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Results: 2596
Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig.
Yulia Rubanova, Ruian Shi, Caitlin F Harrigan, Roujia Li, Jeff Wintersinger, Nil Sahin, Amit G Deshwar, PCAWG Evolution and Heterogeneity Working Group, Quaid D Morris, PCAWG Consortium
Feb 04, 2021
The type and genomic context of cancer mutations depend on their causes. These causes have been characterized using signatures that represent mutation types that co-occur in the same tumours. However, it remains unclear how...
Inferring structural variant cancer cell fraction.
Marek Cmero, Ke Yuan, Cheng Soon Ong, Jan Schröder, PCAWG Evolution and Heterogeneity Working Group, Niall M Corcoran, Tony Papenfuss, Christopher M Hovens, Florian Markowetz, Geoff Macintyre, PCAWG Consortium
Dec 18, 2019
We present SVclone, a computational method for inferring the cancer cell fraction of structural variant (SV) breakpoints from whole-genome sequencing data. SVclone accurately determines the variant allele frequencies of both SV...
Butler enables rapid cloud-based analysis of thousands of human genomes.
Sergei Yakneen, Sebastian M Waszak, PCAWG Technical Working Group, Michael Gertz, Jan O Korbel, PCAWG Consortium
Feb 04, 2021
We present Butler, a computational tool that facilitates large-scale genomic analyses on public and academic clouds. Butler includes innovative anomaly detection and self-healing functions that improve the efficiency of data...
The evolutionary history of 2,658 cancers.
Moritz Gerstung, Clemency Jolly, Ignaty Leshchiner, Stefan C Dentro, Santiago Gonzalez, