Publications

  1. Bayram B, Owen AR, Dudakovic A, Bettencourt JW, Limberg AK, Morrey ME, Sanchez-Sotelo J, Berry DJ, Kocher JP, van Wijnen AJ, Abdel MP. Elevated Expression of Plasminogen Activator Inhibitor (PAI-1/SERPINE1) is Independent from rs1799889 Genotypes in Arthrofibrosis. Meta Gene. 2021 Jun; 28 Epub 2021 Mar 05
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  2. Jessen E, Liu Y, Davila J, Kocher JP, Wang C. Determining mutational burden and signature using RNA-seq from tumor-only samples. BMC Med Genomics. 2021 Mar 1; 14 (1):65 Epub 2021 Mar 01
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  3. Chatzopoulos K, O'Brien DR, Sotiriou S, Khazaie K, Jen J, Kocher JA, Markovic SN, Flotte TJ. Aberrant immunohistochemical expression of CD4 as a rare finding in metastatic melanoma. J Cutan Pathol. 2020 Dec; 47 (12):1223-1226 Epub 2020 Oct 03
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  4. Bayram B, Owen AR, Dudakovic A, Dagneaux L, Turner TW, Bettencourt JW, Limberg AK, Tibbo ME, Morrey ME, Sanchez-Sotelo J, Berry DJ, Kocher JA, Wijnen AJV, Abdel MP. A Potential Theragnostic Regulatory Axis for Arthrofibrosis Involving Adiponectin (ADIPOQ) Receptor 1 and 2 (ADIPOR1 and ADIPOR2), TGFbeta1, and Smooth Muscle alpha-Actin (ACTA2). J Clin Med. 2020 Nov 17; 9 (11)
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  5. Nicolas CT, Kaiser RA, Hickey RD, Allen KL, Du Z, VanLith CJ, Guthman RM, Amiot B, Suksanpaisan L, Han B, Francipane MG, Cheikhi A, Jiang H, Bansal A, Pandey MK, Garg I, Lowe V, Bhagwate A, O'Brien D, Kocher JA, DeGrado TR, Nyberg SL, Lagasse E, Lillegard JB. Ex Vivo Cell Therapy by Ectopic Hepatocyte Transplantation Treats the Porcine Tyrosinemia Model of Acute Liver Failure. Mol Ther Methods Clin Dev. 2020 Sep 11; 18:738-750 Epub 2020 July 10
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  6. Sangtani A, Wang C, Weaver A, Hoppman NL, Kerr SE, Abyzov A, Shridhar V, Staub J, Kocher JA, Voss JS, Podratz KC, Wentzensen N, Kisiel JB, Sherman ME, Bakkum-Gamez JN. Combining copy number, methylation markers, and mutations as a panel for endometrial cancer detection via intravaginal tampon collection. Gynecol Oncol. 2020 Feb; 156 (2):387-392 Epub 2019 Nov 28
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  7. Larson NB, Larson MC, Na J, Sosa CP, Wang C, Kocher JP, Rowsey R. Coverage profile correction of shallow-depth circulating cell-free DNA sequencing via multidistance learning. Pac Symp Biocomput. 2020; 25:599-610
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  8. Wei T, Nie J, Larson NB, Ye Z, Eckel Passow JE, Robertson KD, Kocher JA, Wang L. CpGtools: A Python Package for DNA Methylation Analysis. Bioinformatics. 2019 Dec 6 Epub 2019 Dec 06
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  9. Ahn KS, O'Brien D, Kang YN, Mounajjed T, Kim YH, Kim TS, Kocher JA, Allotey LK, Borad MJ, Roberts LR, Kang KJ. Prognostic subclass of intrahepatic cholangiocarcinoma by integrative molecular-clinical analysis and potential targeted approach. Hepatol Int. 2019 Jul; 13 (4):490-500 Epub 2019 June 18
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  10. Aziz K, Limzerwala JF, Sturmlechner I, Hurley E, Zhang C, Jeganathan KB, Nelson G, Bronk S, Fierro Velasco RO, van Deursen EJ, O'Brien DR, Kocher JA, Youssef SA, van Ree JH, de Bruin A, van den Bos H, Spierings DCJ, Foijer F, van de Sluis B, Roberts LR, Gores GJ, Li H, van Deursen JM. Ccne1 Overexpression Causes Chromosome Instability in Liver Cells and Liver Tumor Development in Mice. Gastroenterology. 2019 Jul; 157 (1):210-226.e12 Epub 2019 Mar 13
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  11. Luchtel RA, Zimmermann MT, Hu G, Dasari S, Jiang M, Oishi N, Jacobs HK, Zeng Y, Hundal T, Rech KL, Ketterling RP, Lee JH, Eckloff BW, Yan H, Gaonkar KS, Tian S, Ye Z, Kadin ME, Sidhu J, Jiang L, Voss J, Link BK, Syrbu SI, Facchetti F, Bennani NN, Slager SL, Ordog T, Kocher JP, Cerhan JR, Ansell SM, Feldman AL. Recurrent MSC (E116K) mutations in ALK-negative anaplastic large cell lymphoma. Blood. 2019 Jun 27; 133 (26):2776-2789 Epub 2019 May 17
