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170 total publications
click field to sort (view as table)Athey BD, Cavalcoli JD, Jagadish HV, Omenn GS, Mirel B, Kretzler M, Burant C, Isokpehi RD, DeLisi C; NCIBI faculty, trainees, and staff. The NIH National Center for Integrative Biomedical Informatics (NCIBI) J Am Med Inform Assoc 2012; 19(2): 166-70. PMID: 22101971.
Bai, Y, Sartor M, Cavalcoli J. Current status and future perspectives for sequencing livestock genomes Journal of Animal Science and Biotechnology 2012; 3(8):
Brandenburg MD, Song J. Broadening Instructional Scope with Network Visualization Journal of the Medical Library Association (In Press) 2012;
Farfan F, Jun M, Sartor MA, Michailidis G, Jagadish HV, THINK Back: Knowledge-based Interpretation of High Throughput Data BMC Bioinformatics 2012; 13(Supp 2): S4. PMID: 22536867.
Karnovsky A, Weymouth T, Hull T, Tarcea VG, Scardoni G, Laudanna C, Sartor A, Stringer KA, Jagadish HV, Burant C, Athey B, Omenn GS. Metscape 2 Bioinformatics Tool for the Analysis and Visualization of Metabolomics and Gene Expression Data Bioinformatics 2012; 28(10): 373-80. PMID: 22135418.
Keller BJ, Eichinger F, Kretzler M. Formal concept analysis of disease similarity 2012 AMIA Summit on Translational Bioinformatics 2012; PMID: 22779049.
Keller BJ, Martini S, Sedor JR, Kretzler M. A systems view of genetics in chronic kidney disease. Kidney International 2012; 81(1): 14-21.
Kim JH, Karnovsky A, Mahavisno V, Weymouth T, Pande M, Dolinoy DC, Rozek LS, Sartor MA. LRpath analysis reveals common pathways dysregulated via DNA methylation across cancer types BMC Genomics 2012; 13(1): 526. PMID: 23033966.
Sartor MA, Ade A, Wright Z, States D, Omenn GS, Athey B and Karnovsky A. Metab2MeSH: Annotating Compounds with Medical Subject Headings (MeSH) Bioinformatics 2012; 28(10): 1408-10. PMID: 22492643.
Shaverdian A, Zhou H, Michailidis G, Jagadish HV. A Graph Algebra for Scalable Visual Analytics IEEE Computer Graphics and Applications's Special Issue - Extreme-Scale Visual Analytics 2012;
Abu-Jbara A, Radev D. Clairlib: A toolkit for Natural Language Processing, Information Retrieval, and Network Analysis ACL HLT 2011 2011; 121-126.
Alvarez A, Woolf PJ. Partially observed bipartite network analysis to identify predictive connections in transcriptional regulatory networks. BMC Syst Biol 2011; 5 86. PMID: 21619639.
Alvarez A, Woolf PJ. RegNetB: predicting relevant regulator-gene relationships in localized prostate tumor samples. BMC Bioinformatics 2011; 12 243. PMID: 21682879.
Farrah T, Deutsch EW, Omenn GS, Campbell DS, Sun Z, Bletz JA, Mallick P, Katz JE, Malmström J, Ossola R, Watts JD, Lin B, Zhang H, Moritz RL, Aebersold R. A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Mol Cell Proteomics 2011; 10(9): M110.006353. PMID: 21632744.
Hur J, Sullivan KA, Pande M, Hong Y, Sima AA, Jagadish HV, Kretzler M, Feldman EL. The identification of gene expression profiles associated with progression of human diabetic neuropathy. Brain 2011; (134): 3222-35. PMID: 21926103.
Hur J, Xiang Z, Feldman EL, He Y. Ontology-based Brucella vaccine literature indexing and systematic analysis of gene-vaccine association network. BMC Immunol 2011; 12 49. PMID: 21871085.
Jafar-Mohammadi B, Groves CJ, Gjesing AP, Herrera BM, Winckler W, Stringham HM, Morris AP, Lauritzen T, Doney AS, Morris AD, Weedon MN, Swift AJ, Kuusisto J, Laakso M, Altshuler D, Hattersley AT, Collins FS, Boehnke M, Hansen T, Pedersen O, Palmer CN, Frayling TM, DIAGRAM Consortium, Gloyn AL, McCarthy MI. A role for coding functional variants in HNF4A in type 2 diabetes susceptibility. Diabetologia 2011; 54(1): 111-9. PMID: 20878384.
Jha, Rahul and Radev, Dragomir R. An unsupervised method for learning probabilistic 1st order logic models from unstructured clinical text. ICML Workshop on Learning from Unstructured Clinical Text 2011;
Kano Y, Björne J, Ginter F, Salakoski T, Buyko E, Hahn U, Cohen KB, Verspoor K, Roeder C, Hunter LE, Kilicoglu H, Bergler S, Van Landeghem S, Van Parys T, Van de Peer Y, Miwa M, Ananiadou S, Neves M, Pascual-Montano A, Özgür A, Radev DR, Riedel S, Sætre R, Chun HW, Kim JD, Pyysalo S, Ohta T, Tsujii J. U-Compare bio-event meta-service: compatible BioNLP event extraction services BMC Bioinformatics 2011; (12): 481. PMID: 22177292.
Kim JH, Dhanasekaran SM, Prensner JR, Cao X, Robinson D, Kalyana-Sundaram S, Huang C, Shankar S, Jing X, Iyer M, Hu M, Sam L, Grasso C, Maher CA, Palanisamy N, Mehra R, Kominsky HD, Siddiqui J, Yu J, Qin ZS, Chinnaiyan AM. Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer. Genome Res 2011; 21(7): 1028-41. PMID: 21724842.
Luo W, Friedman MS, Hankenson KD, Woolf PJ. Time series gene expression profiling and temporal regulatory pathway analysis of BMP6 induced osteoblast differentiation and mineralization. BMC Syst Biol 2011; 5 82. PMID: 21605425.
Ma J, Sartor MA, Jagadish HV. Appearance frequency modulated gene set enrichment testing. BMC Bioinformatics 2011; 12 81. PMID: 21418606.
Menon R, Omenn GS. Identification of alternatively spliced transcripts using a proteomic informatics approach. Data Mining in Proteomics: From Standards to Applications. Methods Mol Biol. 2011; (696): 319-326. PMID: 21063957.
Menon R, Roy A, Mukherjee S, Belkin S, Zhang Y, Omenn GS. Functional implications of structural predictions for alternative splice proteins expressed in Her2/neu-induced breast cancers J Proteome Res 2011; 10(12): 5503-11. PMID: 22003824.
Omenn GS. Data management and data integration in the HUPO Plasma Proteome Project. Data Mining in Proteomics: From Standards to Applications. Methods Mol Biol. 2011; (696): 247-257. PMID: 21063952.
Ozgür A, Xiang Z, Radev DR, He Y. Mining of vaccine-associated IFN-gamma gene interaction networks using the Vaccine Ontology J Biomed Semantics 2011; (2): S8. PMID: 21624163.
Pande M, Hur J, Hong Y, Backus C, Hayes JM, Oh SS, Kretzler M, Feldman EL. Transcriptional profiling of diabetic neuropathy in the BKS db/db mouse: a model of type 2 diabetes. Diabetes 2011; 60(7): 1981-9. PMID: 21617178.
Tenenbaum JD, Whetzel PL, Anderson K, Borromeo CD, Dinov ID, Gabriel D, Kirschner B, Mirel B, Morris T, Noy N, Nyulas C, Rubenson D, Saxman PR, Singh H, Whelan N, Wright Z, Athey BD, Becich MJ, Ginsburg GS, Musen MA, Smith KA, Tarantal AF, Rubin DL, Lyster P. The Biomedical Resource Ontology (BRO) to enable resource discovery in clinical and translational research. J Biomed Inform 2011; 44(1): 137-45. PMID: 20955817.
Wang XS, Shankar S, Dhanasekaran SM, Ateeq B, Sasaki AT, Jing X, Robinson D, Cao Q, Prensner JR, Yocum AK, Wang R, Fries DF, Han B, Asangani IA, Li Y, Omenn GS, Pflueger D, Gopalan A, Reuter VE, Kahoud ER, Cantley LC, Rubin MA, Palanisami N, Varambally S, Chinnaiyan AM. Characterization of KRAS rearrangements in metastatic prostate cancer. Cancer Discovery 2011; 1(1):
Yan X, Ma L, Yi D, Yoon JG, Diercks A, Foltz G, Price ND, Hood LE, Tian Q. A CD133-related gene expression signature identifies an aggressive glioblastoma subtype with excessive mutations. Proc Natl Acad Sci U S A 2011; 108(4): 1591-6. PMID: 21220328.
Ajay SS, Athey BD, Lee I. Unified translation repression mechanism for microRNAs and upstream AUGs. BMC Genomics 2010; 11 155. PMID: 20205738.
Boggy GJ, Woolf PJ. A mechanistic model of PCR for accurate quantification of quantitative PCR data. PLoS One 2010; 5(8): e12355. PMID: 20814578.
Buckner J, Wilson J, Seligman M, Athey B, Watson S, Meng F. The gputools package enables GPU computing in R. Bioinformatics 2010; 26(1): 134-5. PMID: 19850754.
Chapman A, Jagadish HV, Understanding provenance black boxes. Distributed and Parallel Databases 2010; 27(2): 139-167.
Dai M, Thompson RC, Maher C, Contreras-Galindo R, Kaplan MH, Markovitz DM, Omenn G, Meng F. NGSQC: cross-platform quality analysis pipeline for deep sequencing data. BMC Genomics 2010; 11 Suppl 4 S7. PMID: 21143816.
Gao J, Tarcea VG, Karnovsky A, Mirel BR, Weymouth TE, Beecher CW, Cavalcoli JD, Athey BD, Omenn GS, Burant CF, Jagadish HV. Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks. Bioinformatics 2010; 26(7): 971-3. PMID: 20139469.
Hill JA, Smith BE, Papoulias PG, Andrews PC. ProteomeCommons.org collaborative annotation and project management resource integrated with the Tranche repository. J Proteome Res 2010; 9(6): 2809-11. PMID: 20356086.
Hodges AP, Dai D, Xiang Z, Woolf P, Xi C, He Y. Bayesian network expansion identifies new ROS and biofilm regulators. PLoS One 2010; 5(3): e9513. PMID: 20209085.
Hodges AP, Woolf P, He Y. BN+1 bayesian network expansion for identifying molecular pathway elements. Communicative & Integrative Biology 2010; 3(6):
Hodgin JB, Borczuk AC, Nasr SH, Markowitz GS, Nair V, Martini S, Eichinger F, Vining C, Berthier CC, Kretzler M, D'Agati VD. A molecular profile of focal segmental glomerulosclerosis from formalin-fixed, paraffin-embedded tissue. Am J Pathol 2010; 177(4): 1674-86. PMID: 20847290.
Hodgin JB, Cohen CD. Experimental approaches to the human renal transcriptome. Semin Nephrol 2010; 30(5): 455-67. PMID: 21044757.
Hur J, Sullivan KA, Schuyler AD, Hong Y, Pande M, States DJ, Jagadish HV, Feldman EL. Literature-based discovery of diabetes- and ROS-related targets. BMC Med Genomics 2010; 3 49. PMID: 20979611.
Keller B, Martini S, Sedor J, Kretzler M. Linking variants from genome-wide association analysis to function via transcriptional network analysis. Semin Nephrol 2010; 30(2): 177-84. PMID: 20347646.
McEachin RC, Chen H, Sartor MA, Saccone SF, Keller BJ, Prossin AR, Cavalcoli JD, McInnis MG. A genetic network model of cellular responses to lithium treatment and cocaine abuse in bipolar disorder. BMC Syst Biol 2010; 4 158. PMID: 21092101.
McEachin RC, Saccone NL, Saccone SF, Kleyman-Smith YD, Kar T, Kare RK, Ade AS, Sartor MA, Cavalcoli JD, McInnis MG. Modeling complex genetic and environmental influences on comorbid bipolar disorder with tobacco use disorder. BMC Med Genet 2010; 11 14. PMID: 20102619.
Menon R, Omenn GS. Proteomic characterization of novel alternative splice variant proteins in human epidermal growth factor receptor 2/neu-induced breast cancers. Cancer Res 2010; 70(9): 3440-9. PMID: 20388783.
Mo F, Mo Q, Chen Y, Goodlett DR, Hood L, Omenn GS, Li S, Lin B. WaveletQuant, an improved quantification software based on wavelet signal threshold de-noising for labeled quantitative proteomic analysis. BMC Bioinformatics 2010; 11 219. PMID: 20429928.
