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Bhavnani SK, Eichinger F, Martini S, Saxman P, Jagadish HV, Kretzler M. Network analysis of genes regulated in renal diseases: implications for a molecular-based classification. BMC Bioinformatics 2009; 10 Suppl 9(): S3. PMID: 19761573.
Boyd AD, Saxman PR, Hunscher DA, Smith KA, Morris TD, Kaston M, Bayoff F, Rogers B, Hayes P, Rajeev N, Kline-Rogers E, Eagle K, Clauw D, Greden JF, Green LA, Athey BD. The University of Michigan Honest Broker: a Web-based service for clinical and translational research and practice. J Am Med Inform Assoc 2009; 16(6): 784-91. PMID: 19717803.
Chen Y, Lin G, Huo JS, Barney D, Wang Z, Livshiz T, States DJ, Qin ZS, Schwartz J. Computational and functional analysis of growth hormone (GH)-regulated genes identifies the transcriptional repressor B-cell lymphoma 6 (Bc16) as a participant in GH-regulated transcription. Endocrinology 2009; 150(8): 3645-54. PMID: 19406940.
Gao J, Ade AS, Tarcea VG, Weymouth TE, Mirel BR, Jagadish HV, States DJ. Integrating and annotating the interactome using the MiMI plugin for cytoscape. Bioinformatics 2009; 25(1): 137-8. PMID: 18812364.
Ghosh D, Yan X, Tian Q. Gene regulatory networks in embryonic stem cells and brain development. Birth Defects Res C Embryo Today 2009; 87(2): 182-91. PMID: 19530135.
Hur J, Schuyler AD, States DJ, Feldman EL. SciMiner: web-based literature mining tool for target identification and functional enrichment analysis. Bioinformatics 2009; 25(6): 838-40. PMID: 19188191.
Kainkaryam RM, Woolf PJ. Pooling in high-throughput drug screening. Curr Opin Drug Discov Devel 2009; 12(3): 339-50. PMID: 19396735.
Keller BJ, McEachin RC. Identifying hypothetical genetic influences on complex disease phenotypes. BMC Bioinformatics 2009; 10 Suppl 2(): S13. PMID: 19208188.
Kim YJ, Teletia N, Ruotti V, Maher CA, Chinnaiyan AM, Stewart R, Thomson JA, Patel JM. ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches. Bioinformatics 2009; 25(11): 1424-5. PMID: 19351619.
Lee I, Ajay SS, Yook JI, Kim HS, Hong SH, Kim NH, Dhanasekaran SM, Chinnaiyan AM, Athey BD. New class of microRNA targets containing simultaneous 5'-UTR and 3'-UTR interaction sites. Genome Res 2009; 19(7): 1175-83. PMID: 19336450.
Lin B, Wang J, Hong X, Yan X, Hwang D, Cho JH, Yi D, Utleg AG, Fang X, Schones DE, Zhao K, Omenn GS, Hood L. Integrated expression profiling and ChIP-seq analyses of the growth inhibition response program of the androgen receptor. PLoS One 2009; 4(8): e6589. PMID: 19668381.
Luo W, Friedman MS, Shedden K, Hankenson KD, Woolf PJ. GAGE: generally applicable gene set enrichment for pathway analysis. BMC Bioinformatics 2009; 10(): 161. PMID: 19473525.
Maher CA, Kumar-Sinha C, Cao X, Kalyana-Sundaram S, Han B, Jing X, Sam L, Barrette T, Palanisamy N, Chinnaiyan AM. Transcriptome sequencing to detect gene fusions in cancer. Nature 2009; 458(7234): 97-101. PMID: 19136943.
Maher CA, Palanisamy N, Brenner JC, Cao X, Kalyana-Sundaram S, Luo S, Khrebtukova I, Barrette TR, Grasso C, Yu J, Lonigro RJ, Schroth G, Kumar-Sinha C, Chinnaiyan AM. Chimeric transcript discovery by paired-end transcriptome sequencing. Proc Natl Acad Sci U S A 2009; 106(30): 12353-8. PMID: 19592507.
Martini S, Kretzler M. How to build a tight but permeable glomerular junction. J Am Soc Nephrol 2009; 20(7): 1420-1. PMID: 19520750.
Menon R, Zhang Q, Zhang Y, Fermin D, Bardeesy N, DePinho RA, Lu C, Hanash SM, Omenn GS, States DJ. Identification of novel alternative splice isoforms of circulating proteins in a mouse model of human pancreatic cancer. Cancer Res 2009; 69(1): 300-9. PMID: 19118015.
Mirel B. Supporting cognition in systems biology analysis: findings on users' processes and design implications. J Biomed Discov Collab 2009; 4(): 2. PMID: 19216777.
Moll AG, Lindenmeyer MT, Kretzler M, Nelson PJ, Zimmer R, Cohen CD. Transcript-specific expression profiles derived from sequence-based analysis of standard microarrays. PLoS One 2009; 4(3): e4702. PMID: 19277110.
Prokopenko I, Langenberg C, Florez JC, Saxena R, Soranzo N, Thorleifsson G, Loos RJ, Manning AK, Jackson AU, Aulchenko Y, Potter SC, Erdos MR, Sanna S, Hottenga JJ, Wheeler E, Kaakinen M, Lyssenko V, Chen WM, Ahmadi K, Beckmann JS, Bergman RN, Bochud M, Bonnycastle LL, Buchanan TA, Cao A, Cervino A, Coin L, Collins FS, Crisponi L, de Geus EJ, Dehghan A, Deloukas P, Doney AS, Elliott P, Freimer N, Gateva V, Herder C, Hofman A, Hughes TE, Hunt S, Illig T, Inouye M, Isomaa B, Johnson T, Kong A, Krestyaninova M, Kuusisto J, Laakso M, Lim N, Lindblad U, Lindgren CM, McCann OT, Mohlke KL, Morris AD, Naitza S, Orrù M, Palmer CN, Pouta A, Randall J, Rathmann W, Saramies J, Scheet P, Scott LJ, Scuteri A, Sharp S, Sijbrands E, Smit JH, Song K, Steinthorsdottir V, Stringham HM, Tuomi T, Tuomilehto J, Uitterlinden AG, Voight BF, Waterworth D, Wichmann HE, Willemsen G, Witteman JC, Yuan X, Zhao JH, Zeggini E, Schlessinger D, Sandhu M, Boomsma DI, Uda M, Spector TD, Penninx BW, Altshuler D, Vollenweider P, Jarvelin MR, Lakatta E, Waeber G, Fox CS, Peltonen L, Groop LC, Mooser V, Cupples LA, Thorsteinsdottir U, Boehnke M, Barroso I, Van Duijn C, Dupuis J, Watanabe RM, Stefansson K, McCarthy MI, Wareham NJ, Meigs JB, Abecasis GR. Variants in MTNR1B influence fasting glucose levels. Nat Genet 2009; 41(1): 77-81. PMID: 19060907.
States DJ, Ade AS, Wright ZC, Bookvich AV, Athey BD. MiSearch adaptive pubMed search tool. Bioinformatics 2009; 25(7): 974-6. PMID: 18326507.
Tarcea VG, Weymouth T, Ade A, Bookvich A, Gao J, Mahavisno V, Wright Z, Chapman A, Jayapandian M, Ozgür A, Tian Y, Cavalcoli J, Mirel B, Patel J, Radev D, Athey B, States D, Jagadish HV. Michigan molecular interactions r2: from interacting proteins to pathways. Nucleic Acids Res 2009; 37(Database issue): D642-6. PMID: 18978014.
Tu LC, Foltz G, Lin E, Hood L, Tian Q. Targeting stem cells-clinical implications for cancer therapy. Curr Stem Cell Res Ther 2009; 4(2): 147-53. PMID: 19442199.
