Detection and characterization of constitutive replication origins defined by DNA polymerase epsilon

by Roman Jaksik, David A. Wheeler, Marek Kimmel
Published 2023-02-01

Clinical and demographic features of HIV infection in El Salvador

by Elisa García Vázquez, Rolando A. Cedillos, David A. Wheeler
Published 2003-05-01

Genome-wide analysis of binding sites and direct target genes of the orphan nuclear receptor NR2F1/COUP-TFI.

by Celina Montemayor, Oscar A Montemayor, Alex Ridgeway, Feng Lin, David A Wheeler, Scott D Pletcher, Fred A Pereira
Published 2010-01-01

SNPdetector: a software tool for sensitive and accurate SNP detection.

by Jinghui Zhang, David A Wheeler, Imtiaz Yakub, Sharon Wei, Raman Sood, William Rowe, Paul P Liu, Richard A Gibbs, Kenneth H Buetow
Published 2005-10-01

An enhanced genetic model of colorectal cancer progression history

by Lixing Yang, Su Wang, Jake June-Koo Lee, Semin Lee, Eunjung Lee, Eve Shinbrot, David A. Wheeler, Raju Kucherlapati, Peter J. Park
Published 2019-08-01

Integrated Analysis of TP53 Gene and Pathway Alterations in The Cancer Genome Atlas

by Lawrence A. Donehower, Thierry Soussi, Anil Korkut, Yuexin Liu, Andre Schultz, Maria Cardenas, Xubin Li, Ozgun Babur, Teng-Kuei Hsu, Olivier Lichtarge, John N. Weinstein, Rehan Akbani, David A. Wheeler
Published 2019-07-01

SVachra: a tool to identify genomic structural variation in mate pair sequencing data containing inward and outward facing reads

by Oliver A. Hampton, Adam C. English, Mark Wang, William J. Salerno, Yue Liu, Donna M. Muzny, Yi Han, David A. Wheeler, Kim C. Worley, James R. Lupski, Richard A. Gibbs
Published 2017-10-01

Gene expression profiling and immune cell-type deconvolution highlight robust disease progression and survival markers in multiple cohorts of CTCL patients

by Philippe Lefrançois, Pingxing Xie, Linghua Wang, Michael T. Tetzlaff, Linda Moreau, Andrew K. Watters, Elena Netchiporouk, Nathalie Provost, Martin Gilbert, Xiao Ni, Denis Sasseville, David A. Wheeler, Madeleine Duvic, Ivan V. Litvinov
Published 2018-08-01

Glutathione peroxidase 2 is a metabolic driver of the tumor immune microenvironment and immune checkpoint inhibitor response

by Defeng Deng, Ratna Veeramachaneni, Andrew G Sikora, Vlad C Sandulache, William K Decker, Kazi Mokim Ahmed, Nagireddy Putluri, Vasanta Putluri, Maria F Cardenas, David A Wheeler, Andy I Frederick, Sawad Kazi, Mitchell J Frederick
Published 2022-08-01

SMARCA4-inactivating mutations increase sensitivity to Aurora kinase A inhibitor VX-680 in non-small cell lung cancers

by Vural Tagal, Shuguang Wei, Wei Zhang, Rolf A. Brekken, Bruce A. Posner, Michael Peyton, Luc Girard, TaeHyun Hwang, David A. Wheeler, John D. Minna, Michael A. White, Adi F. Gazdar, Michael G. Roth
Published 2017-01-01

Integrated analyses of microRNAs demonstrate their widespread influence on gene expression in high-grade serous ovarian carcinoma.

by Chad J Creighton, Anadulce Hernandez-Herrera, Anders Jacobsen, Douglas A Levine, Parminder Mankoo, Nikolaus Schultz, Ying Du, Yiqun Zhang, Erik Larsson, Robert Sheridan, Weimin Xiao, Paul T Spellman, Gad Getz, David A Wheeler, Charles M Perou, Richard A Gibbs, Chris Sander, D Neil Hayes, Preethi H Gunaratne, Cancer Genome Atlas Research Network
Published 2012-01-01

Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

by Matthew H. Bailey, William U. Meyerson, Lewis Jonathan Dursi, Liang-Bo Wang, Guanlan Dong, Wen-Wei Liang, Amila Weerasinghe, Shantao Li, Yize Li, Sean Kelso, MC3 Working Group, PCAWG novel somatic mutation calling methods working group, Gordon Saksena, Kyle Ellrott, Michael C. Wendl, David A. Wheeler, Gad Getz, Jared T. Simpson, Mark B. Gerstein, Li Ding, PCAWG Consortium
Published 2020-11-01

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

by Matthew H. Bailey, William U. Meyerson, Lewis Jonathan Dursi, Liang-Bo Wang, Guanlan Dong, Wen-Wei Liang, Amila Weerasinghe, Shantao Li, Yize Li, Sean Kelso, MC3 Working Group, PCAWG novel somatic mutation calling methods working group, Gordon Saksena, Kyle Ellrott, Michael C. Wendl, David A. Wheeler, Gad Getz, Jared T. Simpson, Mark B. Gerstein, Li Ding, PCAWG Consortium
Published 2020-09-01

Novel microRNA candidates and miRNA-mRNA pairs in embryonic stem (ES) cells.

by Peili Gu, Jeffrey G Reid, Xiaolian Gao, Chad A Shaw, Chad Creighton, Peter L Tran, Xiaochuan Zhou, Rafal B Drabek, David L Steffen, David M Hoang, Michelle K Weiss, Arash O Naghavi, Jad El-daye, Mahjabeen F Khan, Glen B Legge, David A Wheeler, Richard A Gibbs, Jonathan N Miller, Austin J Cooney, Preethi H Gunaratne
Published 2008-07-01

Author Correction: Pathway and network analysis of more than 2500 whole cancer genomes

by Matthew A. Reyna, David Haan, Marta Paczkowska, Lieven P. C. Verbeke, Miguel Vazquez, Abdullah Kahraman, Sergio Pulido-Tamayo, Jonathan Barenboim, Lina Wadi, Priyanka Dhingra, Raunak Shrestha, Gad Getz, Michael S. Lawrence, Jakob Skou Pedersen, Mark A. Rubin, David A. Wheeler, Søren Brunak, Jose M. G. Izarzugaza, Ekta Khurana, Kathleen Marchal, Christian von Mering, S. Cenk Sahinalp, Alfonso Valencia, PCAWG Drivers and Functional Interpretation Working Group, Jüri Reimand, Joshua M. Stuart, Benjamin J. Raphael, PCAWG Consortium
Published 2022-12-01

Pathway and network analysis of more than 2500 whole cancer genomes

by Matthew A. Reyna, David Haan, Marta Paczkowska, Lieven P. C. Verbeke, Miguel Vazquez, Abdullah Kahraman, Sergio Pulido-Tamayo, Jonathan Barenboim, Lina Wadi, Priyanka Dhingra, Raunak Shrestha, Gad Getz, Michael S. Lawrence, Jakob Skou Pedersen, Mark A. Rubin, David A. Wheeler, Søren Brunak, Jose M. G. Izarzugaza, Ekta Khurana, Kathleen Marchal, Christian von Mering, S. Cenk Sahinalp, Alfonso Valencia, PCAWG Drivers and Functional Interpretation Working Group, Jüri Reimand, Joshua M. Stuart, Benjamin J. Raphael, PCAWG Consortium
Published 2020-02-01

Etiology of oncogenic fusions in 5,190 childhood cancers and its clinical and therapeutic implication

by Yanling Liu, Jonathon Klein, Richa Bajpai, Li Dong, Quang Tran, Pandurang Kolekar, Jenny L. Smith, Rhonda E. Ries, Benjamin J. Huang, Yi-Cheng Wang, Todd A. Alonzo, Liqing Tian, Heather L. Mulder, Timothy I. Shaw, Jing Ma, Michael P. Walsh, Guangchun Song, Tamara Westover, Robert J. Autry, Alexander M. Gout, David A. Wheeler, Shibiao Wan, Gang Wu, Jun J. Yang, William E. Evans, Mignon Loh, John Easton, Jinghui Zhang, Jeffery M. Klco, Soheil Meshinchi, Patrick A. Brown, Shondra M. Pruett-Miller, Xiaotu Ma
Published 2023-04-01

DNA methylation patterns identify subgroups of pancreatic neuroendocrine tumors with clinical association

by Vanessa Lakis, Rita T. Lawlor, Felicity Newell, Ann-Marie Patch, Andrea Mafficini, Anguraj Sadanandam, Lambros T. Koufariotis, Rebecca L. Johnston, Conrad Leonard, Scott Wood, Borislav Rusev, Vincenzo Corbo, Claudio Luchini, Sara Cingarlini, Luca Landoni, Roberto Salvia, Michele Milella, David Chang, Peter Bailey, Nigel B. Jamieson, Fraser Duthie, Marie-Claude Gingras, Donna M. Muzny, David A. Wheeler, Richard A. Gibbs, Massimo Milione, APGI, ARC-Net, Paolo Pederzoli, Jaswinder S. Samra, Anthony J. Gill, Amber L. Johns, John V. Pearson, Andrew V. Biankin, Sean M. Grimmond, Nicola Waddell, Katia Nones, Aldo Scarpa
Published 2021-02-01

Cross-species identification of genomic drivers of squamous cell carcinoma development across preneoplastic intermediates

by Vida Chitsazzadeh, Cristian Coarfa, Jennifer A. Drummond, Tri Nguyen, Aaron Joseph, Suneel Chilukuri, Elizabeth Charpiot, Charles H. Adelmann, Grace Ching, Tran N. Nguyen, Courtney Nicholas, Valencia D. Thomas, Michael Migden, Deborah MacFarlane, Erika Thompson, Jianjun Shen, Yoko Takata, Kayla McNiece, Maxim A. Polansky, Hussein A. Abbas, Kimal Rajapakshe, Adam Gower, Avrum Spira, Kyle R. Covington, Weimin Xiao, Preethi Gunaratne, Curtis Pickering, Mitchell Frederick, Jeffrey N. Myers, Li Shen, Hui Yao, Xiaoping Su, Ronald P. Rapini, David A. Wheeler, Ernest T. Hawk, Elsa R. Flores, Kenneth Y. Tsai
Published 2016-08-01

Multilevel Genomics-Based Taxonomy of Renal Cell Carcinoma

by Fengju Chen, Yiqun Zhang, Yasin Şenbabaoğlu, Giovanni Ciriello, Lixing Yang, Ed Reznik, Brian Shuch, Goran Micevic, Guillermo De Velasco, Eve Shinbrot, Michael S. Noble, Yiling Lu, Kyle R. Covington, Liu Xi, Jennifer A. Drummond, Donna Muzny, Hyojin Kang, Junehawk Lee, Pheroze Tamboli, Victor Reuter, Carl Simon Shelley, Benny A. Kaipparettu, Donald P. Bottaro, Andrew K. Godwin, Richard A. Gibbs, Gad Getz, Raju Kucherlapati, Peter J. Park, Chris Sander, Elizabeth P. Henske, Jane H. Zhou, David J. Kwiatkowski, Thai H. Ho, Toni K. Choueiri, James J. Hsieh, Rehan Akbani, Gordon B. Mills, A. Ari Hakimi, David A. Wheeler, Chad J. Creighton
Published 2016-03-01