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Did you mean: (open cravat OR cravat OR mupi) AND (software OR tool OR bioinformatics OR disease OR "variant analysis" OR "mutation analysis" OR genetics OR cancer OR genomics OR protein OR sequencing) (513 items)

Select item 60294501.

Comprehensive Characterization of Cancer Driver Genes and Mutations

Matthew H. Bailey, Collin Tokheim, Eduard Porta-Pardo, Sohini Sengupta, Denis Bertrand, Amila Weerasinghe, Antonio Colaprico, Michael C. Wendl, Jaegil Kim, Brendan Reardon, Kwok-Shing Ng, Kang Jin Jeong, Song Cao, Zixing Wang, JianJiong Gao, Qingsong Gao, Fang Wang, Eric Minwei Liu, Loris Mularoni, Carlota Rubio-Perez, Niranjan Nagarajan, Isidro Cortés-Ciriano, Daniel Cui Zhou, Wen-Wei Liang, Julian M. Hess, Venkata D. Yellapantula, David Tamborero, Abel Gonzalez-Perez, Chayaporn Suphavilai, Jia Yu Ko, Ekta Khurana, Peter J. Park, Eliezer Van Allen, Han Liang, The MC3 Working Group, The Cancer Genome Atlas Research Network, Michael Lawrence, Adam Godzik, Nuria Lopez-Bigas, Josh Stuart, David Wheeler, Gad Getz, Ken Chen, Alexander J. Lazar, Gordon B Mills, Rachel Karchin, Li Ding

Cell. Author manuscript; available in PMC 2019 Apr 5.

Published in final edited form as: Cell. 2018 Apr 5; 173(2): 371–385.e18. doi: 10.1016/j.cell.2018.02.060

Correction in:: Cell. 2018 Aug 9; 174(4): 1034–1035.

PMCID:: PMC6029450

Abstract Article PDF–3.6M

Select item 71131032.

Integrated Informatics Analysis of Cancer-Related Variants

Kymberleigh A. Pagel, Rick Kim, Kyle Moad, Ben Busby, Lily Zheng, Collin Tokheim, Michael Ryan, Rachel Karchin

JCO Clin Cancer Inform. 2020; 4: CCI.19.00132. Published online 2020 Mar 30. doi: 10.1200/CCI.19.00132

PMCID:: PMC7113103

Abstract Article PDF–1.4M

Select item 58509453.

CRAVAT 4: Cancer-Related Analysis of Variants Toolkit

David L. Masica, Christopher Douville, Collin Tokheim, Rohit Bhattacharya, RyangGuk Kim, Kyle Moad, Michael C. Ryan, Rachel Karchin

Cancer Res. Author manuscript; available in PMC 2018 Nov 1.

Published in final edited form as: Cancer Res. 2017 Nov 1; 77(21): e35–e38. doi: 10.1158/0008-5472.CAN-17-0338

PMCID:: PMC5850945

Abstract Article PDF–618K

Select item 39195554.

Computational approaches to identify functional genetic variants in cancer genomes

Abel Gonzalez-Perez, Ville Mustonen, Boris Reva, Graham R.S. Ritchie, Pau Creixell, Rachel Karchin, Miguel Vazquez, J. Lynn Fink, Karin S. Kassahn, John V. Pearson, Gary Bader, Paul C. Boutros, Lakshmi Muthuswamy, B.F. Francis Ouellette, Jüri Reimand, Rune Linding, Tatsuhiro Shibata, Alfonso Valencia, Adam Butler, Serge Dronov, Paul Flicek, Nick B. Shannon, Hannah Carter, Li Ding, Chris Sander, Josh M. Stuart, Lincoln D. Stein, Nuria Lopez-Bigas, the ICGC Mutation Pathways and Consequences Subgroup of the Bioinformatics Analyses Working Group

Nat Methods. Author manuscript; available in PMC 2014 Aug 1.

Published in final edited form as: Nat Methods. 2013 Aug; 10(8): 723–729. doi: 10.1038/nmeth.2562

PMCID:: PMC3919555

Abstract Article PDF–596K

Select item 37978535.

MuPIT Interactive: Webserver for mapping variant positions to annotated, interactive 3D structures

Noushin Niknafs, Dewey Kim, Ryang Guk Kim, Mark Diekhans, Michael Ryan, Peter D. Stenson, David N. Cooper, Rachel Karchin

Hum Genet. Author manuscript; available in PMC 2014 Nov 1.

