Publications

  1. Baheti S, Singh P, Zhang Y, Evans J, Jensen MD, Somers VK, Kocher JA, Sun Z, Chakkera HA. Adipose tissue DNA methylome changes in development of new-onset diabetes after kidney transplantation. Epigenomics. 2017 Nov; 9 (11):1423-1435 Epub 2017 Oct 02
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  2. Sun Z, Nair A, Chen X, Prodduturi N, Wang J, Kocher JP. UClncR: Ultrafast and comprehensive long non-coding RNA detection from RNA-seq. Sci Rep. 2017 Oct 27; 7 (1):14196
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  3. Druliner BR, Ruan X, Sicotte H, O'Brien D, Liu H, Kocher JA, Boardman L. Early genetic aberrations in patients with sporadic colorectal cancer. Mol Carcinog. 2017 Sep 19 Epub 2017 Sept 19
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  4. Yip SH, Wang P, Kocher JA, Sham PC, Wang J. Linnorm: improved statistical analysis for single cell RNA-seq expression data. Nucleic Acids Res. 2017 Sep 18 Epub 2017 Sept 18
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  5. Davila JI, Starr JS, Attia S, Wang C, Knudson RA, Necela BM, Sarangi V, Sun Z, Ren Y, Casler JD, Menke DM, Oliver GR, Joseph RW, Copland JA, Parker AS, Kocher JA, Thompson EA, Smallridge RC, Asmann YW. Comprehensive Genomic Profiling of a Rare Thyroid Follicular Dendritic Cell Sarcoma. Rare Tumors. 2017 Jul 03; 9 (2):6834 Epub 2017 Sept 15
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  6. Goetz MP, Kalari KR, Suman VJ, Moyer AM, Yu J, Visscher DW, Dockter TJ, Vedell PT, Sinnwell JP, Tang X, Thompson KJ, McLaughlin SA, Moreno-Aspitia A, Copland JA, Northfelt DW, Gray RJ, Hunt K, Conners A, Sicotte H, Eckel-Passow JE, Kocher JP, Ingle JN, Ellingson MS, McDonough M, Wieben ED, Weinshilboum R, Wang L, Boughey JC. Tumor Sequencing and Patient-Derived Xenografts in the Neoadjuvant Treatment of Breast Cancer. J Natl Cancer Inst. 2017 Jul 01; 109 (7)
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  7. Farshidfar F, Zheng S, Gingras MC, Newton Y, Shih J, Robertson AG, Hinoue T, Hoadley KA, Gibb EA, Roszik J, Covington KR, Wu CC, Shinbrot E, Stransky N, Hegde A, Yang JD, Reznik E, Sadeghi S, Pedamallu CS, Ojesina AI, Hess JM, Auman JT, Rhie SK, Bowlby R, Borad MJ, Zhu AX, Stuart JM, Sander C, Akbani R, Cherniack AD, Deshpande V, Mounajjed T, Foo WC, Torbenson MS, Kleiner DE, Laird PW, Wheeler DA, McRee AJ, Bathe OF, Andersen JB, Bardeesy N, Roberts LR, Kwong LN, Cancer Genome Atlas Network. Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles. Cell Rep. 2017 Jun 27; 19 (13):2878-2880
