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Michael C. Ryan
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Journal Articles

CRAVAT 4: Cancer-Related Analysis of Variants Toolkit

Free
David L. Masica, Christopher Douville, Collin Tokheim, Rohit Bhattacharya, RyangGuk Kim, Kyle Moad, Michael C. Ryan, Rachel Karchin
Journal: Cancer Research
Cancer Res (2017) 77 (21): e35–e38.
https://doi.org/10.1158/0008-5472.CAN-17-0338
Published: 01 November 2017
View articletitled, CRAVAT 4: Cancer-Related Analysis of Variants Toolkit
Open the PDF for CRAVAT 4: Cancer-Related Analysis of Variants Toolkit in another window
Includes: Multimedia, Supplementary data
Journal Articles

A Galaxy Implementation of Next-Generation Clustered Heatmaps for Interactive Exploration of Molecular Profiling Data

Free
Bradley M. Broom, Michael C. Ryan, Robert E. Brown, Futa Ikeda, Mark Stucky, David W. Kane, James Melott, Chris Wakefield, Tod D. Casasent, Rehan Akbani, John N. Weinstein
Journal: Cancer Research
Cancer Res (2017) 77 (21): e23–e26.
https://doi.org/10.1158/0008-5472.CAN-17-0318
Published: 01 November 2017
View articletitled, A Galaxy Implementation of Next-Generation Clustered Heatmaps for Interactive Exploration of Molecular Profiling Data
Open the PDF for A Galaxy Implementation of Next-Generation Clustered Heatmaps for Interactive Exploration of Molecular Profiling Data in another window
Includes: Multimedia, Supplementary data
Journal Articles

Abstract 128: Comprehensive molecular characterization of 412 muscle-invasive urothelial bladder carcinomas: final analysis of The Cancer Genome Atlas (TCGA) project

Free
John N. Weinstein, Seth P. Lerner, David J. Kwiatkowski, Gad Getz, Jaegil Kim, Hikmat A. Al-ahmadie, Andrew D. Cherniack, Guangwu Guo, Rehan Akbani, Katherine A. Hoadley, William Y. Kim, Gordon Robertson, Andrew J. Mungall, Toshinori Hinoue, Peter W. Laird, Jonathan E. Rosenberg, Joaquim Bellmunt, Dean F. Bajorin, Margaret B. Morgan, Chad J. Creighton, Dmitry Gordenin, Joshua M. Stuart, Xiaoping Su, Michael C. Ryan, Jeffrey S. Damrauer, Wei Zhang, Yuexin Liu, Yiling Lu, Nikolaus Schultz, Raju Kucherlapati, Gordon B. Mills, Donna E. Hansel, Brian D. Robinson, Bodgen A. Czerniak, Victor E. Reuter
Journal: Cancer Research
Cancer Res (2016) 76 (14_Supplement): 128.
https://doi.org/10.1158/1538-7445.AM2016-128
Published: 15 July 2016
View articletitled, Abstract 128: Comprehensive molecular characterization of 412 muscle-invasive urothelial bladder carcinomas: final analysis of The Cancer Genome Atlas (TCGA) project
Journal Articles

Abstract 2895: Radiation-induced alternative splicing as detected in total and polysome-bound mRNA in glioblastoma stem-like cells

Free
Amy Wahba, Michael C. Ryan, Uma Shankavaram, Kevin Camphausen, Philip J. Tofilon
Journal: Cancer Research
Cancer Res (2016) 76 (14_Supplement): 2895.
https://doi.org/10.1158/1538-7445.AM2016-2895
Published: 15 July 2016
View articletitled, Abstract 2895: Radiation-induced alternative splicing as detected in total and polysome-bound mRNA in glioblastoma stem-like cells
Journal Articles

Abstract 2979: A web portal of ‘next-generation’ clustered heat maps for user-friendly, interactive exploration of patterns in TCGA data

Free
John N. Weinstein, Rehan Akbani, David W. Kane, James M. Melott, Tod D. Casasent, Rong Yao, Paul L. Roebuck, Gordon B. Mills, Michael C. Ryan, Christopher Wakefield, Bradley M. Broom
Journal: Cancer Research
Cancer Res (2015) 75 (15_Supplement): 2979.
https://doi.org/10.1158/1538-7445.AM2015-2979
Published: 01 August 2015
View articletitled, Abstract 2979: A web portal of ‘next-generation’ clustered heat maps for user-friendly, interactive exploration of patterns in TCGA data
Journal Articles

