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  • Patlak M, Balogh E, & Nass S (2012) Facilitating Collaborations to Develop Combination Investigational Cancer Therapies. National Cancer Policy Forum.
  • Jeon Y, Xun Z, Su P, & Rogers P (2012) Genome-wide transcriptomic analysis of a flocculent strain of Zymomonas mobilis. Applied Microbiology and Biotechnology:1-6.
  • Lembo A, Di Cunto F, & Provero P (2012) Shortening of 3UTRs Correlates with Poor Prognosis in Breast and Lung Cancer. Plos One 7(2):e31129.
  • Lockwood WW, et al. (2012) Integrative Genomics Identified RFC3 as an Amplified Candidate Oncogene in Esophageal Adenocarcinoma. Clinical Cancer Research.
  • Lu Y, Wang L, Liu P, Yang P, & You M (2012) Gene-Expression Signature Predicts Postoperative Recurrence in Stage I Non-Small Cell Lung Cancer Patients. Plos One 7(1):e30880.
  • Tseng GC, Ghosh D, & Feingold E (2012) Comprehensive literature review and statistical considerations for microarray meta-analysis. Nucleic Acids Research.
  • Imielinski M, et al. (2012) Integrated proteomic, transcriptomic, and biological network analysis of breast carcinoma reveals molecular features of tumorigenesis and clinical relapse. Molecular & Cellular Proteomics.
  • Roy A, McDonald PR, & Chaguturu R (2011) The Open Conference Proceedings Journal. The Open Conference Proceedings Journal 2:130-136.
  • Land W, et al. (2011) Kernelized partial least squares for feature reduction and classification of gene microarray data. BMC Systems Biology 5(Suppl 3):S13.
  • Zheng J, Stoyanovich J, Manduchi E, Liu J, & Stoeckert CJ (2011) AnnotCompute: annotation-based exploration and meta-analysis of genomics experiments. Database 2011.
  • Chen D-T, et al. (2011) Prognostic and Predictive Value of a Malignancy-Risk Gene Signature in Early-Stage Non--Small Cell Lung Cancer. Journal of the National Cancer Institute.
  • Azare J, et al. (2011) Stat3 Mediates Expression of Autotaxin in Breast Cancer. Plos One 6(11):e27851.
  • Floratos A, Honig B, Pe'er D, & Califano A (2011) Using systems and structure biology tools to dissect cellular phenotypes. Journal of the American Medical Informatics Association.
  • Suzuki Hiroshi I, et al. (2011) MCPIP1 Ribonuclease Antagonizes Dicer and Terminates MicroRNA Biogenesis through Precursor MicroRNA Degradation. Molecular Cell 44(3):424-436.
  • Wan Y-W, Beer DG, & Guo NL (2011) Signaling pathway-based identification of extensive prognostic gene signatures for lung adenocarcinoma. Lung Cancer (0).
  • Zhang J, Tan W, Alexander J, Foster I, & Madduri R (2011) Recommend-As-You-Go: A Novel Approach Supporting Services-Oriented Scientific Workflow Reuse. Services Computing (SCC), 2011 IEEE International Conference on, pp 48-55.
  • Martin Wiesinger MH, Marco Behr, Henrique Lopes de Abreu Madeira, Gernot Glockler, Paul Perco and Arno Lukas (2011) Data and Knowledge Management in Cross-Omics Research Projects Bioinformatics for Omics Data Methods and Protocols,  (Methods in Molecular Biology), Vol 719.
  • Mader M, Simon R, Steinbiss S, & Kurtz S (2011) FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context. Journal of Clinical Bioinformatics 1(1):20.
  • Komatsoulis GA (2011) Collaboration in Cancer Research Community: Cancer Biomedical Informatics Grid (caBIG). Collaborative Computational Technologies for Biomedical Research,  (John Wiley & Sons, Inc.), pp 261-280.
  • Hu H, et al. (2011) DW4TR: A Data Warehouse for Translational Research. Journal of Biomedical Informatics (0).