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  8. Adrian Ally, Miruna Balasundaram, Rebecca Carlsen, Eric Chuah, Amanda Clarke, Noreen Dhalla, Robert A. Holt, Steven J.M. Jones, Darlene Lee, Yussanne Ma, Marco A. Marra, Michael Mayo, Richard A. Moore, Andrew J. Mungall, Jacqueline E. Schein, Payal Sipahimalani, Angela Tam, Nina Thiessen, Dorothy Cheung, Tina Wong, Denise Brooks, A. Gordon Robertson, Reanne Bowlby, Karen Mungall, Sara Sadeghi, Liu Xi, Kyle Covington, Eve Shinbrot, David A. Wheeler, Richard A. Gibbs, Lawrence A. Donehower, Linghua Wang, Jay Bowen, Julie M. Gastier-Foster, Mark Gerken, Carmen Helsel, Kristen M. Leraas, Tara M. Lichtenberg, Nilsa C. Ramirez, Lisa Wise, Erik Zmuda, Stacey B. Gabriel, Matthew Meyerson, Carrie Cibulskis, Bradley A. Murray, Juliann Shih, Rameen Beroukhim, Andrew D. Cherniack, Steven E. Schumacher, Gordon Saksena, Chandra Sekhar Pedamallu, Lynda Chin, Gad Getz, Michael Noble, Hailei Zhang, David Heiman, Juok Cho, Nils Gehlenborg, Gordon Saksena, Douglas Voet, Pei Lin, Scott Frazer, Timothy Defreitas, Sam Meier, Michael Lawrence, Jaegil Kim, Chad J. Creighton, Donna Muzny, HarshaVardhan Doddapaneni, Jianhong Hu, Min Wang, Donna Morton, Viktoriya Korchina, Yi Han, Huyen Dinh, Lora Lewis, Michelle Bellair, Xiuping Liu, Jireh Santibanez, Robert Glenn, Sandra Lee, Walker Hale, Joel S. Parker, Matthew D. Wilkerson, D. Neil Hayes, Sheila M. Reynolds, Ilya Shmulevich, Wei Zhang, Yuexin Liu, Lisa Iype, Hala Makhlouf, Michael S. Torbenson, Sanjay Kakar, Matthew M. Yeh, David E. Kleiner, Dhanpat Jain, Renumathy Dhanasekaran, Hashem B. El-Serag, Sun Young Yim, John N. Weinstein, Lopa Mishra, Jianping Zhang, Rehan Akbani, Shiyun Ling, Zhenlin Ju, Xiaoping Su, Apurva M. Hegde, Gordon B. Mills, Yiling Lu, Jian Chen, Ju-Seog Lee, Bo Hwa Sohn, Jae Jun Shim, Pan Tong, Hiroyuki Aburatani, Shogo Yamamoto, Kenji Tatsuno, Wei Li, Zheng Xia, Nicolas Stransky, Eric Seiser, Federico Innocenti, Jianjiong Gao, Ritika Kundra, Hongxin Zhang, Zachary Heins, Angelica Ochoa, Chris Sander, Marc Ladanyi, Ronglai Shen, Arshi Arora, Francisco Sanchez-Vega, Nikolaus Schultz, Katayoon Kasaian, Amie Radenbaugh, Karl-Dimiter Bissig, David D. Moore, Yasushi Totoki, Hiromi Nakamura, Tatsuhiro Shibata, Christina Yau, Kiley Graim, Josh Stuart, David Haussler, Betty L. Slagle, Akinyemi I. Ojesina, Panagiotis Katsonis, Amanda Koire, Olivier Lichtarge, Teng-Kuei Hsu, Martin L. Ferguson, John A. Demchok, Ina Felau, Margi Sheth, Roy Tarnuzzer, Zhining Wang, Liming Yang, Jean C. Zenklusen, Jiashan Zhang, Carolyn M. Hutter, Heidi J. Sofia, Roel G.W. Verhaak, Siyuan Zheng, Frederick Lang, Sudha Chudamani, Jia Liu, Laxmi Lolla, Ye Wu, Rashi Naresh, Todd Pihl, Charlie Sun, Yunhu Wan, Christopher Benz, Amy H. Perou, Leigh B. Thorne, Lori Boice, Mei Huang, W. Kimryn Rathmell, Houtan Noushmehr, Fabiano Pinto Saggioro, Daniela Pretti da Cunha Tirapelli, Carlos Gilberto Carlotti Junior, Enio David Mente, Orlando de Castro Silva Jr., Felipe Amstalden Trevisan, Koo Jeong Kang, Keun Soo Ahn, Nasra H. Giama, Catherine D. Moser, Thomas J. Giordano, Michelle Vinco, Theodore H. Welling, Daniel Crain, Erin Curley, Johanna Gardner, David Mallery, Scott Morris, Joseph Paulauskis, Robert Penny, Candace Shelton, Troy