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  12. Wang X, Sun Z, Zimmermann MT, Bugrim A, Kocher JP. Predict drug sensitivity of cancer cells with pathway activity inference. BMC Med Genomics. 2019 Jan 31; 12 (Suppl 1):15
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  13. Stephens Z, Wang C, Iyer RK, Kocher JP. Detection and visualization of complex structural variants from long reads. BMC Bioinformatics. 2018 Dec 21; 19 (Suppl 20):508
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  14. Lin S, Wang C, Zarei S, Bell DA, Kerr SE, Runger GC, Kocher JA. A data science approach for the classification of low-grade and high-grade ovarian serous carcinomas. BMC Genomics. 2018 Nov 27; 19 (1):841
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  15. Prodduturi N, Bhagwate A, Kocher JA, Sun Z. Indel sensitive and comprehensive variant/mutation detection from RNA sequencing data for precision medicine. BMC Med Genomics. 2018 Sep 14; 11 (Suppl 3):67 Epub 2018 Sept 14
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  16. Kang SS, Ebbert MTW, Baker KE, Cook C, Wang X, Sens JP, Kocher JP, Petrucelli L, Fryer JD. Microglial translational profiling reveals a convergent APOE pathway from aging, amyloid, and tau. J Exp Med. 2018 Sep 3; 215 (9):2235-2245 Epub 2018 Aug 06
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  17. Larson NB, Wang C, Na J, Rowsey RA, Highsmith WE, Hoppman NL, Kocher JP, Klee EW. Improving Single-Nucleotide Polymorphism-Based Fetal Fraction Estimation of Maternal Plasma Circulating Cell-Free DNA Using Bayesian Hierarchical Models. J Comput Biol. 2018 Sep; 25 (9):1040-1049 Epub 2018 June 22
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  18. Zimmermann MT, Therneau TM, Kocher JA. Correction to: the impact of pharmacokinetic gene profiles across human cancers. BMC Cancer. 2018 Jul 18; 18 (1):743 Epub 2018 July 18
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  19. Baheti S, Tang X, O'Brien DR, Chia N, Roberts LR, Nelson H, Boughey JC, Wang L, Goetz MP, Kocher JA, Kalari KR. HGT-ID: an efficient and sensitive workflow to detect human-viral insertion sites using next-generation sequencing data. BMC Bioinformatics. 2018 Jul 17; 19 (1):271 Epub 2018 July 17
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  20. Ye Z, Dong H, Li Y, Ma T, Huang H, Leong HS, Eckel-Passow J, Kocher JA, Liang H, Wang L. Prevalent Homozygous Deletions of Type I Interferon and Defensin Genes in Human Cancers Associate with Immunotherapy Resistance. Clin Cancer Res. 2018 Jul 15; 24 (14):3299-3308 Epub 2018 Apr 04
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  21. Zimmermann MT, Therneau TM, Kocher JA. The impact of pharmacokinetic gene profiles across human cancers. BMC Cancer. 2018 May 21; 18 (1):577
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  22. Taylor AM, Shih J, Ha G, Gao GF, Zhang X, Berger AC, Schumacher SE, Wang C, Hu H, Liu J, Lazar AJ, Cherniack AD, Beroukhim R, Meyerson M, Cancer Genome Atlas Research Network. Genomic and Functional Approaches to Understanding Cancer Aneuploidy. Cancer Cell. 2018 Apr 9; 33 (4):676-689.e3 Epub 2018 Apr 02
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  23. Liu Y, Sethi NS, Hinoue T, Schneider BG, Cherniack AD, Sanchez-Vega F, Seoane JA, Farshidfar F, Bowlby R, Islam M, Kim J, Chatila W, Akbani R, Kanchi RS, Rabkin CS, Willis JE, Wang KK, McCall SJ, Mishra L, Ojesina AI, Bullman S, Pedamallu CS, Lazar AJ, Sakai R, Thorsson V, Bass AJ, Laird PW, Cancer Genome Atlas Research Network. Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas. Cancer Cell. 2018 Apr 9; 33 (4):721-735.e8 Epub 2018 Apr 02
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  24. Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Ng PK, Jeong KJ, Cao S, Wang Z, Gao J, Gao Q, Wang F, Liu EM, Mularoni L, Rubio-Perez C, Nagarajan N, Cortes-Ciriano I, Zhou DC, Liang WW, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko JY, Khurana E, Park PJ, Van Allen EM, Liang H, Lawrence MS, Godzik A, Lopez-Bigas N, Stuart J, Wheeler D, Getz G, Chen K, Lazar AJ, Mills GB, Karchin R, Ding L, MC3 Working Group//Cancer Genome Atlas Research Network. Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell. 2018 Apr 5; 173 (2):371-385.e18
