Correction to: the impact of pharmacokinetic gene profiles across human cancers

by Michael T. Zimmermann, Terry M. Therneau, Jean-Pierre A. Kocher
Published 2018-07-01

The impact of pharmacokinetic gene profiles across human cancers

by Michael T. Zimmermann, Terry M. Therneau, Jean-Pierre A. Kocher
Published 2018-05-01

Indel sensitive and comprehensive variant/mutation detection from RNA sequencing data for precision medicine

by Naresh Prodduturi, Aditya Bhagwate, Jean-Pierre A. Kocher, Zhifu Sun
Published 2018-09-01

Genome-wide analysis of loss of heterozygosity in breast infiltrating ductal carcinoma distant normal tissue highlights arm specific enrichment and expansion across tumor stages.

by Xiaoyang Ruan, Hongfang Liu, Lisa Boardman, Jean-Pierre A Kocher
Published 2014-01-01

From days to hours: reporting clinically actionable variants from whole genome sequencing.

by Sumit Middha, Saurabh Baheti, Steven N Hart, Jean-Pierre A Kocher
Published 2014-01-01

Mass homozygotes accumulation in the NCI-60 cancer cell lines as compared to HapMap Trios, and relation to fragile site location.

by Xiaoyang Ruan, Jean-Pierre A Kocher, Yves Pommier, Hongfang Liu, William C Reinhold
Published 2012-01-01

CircularLogo: A lightweight web application to visualize intra-motif dependencies

by Zhenqing Ye, Tao Ma, Michael T. Kalmbach, Surendra Dasari, Jean-Pierre A. Kocher, Liguo Wang
Published 2017-05-01

PB-Motif—A Method for Identifying Gene/Pseudogene Rearrangements With Long Reads: An Application to CYP21A2 Genotyping

by Zachary Stephens, Dragana Milosevic, Benjamin Kipp, Stefan Grebe, Ravishankar K. Iyer, Jean-Pierre A. Kocher
Published 2021-07-01

A data science approach for the classification of low-grade and high-grade ovarian serous carcinomas

by Sangdi Lin, Chen Wang, Shabnam Zarei, Debra A. Bell, Sarah E. Kerr, George C. Runger, Jean-Pierre A. Kocher
Published 2018-11-01

SoftSearch: integration of multiple sequence features to identify breakpoints of structural variations.

by Steven N Hart, Vivekananda Sarangi, Raymond Moore, Saurabh Baheti, Jaysheel D Bhavsar, Fergus J Couch, Jean-Pierre A Kocher
Published 2013-01-01

PANDA: pathway and annotation explorer for visualizing and interpreting gene-centric data

by Steven N. Hart, Raymond M. Moore, Michael T. Zimmermann, Gavin R. Oliver, Jan B. Egan, Alan H. Bryce, Jean-Pierre A. Kocher
Published 2015-05-01

HGT-ID: an efficient and sensitive workflow to detect human-viral insertion sites using next-generation sequencing data

by Saurabh Baheti, Xiaojia Tang, Daniel R. O’Brien, Nicholas Chia, Lewis R. Roberts, Heidi Nelson, Judy C. Boughey, Liewei Wang, Matthew P. Goetz, Jean-Pierre A. Kocher, Krishna R. Kalari
Published 2018-07-01

Impact of library preparation on downstream analysis and interpretation of RNA-Seq data: comparison between Illumina PolyA and NuGEN Ovation protocol.

by Zhifu Sun, Yan W Asmann, Asha Nair, Yuji Zhang, Liguo Wang, Krishna R Kalari, Aditya V Bhagwate, Tiffany R Baker, Jennifer M Carr, Jean-Pierre A Kocher, Edith A Perez, E Aubrey Thompson
Published 2013-01-01

A Potential Theragnostic Regulatory Axis for Arthrofibrosis Involving Adiponectin (ADIPOQ) Receptor 1 and 2 (ADIPOR1 and ADIPOR2), TGFβ1, and Smooth Muscle α-Actin (ACTA2)

by Banu Bayram, Aaron R. Owen, Amel Dudakovic, Louis Dagneaux, Travis W. Turner, Jacob W. Bettencourt, Afton K. Limberg, Meagan E. Tibbo, Mark E. Morrey, Joaquin Sanchez-Sotelo, Daniel J. Berry, Jean-Pierre A. Kocher, Andre J. van Wijnen, Matthew P. Abdel
Published 2020-11-01

Comprehensive genomic profiling of a rare thyroid follicular dendritic cell sarcoma

by Jaime I. Davila, Jason S. Starr, Steven Attia, Chen Wang, Ryan A. Knudson, Brian M. Necela, Vivekananda Sarangi, Zhifu Sun, Yingxue Ren, John D. Casler, David M. Menke, Gavin R. Oliver, Richard W. Joseph, John A. Copland, Alexander S. Parker, Jean-Pierre A. Kocher, E. Aubrey Thompson, Robert C. Smallridge, Yan W. Asmann
Published 2017-09-01

CRISPR/Cas9-mediated excision of ALS/FTD-causing hexanucleotide repeat expansion in C9ORF72 rescues major disease mechanisms in vivo and in vitro

by Katharina E. Meijboom, Abbas Abdallah, Nicholas P. Fordham, Hiroko Nagase, Tomás Rodriguez, Carolyn Kraus, Tania F. Gendron, Gopinath Krishnan, Rustam Esanov, Nadja S. Andrade, Matthew J. Rybin, Melina Ramic, Zachary D. Stephens, Alireza Edraki, Meghan T. Blackwood, Aydan Kahriman, Nils Henninger, Jean-Pierre A. Kocher, Michael Benatar, Michael H. Brodsky, Leonard Petrucelli, Fen-Biao Gao, Erik J. Sontheimer, Robert H. Brown, Zane Zeier, Christian Mueller
Published 2022-10-01

Ex Vivo Cell Therapy by Ectopic Hepatocyte Transplantation Treats the Porcine Tyrosinemia Model of Acute Liver Failure

by Clara T. Nicolas, Robert A. Kaiser, Raymond D. Hickey, Kari L. Allen, Zeji Du, Caitlin J. VanLith, Rebekah M. Guthman, Bruce Amiot, Lukkana Suksanpaisan, Bing Han, Maria Giovanna Francipane, Amin Cheikhi, Huailei Jiang, Aditya Bansal, Mukesh K. Pandey, Ishan Garg, Val Lowe, Aditya Bhagwate, Daniel O’Brien, Jean-Pierre A. Kocher, Timothy R. DeGrado, Scott L. Nyberg, Eric Lagasse, Joseph B. Lillegard
Published 2020-09-01

Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles

by Farshad Farshidfar, Siyuan Zheng, Marie-Claude Gingras, Yulia Newton, Juliann Shih, A. Gordon Robertson, Toshinori Hinoue, Katherine A. Hoadley, Ewan A. Gibb, Jason Roszik, Kyle R. Covington, Chia-Chin Wu, Eve Shinbrot, Nicolas Stransky, Apurva Hegde, Ju Dong Yang, Ed Reznik, Sara Sadeghi, Chandra Sekhar Pedamallu, Akinyemi I. Ojesina, Julian M. Hess, J. Todd Auman, Suhn K. Rhie, Reanne Bowlby, Mitesh J. Borad, Rehan Akbani, Loretta K. Allotey, Adrian Ally, Domenico Alvaro, Jesper B. Andersen, Elizabeth L. Appelbaum, Arshi Arora, J. Todd Auman, Miruna Balasundaram, Saianand Balu, Nabeel Bardeesy, Oliver F. Bathe, Stephen B. Baylin, Rameen Beroukhim, Mario Berrios, Tom Bodenheimer, Lori Boice, Moiz S. Bootwalla, Mitesh J. Borad, Jay Bowen, Reanne Bowlby, Maria Consiglia Bragazzi, Denise Brooks, Vincenzo Cardinale, Rebecca Carlsen, Guido Carpino, Andre L. Carvalho, Roongruedee Chaiteerakij, Vishal C. Chandan, Andrew D. Cherniack, Lynda Chin, Juok Cho, Gina Choe, Eric Chuah, Sudha Chudamani, Carrie Cibulskis, Matthew G. Cordes, Kyle R. Covington, Daniel Crain, Erin Curley, Agostino Maria De Rose, Timothy Defreitas, John A. Demchok, Vikram Deshpande, Noreen Dhalla, Li Ding, Kimberley Evason, Farshad Farshidfar, Ina Felau, Martin L. Ferguson, Wai Chin Foo, Antonio Franchitto, Scott Frazer, Catrina C. Fronick, Lucinda A. Fulton, Robert S. Fulton, Stacey B. Gabriel, Johanna Gardner, Julie M. Gastier-Foster, Eugenio Gaudio, Nils Gehlenborg, Giannicola Genovese, Mark Gerken, Gad Getz, Nasra H. Giama, Richard A. Gibbs, Marie-Claude Gingras, Felice Giuliante, Gian Luca Grazi, D. Neil Hayes, Apurva M. Hegde, David I. Heiman, Julian M. Hess, Toshinori Hinoue, Katherine A. Hoadley, Andrea Holbrook, Robert A. Holt, Alan P. Hoyle, Mei Huang, Carolyn M. Hutter, Stuart R. Jefferys, Steven J.M. Jones, Corbin D. Jones, Katayoon Kasaian, Robin K. Kelley, Jaegil Kim, David E. Kleiner, Jean-Pierre A. Kocher, Lawrence N. Kwong, Phillip H. Lai, Peter W. Laird, Michael S. Lawrence, Kristen M. Leraas, Tara M. Lichtenberg, Pei Lin, Wenbin Liu, Jia Liu, Laxmi Lolla, Yiling Lu, Yussanne Ma, David Mallery, Elaine R. Mardis, Marco A. Marra, Marcus M. Matsushita, Michael Mayo, Michael D. McLellan, Autumn J. McRee, Sam Meier, Shaowu Meng, Matthew Meyerson, Piotr A. Mieczkowski, Christopher A. Miller, Gordon B. Mills, Richard A. Moore, Scott Morris, Lisle E. Mose, Catherine D. Moser, Taofic Mounajjed, Andrew J. Mungall, Karen Mungall, Bradley A. Murray, Rashi Naresh, Yulia Newton, Michael S. Noble, Daniel R. O’Brien, Akinyemi I. Ojesina, Joel S. Parker, Tushar C. Patel, Joseph Paulauskis, Chandra Sekhar Pedamallu, Robert Penny, Charles M. Perou, Amy H. Perou, Todd Pihl, Amie J. Radenbaugh, Nilsa C. Ramirez, W. Kimryn Rathmell, Ed Reznik, Suhn K. Rhie, Jeffrey Roach, Lewis R. Roberts, A. Gordon Robertson, Sara Sadeghi, Gordon Saksena, Chris Sander, Jacqueline E. Schein, Heather K. Schmidt, Steven E. Schumacher, Candace Shelton, Troy Shelton, Ronglai Shen, Margi Sheth, Yan Shi, Juliann Shih, Eve Shinbrot, Rachna Shroff, Janae V. Simons, Payal Sipahimalani, Tara Skelly, Heidi J. Sofia, Matthew G. Soloway, Hubert Stoppler, Nicolas Stransky, Josh Stuart, Qiang Sun, Angela Tam, Donghui Tan, Roy Tarnuzzer, Nina Thiessen, Leigh B. Thorne, Michael S. Torbenson, David J. Van Den Berg, Umadevi Veluvolu, Roel G.W. Verhaak, Doug Voet, Yunhu Wan, Zhining Wang, John N. Weinstein, Daniel J. Weisenberger, David A. Wheeler, Richard K. Wilson, Lisa Wise, Tina Wong, Chia-Chin Wu, Ye Wu, Liu Xi, Ju Dong Yang, Liming Yang, Jean C. Zenklusen, Hailei Zhang, Jiashan (Julia) Zhang, Siyuan Zheng, Erik Zmuda
Published 2017-06-01