Shelton, Robin K. Kelley, Joong-Won Park, Vishal S. Chandan, Lewis R. Roberts, Oliver F. Bathe, Curt H. Hagedorn, J. Todd Auman, Daniel R. O'Brien, Jean-Pierre A. Kocher, Corbin D. Jones, Piotr A. Mieczkowski, Charles M. Perou, Tara Skelly, Donghui Tan, Umadevi Veluvolu, Saianand Balu, Tom Bodenheimer, Alan P. Hoyle, Stuart R. Jefferys, Shaowu Meng, Lisle E. Mose, Yan Shi, Janae V. Simons, Matthew G. Soloway, Jeffrey Roach, Katherine A. Hoadley, Stephen B. Baylin, Hui Shen, Toshinori Hinoue, Moiz S. Bootwalla, David J. Van Den Berg, Daniel J. Weisenberger, Phillip H. Lai, Andrea Holbrook, Mario Berrios, and Peter W. Laird. Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma Cell.2017;
  9. Li MJ, Zhang J, Liang Q, Xuan C, Wu J, Jiang P, Li W, Zhu Y, Wang P, Fernandez D, Shen Y, Chen Y, Kocher JA, Yu Y, Sham PC, Wang J, Liu JS, Liu XS. Exploring genetic associations with ceRNA regulation in the human genome. Nucleic Acids Res. 2017 Jun 02; 45 (10):5653-5665
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  10. Ye Z, Ma T, Kalmbach MT, Dasari S, Kocher JA, Wang L. CircularLogo: A lightweight web application to visualize intra-motif dependencies. BMC Bioinformatics. 2017 May 22; 18 (1):269
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  11. Li MJ, Yao H, Huang D, Liu H, Liu Z, Xu H, Qin Y, Prinz J, Xia W, Wang P, Yan B, Tran NL, Kocher JP, Sham PC, Wang J. mTCTScan: a comprehensive platform for annotation and prioritization of mutations affecting drug sensitivity in cancers. Nucleic Acids Res. 2017 May 08;
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  12. Bryce AH, Egan JB, Borad MJ, Stewart AK, Nowakowski GS, Chanan-Khan A, Patnaik MM, Ansell SM, Banck MS, Robinson SI, Mansfield AS, Klee EW, Oliver GR, McCormick JB, Huneke NE, Tagtow CM, Jenkins RB, Rumilla KM, Kerr SE, Kocher JA, Beck SA, Fernandez-Zapico ME, Farrugia G, Lazaridis KN, McWilliams RR. Experience with precision genomics and tumor board, indicates frequent target identification, but barriers to delivery. Oncotarget. 2017 Apr 18; 8: (16)27145-27154.
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  13. Li MJ, Li M, Liu Z, Yan B, Pan Z, Huang D, Liang Q, Ying D, Xu F, Yao H, Wang P, Kocher JA, Xia Z, Sham PC, Liu JS, Wang J. cepip: context-dependent epigenomic weighting for prioritization of regulatory variants and disease-associated genes. Genome Biol. 2017 Mar 16; 18: (1)52.
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  14. Nair AA, Niu N, Tang X, Thompson KJ, Wang L, Kocher JP, Subramanian S, Kalari KR. Circular RNAs and their associations with breast cancer subtypes. Oncotarget. 2016 Dec 06; 7 (49):80967-80979
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  15. Pan Z, Wu J, Wang P, Zhu Y, Xia Z, Sham PC, Kocher JP, Li M, Liu JS, Wang J. Predicting regulatory variants with composite statistic. Bioinformatics. 2016 Sep 15; 32: (18)2729-36.
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  16. Sun Z, Bhagwate A, Prodduturi N, Yang P, Kocher JA. Indel detection from RNA-seq data: tool evaluation and strategies for accurate detection of actionable mutations. Brief Bioinform. 2016 Jul 29;
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  17. Ravikumar KE, Wagholikar KB, Li D, Kocher JP, Liu H. Erratum to: Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature. BMC Bioinformatics. 2016 Apr 13; 17:162
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  18. Hart SN, Duffy P, Quest DJ, Hossain A, Meiners MA, Kocher JP. VCF-Miner: GUI-based application for mining variants and annotations stored in VCF files. Brief Bioinform. 2016 Mar; 17: (2)346-51.
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  19. Baheti S, Kanwar R, Goelzenleuchter M, Kocher JP, Beutler AS, Sun Z. Targeted alignment and end repair elimination increase alignment and methylation measure accuracy for reduced representation bisulfite sequencing data. BMC Genomics. 2016 Feb 27; 17: 149.
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  20. Wang L, Nie J, Sicotte H, Li Y, Eckel-Passow JE, Dasari S, Vedell PT, Barman P, Wang L, Weinshiboum R, Jen J, Huang H, Kohli M, Kocher JP. Measure transcript integrity using RNA-seq data. BMC Bioinformatics. 2016 Feb 03; 17:58.
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  21. Chen J, Just AC, Schwartz J, Hou L, Jafari N, Sun Z, Kocher JP, Baccarelli A, Lin X. CpGFilter: model-based CpG probe filtering with replicates for epigenome-wide association studies. Bioinformatics. 2016 Feb 01; 32: (3)469-71.
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  22. Li MJ, Liu Z, Wang P, Wong MP, Nelson MR, Kocher JP, Yeager M, Sham PC, Chanock SJ, Xia Z, Wang J. GWASdb v2: an update database for human genetic variants identified by genome-wide association studies. Nucleic Acids Res. 2016 Jan 4; 44: (D1)D869-76.
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  23. Chen L, Liu H, Kocher JP, Li H, Chen J. glmgraph: an R package for variable selection and predictive modeling of structured genomic data. Bioinformatics. 2015 Dec 15; 31: (24)3991-3.
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  24. Sun Z, Prodduturi N, Sun SY, Thompson EA, Kocher JP. Chromosome X genomic and epigenomic aberrations and clinical implications in breast cancer by base resolution profiling. Epigenomics. 2015 Oct; 7: (7)1099-110.
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  25. Chien J, Sicotte H, Fan JB, Humphray S, Cunningham JM, Kalli KR, Oberg AL, Hart SN, Li Y, Davila JI, Baheti S, Wang C, Dietmann S, Atkinson EJ, Asmann YW, Bell DA, Ota T, Tarabishy Y, Kuang R, Bibikova M, Cheetham RK, Grocock RJ, Swisher EM, Peden J, Bentley D, Kocher JP, Kaufmann SH, Hartmann LC, Shridhar V, Goode EL. TP53 mutations, tetraploidy and homologous recombination repair defects in early stage high-grade serous ovarian cancer. Nucleic Acids Res. 2015 Aug 18; 43: (14)6945-58.
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  26. Sun Z, Cunningham J, Slager S, Kocher JP. Base resolution methylome profiling: considerations in platform selection, data preprocessing and analysis. Epigenomics. 2015 Aug; 7: (5)813-28.
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  27. Ravikumar KE, Wagholikar KB, Li D, Kocher JP, Liu H. Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature. BMC Bioinformatics. 2015 Jun 06; 16:185.
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  28. Wang Y, Cao Y, Yamada S, Thirunavukkarasu M, Nin V, Joshi M, Rishi MT, Bhattacharya S, Camacho-Pereira J, Sharma AK, Shameer K, Kocher JP, Sanchez JA, Wang E, Hoeppner LH, Dutta SK, Leof EB, Shah V, Claffey KP, Chini EN, Simons M, Terzic A, Maulik N, Mukhopadhyay D. Cardiomyopathy and Worsened Ischemic Heart Failure in SM22-alpha Cre-Mediated Neuropilin-1 Null Mice: Dysregulation of PGC1alpha and Mitochondrial Homeostasis. Arterioscler Thromb Vasc Biol. 2015 Jun; 35: (6)1401-12.