Omenn GS. Bioinformatics and systems biology of cancers. Progress in Molecular Biology and Translational Science 2010; (95): 159-192. PMID: 21075332.
Ozgür A, Xiang Z, Radev DR, He Y. Literature-based discovery of IFN-gamma and vaccine-mediated gene interaction networks. J Biomed Biotechnol 2010; 2010 426479. PMID: 20625487.
Perry JR, Weedon MN, Langenberg C, Jackson AU, Lyssenko V, Sparsø T, Thorleifsson G, Grallert H, Ferrucci L, Maggio M, Paolisso G, Walker M, Palmer CN, Payne F, Young E, Herder C, Narisu N, Morken MA, Bonnycastle LL, Owen KR, Shields B, Knight B, Bennett A, Groves CJ, Ruokonen A, Jarvelin MR, Pearson E, Pascoe L, Ferrannini E, Bornstein SR, Stringham HM, Scott LJ, Kuusisto J, Nilsson P, Neptin M, Gjesing AP, Pisinger C, Lauritzen T, Sandbaek A, Sampson M, MAGIC, Zeggini E, Lindgren CM, Steinthorsdottir V, Thorsteinsdottir U, Hansen T, Schwarz P, Illig T, Laakso M, Stefansson K, Morris AD, Groop L, Pedersen O, Boehnke M, Barroso I, Wareham NJ, Hattersley AT, McCarthy MI, Frayling TM. Genetic evidence that raised sex hormone binding globulin (SHBG) levels reduce the risk of type 2 diabetes. Hum Mol Genet 2010; 19(3): 535-44. PMID: 19933169.
Sartor MA, Mahavisno V, Keshamouni VG, Cavalcoli J, Wright Z, Karnovsky A, Kuick R, Jagadish HV, Mirel B, Weymouth T, Athey B, Omenn GS. ConceptGen: a gene set enrichment and gene set relation mapping tool. Bioinformatics 2010; 26(4): 456-63. PMID: 20007254.
Saxena R, Hivert MF, Langenberg C, Tanaka T, Pankow JS, Vollenweider P, Lyssenko V, Bouatia-Naji N, Dupuis J, Jackson AU, Kao WH, Li M, Glazer NL, Manning AK, Luan J, Stringham HM, Prokopenko I, Johnson T, Grarup N, Boesgaard TW, Lecoeur C, Shrader P, O'Connell J, Ingelsson E, Couper DJ, Rice K, Song K, Andreasen CH, Dina C, Köttgen A, Le Bacquer O, Pattou F, Taneera J, Steinthorsdottir V, Rybin D, Ardlie K, Sampson M, Qi L, van Hoek M, Weedon MN, Aulchenko YS, Voight BF, Grallert H, Balkau B, Bergman RN, Bielinski SJ, Bonnefond A, Bonnycastle LL, Borch-Johnsen K, Böttcher Y, Brunner E, Buchanan TA, Bumpstead SJ, Cavalcanti-Proença C, Charpentier G, Chen YD, Chines PS, Collins FS, Cornelis M, J Crawford G, Delplanque J, Doney A, Egan JM, Erdos MR, Firmann M, Forouhi NG, Fox CS, Goodarzi MO, Graessler J, Hingorani A, Isomaa B, Jørgensen T, Kivimaki M, Kovacs P, Krohn K, Kumari M, Lauritzen T, Lévy-Marchal C, Mayor V, McAteer JB, Meyre D, Mitchell BD, Mohlke KL, Morken MA, Narisu N, Palmer CN, Pakyz R, Pascoe L, Payne F, Pearson D, Rathmann W, Sandbaek A, Sayer AA, Scott LJ, Sharp SJ, Sijbrands E, Singleton A, Siscovick DS, Smith NL, Sparsø T, Swift AJ, Syddall H, Thorleifsson G, Tönjes A, Tuomi T, Tuomilehto J, Valle TT, Waeber G, Walley A, Waterworth DM, Zeggini E, Zhao JH, GIANT consortium, MAGIC investigators, Illig T, Wichmann HE, Wilson JF, van Duijn C, Hu FB, Morris AD, Frayling TM, Hattersley AT, Thorsteinsdottir U, Stefansson K, Nilsson P, Syvänen AC, Shuldiner AR, Walker M, Bornstein SR, Schwarz P, Williams GH, Nathan DM, Kuusisto J, Laakso M, Cooper C, Marmot M, Ferrucci L, Mooser V, Stumvoll M, Loos RJ, Altshuler D, Psaty BM, Rotter JI, Boerwinkle E, Hansen T, Pedersen O, Florez JC, McCarthy MI, Boehnke M, Barroso I, Sladek R, Froguel P, Meigs JB, Groop L, Wareham NJ, Watanabe RM. Genetic variation in GIPR influences the glucose and insulin responses to an oral glucose challenge. Nat Genet 2010; 42(2): 142-8. PMID: 20081857.
