasets selector web tool. BMC Bioinformatics 2010 Oct 22;11:528. PMID: 20969778
  • Miecznikowski JC, Wang D, Liu S, Sucheston L et al. Comparative survival analysis of breast cancer microarray studies identifies important prognostic genetic pathways. BMC Cancer 2010 Oct 21;10:573. PMID: 20964848
  • Kleger A, Seufferlein T, Malan D, Tischendorf M et al. Modulation of calcium-activated potassium channels induces cardiogenesis of pluripotent stem cells and enrichment of pacemaker-like cells. Circulation 2010 Nov 2;122(18):1823-36. PMID: 20956206
  • Gatti DM, Barry WT, Nobel AB, Rusyn I et al. Heading down the wrong pathway: on the influence of correlation within gene sets. BMC Genomics 2010 Oct 18;11:574. PMID: 20955544
  • Thorner AR, Parker JS, Hoadley KA, Perou CM. Potential tumor suppressor role for the c-Myb oncogene in luminal breast cancer. PLoS One 2010 Oct 7;5(10):e13073. PMID: 20949095
  • Wang Y, Robbins KR, Rekaya R. Comparison of computational models for assessing conservation of gene expression across species. PLoS One 2010 Oct 8;5(10):e13239. PMID: 20949029
  • Gunaratne GH, Gunaratne PH, Seemann L, Török A. Using effective subnetworks to predict selected properties of gene networks. PLoS One 2010 Oct 8;5(10):e13080. PMID: 20949025
  • Nguyen TT, Almon RR, Dubois DC, Jusko WJ et al. Comparative analysis of acute and chronic corticosteroid pharmacogenomic effects in rat liver: transcriptional dynamics and regulatory structures. BMC Bioinformatics 2010 Oct 14;11:515. PMID: 20946642
  • Kelly VR, Xu B, Kuick R, Koenig RJ et al. Dax1 up-regulates Oct4 expression in mouse embryonic stem cells via LRH-1 and SRA. Mol Endocrinol 2010 Dec;24(12):2281-91. PMID: 20943815
  • Berger F, De Meulder B, Gaigneaux A, Depiereux S et al. Functional analysis: evaluation of response intensities--tailoring ANOVA for lists of expression subsets. BMC Bioinformatics 2010 Oct 13;11:510. PMID: 20942918
  • Gurtowski J, Cancio A, Shah H, Levovitz C et al. Geoseq: a tool for dissecting deep-sequencing datasets. BMC Bioinformatics 2010 Oct 12;11:506. PMID: 20939882
  • Weber CC, Hurst LD. Intronic AT skew is a defendable proxy for germline transcription but does not predict crossing-over or protein evolution rates in Drosophila melanogaster. J Mol Evol 2010 Dec;71(5-6):415-26. PMID: 20938653
  • Thorsen K, Mansilla F, Schepeler T, Øster B et al. Alternative splicing of SLC39A14 in colorectal cancer is regulated by the Wnt pathway. Mol Cell Proteomics 2011 Jan;10(1):M110.002998. PMID: 20938052
  • Gaspar N, Marshall L, Perryman L, Bax DA et al. MGMT-independent temozolomide resistance in pediatric glioblastoma cells associated with a PI3-kinase-mediated HOX/stem cell gene signature. Cancer Res 2010 Nov 15;70(22):9243-52. PMID: 20935218
  • Ciraci C, Tuggle CK, Wannemuehler MJ, Nettleton D et al. Unique genome-wide transcriptome profiles of chicken macrophages exposed to Salmonella-derived endotoxin. BMC Genomics 2010 Oct 8;11:545. PMID: 20929591
  • Kupershmidt I, Su QJ, Grewal A, Sundaresh S et al. Ontology-based meta-analysis of global collections of high-throughput public data. PLoS One 2010 Sep 29;5(9). PMID: 20927376
  • Cao K, Chen-Plotkin AS, Plotkin JB, Wang LS. Age-correlated gene expression in normal and neurodegenerative human brain tissues. PLoS One 2010 Sep 29;5(9). PMID: 20927326
  • Mangelsen E, Kilian J, Harter K, Jansson C et al. Transcriptome analysis of high-temperature stress in developing barley caryopses: early stress responses and effects on storage compound biosynthesis. Mol Plant 2011 Jan;4(1):97-115. PMID: 20924027
  • Huang JX, Wang L, Jiang MH. TNFRSF11B computational development network construction and analysis between frontal cortex of HIV encephalitis (HIVE) and HIVE-control patients. J Inflamm (Lond) 2010 Sep 30;7:50. PMID: 20920282
  • Chen R, Sigdel TK, Li L, Kambham N et al. Differentially expressed RNA from public microarray data identifies serum protein biomarkers for cross-organ transplant rejection and other conditions. PLoS Comput Biol 2010 Sep 23;6(9). PMID: 20885780