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  25. Huang KL, Mashl RJ, Wu Y, Ritter DI, Wang J, Oh C, Paczkowska M, Reynolds S, Wyczalkowski MA, Oak N, Scott AD, Krassowski M, Cherniack AD, Houlahan KE, Jayasinghe R, Wang LB, Zhou DC, Liu D, Cao S, Kim YW, Koire A, McMichael JF, Hucthagowder V, Kim TB, Hahn A, Wang C, McLellan MD, Al-Mulla F, Johnson KJ, Lichtarge O, Boutros PC, Raphael B, Lazar AJ, Zhang W, Wendl MC, Govindan R, Jain S, Wheeler D, Kulkarni S, Dipersio JF, Reimand J, Meric-Bernstam F, Chen K, Shmulevich I, Plon SE, Chen F, Ding L, Cancer Genome Atlas Research Network. Pathogenic Germline Variants in 10,389 Adult Cancers. Cell. 2018 Apr 5; 173 (2):355-370.e14
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  26. Knijnenburg TA, Wang L, Zimmermann MT, Chambwe N, Gao GF, Cherniack AD, Fan H, Shen H, Way GP, Greene CS, Liu Y, Akbani R, Feng B, Donehower LA, Miller C, Shen Y, Karimi M, Chen H, Kim P, Jia P, Shinbrot E, Zhang S, Liu J, Hu H, Bailey MH, Yau C, Wolf D, Zhao Z, Weinstein JN, Li L, Ding L, Mills GB, Laird PW, Wheeler DA, Shmulevich I, Monnat RJ Jr, Xiao Y, Wang C, Cancer Genome Atlas Research Network. Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas. Cell Rep. 2018 Apr 3; 23 (1):239-254.e6
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  27. Campbell JD, Yau C, Bowlby R, Liu Y, Brennan K, Fan H, Taylor AM, Wang C, Walter V, Akbani R, Byers LA, Creighton CJ, Coarfa C, Shih J, Cherniack AD, Gevaert O, Prunello M, Shen H, Anur P, Chen J, Cheng H, Hayes DN, Bullman S, Pedamallu CS, Ojesina AI, Sadeghi S, Mungall KL, Robertson AG, Benz C, Schultz A, Kanchi RS, Gay CM, Hegde A, Diao L, Wang J, Ma W, Sumazin P, Chiu HS, Chen TW, Gunaratne P, Donehower L, Rader JS, Zuna R, Al-Ahmadie H, Lazar AJ, Flores ER, Tsai KY, Zhou JH, Rustgi AK, Drill E, Shen R, Wong CK, Stuart JM, Laird PW, Hoadley KA, Weinstein JN, Peto M, Pickering CR, Chen Z, Van Waes C, Cancer Genome Atlas Research Network. Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas. Cell Rep. 2018 Apr 3; 23 (1):194-212.e6
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  28. Chen X, Johnson S, Jeraldo P, Wang J, Chia N, Kocher JA, Chen J. Hybrid-denovo: a de novo OTU-picking pipeline integrating single-end and paired-end 16S sequence tags. Gigascience. 2018 Mar 1; 7 (3):1-7
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  29. 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. 2018 Jan; 57 (1):114-124 Epub 2017 Oct 18
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  30. Prinz J, Koohi-Moghadam M, Sun H, Kocher JA, Wang J. Novel Neural Network Approach to Predict Drug-Target Interactions Based on Drug Side Effects and Genome-Wide Association Studies. Hum Hered. 2018; 83 (2):79-91 Epub 2018 Oct 22
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  31. 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 Dec 15; 45 (22):e179
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  32. Yip SH, Wang P, Kocher JA, Sham PC, Wang J. Corrigendum: Linnorm: improved statistical analysis for single cell RNA-seq expression data. Nucleic Acids Res. 2017 Dec 15; 45 (22):13097
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  33. 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. 2017 Nov 1; 18 (6):973-983
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  34. 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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  35. 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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  36. 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 Jul 3; 45 (W1):W215-W221
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  37. 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 3; 9 (2):6834 Epub 2017 Sept 15
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  38. 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 1; 109 (7)