  • Amin W, Chandran U, Parwani AV, & Becich MJ (2011) Biomedical Informatics for Anatomic Pathology: Essentials of Anatomic Pathology. eds Cheng L & Bostwick DG (Springer New York), pp 469-480.
  • Tan W, et al. (2010) CaGrid Workflow Toolkit: A taverna based workflow tool for cancer grid. BMC Bioinformatics 11(1):542.
  • Shankar R, et al. (2010) Annotare---a tool for annotating high-throughput biomedical investigations and resulting data. Bioinformatics 26(19):2470-2471.
  • Sara H, Kallioniemi O, & Nees M (2010) A decade of cancer gene profiling: from molecular portraits to molecular function. (Translated from eng) Methods Mol Biol 576:61-87 (in eng).
  • McCusker J & McGuinness D (2010) Explorations into the Provenance of High Throughput Biomedical Experiments. Provenance and Annotation of Data and Processes, Lecture Notes in Computer Science, eds McGuinness D, Michaelis J, & Moreau L (Springer Berlin / Heidelberg), Vol 6378, pp 120-128.
  • Klemm J, Basu A, Fore I, Floratos A, & Komatsoulis G (2010) The caBIG Life Sciences Distribution. Biomedical Informatics for Cancer Research, eds Ochs MF, Casagrande JT, & Davuluri RV (Springer US), pp 253-266.
  • Etcheverry L, Khatchadourian S, & Consens M (2010) Quality Assessment of MAGE-ML Genomic Datasets Using DescribeX. Data Integration in the Life Sciences, Lecture Notes in Computer Science, eds Lambrix P & Kemp G (Springer Berlin / Heidelberg), Vol 6254, pp 192-206.
  • Borromeo C, Kang H, Berman J, & Becich M (2010) The tissue microarray OWL schema: An open-source tool for sharing tissue microarray data  pp 9-9.
  • Xingmin L (2009) Clustering and Tailoring User Session Data for Testing Web Applications. eds Fan P & Mei-Hwa C, pp 336-345.
  • Wei T, et al. (2009) Scientific Workflows as Services in caGrid: A Taverna and gRAVI Approach. Web Services, 2009. ICWS 2009. IEEE International Conference on, pp 413-420.
  • Phan JH, et al. (2009) Convergence of biomarkers, bioinformatics and nanotechnology for individualized cancer treatment. Trends in Biotechnology 27(6):350-358.
  • Chervitz SA, et al. (2009) Standards for Functional Genomics. Bioinformatics, eds Edwards D, Stajich J, & Hansen D (Springer New York), pp 293-329.
  • Bian X, et al. (2009) Data submission and curation for caArray, a standard based microarray data repository system. In 3rd International Biocuration Conference. Nature Publishing Group.
  • Zhao X-M, Chen L, & Aihara K (2008) Protein function prediction with high-throughput data. Amino Acids 35(3):517-530.
  • Wei T, Foster I, & Madduri R (2008) Combining the Power of Taverna and caGrid: Scientific Workflows that Enable Web-Scale Collaboration. Internet Computing, IEEE 12(6):61-68.
  • Stokes T, Torrance J, Li H, & Wang M (2008) ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses. BMC Bioinformatics 9(Suppl 6):S18.
  • Stein LD (2008) Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges. Nat Rev Genet 9(9):678-688.
  • Shironoshita EP, Jean-Mary YR, Bradley RM, & Kabuka MR (2008) semCDI: A Query Formulation for Semantic Data Integration in caBIG. Journal of the American Medical Informatics Association 15(4):559-568.
  • Coulibaly GPPaI (2008) Bioinformatic Tools for Inferring Functional Information from Plant Microarray Data: Tools for the First Steps. Int J Plant Genomics.
  • Yu Rang Park HWL, Sung Bum Cho, Ju Han Kim (2007) Cancer Genomics Object Model: An Object Model for Multiple Functional Genomics Data for Cancer Research. 12th World Congress on Health (Medical) Informatics.