Vellaichamy A, Sreekumar A, Strahler JR, Rajendiran T, Yu J, Varambally S, Li Y, Omenn GS, Chinnaiyan AM, Nesvizhskii AI. Proteomic interrogation of androgen action in prostate cancer cells reveals roles of aminoacyl tRNA synthetases. PLoS One 2009; 4(9): e7075. PMID: 19763266.
Wang XS, Prensner JR, Chen G, Cao Q, Han B, Dhanasekaran SM, Ponnala R, Cao X, Varambally S, Thomas DG, Giordano TJ, Beer DG, Palanisamy N, Sartor MA, Omenn GS, Chinnaiyan AM. An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer. Nat Biotechnol 2009; 27(11): 1005-11. PMID: 19881495.
Wiggin TD, Sullivan KA, Pop-Busui R, Amato A, Sima AA, Feldman EL. Elevated triglycerides correlate with progression of diabetic neuropathy. Diabetes 2009; 58(7): 1634-40. PMID: 19411614.
Xuan W, Dai M, Mirel B, Song J, Athey B, Watson SJ, Meng F. Open Biomedical Ontology-based Medline exploration. BMC Bioinformatics 2009; 10 Suppl 5(): S6. PMID: 19426463.
Yang CY, Sun H, Chen J, Nikolovska-Coleska Z, Wang S. Importance of ligand reorganization free energy in protein-ligand binding-affinity prediction. J Am Chem Soc 2009; 131(38): 13709-21. PMID: 19736924.
Ashkenazi M, Bader GD, Kuchinsky A, Moshelion M, States DJ. Cytoscape ESP: simple search of complex biological networks. Bioinformatics 2008; 24(12): 1465-6. PMID: 18445605.
Black MH, Fingerlin TE, Allayee H, Zhang W, Xiang AH, Trigo E, Hartiala J, Lehtinen AB, Haffner SM, Bergman RN, McEachin RC, Kjos SL, Lawrence JM, Buchanan TA, Watanabe RM. Evidence of interaction between PPARG2 and HNF4A contributing to variation in insulin sensitivity in Mexican Americans. Diabetes 2008; 57(4): 1048-56. PMID: 18162503.
Chen WM, Erdos MR, Jackson AU, Saxena R, Sanna S, Silver KD, Timpson NJ, Hansen T, Orrù M, Grazia Piras M, Bonnycastle LL, Willer CJ, Lyssenko V, Shen H, Kuusisto J, Ebrahim S, Sestu N, Duren WL, Spada MC, Stringham HM, Scott LJ, Olla N, Swift AJ, Najjar S, Mitchell BD, Lawlor DA, Smith GD, Ben-Shlomo Y, Andersen G, Borch-Johnsen K, Jørgensen T, Saramies J, Valle TT, Buchanan TA, Shuldiner AR, Lakatta E, Bergman RN, Uda M, Tuomilehto J, Pedersen O, Cao A, Groop L, Mohlke KL, Laakso M, Schlessinger D, Collins FS, Altshuler D, Abecasis GR, Boehnke M, Scuteri A, Watanabe RM. Variations in the G6PC2/ABCB11 genomic region are associated with fasting glucose levels. J Clin Invest 2008; 118(7): 2620-8. PMID: 18521185.
Dinov ID, Rubin D, Lorensen W, Dugan J, Ma J, Murphy S, Kirschner B, Bug W, Sherman M, Floratos A, Kennedy D, Jagadish HV, Schmidt J, Athey B, Califano A, Musen M, Altman R, Kikinis R, Kohane I, Delp S, Parker DS, Toga AW. iTools: a framework for classification, categorization and integration of computational biology resources. PLoS One 2008; 3(5): e2265. PMID: 18509477.