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  29. Wang L, Nie JJ, Kocher JP. PVAAS: identify variants associated with aberrant splicing from RNA-seq. Bioinformatics. 2015 May 15; 31: (10)1668-70.
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  30. Du J, Aleff RA, Soragni E, Kalari K, Nie J, Tang X, Davila J, Kocher JP, Patel SV, Gottesfeld JM, Baratz KH, Wieben ED. RNA toxicity and missplicing in the common eye disease fuchs endothelial corneal dystrophy. J Biol Chem. 2015 Mar 06; 290: (10)5979-90.
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  31. Wang L, Huang H, Dougherty G, Zhao Y, Hossain A, Kocher JP. Epidaurus: aggregation and integration analysis of prostate cancer epigenome. Nucleic Acids Res. 2015 Jan; 43: (2)e7.
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  32. Hart SN, Moore RM, Zimmermann MT, Oliver GR, Egan JB, Bryce AH, Kocher JA. PANDA: pathway and annotation explorer for visualizing and interpreting gene-centric data. PeerJ. 2015; 3:e970.
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  33. Champion MD, Hlady RA, Yan H, Evans J, Nie J, Lee JH, Bogenberger J, Nandakumar K, Davila J, Moore R, Nair A, O'Brien D, Zhu YX, Kortum KM, Ordog T, Zhang Z, Joseph RW, Stewart AK, Kocher JP, Jonasch E, Robertson KD, Tibes R, Ho TH. Bioinformatics strategies for identifying regions of epigenetic deregulation associated with aberrant transcript splicing and RNA-editing. BIOINFORMATICS 2015 - 6th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 8th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2015. 2015:163-70.
  34. Tang X, Baheti S, Shameer K, Thompson KJ, Wills Q, Niu N, Holcomb IN, Boutet SC, Ramakrishnan R, Kachergus JM, Kocher JP, Weinshilboum RM, Wang L, Thompson EA, Kalari KR. The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data. Nucleic Acids Res. 2014 Dec 16; 42: (22)e172.
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  35. Wang C, Davila JI, Baheti S, Bhagwate AV, Wang X, Kocher JP, Slager SL, Feldman AL, Novak AJ, Cerhan JR, Thompson EA, Asmann YW. RVboost: RNA-seq variants prioritization using a boosting method. Bioinformatics. 2014 Dec 1; 30: (23)3414-6.
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  36. Wang L, Chen J, Wang C, Uuskula-Reimand L, Chen K, Medina-Rivera A, Young EJ, Zimmermann MT, Yan H, Sun Z, Zhang Y, Wu ST, Huang H, Wilson MD, Kocher JP, Li W. MACE: model based analysis of ChIP-exo. Nucleic Acids Res. 2014 Nov 10; 42: (20)e156.
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  37. Klein CJ, Middha S, Duan X, Wu Y, Litchy WJ, Gu W, Dyck PJ, Gavrilova RH, Smith DI, Kocher JP, Dyck PJ. Application of whole exome sequencing in undiagnosed inherited polyneuropathies. J Neurol Neurosurg Psychiatry. 2014 Nov; 85 (11):1265-72 Epub 2014 Mar 06
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  38. Wang C, Evans JM, Bhagwate AV, Prodduturi N, Sarangi V, Middha M, Sicotte H, Vedell PT, Hart SN, Oliver GR, Kocher JP, Maurer MJ, Novak AJ, Slager SL, Cerhan JR, Asmann YW. PatternCNV: a versatile tool for detecting copy number changes from exome sequencing data. Bioinformatics. 2014 Sep 15; 30: (18)2678-80.