  • Agam A, Yalcin B, Bhomra A, Cubin M et al. Elusive copy number variation in the mouse genome. PLoS One 2010 Sep 21;5(9):e12839. PMID: 20877625
  • Dawany NB, Tozeren A. Asymmetric microarray data produces gene lists highly predictive of research literature on multiple cancer types. BMC Bioinformatics 2010 Sep 27;11:483. PMID: 20875095
  • Toedling J, Ciaudo C, Voinnet O, Heard E et al. Girafe--an R/Bioconductor package for functional exploration of aligned next-generation sequencing reads. Bioinformatics 2010 Nov 15;26(22):2902-3. PMID: 20861030
  • Yau C, Mouradov D, Jorissen RN, Colella S et al. A statistical approach for detecting genomic aberrations in heterogeneous tumor samples from single nucleotide polymorphism genotyping data. Genome Biol 2010;11(9):R92. PMID: 20858232
  • Cai YD, Huang T, Feng KY, Hu L et al. A unified 35-gene signature for both subtype classification and survival prediction in diffuse large B-cell lymphomas. PLoS One 2010 Sep 13;5(9):e12726. PMID: 20856936
  • Spade DJ, Griffitt RJ, Liu L, Brown-Peterson NJ et al. Queen conch (Strombus gigas) testis regresses during the reproductive season at nearshore sites in the Florida Keys. PLoS One 2010 Sep 15;5(9):e12737. PMID: 20856805
  • Zheng M, Liu GX, Zhou CG, Liang YC et al. Gravitation field algorithm and its application in gene cluster. Algorithms Mol Biol 2010 Sep 20;5:32. PMID: 20854683
  • Zaravinos A, Chatziioannou M, Lambrou GI, Boulalas I et al. Implication of RAF and RKIP genes in urinary bladder cancer. Pathol Oncol Res 2011 Jun;17(2):181-90. PMID: 20853079
  • Park YY, Choi HS, Lee JS. Systems-level analysis of gene expression data revealed NR0B2/SHP as potential tumor suppressor in human liver cancer. Mol Cells 2010 Nov;30(5):485-91. PMID: 20853064
  • Teider N, Scott DK, Neiss A, Weeraratne SD et al. Neuralized1 causes apoptosis and downregulates Notch target genes in medulloblastoma. Neuro Oncol 2010 Dec;12(12):1244-56. PMID: 20847082
  • Sun H, Wu J, Wickramasinghe P, Pal S et al. Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq. Nucleic Acids Res 2011 Jan;39(1):190-201. PMID: 20843783
  • Nitsch D, Gonçalves JP, Ojeda F, de Moor B et al. Candidate gene prioritization by network analysis of differential expression using machine learning approaches. BMC Bioinformatics 2010 Sep 14;11:460. PMID: 20840752
  • Rao S, Zhen S, Roumiantsev S, McDonald LT et al. Differential roles of Sall4 isoforms in embryonic stem cell pluripotency. Mol Cell Biol 2010 Nov;30(22):5364-80. PMID: 20837710
  • Gelly JC, Orgeur M, Jacq C, Lelandais G. MitoGenesisDB: an expression data mining tool to explore spatio-temporal dynamics of mitochondrial biogenesis. Nucleic Acids Res 2011 Jan;39(Database issue):D1079-84. PMID: 20833631
  • Dexter TJ, Sims D, Mitsopoulos C, Mackay A et al. Genomic distance entrained clustering and regression modelling highlights interacting genomic regions contributing to proliferation in breast cancer. BMC Syst Biol 2010 Sep 8;4:127. PMID: 20825665
  • Patel VN, Bebek G, Mariadason JM, Wang D et al. Prediction and testing of biological networks underlying intestinal cancer. PLoS One 2010 Sep 1;5(9). PMID: 20824133
  • Serb JM, Orr MC, West Greenlee MH. Using evolutionary conserved modules in gene networks as a strategy to leverage high throughput gene expression queries. PLoS One 2010 Sep 2;5(9). PMID: 20824082
  • Gille C, Bölling C, Hoppe A, Bulik S et al. HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology. Mol Syst Biol 2010 Sep 7;6:411. PMID: 20823849
  • Dao P, Colak R, Salari R, Moser F et al. Inferring cancer subnetwork markers using density-constrained biclustering. Bioinformatics 2010 Sep 15;26(18):i625-31. PMID: 20823331
  • Zavadil J, Ye H, Liu Z, Wu J et al. Profiling and functional analyses of microRNAs and their target gene products in human uterine leiomyomas. PLoS One 2010 Aug 24;5(8):e12362. PMID: 20808773
  • Fernandez-Valverde SL, Taft RJ, Mattick JS. Dynamic isomiR regulation in Drosophila development. RNA 2010 Oct;16(10):1881-8. PMID: 20805289
  • Lu TP, Tsai MH, Lee JM, Hsu CP et al. Identification of a novel biomarker, SEMA5A, for non-small cell lung carcinoma in nonsmoking women. Cancer Epidemiol Biomarkers Prev 2010 Oct;19(10):2590-7. PMID: 20802022