Gaulton KJ, Willer CJ, Li Y, Scott LJ, Conneely KN, Jackson AU, Duren WL, Chines PS, Narisu N, Bonnycastle LL, Luo J, Tong M, Sprau AG, Pugh EW, Doheny KF, Valle TT, Abecasis GR, Tuomilehto J, Bergman RN, Collins FS, Boehnke M, Mohlke KL. Comprehensive association study of type 2 diabetes and related quantitative traits with 222 candidate genes. Diabetes 2008; 57(11): 3136-44. PMID: 18678618.
Kainkaryam RM, Woolf PJ. poolHiTS: a shifted transversal design based pooling strategy for high-throughput drug screening. BMC Bioinformatics 2008; 9(): 256. PMID: 18513431.
Laxman B, Morris DS, Yu J, Siddiqui J, Cao J, Mehra R, Lonigro RJ, Tsodikov A, Wei JT, Tomlins SA, Chinnaiyan AM. A first-generation multiplex biomarker analysis of urine for the early detection of prostate cancer. Cancer Res 2008; 68(3): 645-9. PMID: 18245462.
Lee I, Ajay SS, Chen H, Maruyama A, Wang N, McInnis MG, Athey BD. Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG). Nucleic Acids Res 2008; 36(5): e27. PMID: 18208839.
Leitner F, Krallinger M, Rodriguez-Penagos C, Hakenberg J, Plake C, Kuo CJ, Hsu CN, Tsai RT, Hung HC, Lau WW, Johnson CA, Saetre R, Yoshida K, Chen YH, Kim S, Shin SY, Zhang BT, Baumgartner WA, Hunter L, Haddow B, Matthews M, Wang X, Ruch P, Ehrler F, Ozgür A, Erkan G, Radev DR, Krauthammer M, Luong T, Hoffmann R, Sander C, Valencia A. Introducing meta-services for biomedical information extraction. Genome Biol 2008; 9 Suppl 2(): S6. PMID: 18834497.
Luo W, Hankenson KD, Woolf PJ. Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information. BMC Bioinformatics 2008; 9(): 467. PMID: 18980677.
Martini S, Eichinger F, Nair V, Kretzler M. Defining human diabetic nephropathy on the molecular level: integration of transcriptomic profiles with biological knowledge. Rev Endocr Metab Disord 2008; 9(4): 267-74. PMID: 18704688.
McEachin RC, Keller BJ, Saunders EF, McInnis MG. Modeling gene-by-environment interaction in comorbid depression with alcohol use disorders via an integrated bioinformatics approach. BioData Min 2008; 1(1): 2. PMID: 18822146.
Mo F, Hong X, Gao F, Du L, Wang J, Omenn GS, Lin B. A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data. BMC Bioinformatics 2008; 9(): 537. PMID: 19087293.
Ozgür A, Vu T, Erkan G, Radev DR. Identifying gene-disease associations using centrality on a literature mined gene-interaction network. Bioinformatics 2008; 24(13): i277-85. PMID: 18586725.
Qian Y, Murphy RF. Improved recognition of figures containing fluorescence microscope images in online journal articles using graphical models. Bioinformatics 2008; 24(4): 569-76. PMID: 18033795.
Sarntivijai S, Ade AS, Athey BD, States DJ. A bioinformatics analysis of the cell line nomenclature. Bioinformatics 2008; 24(23): 2760-6. PMID: 18849319.
Taylor BS, Pal M, Yu J, Laxman B, Kalyana-Sundaram S, Zhao R, Menon A, Wei JT, Nesvizhskii AI, Ghosh D, Omenn GS, Lubman DM, Chinnaiyan AM, Sreekumar A. Humoral response profiling reveals pathways to prostate cancer progression. Mol Cell Proteomics 2008; 7(3): 600-11. PMID: 18077443.