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  39. Wieben ED, Aleff RA, Eckloff BW, Atkinson EJ, Baheti S, Middha S, Brown WL, Patel SV, Kocher JP, Baratz KH. Comprehensive assessment of genetic variants within TCF4 in Fuchs' endothelial corneal dystrophy. Invest Ophthalmol Vis Sci. 2014 Aug 28; 55: (9)6101-7.
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  40. Sun Z, Wu Y, Ordog T, Baheti S, Nie J, Duan X, Hojo K, Kocher JP, Dyck PJ, Klein CJ. Aberrant signature methylome by DNMT1 hot spot mutation in hereditary sensory and autonomic neuropathy 1E. Epigenetics. 2014 Aug; 9: (8)1184-93.
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  41. Kocher JP, Quest DJ, Duffy P, Meiners MA, Moore RM, Rider D, Hossain A, Hart SN, Dinu V. The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation. Bioinformatics. 2014 Jul 1; 30(13):1920-2. Epub 2014 Mar 10.
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  42. Li X, Martinez-Fernandez A, Hartjes KA, Kocher JP, Olson TM, Terzic A, Nelson TJ. Transcriptional atlas of cardiogenesis maps congenital heart disease interactome. Physiol Genomics. 2014 Jul 01; 46: (13)482-95.
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  43. Kalari KR, Nair AA, Bhavsar JD, O'Brien DR, Davila JI, Bockol MA, Nie J, Tang X, Baheti S, Doughty JB, Middha S, Sicotte H, Thompson AE, Asmann YW, Kocher JP. MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing. BMC Bioinformatics. 2014 Jun 27; 15:224.
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  44. Giri K, Shameer K, Zimmermann MT, Saha S, Chakraborty PK, Sharma A, Arvizo RR, Madden BJ, Mccormick DJ, Kocher JP, Bhattacharya R, Mukherjee P. Understanding protein-nanoparticle interaction: a new gateway to disease therapeutics. Bioconjug Chem. 2014 Jun 18; 25: (6)1078-90.
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  45. Dasari S, Theis JD, Vrana JA, Zenka RM, Zimmermann MT, Kocher JP, Highsmith WE Jr, Kurtin PJ, Dogan A. Clinical proteome informatics workbench detects pathogenic mutations in hereditary amyloidoses. J Proteome Res. 2014 May 2; 13(5):2352-8. Epub 2014 Apr 03.
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  46. Zhao H, Sun Z, Wang J, Huang H, Kocher JP, Wang L. CrossMap: a versatile tool for coordinate conversion between genome assemblies. Bioinformatics. 2014 Apr 1; 30(7):1006-7. Epub 2013 Dec 18.
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  47. Sakuma T, Davila JI, Malcolm JA, Kocher JP, Tonne JM, Ikeda Y. Murine leukemia virus uses NXF1 for nuclear export of spliced and unspliced viral transcripts. J Virol. 2014 Apr; 88: (8)4069-82.
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  48. Ansell SM, Hodge LS, Secreto FJ, Manske M, Braggio E, Price-Troska T, Ziesmer S, Li Y, Johnson SH, Hart SN, Kocher JP, Vasmatzis G, Chanan-Kahn A, Gertz M, Fonseca R, Dogan A, Cerhan JR, Novak AJ. Activation of TAK1 by MYD88 L265P drives malignant B-cell Growth in non-Hodgkin lymphoma. Blood Cancer J. 2014 Feb 14; 4:e183.
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  49. Borad MJ, Champion MD, Egan JB, Liang WS, Fonseca R, Bryce AH, McCullough AE, Barrett MT, Hunt K, Patel MD, Young SW, Collins JM, Silva AC, Condjella RM, Block M, McWilliams RR, Lazaridis KN, Klee EW, Bible KC, Harris P, Oliver GR, Bhavsar JD, Nair AA, Middha S, Asmann Y, Kocher JP, Schahl K, Kipp BR, Barr Fritcher EG, Baker A, Aldrich J, Kurdoglu A, Izatt T, Christoforides A, Cherni I, Nasser S, Reiman R, Phillips L, McDonald J, Adkins J, Mastrian SD, Placek P, Watanabe AT, Lobello J, Han H, Von Hoff D, Craig DW, Stewart AK, Carpten JD. Integrated genomic characterization reveals novel, therapeutically relevant drug targets in FGFR and EGFR pathways in sporadic intrahepatic cholangiocarcinoma. PLoS Genet. 2014 Feb; 10: (2)e1004135.