  • Wang J, et al. (2007) VISDA: an open-source caBIG (TM) analytical tool for data clustering and beyond. Bioinformatics 23(15):2024-2027.
  • Torrance JT, Moffitt R, Stokes T, & Wang MD (2007) Can we trust biomarkers? visualization and quantification of outlier probes in high density oligonucleotide microarrays. Life Science Systems and Applications Workshop, 2007. LISA 2007. IEEE/NIH, pp 196-199.
  • Studer SM & Kaminski N (2007) Towards Systems Biology of Human Pulmonary Fibrosis. Proc Am Thorac Soc 4(1):85-91.
  • Stokes T, Moffitt R, Phan J, & Wang M (2007) Chip Artifact CORRECTion (caCORRECT): A Bioinformatics System for Quality Assurance of Genomics and Proteomics Array Data. Annals of Biomedical Engineering 35(6):1068-1080.
  • Martin SB, et al. (2007) Gene expression overlap affects karyotype prediction in pediatric acute lymphoblastic leukemia. (Translated from English) Leukemia 21(6):1341-1344 (in English).
  • Hanauer DA, Rhodes DR, Sinha-Kumar C, & Chinnaiyan AM (2007) Bioinformatics approaches in the study of cancer. (Translated from eng) Curr Mol Med 7(1):133-141 (in eng).
  • Ellis MJ, Dixon M, Dowsett M, Nagarajan R, & Mardis E (2007) A luminal breast cancer genome atlas: Progress and barriers. The Journal of Steroid Biochemistry and Molecular Biology 106(1-5):125-129.
  • Whetzel PL, et al. (2006) The MGED Ontology: a resource for semantics-based description of microarray experiments. Bioinformatics 22(7):866-873.
  • Saltz J, et al. (2006) caGrid: design and implementation of the core architecture of the cancer biomedical informatics grid. Bioinformatics 22(15):1910-1916.
  • Rhee SY, Dickerson J, & Xu D (2006) BIOINFORMATICS AND ITS APPLICATIONS IN PLANT BIOLOGY. Annual Review of Plant Biology 57(1):335-360.
  • Perrone VaF, A and Goldin, L and Kramer, J and Parkinson, H and Reddington, F (2006) Developing an Integrative Platform for Cancer Research: a Requirements Engineering Perspective. the UK e-Science All Hands Meeting 2006.
  • Goldin L (2006) Bioinformatics Integration for Cancer Research-Goal Question analysis. Information Technology: Research and Education, 2006. ITRE '06. International Conference on, pp 248-252.
  • Fenstermacher D, et al. (2005) The Cancer Biomedical Informatics Grid (caBIG (TM) ). Engineering in Medicine and Biology Society, 2005. IEEE-EMBS 2005. 27th Annual International Conference of the, pp 743-746.
  • Brazma A & Sarkans U (2001) Gene Expression Databases. eLS,  (John Wiley & Sons, Ltd).
  • Phillips JL (Integrated Biomedical Databases: Microarray, Molecular Biology Integra-tion, Natural Language Processing, and Ontology Mapping. Signal 5:69.
  • Xie Y, et al. (2011) Robust Gene Expression Signature from Formalin-Fixed Paraffin-Embedded Samples Predicts Prognosis of Non-Small-Cell Lung Cancer Patients. Clinical Cancer Research.
  • Soon WW, et al. (2011) Combined genomic and phenotype screening reveals secretory factor SPINK1 as an invasion and survival factor associated with patient prognosis in breast cancer. EMBO Molecular Medicine 3(8):451-464.
  • Shiau C-K, Gu D-L, Chen C-F, Lin C-H, & Jou Y-S (2011) IGRhCellID: integrated genomic resources of human cell lines for identification. Nucleic Acids Research 39(suppl 1):D520-D524.
  • Robbins CM, et al. (2011) Copy number and targeted mutational analysis reveals novel somatic events in metastatic prostate tumors. Genome Research 21(1):47-55.