Tomlins SA, Rhodes DR, Yu J, Varambally S, Mehra R, Perner S, Demichelis F, Helgeson BE, Laxman B, Morris DS, Cao Q, Cao X, Andrén O, Fall K, Johnson L, Wei JT, Shah RB, Al-Ahmadie H, Eastham JA, Eggener SE, Fine SW, Hotakainen K, Stenman UH, Tsodikov A, Gerald WL, Lilja H, Reuter VE, Kantoff PW, Scardino PT, Rubin MA, Bjartell AS, Chinnaiyan AM. The role of SPINK1 in ETS rearrangement-negative prostate cancers. Cancer Cell 2008; 13(6): 519-28. PMID: 18538735.
Wiggin TD, Kretzler M, Pennathur S, Sullivan KA, Brosius FC, Feldman EL. Rosiglitazone treatment reduces diabetic neuropathy in streptozotocin-treated DBA/2J mice. Endocrinology 2008; 149(10): 4928-37. PMID: 18583417.
Yu J, Yu J, Cordero KE, Johnson MD, Ghosh D, Rae JM, Chinnaiyan AM, Lippman ME. A transcriptional fingerprint of estrogen in human breast cancer predicts patient survival. Neoplasia 2008; 10(1): 79-88. PMID: 18231641.
Zandi PP, Zöllner S, Avramopoulos D, Willour VL, Chen Y, Qin ZS, Burmeister M, Miao K, Gopalakrishnan S, McEachin R, Potash JB, Depaulo JR, McInnis MG. Family-based SNP association study on 8q24 in bipolar disorder. Am J Med Genet B Neuropsychiatr Genet 2008; 147B(5): 612-8. PMID: 18163389.
Zeggini E, Scott LJ, Saxena R, Voight BF, Marchini JL, Hu T, de Bakker PI, Abecasis GR, Almgren P, Andersen G, Ardlie K, Boström KB, Bergman RN, Bonnycastle LL, Borch-Johnsen K, Burtt NP, Chen H, Chines PS, Daly MJ, Deodhar P, Ding CJ, Doney AS, Duren WL, Elliott KS, Erdos MR, Frayling TM, Freathy RM, Gianniny L, Grallert H, Grarup N, Groves CJ, Guiducci C, Hansen T, Herder C, Hitman GA, Hughes TE, Isomaa B, Jackson AU, Jørgensen T, Kong A, Kubalanza K, Kuruvilla FG, Kuusisto J, Langenberg C, Lango H, Lauritzen T, Li Y, Lindgren CM, Lyssenko V, Marvelle AF, Meisinger C, Midthjell K, Mohlke KL, Morken MA, Morris AD, Narisu N, Nilsson P, Owen KR, Palmer CN, Payne F, Perry JR, Pettersen E, Platou C, Prokopenko I, Qi L, Qin L, Rayner NW, Rees M, Roix JJ, Sandbaek A, Shields B, Sjögren M, Steinthorsdottir V, Stringham HM, Swift AJ, Thorleifsson G, Thorsteinsdottir U, Timpson NJ, Tuomi T, Tuomilehto J, Walker M, Watanabe RM, Weedon MN, Willer CJ, Wellcome Trust Case Control Consortium, Illig T, Hveem K, Hu FB, Laakso M, Stefansson K, Pedersen O, Wareham NJ, Barroso I, Hattersley AT, Collins FS, Groop L, McCarthy MI, Boehnke M, Altshuler D. Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes. Nat Genet 2008; 40(5): 638-45. PMID: 18372903.
Chen J, Blackwell TW, Fermin D, Menon R, Chen Y, Gao J, Lee AW, States DJ. Evolutionary-conserved gene expression response profiles across mammalian tissues. OMICS 2007; 11(1): 96-115. PMID: 17411398.
Chen SC, Zhao T, Gordon GJ, Murphy RF. Automated image analysis of protein localization in budding yeast. Bioinformatics 2007; 23(13): i66-71. PMID: 17646347.
Chen Y, Blackwell TW, Chen J, Gao J, Lee AW, States DJ. Integration of genome and chromatin structure with gene expression profiles to predict c-MYC recognition site binding and function. PLoS Comput Biol 2007; 3(4): e63. PMID: 17411336.