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  50. Middha S, Baheti S, Hart SN, Kocher JP. From days to hours: reporting clinically actionable variants from whole genome sequencing. PLoS One. 2014; 9(2):e86803. Epub 2014 Feb 05.
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  51. Ruan X, Liu H, Boardman L, Kocher JP. Genome-wide analysis of loss of heterozygosity in breast infiltrating ductal carcinoma distant normal tissue highlights arm specific enrichment and expansion across tumor stages. PLoS One. 2014; 9: (4)e95783.
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  52. Sun Z, Evans J, Bhagwate A, Middha S, Bockol M, Yan H, Kocher JP. CAP-miRSeq: a comprehensive analysis pipeline for microRNA sequencing data. BMC Genomics. 2014; 15:423. Epub 2014 Jun 03.
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  53. Yan H, Evans J, Kalmbach M, Moore R, Middha S, Luban S, Wang L, Bhagwate A, Li Y, Sun Z, Chen X, Kocher JP. HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data. BMC Bioinformatics. 2014; 15:280. Epub 2014 Aug 15.
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  54. Jeraldo P, Kalari K, Chen X, Bhavsar J, Mangalam A, White B, Nelson H, Kocher JP, Chia N. IM-TORNADO: a tool for comparison of 16S reads from paired-end libraries. PLoS One. 2014; 9: (12)e114804.
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  55. Hart SN, Therneau TM, Zhang Y, Poland GA, Kocher JP. Calculating sample size estimates for RNA sequencing data. J Comput Biol. 2013 Dec; 20: (12)970-8.
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  56. Reese SE, Archer KJ, Therneau TM, Atkinson EJ, Vachon CM, de Andrade M, Kocher JP, Eckel-Passow JE. A new statistic for identifying batch effects in high-throughput genomic data that uses guided principal component analysis. Bioinformatics. 2013 Nov 15; 29: (22)2877-83.
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  57. Wang L, Park HJ, Dasari S, Wang S, Kocher JP, Li W. CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model. Nucleic Acids Res. 2013 Apr 01; 41: (6)e74.
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  58. Patowary A, Purkanti R, Singh M, Chauhan R, Singh AR, Swarnkar M, Singh N, Pandey V, Torroja C, Clark MD, Kocher JP, Clark KJ, Stemple DL, Klee EW, Ekker SC, Scaria V, Sivasubbu S. A sequence-based variation map of zebrafish. Zebrafish. 2013 Mar; 10: (1)15-20.
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  59. Mahoney DW, Therneau TM, Anderson SK, Jen J, Kocher JP, Reinholz MM, Perez EA, Eckel-Passow JE. Quality assessment metrics for whole genome gene expression profiling of paraffin embedded samples. BMC Res Notes. 2013 Jan 30; 6:33.
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  60. Sun Z, Asmann YW, Nair A, Zhang Y, Wang L, Kalari KR, Bhagwate AV, Baker TR, Carr JM, Kocher JP, Perez EA, Thompson EA. Impact of library preparation on downstream analysis and interpretation of RNA-Seq data: comparison between Illumina PolyA and NuGEN Ovation protocol. PLoS One. 2013; 8(8):e71745. Epub 2013 Aug 19.
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  61. Hart SN, Sarangi V, Moore R, Baheti S, Bhavsar JD, Couch FJ, Kocher JP. SoftSearch: integration of multiple sequence features to identify breakpoints of structural variations. PLoS One. 2013; 8(12):e83356. Epub 2013 Dec 16.