Abstract 2969: Progress in The Cancer Genome Atlas bladder cancer project

Free
John N. Weinstein, Jaegil Kim, Chad J. Creighton, Rehan Akbani, Katherine A. Hoadley, William Y. Kim, Margaret B. Morgan, Toshinori Hinoue, Andrew Cherniack, Xiaoping Su, Andrew J. Mungall, Michael C. Ryan, Dean F. Bajorin, Jonathan E. Rosenberg, Bogdan Czerniak, Donna Hansel, Victor E. Reuter, Brian D. Robinson, Hikmat A. Al-Ahmadie, Jeffrey S. Damrauer, Wei Zhang, Yuexin Liu, Dmitry R. Gordenin, Joshua M. Stuart, Nikolaus Schultz, Gordon Robertson, Steven JM Jones, Raju R. Kucherlapati, David J. McConkey, Peter W. Laird, Gordon B. Mills, David J. Kwiatkowski, Seth P. Lerner, TCGA Bladder Cancer Working Group, TCGA Research Network
Journal: Cancer Research
Cancer Res (2015) 75 (15_Supplement): 2969.
https://doi.org/10.1158/1538-7445.AM2015-2969
Published: 01 August 2015
View articletitled, Abstract 2969: Progress in The Cancer Genome Atlas bladder cancer project
Journal Articles

Abstract 987: Comprehensive characterization of urothelial bladder cancer: a TCGA Project update

Free
John N. Weinstein, Jaegil Kim, Chad J. Creighton, Rehan Akbani, Katherine A. Hoadley, William Y. Kim, Margaret B. Morgan, Toshinori Hinoue, Andrew Cherniack, Xiaoping Su, Andrew J. Mungall, Michael C. Ryan, Jonathan E. Rosenberg, Dean F. Bajorin, Bogdan Czerniak, Donna Hansel, Victor E. Reuter, Brian D. Robinson, Hikmat A. Al-Ahmadie, Jeffrey S. Damrauer, Wei Zhang, Yuexin Liu, Dmitry Gordenin, Joshua M. Stuart, Nikolaus Schultz, Gordon Robertson, Raju Kucherlapati, Peter W. Laird, Gordon B. Mills, David J. Kwiatkowski, Seth P. Lerner, representing TCGA's Bladder Cancer Working Group
Journal: Cancer Research
Cancer Res (2014) 74 (19_Supplement): 987.
https://doi.org/10.1158/1538-7445.AM2014-987
Published: 01 October 2014
View articletitled, Abstract 987: Comprehensive characterization of urothelial bladder cancer: a TCGA Project update
Journal Articles

Transcription Poisoning by Topoisomerase I Is Controlled by Gene Length, Splice Sites, and miR-142-3p

Free
Stéphanie Solier, Michael C. Ryan, Scott E. Martin, Sudhir Varma, Kurt W. Kohn, Hongfang Liu, Barry R. Zeeberg, Yves Pommier
Journal: Cancer Research
Cancer Res (2013) 73 (15): 4830–4839.
https://doi.org/10.1158/0008-5472.CAN-12-3504
Published: 31 July 2013
View articletitled, Transcription Poisoning by Topoisomerase I Is Controlled by Gene Length, Splice Sites, and miR-142-3p
Open the PDF for Transcription Poisoning by Topoisomerase I Is Controlled by Gene Length, Splice Sites, and miR-142-3p in another window
Includes: Supplementary data
Journal Articles

Abstract 1796: Analysis of TCGA RNASeq data using SpliceSeq provides a survey of alternative splicing in cancer.

Free
Michael C. Ryan, John N. Weinstein
Journal: Cancer Research
Cancer Res (2013) 73 (8_Supplement): 1796.
https://doi.org/10.1158/1538-7445.AM2013-1796
Published: 15 April 2013
View articletitled, Abstract 1796: Analysis of TCGA RNASeq data using SpliceSeq provides a survey of alternative splicing in cancer.
Journal Articles

Abstract 5132: Interactively exploring patterns in TCGA data: a web-based compendium of ‘next-generation’ clustered heat maps.

Free
John N. Weinstein, David W. Kane, Rehan Akbani, Deepti Dodda, Lam Nguyen, Michael C. Ryan, Chris Wakefield, Bradley M. Broom
Journal: Cancer Research
Cancer Res (2013) 73 (8_Supplement): 5132.
https://doi.org/10.1158/1538-7445.AM2013-5132
Published: 15 April 2013
View articletitled, Abstract 5132: Interactively exploring patterns in TCGA data: a web-based compendium of ‘next-generation’ clustered heat maps.