Dai M, Wang P, Jakupovic E, Watson SJ, Meng F. Web-based GeneChip analysis system for large-scale collaborative projects. Bioinformatics 2007; 23(16): 2185-7. PMID: 17586830.
Gao WM, Chadha MS, Berger RP, Omenn GS, Allen DL, Pisano M, Adelson PD, Clark RS, Jenkins LW, Kochanek PM. A gel-based proteomic comparison of human cerebrospinal fluid between inflicted and non-inflicted pediatric traumatic brain injury. J Neurotrauma 2007; 24(1): 43-53. PMID: 17263669.
Jayapandian M, Chapman A, Tarcea VG, Yu C, Elkiss A, Ianni A, Liu B, Nandi A, Santos C, Andrews P, Athey B, States D, Jagadish HV. Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. Nucleic Acids Res 2007; 35(Database issue): D566-71. PMID: 17130145.
McEachin RC, Keller BJ, Zandi PP, Almani M, McInnis MG. Prioritizing Disease Genes by Analysis of Common Elements (PDG-ACE). AMIA Annu Symp Proc 2007; (): 1068. PMID: 18694166.
Morris DS, Tomlins SA, Rhodes DR, Mehra R, Shah RB, Chinnaiyan AM. Integrating biomedical knowledge to model pathways of prostate cancer progression. Cell Cycle 2007; 6(10): 1177-87. PMID: 17495538.
Rhodes DR, Kalyana-Sundaram S, Mahavisno V, Varambally R, Yu J, Briggs BB, Barrette TR, Anstet MJ, Kincead-Beal C, Kulkarni P, Varambally S, Ghosh D, Chinnaiyan AM. Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia 2007; 9(2): 166-80. PMID: 17356713.
Scott LJ, Mohlke KL, Bonnycastle LL, Willer CJ, Li Y, Duren WL, Erdos MR, Stringham HM, Chines PS, Jackson AU, Prokunina-Olsson L, Ding CJ, Swift AJ, Narisu N, Hu T, Pruim R, Xiao R, Li XY, Conneely KN, Riebow NL, Sprau AG, Tong M, White PP, Hetrick KN, Barnhart MW, Bark CW, Goldstein JL, Watkins L, Xiang F, Saramies J, Buchanan TA, Watanabe RM, Valle TT, Kinnunen L, Abecasis GR, Pugh EW, Doheny KF, Bergman RN, Tuomilehto J, Collins FS, Boehnke M. A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants. Science 2007; 316(5829): 1341-5. PMID: 17463248.
Sullivan KA, Hayes JM, Wiggin TD, Backus C, Su Oh S, Lentz SI, Brosius F, Feldman EL. Mouse models of diabetic neuropathy. Neurobiol Dis 2007; 28(3): 276-85. PMID: 17804249.
Sun B, Ranish JA, Utleg AG, White JT, Yan X, Lin B, Hood L. Shotgun glycopeptide capture approach coupled with mass spectrometry for comprehensive glycoproteomics. Mol Cell Proteomics 2007; 6(1): 141-9. PMID: 17074749.
Tian Y, McEachin RC, Santos C, States DJ, Patel JM. SAGA: a subgraph matching tool for biological graphs. Bioinformatics 2007; 23(2): 232-9. PMID: 17110368.
Tomlins SA, Mehra R, Rhodes DR, Cao X, Wang L, Dhanasekaran SM, Kalyana-Sundaram S, Wei JT, Rubin MA, Pienta KJ, Shah RB, Chinnaiyan AM. Integrative molecular concept modeling of prostate cancer progression. Nat Genet 2007; 39(1): 41-51. PMID: 17173048.
Tu LC, Yan X, Hood L, Lin B. Proteomics analysis of the interactome of N-myc downstream regulated gene 1 and its interactions with the androgen response program in prostate cancer cells. Mol Cell Proteomics 2007; 6(4): 575-88. PMID: 17220478.