Su G, Athey BD, Meng F. GSearcher: agile attribute querying for biological networks. Bioinformatics 2010; 26(24): 3138-9. PMID: 21088028.
Su G, Kuchinsky A, Morris JH, States DJ, Meng F. GLay: community structure analysis of biological networks. Bioinformatics 2010; 26(24): 3135-7. PMID: 21123224.
Voight BF, Scott LJ, Steinthorsdottir V, Morris AP, Dina C, Welch RP, Zeggini E, Huth C, Aulchenko YS, Thorleifsson G, McCulloch LJ, Ferreira T, Grallert H, Amin N, Wu G, Willer CJ, Raychaudhuri S, McCarroll SA, Langenberg C, Hofmann OM, Dupuis J, Qi L, Segrè AV, van Hoek M, Navarro P, Ardlie K, Balkau B, Benediktsson R, Bennett AJ, Blagieva R, Boerwinkle E, Bonnycastle LL, Bengtsson Boström K, Bravenboer B, Bumpstead S, Burtt NP, Charpentier G, Chines PS, Cornelis M, Couper DJ, Crawford G, Doney AS, Elliott KS, Elliott AL, Erdos MR, Fox CS, Franklin CS, Ganser M, Gieger C, Grarup N, Green T, Griffin S, Groves CJ, Guiducci C, Hadjadj S, Hassanali N, Herder C, Isomaa B, Jackson AU, Johnson PR, Jørgensen T, Kao WH, Klopp N, Kong A, Kraft P, Kuusisto J, Lauritzen T, Li M, Lieverse A, Lindgren CM, Lyssenko V, Marre M, Meitinger T, Midthjell K, Morken MA, Narisu N, Nilsson P, Owen KR, Payne F, Perry JR, Petersen AK, Platou C, Proença C, Prokopenko I, Rathmann W, Rayner NW, Robertson NR, Rocheleau G, Roden M, Sampson MJ, Saxena R, Shields BM, Shrader P, Sigurdsson G, Sparsø T, Strassburger K, Stringham HM, Sun Q, Swift AJ, Thorand B, Tichet J, Tuomi T, van Dam RM, van Haeften TW, van Herpt T, van Vliet-Ostaptchouk JV, Walters GB, Weedon MN, Wijmenga C, Witteman J, Bergman RN, Cauchi S, Collins FS, Gloyn AL, Gyllensten U, Hansen T, Hide WA, Hitman GA, Hofman A, Hunter DJ, Hveem K, Laakso M, Mohlke KL, Morris AD, Palmer CN, Pramstaller PP, Rudan I, Sijbrands E, Stein LD, Tuomilehto J, Uitterlinden A, Walker M, Wareham NJ, Watanabe RM, Abecasis GR, Boehm BO, Campbell H, Daly MJ, Hattersley AT, Hu FB, Meigs JB, Pankow JS, Pedersen O, Wichmann HE, Barroso I, Florez JC, Frayling TM, Groop L, Sladek R, Thorsteinsdottir U, Wilson JF, Illig T, Froguel P, van Duijn CM, Stefansson K, Altshuler D, Boehnke M, McCarthy MI, MAGIC investigators, GIANT Consortium. Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Nat Genet 2010; 42(7): 579-89. PMID: 20581827.
Watanabe RM. The genetics of insulin resistance: Where's Waldo? Curr Diab Rep 2010; 10(6): 476-84. PMID: 20820957.
Xuan W, Dai M, Buckner J, Mirel B, Song J, Athey B, Watson SJ, Meng F. Cross-domain neurobiology data integration and exploration. BMC Genomics 2010; 11 Suppl 3 S6. PMID: 21143788.