Published in final edited form as: Hum Genet. 2013 Nov; 132(11): 1235–1243. Published online 2013 Jun 23. doi: 10.1007/s00439-013-1325-0

PMCID:: PMC3797853

Abstract Article PDF–2.1M

Select item 57359286.

Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework

Gustavo Glusman, Peter W. Rose, Andreas Prlić, Jennifer Dougherty, José M. Duarte, Andrew S. Hoffman, Geoffrey J. Barton, Emøke Bendixen, Timothy Bergquist, Christian Bock, Elizabeth Brunk, Marija Buljan, Stephen K. Burley, Binghuang Cai, Hannah Carter, JianJiong Gao, Adam Godzik, Michael Heuer, Michael Hicks, Thomas Hrabe, Rachel Karchin, Julia Koehler Leman, Lydie Lane, David L. Masica, Sean D. Mooney, John Moult, Gilbert S. Omenn, Frances Pearl, Vikas Pejaver, Sheila M. Reynolds, Ariel Rokem, Torsten Schwede, Sicheng Song, Hagen Tilgner, Yana Valasatava, Yang Zhang, Eric W. Deutsch

Genome Med. 2017; 9: 113. Published online 2017 Dec 18. doi: 10.1186/s13073-017-0509-y

PMCID:: PMC5735928

Abstract Article PDF–456K

Select item 102515777.

3DVizSNP: a tool for rapidly visualizing missense mutations identified in high throughput experiments in iCn3D

Michael Sierk, Shashikala Ratnayake, Manoj M. Wagle, Ben Chen, Brian Park, Jiyao Wang, Philippe Youkharibache, Daoud Meerzaman

BMC Bioinformatics. 2023; 24: 244. Published online 2023 Jun 9. doi: 10.1186/s12859-023-05370-5

PMCID:: PMC10251577

Abstract Article PDF–1.2M

Select item 35822728.

CRAVAT: cancer-related analysis of variants toolkit

Christopher Douville, Hannah Carter, Rick Kim, Noushin Niknafs, Mark Diekhans, Peter D. Stenson, David N. Cooper, Michael Ryan, Rachel Karchin

Bioinformatics. 2013 Mar 1; 29(5): 647–648. Published online 2013 Jan 16. doi: 10.1093/bioinformatics/btt017

PMCID:: PMC3582272

Abstract Article PDF–126K

Select item 95571419.

The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms

Kimberly Walker, Divya Kalra, Rebecca Lowdon, Guangyi Chen, David Molik, Daniela C. Soto, Fawaz Dabbaghie, Ahmad Al Khleifat, Medhat Mahmoud, Luis F Paulin, Muhammad Sohail Raza, Susanne P. Pfeifer, Daniel Paiva Agustinho, Elbay Aliyev, Pavel Avdeyev, Enrico R. Barrozo, Sairam Behera, Kimberley Billingsley, Li Chuin Chong, Deepak Choubey, Wouter De Coster, Yilei Fu, Alejandro R. Gener, Timothy Hefferon, David Morgan Henke, Wolfram Höps, Anastasia Illarionova, Michael D. Jochum, Maria Jose, Rupesh K. Kesharwani, Sree Rohit Raj Kolora, Jędrzej Kubica, Priya Lakra, Damaris Lattimer, Chia-Sin Liew, Bai-Wei Lo, Chunhsuan Lo, Anneri Lötter, Sina Majidian, Suresh Kumar Mendem, Rajarshi Mondal, Hiroko Ohmiya, Nasrin Parvin, Carolina Peralta, Chi-Lam Poon, Ramanandan Prabhakaran, Marie Saitou, Aditi Sammi, Philippe Sanio, Nicolae Sapoval, Najeeb Syed, Todd Treangen, Gaojianyong Wang, Tiancheng Xu, Jianzhi Yang, Shangzhe Zhang, Weiyu Zhou, Fritz J Sedlazeck, Ben Busby

Version 1. F1000Res. 2022; 11: 530. Published online 2022 May 16. doi: 10.12688/f1000research.110194.1

PMCID:: PMC9557141

Abstract Article PDF–5.8M

Select item 643845610.

Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers

Ruth Nussinov, Hyunbum Jang, Chung-Jung Tsai, Feixiong Cheng

PLoS Comput Biol. 2019 Mar; 15(3): e1006658. Published online 2019 Mar 28. doi: 10.1371/journal.pcbi.1006658

Correction in:: PLoS Comput Biol. 2019 Jun; 15(6): e1007114.

PMCID:: PMC6438456

Abstract Article PDF–5.9M

Select item 659794411.

PhyreRisk: A Dynamic Web Application to Bridge Genomics, Proteomics and 3D Structural Data to Guide Interpretation of Human Genetic Variants

Tochukwu C. Ofoegbu, Alessia David, Lawrence A. Kelley, Stefans Mezulis, Suhail A. Islam, Sophia F. Mersmann, Léonie Strömich, Ilya A. Vakser, Richard S. Houlston, Michael J.E. Sternberg

J Mol Biol. 2019 Jun 14; 431(13): 2460–2466. doi: 10.1016/j.jmb.2019.04.043

PMCID:: PMC6597944

Abstract Article PDF–1.0M

Select item 592620112.

Systematic Functional Annotation of Somatic Mutations in Cancer

Patrick Kwok-Shing Ng, Jun Li, Kang Jin Jeong, Shan Shao, Hu Chen, Yiu Huen Tsang, Sohini Sengupta, Zixing Wang, Venkata Hemanjani Bhavana, Richard Tran, Stephanie Soewito, Darlan Conterno Minussi, Daniela Moreno, Kathleen Kong, Turgut Dogruluk, Hengyu Lu, Jianjiong Gao, Collin Tokheim, Daniel Cui Zhou, Amber M. Johnson, Jia Zeng, Carman Ka Man Ip, Zhenlin Ju, Matthew Wester, Shuangxing Yu, Yongsheng Li, Christopher P. Vellano, Nikolaus Schultz, Rachel Karchin, Li Ding, Yiling Lu, Lydia Wai Ting Cheung, Ken Chen, Kenna R. Shaw, Funda Meric-Bernstam, Kenneth L. Scott, Song Yi, Nidhi Sahni, Han Liang, Gordon B. Mills

Cancer Cell. Author manuscript; available in PMC 2019 Mar 12.

Published in final edited form as: Cancer Cell. 2018 Mar 12; 33(3): 450–462.e10. doi: 10.1016/j.ccell.2018.01.021

PMCID:: PMC5926201

Abstract Article PDF–1.0M

Select item 1109874113.

Single-nucleotide variant calling in single-cell sequencing data with Monopogen

Jinzhuang Dou, Yukun Tan, Kian Hong Kock, Jun Wang, Xuesen Cheng, Le Min Tan, Kyung Yeon Han, Chung-Chau Hon, Woong-Yang Park, Jay W. Shin, Haijing Jin, Yujia Wang, Han Chen, Li Ding, Shyam Prabhakar, Nicholas Navin, Rui Chen, Ken Chen

Nat Biotechnol. 2024; 42(5): 803–812. Published online 2023 Aug 17. doi: 10.1038/s41587-023-01873-x

PMCID:: PMC11098741

Abstract Article PDF–3.4M

Select item 449921614.

Identification of cancer predisposition variants in apparently healthy individuals using a next-generation sequencing-based family genomics approach

Ioannis Karageorgos, Clint Mizzi, Efstathia Giannopoulou, Cristiana Pavlidis, Brock A. Peters, Zoi Zagoriti, Peter D. Stenson, Konstantinos Mitropoulos, Joseph Borg, Haralabos P. Kalofonos, Radoje Drmanac, Andrew Stubbs, Peter van der Spek, David N. Cooper, Theodora Katsila, George P. Patrinos

Hum Genomics. 2015; 9(1): 12. Published online 2015 Jun 20. doi: 10.1186/s40246-015-0034-2

PMCID:: PMC4499216

Abstract Article PDF–1.2M

Select item 819986215.

Identifying Cancer Drivers Using DRIVE: A Feature-Based Machine Learning Model for a Pan-Cancer Assessment of Somatic Missense Mutations

Ionut Dragomir, Adnan Akbar, John W. Cassidy, Nirmesh Patel, Harry W. Clifford, Gianmarco Contino

Cancers (Basel) 2021 Jun; 13(11): 2779. Published online 2021 Jun 3. doi: 10.3390/cancers13112779

PMCID:: PMC8199862

Abstract Article PDF–1016K

Select item 951403316.