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  62. Sun Z, Baheti S, Middha S, Kanwar R, Zhang Y, Li X, Beutler AS, Klee E, Asmann YW, Thompson EA, Kocher JP. SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing. Bioinformatics. 2012 Aug 15; 28(16):2180-1. Epub 2012 Jun 10.
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  63. Dutta T, Chai HS, Ward LE, Ghosh A, Persson XM, Ford GC, Kudva YC, Sun Z, Asmann YW, Kocher JP, Nair KS. Concordance of changes in metabolic pathways based on plasma metabolomics and skeletal muscle transcriptomics in type 1 diabetes. Diabetes. 2012 May; 61: (5)1004-16.
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  64. Asmann YW, Middha S, Hossain A, Baheti S, Li Y, Chai HS, Sun Z, Duffy PH, Hadad AA, Nair A, Liu X, Zhang Y, Klee EW, Kalari KR, Kocher JP. TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data. Bioinformatics. 2012 Jan 15; 28(2):277-8. Epub 2011 Nov 15.
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  65. Ruan X, Kocher JP, Pommier Y, Liu H, Reinhold WC. Mass homozygotes accumulation in the NCI-60 cancer cell lines as compared to HapMap Trios, and relation to fragile site location. PLoS One. 2012; 7: (2)e31628.
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  66. Arvizo RR, Giri K, Moyano D, Miranda OR, Madden B, McCormick DJ, Bhattacharya R, Rotello VM, Kocher JP, Mukherjee P. Identifying new therapeutic targets via modulation of protein corona formation by engineered nanoparticles. PLoS One. 2012; 7: (3)e33650.
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  67. Kalari KR, Rossell D, Necela BM, Asmann YW, Nair A, Baheti S, Kachergus JM, Younkin CS, Baker T, Carr JM, Tang X, Walsh MP, Chai HS, Sun Z, Hart SN, Leontovich AA, Hossain A, Kocher JP, Perez EA, Reisman DN, Fields AP, Thompson EA. Deep Sequence Analysis of Non-Small Cell Lung Cancer: Integrated Analysis of Gene Expression, Alternative Splicing, and Single Nucleotide Variations in Lung Adenocarcinomas with and without Oncogenic KRAS Mutations. Front Oncol. 2012; 2:12.
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  68. Sun Z, Chai HS, Wu Y, White WM, Donkena KV, Klein CJ, Garovic VD, Therneau TM, Kocher JP. Batch effect correction for genome-wide methylation data with Illumina Infinium platform. BMC Med Genomics. 2011 Dec 16; 4:84.
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  69. Sohn S, Kocher JP, Chute CG, Savova GK. Drug side effect extraction from clinical narratives of psychiatry and psychology patients. J Am Med Inform Assoc. 2011 Dec; 18 Suppl 1:i144-9. Epub 2011 Sep 21.
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  70. Asmann YW, Hossain A, Necela BM, Middha S, Kalari KR, Sun Z, Chai HS, Williamson DW, Radisky D, Schroth GP, Kocher JP, Perez EA, Thompson EA. A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines. Nucleic Acids Res. 2011 Aug; 39(15):e100. Epub 2011 May 27.
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  71. Bielinski SJ, Chai HS, Pathak J, Talwalkar JA, Limburg PJ, Gullerud RE, Sicotte H, Klee EW, Ross JL, Kocher JP, Kullo IJ, Heit JA, Petersen GM, de Andrade M, Chute CG. Mayo Genome Consortia: a genotype-phenotype resource for genome-wide association studies with an application to the analysis of circulating bilirubin levels. Mayo Clin Proc. 2011 Jul; 86: (7)606-14.
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  72. Sicotte H, Rider DN, Poland GA, Dhiman N, Kocher JP. SNPPicker: high quality tag SNP selection across multiple populations. BMC Bioinformatics. 2011 May 02; 12:129.
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