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  39. 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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  40. 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;
  41. 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 2; 45 (10):5653-5665
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  42. 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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  43. 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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  44. 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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  45. Stephens ZD, Iyer RK, Wang C, Kocher JPA. Unraveling complex local genomic rearrangements from long-read data Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. 2017; 2017-January:181-7
  46. Thompson KJ, Ingle JN, Tang X, Chia N, Jeraldo PR, Walther-Antonio MR, Kandimalla KK, Johnson S, Yao JZ, Harrington SC, Suman VJ, Wang L, Weinshilboum RL, Boughey JC, Kocher JP, Nelson H, Goetz MP, Kalari KR. A comprehensive analysis of breast cancer microbiota and host gene expression. PLoS One. 2017; 12 (11):e0188873 Epub 2017 Nov 30
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  47. Egan JB, Marks DL, Hogenson TL, Vrabel AM, Sigafoos AN, Tolosa EJ, Carr RM, Safgren SL, Hesles EE, Almada LL, Romecin-Duran PA, Iguchi E, Ala'Aldeen A, Kocher JA, Oliver GR, Prodduturi N, Mead DW, Hossain A, Huneke NE, Tagtow CM, Ailawadhi S, Ansell SM, Banck MS, Bryce AH, Carballido EM, Chanan-Khan AA, Curtis KK, Resnik E, Gawryletz CD, Go RS, Halfdanarson TR, Ho TH, Joseph RW, Kapoor P, Mansfield AS, Meurice N, Nageswara Rao AA, Nowakowski GS, Pardanani A, Parikh SA, Cheville JC, Feldman AL, Ramanathan RK, Robinson SI, Tibes R, Finnes HD, McCormick JB, McWilliams RR, Jatoi A, Patnaik MM, Silva AC, Wieben ED, McAllister TM, Rumilla KM, Kerr SE, Lazaridis KN, Farrugia G, Stewart AK, Clark KJ, Kennedy EJ, Klee EW, Borad MJ, Fernandez-Zapico ME. Molecular Modeling and Functional Analysis of Exome Sequencing-Derived Variants of Unknown Significance Identify a Novel, Constitutively Active FGFR2 Mutant in Cholangiocarcinoma. JCO Precis Oncol. 2017; 2017 Epub 2017 Aug 01
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  48. 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 6; 7 (49):80967-80979
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  49. Li MJ, Pan Z, Liu Z, Wu J, Wang P, Zhu Y, Xu F, 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 Epub 2016 June 06
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  50. 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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  51. 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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  52. 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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  53. 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 3; 17:58 Epub 2016 Feb 03
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  54. 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 1; 32 (3):469-71 Epub 2015 Oct 07
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  55. 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 Epub 2015 Nov 28
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  56. 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 Epub 2015 Aug 26
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  57. 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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  58. 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 Epub 2015 Apr 27
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  59. 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 Epub 2015 Sept 14
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  60. 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 6; 16:185 Epub 2015 June 06
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  61. 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 Epub 2015 Apr 16
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