  • Onaitis M, et al. (2011) A 10-Gene Progenitor Cell Signature Predicts Poor Prognosis in Lung Adenocarcinoma. The Annals of Thoracic Surgery 91(4):1046-1050.
  • Meng X, et al. (2011) GSI-I (Z-LLNle-CHO) inhibits [gamma]-secretase and the proteosome to trigger cell death in precursor-B acute lymphoblastic leukemia. Leukemia 25(7):1135-1146.
  • Kadara H, et al. (2011) A Five-Gene and Corresponding Protein Signature for Stage-I Lung Adenocarcinoma Prognosis. Clinical Cancer Research 17(6):1490-1501.
  • Faratian D, et al. (2011) Trastuzumab and Pertuzumab Produce Changes in Morphology and Estrogen Receptor Signaling in Ovarian Cancer Xenografts Revealing New Treatment Strategies. Clinical Cancer Research 17(13):4451-4461.
  • Cohen AL, et al. (2011) A pharmacogenomic method for individualized prediction of drug sensitivity. Mol Syst Biol 7.
  • Chen C, et al. (2011) Varied pathways of stage IA lung adenocarcinomas discovered by integrated gene expression analysis. (Translated from eng) Int J Biol Sci 7(5):551-566 (in eng).
  • Yoo J-K, Galligan CL, Virtanen C, & Fish EN (2010) Identification of a novel antigen-presenting cell population modulating antiinfluenza type 2 immunity. The Journal of Experimental Medicine 207(7):1435-1451.
  • Xie T, et al. (2010) A Survey of Cancer Cell Lines Reveals Highly Structured and Hierarchical Relationships within and between DNA and mRNA That May Be the Result of Selection. OMICS: A Journal of Integrative Biology 14(1):91-97.
  • Wan Y-W, et al. (2010) Hybrid Models Identified a 12-Gene Signature for Lung Cancer Prognosis and Chemoresponse Prediction. Plos One 5(8):e12222.
  • Sabine V, et al. (2010) Gene expression profiling of response to mTOR inhibitor everolimus in pre-operatively treated post-menopausal women with oestrogen receptor-positive breast cancer. Breast Cancer Research and Treatment 122(2):419-428.
  • Potratz JC, et al. (2010) Synthetic Lethality Screens Reveal RPS6 and MST1R as Modifiers of Insulin-like Growth Factor-1 Receptor Inhibitor Activity in Childhood Sarcomas. Cancer Research 70(21):8770-8781.
  • Luo J & Ellis MJ (2010) Microarray data analysis in neoadjuvant biomarker studies in estrogen receptor-positive breast cancer. (Translated from eng) Breast Cancer Res 12(4):112 (in eng).
  • Loboda A, et al. (2010) A gene expression signature of RAS pathway dependence predicts response to PI3K and RAS pathway inhibitors and expands the population of RAS pathway activated tumors. BMC Medical Genomics 3(1):26.
  • Kitchen R, et al. (2010) Correcting for intra-experiment variation in Illumina BeadChip data is necessary to generate robust gene-expression profiles. BMC Genomics 11(1):134.
  • Katz E, et al. (2010) A gene on the HER2 amplicon, C35, is an oncogene in breast cancer whose actions are prevented by inhibition of Syk. Br J Cancer 103(3):401-410.
  • Jeong Y, et al. (2010) Nuclear Receptor Expression Defines a Set of Prognostic Biomarkers for Lung Cancer. PLoS Med 7(12):e1000378.
  • Harvey RC, et al. (2010) Rearrangement of CRLF2 is associated with mutation of JAK kinases, alteration of IKZF1, Hispanic/Latino ethnicity, and a poor outcome in pediatric B-progenitor acute lymphoblastic leukemia. Blood 115(26):5312-5321.
  • Floratos A, Smith K, Ji Z, Watkinson J, & Califano A (2010) geWorkbench: an open source platform for integrative genomics. Bioinformatics 26(14):1779-1780.