Wilson J, Dai M, Jakupovic E, Watson S, Meng F. Supercomputing with toys: harnessing the power of NVIDIA 8800GTX and playstation 3 for bioinformatics problem. Comput Syst Bioinformatics Conf 2007; 6(): 387-90. PMID: 17951841.
Xiang Z, Minter RM, Bi X, Woolf PJ, He Y. miniTUBA: medical inference by network integration of temporal data using Bayesian analysis. Bioinformatics 2007; 23(18): 2423-32. PMID: 17644819.
Xuan W, Dai M, Mirel B, Wilson J, Athey B, Watson SJ, Meng F. An active visual search interface for Medline. Comput Syst Bioinformatics Conf 2007; 6(): 359-69. PMID: 17951838.
Xuan W, Wang P, Watson SJ, Meng F. Medline search engine for finding genetic markers with biological significance. Bioinformatics 2007; 23(18): 2477-84. PMID: 17823133.
Yu J, Yu J, Almal AA, Dhanasekaran SM, Ghosh D, Worzel WP, Chinnaiyan AM. Feature selection and molecular classification of cancer using genetic programming. Neoplasia 2007; 9(4): 292-303. PMID: 17460773.
Zhao T, Murphy RF. Automated learning of generative models for subcellular location: building blocks for systems biology. Cytometry A 2007; 71(12): 978-90. PMID: 17972315.
Barker PE, Wagner PD, Stein SE, Bunk DM, Srivastava S, Omenn GS. Standards for plasma and serum proteomics in early cancer detection: a needs assessment report from the national institute of standards and technology--National Cancer Institute Standards, Methods, Assays, Reagents and Technologies Workshop, August 18-19, 2005. Clin Chem 2006; 52(9): 1669-74. PMID: 16840585.
Bookstein FL, Streissguth AP, Connor PD, Sampson PD. Damage to the human cerebellum from prenatal alcohol exposure: the anatomy of a simple biometrical explanation. Anat Rec B New Anat 2006; 289(5): 195-209. PMID: 16955499.
Fermin D, Allen BB, Blackwell TW, Menon R, Adamski M, Xu Y, Ulintz P, Omenn GS, States DJ. Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics. Genome Biol 2006; 7(4): R35. PMID: 16646984.
Goodman GE, Thornquist MD, Edelstein C, Omenn GS. Biorepositories: let's not lose what we have so carefully gathered! Cancer Epidemiol Biomarkers Prev 2006; 15(4): 599-601. PMID: 16614097.
Keshamouni VG, Michailidis G, Grasso CS, Anthwal S, Strahler JR, Walker A, Arenberg DA, Reddy RC, Akulapalli S, Thannickal VJ, Standiford TJ, Andrews PC, Omenn GS. Differential protein expression profiling by iTRAQ-2DLC-MS/MS of lung cancer cells undergoing epithelial-mesenchymal transition reveals a migratory/invasive phenotype. J Proteome Res 2006; 5(5): 1143-54. PMID: 16674103.
Kim YJ, Patel JM. A framework for protein structure classification and identification of novel protein structures. BMC Bioinformatics 2006; 7(): 456. PMID: 17042958.
Lee AW, States DJ. Colony-stimulating factor-1 requires PI3-kinase-mediated metabolism for proliferation and survival in myeloid cells. Cell Death Differ 2006; 13(11): 1900-14. PMID: 16514418.
Omenn GS. Report from the 2nd Annual US HUPO Meeting on the HUPO Human Plasma Proteome Project. Expert Rev Proteomics 2006; 3(2): 165-8. PMID: 16608429.
Omenn GS. Strategies for plasma proteomic profiling of cancers. Proteomics 2006; 6(20): 5662-73. PMID: 16991194.
Omenn GS, Paik YK, Speicher D. The HUPO Plasma Proteome Project: a report from the Munich congress. Proteomics 2006; 6(1): 9-11. PMID: 16400715.