  • Yu Y, Ping J, Chen H, Jiao L et al. A comparative analysis of liver transcriptome suggests divergent liver function among human, mouse and rat. Genomics 2010 Nov;96(5):281-9. PMID: 20800674
  • Zhang XY, Shi L, Liu Y, Tian F et al. ICPS: an integrative cancer profiler system. Bioinformatics 2010 Oct 15;26(20):2649-50. PMID: 20736342
  • Blow MJ, McCulley DJ, Li Z, Zhang T et al. ChIP-Seq identification of weakly conserved heart enhancers. Nat Genet 2010 Sep;42(9):806-10. PMID: 20729851
  • Zhang M, Zhang Y, Liu L, Yu L et al. Gene Expression Browser: large-scale and cross-experiment microarray data integration, management, search & visualization. BMC Bioinformatics 2010 Aug 20;11:433. PMID: 20727159
  • Takasugi M, Yagi S, Hirabayashi K, Shiota K. DNA methylation status of nuclear-encoded mitochondrial genes underlies the tissue-dependent mitochondrial functions. BMC Genomics 2010 Aug 19;11:481. PMID: 20723256
  • Wong EH, Smith DK, Rabadan R, Peiris M et al. Codon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza Virus. BMC Evol Biol 2010 Aug 19;10:253. PMID: 20723216
  • Assou S, Boumela I, Haouzi D, Anahory T et al. Dynamic changes in gene expression during human early embryo development: from fundamental aspects to clinical applications. Hum Reprod Update 2011 Mar-Apr;17(2):272-90. PMID: 20716614
  • Jennen DG, Gaj S, Giesbertz PJ, van Delft JH et al. Biotransformation pathway maps in WikiPathways enable direct visualization of drug metabolism related expression changes. Drug Discov Today 2010 Oct;15(19-20):851-8. PMID: 20708095
  • Le HS, Oltvai ZN, Bar-Joseph Z. Cross-species queries of large gene expression databases. Bioinformatics 2010 Oct 1;26(19):2416-23. PMID: 20702396
  • Sa Q, Hart E, Nadeau JH, Hoover-Plow JL. Mouse chromosome 17 candidate modifier genes for thrombosis. Mamm Genome 2010 Aug;21(7-8):337-49. PMID: 20700597
  • Cheng WC, Tsai ML, Chang CW, Huang CL et al. Microarray meta-analysis database (M(2)DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database. BMC Bioinformatics 2010 Aug 10;11:421. PMID: 20698961
  • Verzi MP, Hatzis P, Sulahian R, Philips J et al. TCF4 and CDX2, major transcription factors for intestinal function, converge on the same cis-regulatory regions. Proc Natl Acad Sci U S A 2010 Aug 24;107(34):15157-62. PMID: 20696899
  • Zhang W, Gao S, Zhou X, Xia J et al. Multiple distinct small RNAs originate from the same microRNA precursors. Genome Biol 2010;11(8):R81. PMID: 20696037
  • Finka A, Mattoo RU, Goloubinoff P. Meta-analysis of heat- and chemically upregulated chaperone genes in plant and human cells. Cell Stress Chaperones 2011 Jan;16(1):15-31. PMID: 20694844
  • Park SG, Choi SS. Expression breadth and expression abundance behave differently in correlations with evolutionary rates. BMC Evol Biol 2010 Aug 7;10:241. PMID: 20691101
  • Salmon-Divon M, Dvinge H, Tammoja K, Bertone P. PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci. BMC Bioinformatics 2010 Aug 6;11:415. PMID: 20691053
  • Swindell WR, Johnston A, Gudjonsson JE. Transcriptional profiles of leukocyte populations provide a tool for interpreting gene expression patterns associated with high fat diet in mice. PLoS One 2010 Jul 29;5(7):e11861. PMID: 20686622
  • Ochsner SA, Watkins CM, LaGrone BS, Steffen DL et al. Research resource: Tissue-specific transcriptomics and cistromics of nuclear receptor signaling: a web research resource. Mol Endocrinol 2010 Oct;24(10):2065-9. PMID: 20685849
  • De S, Zhang Y, Garner JR, Wang SA et al. Disease and phenotype gene set analysis of disease-based gene expression in mouse and human. Physiol Genomics 2010 Oct;42A(2):162-7. PMID: 20682848
  • Newman AM, Cooper JB. Lab-specific gene expression signatures in pluripotent stem cells. Cell Stem Cell 2010 Aug 6;7(2):258-62. PMID: 20682451
  • Weng YI, Hsu PY, Liyanarachchi S, Liu J et al. Epigenetic influences of low-dose bisphenol A in primary human breast epithelial cells. Toxicol Appl Pharmacol 2010 Oct 15;248(2):111-21. PMID: 20678512
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