  • Dews M, et al. (2010) The Myc--miR-17-92 Axis Blunts TGF-beta Signaling and Production of Multiple TGF-beta-Dependent Antiangiogenic Factors. Cancer Research 70(20):8233-8246.
  • Wang X-S, et al. (2009) An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer. Nat Biotech 27(11):1005-1011.
  • Sanga S, Broom B, Cristini V, & Edgerton M (2009) Gene expression meta-analysis supports existence of molecular apocrine breast cancer with a role for androgen receptor and implies interactions with ErbB family. BMC Medical Genomics 2(1):59.
  • Reinholdt L, et al. (2009) Meiotic behavior of aneuploid chromatin in mouse models of Down syndrome. Chromosoma 118(6):723-736.
  • Rahman M, et al. (2009) TRAIL induces apoptosis in triple-negative breast cancer cells with a mesenchymal phenotype. Breast Cancer Research and Treatment 113(2):217-230.
  • Murat A, et al. (2009) Modulation of Angiogenic and Inflammatory Response in Glioblastoma by Hypoxia. (Translated from English) Plos One 4(6) (in English).
  • Lavarino C, et al. (2009) Specific gene expression profiles and chromosomal abnormalities are associated with infant disseminated neuroblastoma. BMC Cancer 9(1):44.
  • Krauthammer M, McCusker JP, Phillips JA, Beltran AG, & Finkelstein A (2009) Semantic web data warehousing for caGrid. (Translated from English) BMC Bioinformatics 10 (in English).
  • Kotliarov Y, et al. (2009) Correlation analysis between single-nucleotide polymorphism and expression arrays in gliomas identifies potentially relevant target genes. (Translated from eng) Cancer Res 69(4):1596-1603 (in eng).
  • Kim WY, et al. (2009) HIF2alpha cooperates with RAS to promote lung tumorigenesis in mice. (Translated from eng) J Clin Invest 119(8):2160-2170 (in eng).
  • Itadani H, Oshima H, Oshima M, & Kotani H (2009) Mouse gastric tumor models with prostaglandin E2 pathway activation show similar gene expression profiles to intestinal-type human gastric cancer. BMC Genomics 10(1):615.
  • Gershon TR, et al. (2009) Enteric Neural Crest Differentiation in Ganglioneuromas Implicates Hedgehog Signaling in Peripheral Neuroblastic Tumor Pathogenesis. Plos One 4(10):e7491.
  • Cheng H, et al. (2009) SIK1 couples LKB1 to p53-dependent anoikis and suppresses metastasis. (Translated from eng) Sci Signal 2(80):ra35 (in eng).
  • Lavarino C, et al. (2008) Differential expression of genes mapping to recurrently abnormal chromosomal regions characterize neuroblastic tumours with distinct ploidy status. BMC Medical Genomics 1(1):36.
  • Huh J-I, et al. (2007) 2-Methoxyestradiol Induces Mammary Gland Differentiation through Amphiregulin-Epithelial Growth Factor Receptor-Mediated Signaling: Molecular Distinctions from the Mammary Gland of Pregnant Mice. Endocrinology 148(3):1266-1277.
  • Kotliarov Y, et al. (2006) High-resolution Global Genomic Survey of 178 Gliomas Reveals Novel Regions of Copy Number Alteration and Allelic Imbalances. Cancer Research 66(19):9428-9436.
  • Doane AS, et al. (2006) An estrogen receptor-negative breast cancer subset characterized by a hormonally regulated transcriptional program and response to androgen. Oncogene 25(28):3994-4008.
  • Chelvarajan RL, et al. (2006) Molecular basis of age-associated cytokine dysregulation in LPS-stimulated macrophages. Journal of Leukocyte Biology 79(6):1314-1327.
  • Sui G, et al. (2011) Yin Yang 1 contains G-quadruplex structures in its promoter and 5-prime-UTR and its expression is modulated by G4 resolvase 1. Nucleic Acids Research 39(18):1-17.
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