Scott LJ, Bonnycastle LL, Willer CJ, Sprau AG, Jackson AU, Narisu N, Duren WL, Chines PS, Stringham HM, Erdos MR, Valle TT, Tuomilehto J, Bergman RN, Mohlke KL, Collins FS, Boehnke M. Association of transcription factor 7-like 2 (TCF7L2) variants with type 2 diabetes in a Finnish sample. Diabetes 2006; 55(9): 2649-53. PMID: 16936217.
States DJ, Omenn GS, Blackwell TW, Fermin D, Eng J, Speicher DW, Hanash SM. Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nat Biotechnol 2006; 24(3): 333-8. PMID: 16525410.
Tomlins SA, Chinnaiyan AM. Of mice and men: cancer gene discovery using comparative oncogenomics. Cancer Cell 2006; 10(1): 2-4. PMID: 16843259.
Tomlins SA, Mehra R, Rhodes DR, Smith LR, Roulston D, Helgeson BE, Cao X, Wei JT, Rubin MA, Shah RB, Chinnaiyan AM. TMPRSS2:ETV4 gene fusions define a third molecular subtype of prostate cancer. Cancer Res 2006; 66(7): 3396-400. PMID: 16585160.
Wang P, Dai M, Xuan W, McEachin RC, Jackson AU, Scott LJ, Athey B, Watson SJ, Meng F. SNP Function Portal: a web database for exploring the function implication of SNP alleles. Bioinformatics 2006; 22(14): e523-9. PMID: 16873516.
Willer CJ, Scott LJ, Bonnycastle LL, Jackson AU, Chines P, Pruim R, Bark CW, Tsai YY, Pugh EW, Doheny KF, Kinnunen L, Mohlke KL, Valle TT, Bergman RN, Tuomilehto J, Collins FS, Boehnke M. Tag SNP selection for Finnish individuals based on the CEPH Utah HapMap database. Genet Epidemiol 2006; 30(2): 180-90. PMID: 16374835.
Dai M, Wang P, Boyd AD, Kostov G, Athey B, Jones EG, Bunney WE, Myers RM, Speed TP, Akil H, Watson SJ, Meng F. Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res 2005; 33(20): e175. PMID: 16284200.
Gao WM, Kuick R, Orchekowski RP, Misek DE, Qiu J, Greenberg AK, Rom WN, Brenner DE, Omenn GS, Haab BB, Hanash SM. Distinctive serum protein profiles involving abundant proteins in lung cancer patients based upon antibody microarray analysis. BMC Cancer 2005; 5(): 110. PMID: 16117833.
Kim YJ, Boyd A, Athey BD, Patel JM. miBLAST: scalable evaluation of a batch of nucleotide sequence queries with BLAST. Nucleic Acids Res 2005; 33(13): 4335-44. PMID: 16061938.
Lin B, White JT, Lu W, Xie T, Utleg AG, Yan X, Yi EC, Shannon P, Khrebtukova I, Lange PH, Goodlett DR, Zhou D, Vasicek TJ, Hood L. Evidence for the presence of disease-perturbed networks in prostate cancer cells by genomic and proteomic analyses: a systems approach to disease. Cancer Res 2005; 65(8): 3081-91. PMID: 15833837.
Mohlke KL, Jackson AU, Scott LJ, Peck EC, Suh YD, Chines PS, Watanabe RM, Buchanan TA, Conneely KN, Erdos MR, Narisu N, Enloe S, Valle TT, Tuomilehto J, Bergman RN, Boehnke M, Collins FS. Mitochondrial polymorphisms and susceptibility to type 2 diabetes-related traits in Finns. Hum Genet 2005; 118(2): 245-54. PMID: 16142453.
Tomlins SA, Rhodes DR, Perner S, Dhanasekaran SM, Mehra R, Sun XW, Varambally S, Cao X, Tchinda J, Kuefer R, Lee C, Montie JE, Shah RB, Pienta KJ, Rubin MA, Chinnaiyan AM. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 2005; 310(5748): 644-8. PMID: 16254181.
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