VIVID: A Web Application for Variant Interpretation and Visualization in Multi-dimensional Analyses

Swapnil Tichkule, Yoochan Myung, Myo T Naung, Brendan R E Ansell, Andrew J Guy, Namrata Srivastava, Somya Mehra, Simone M Cacciò, Ivo Mueller, Alyssa E Barry, Cock van Oosterhout, Bernard Pope, David B Ascher, Aaron R Jex

Mol Biol Evol. 2022 Sep; 39(9): msac196. Published online 2022 Sep 14. doi: 10.1093/molbev/msac196

PMCID:: PMC9514033

Abstract Article PDF–737K

Select item 672466917.

Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE): a cloud-based platform for curating and classifying germline variants

Michael N. Edmonson, Aman N. Patel, Dale J. Hedges, Zhaoming Wang, Evadnie Rampersaud, Chimene A. Kesserwan, Xin Zhou, Yanling Liu, Scott Newman, Michael C. Rusch, Clay L. McLeod, Mark R. Wilkinson, Stephen V. Rice, Thierry Soussi, J. Paul Taylor, Michael Benatar, Jared B. Becksfort, Kim E. Nichols, Leslie L. Robison, James R. Downing, Jinghui Zhang

Genome Res. 2019 Sep; 29(9): 1555–1565. doi: 10.1101/gr.250357.119

PMCID:: PMC6724669

Abstract Article PDF–3.0M

Select item 366558118.

Assessment of computational methods for predicting the effects of missense mutations in human cancers

Florian Gnad, Albion Baucom, Kiran Mukhyala, Gerard Manning, Zemin Zhang

BMC Genomics. 2013; 14(Suppl 3): S7. Published online 2013 May 28. doi: 10.1186/1471-2164-14-S3-S7

PMCID:: PMC3665581

Abstract Article PDF–2.3M

Select item 837185619.

PhenoDB, GeneMatcher and VariantMatcher, tools for analysis and sharing of sequence data

Elizabeth Wohler, Renan Martin, Sean Griffith, Eliete da S. Rodrigues, Corina Antonescu, Jennifer E. Posey, Zeynep Coban-Akdemir, Shalini N. Jhangiani, Kimberly F. Doheny, James R. Lupski, David Valle, Ada Hamosh, Nara Sobreira

Orphanet J Rare Dis. 2021; 16: 365. Published online 2021 Aug 18. doi: 10.1186/s13023-021-01916-z

PMCID:: PMC8371856

Abstract Article PDF–1.3M

Select item 982560820.

CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase

Kilannin Krysiak, Arpad M Danos, Jason Saliba, Joshua F McMichael, Adam C Coffman, Susanna Kiwala, Erica K Barnell, Lana Sheta, Cameron J Grisdale, Lynzey Kujan, Shahil Pema, Jake Lever, Sarah Ridd, Nicholas C Spies, Veronica Andric, Andreea Chiorean, Damian T Rieke, Kaitlin A Clark, Caralyn Reisle, Ajay C Venigalla, Mark Evans, Payal Jani, Hideaki Takahashi, Avila Suda, Peter Horak, Deborah I Ritter, Xin Zhou, Benjamin J Ainscough, Sean Delong, Chimene Kesserwan, Mario Lamping, Haolin Shen, Alex R Marr, My H Hoang, Kartik Singhal, Mariam Khanfar, Brian V Li, Wan-Hsin Lin, Panieh Terraf, Laura B Corson, Yasser Salama, Katie M Campbell, Kirsten M Farncombe, Jianling Ji, Xiaonan Zhao, Xinjie Xu, Rashmi Kanagal-Shamanna, Ian King, Kelsy C Cotto, Zachary L Skidmore, Jason R Walker, Jinghui Zhang, Aleksandar Milosavljevic, Ronak Y Patel, Rachel H Giles, Raymond H Kim, Lynn M Schriml, Elaine R Mardis, Steven J M Jones, Gordana Raca, Shruti Rao, Subha Madhavan, Alex H Wagner, Malachi Griffith, Obi L Griffith

Nucleic Acids Res. 2023 Jan 6; 51(D1): D1230–D1241. Published online 2022 Nov 14. doi: 10.1093/nar/gkac979

PMCID:: PMC9825608

Abstract Article PDF–2.4M

Did you mean: (open cravat OR cravat OR mupi) AND (software OR tool OR bioinformatics OR disease OR "variant analysis" OR "mutation analysis" OR genetics OR cancer OR genomics OR protein OR sequencing) (513 items)

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