Zhang J, Jagadish HV. Lost Source Provenance. ACM International Conference Proceeding Series; Proceedings of the 13th International Conference on Extending Database Technology 2010; 426
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.
Chen H, Wang N, Burmeister M, McInnis MG. MicroRNA expression changes in lymphoblastoid cell lines in response to lithium treatment. Int J Neuropsychopharmacol 2009; 12(7): 975-81. PMID: 19254429.
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.
Nandi A. Qunits: Queried units for database search CIDR 2009 - 4th Biennal Conference on Innovative Data Systems Research 2009;
Newton-Cheh C, Johnson T, Gateva V, Tobin MD, Bochud M, Coin L, Najjar SS, Zhao JH, Heath SC, Eyheramendy S, Papadakis K, Voight BF, Scott LJ, Zhang F, Farrall M, Tanaka T, Wallace C, Chambers JC, Khaw KT, Nilsson P, van der Harst P, Polidoro S, Grobbee DE, Onland-Moret NC, Bots ML, Wain LV, Elliott KS, Teumer A, Luan J, Lucas G, Kuusisto J, Burton PR, Hadley D, McArdle WL, Wellcome Trust Case Control Consortium, Brown M, Dominiczak A, Newhouse SJ, Samani NJ, Webster J, Zeggini E, Beckmann JS, Bergmann S, Lim N, Song K, Vollenweider P, Waeber G, Waterworth DM, Yuan X, Groop L, Orho-Melander M, Allione A, Di Gregorio A, Guarrera S, Panico S, Ricceri F, Romanazzi V, Sacerdote C, Vineis P, Barroso I, Sandhu MS, Luben RN, Crawford GJ, Jousilahti P, Perola M, Boehnke M, Bonnycastle LL, Collins FS, Jackson AU, Mohlke KL, Stringham HM, Valle TT, Willer CJ, Bergman RN, Morken MA, Döring A, Gieger C, Illig T, Meitinger T, Org E, Pfeufer A, Wichmann HE, Kathiresan S, Marrugat J, O'Donnell CJ, Schwartz SM, Siscovick DS, Subirana I, Freimer NB, Hartikainen AL, McCarthy MI, O'Reilly PF, Peltonen L, Pouta A, de Jong PE, Snieder H, van Gilst WH, Clarke R, Goel A, Hamsten A, Peden JF, Seedorf U, Syvänen AC, Tognoni G, Lakatta EG, Sanna S, Scheet P, Schlessinger D, Scuteri A, Dörr M, Ernst F, Felix SB, Homuth G, Lorbeer R, Reffelmann T, Rettig R, Völker U, Galan P, Gut IG, Hercberg S, Lathrop GM, Zelenika D, Deloukas P, Soranzo N, Williams FM, Zhai G, Salomaa V, Laakso M, Elosua R, Forouhi NG, Völzke H, Uiterwaal CS, van der Schouw YT, Numans ME, Matullo G, Navis G, Berglund G, Bingham SA, Kooner JS, Connell JM, Bandinelli S, Ferrucci L, Watkins H, Spector TD, Tuomilehto J, Altshuler D, Strachan DP, Laan M, Meneton P, Wareham NJ, Uda M, Jarvelin MR, Mooser V, Melander O, Loos RJ, Elliott P, Abecasis GR, Caulfield M, Munroe PB. Genome-wide association study identifies eight loci associated with blood pressure. Nat Genet 2009; 41(6): 666-76. PMID: 19430483.
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.
Shah A, Tenzen T, McMahon AP, Woolf PJ. Using mechanistic Bayesian networks to identify downstream targets of the sonic hedgehog pathway. BMC Bioinformatics 2009; 10 433. PMID: 20021670.
States DJ, Ade AS, Wright ZC, Bookvich AV, Athey BD. MiSearch adaptive pubMed search tool. Bioinformatics 2009; 25(7): 974-6. PMID: 18326507.
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Xiang Z, Todd T, Ku KP, Kovacic BL, Larson CB, Chen F, Hodges AP, Tian Y, Olenzek EA, Zhao B, Colby LA, Rush HG, Gilsdorf JR, Jourdian GW, He Y. VIOLIN: vaccine investigation and online information network. Nucleic Acids Res 2008; 36(Database issue): D923-8. PMID: 18025042.
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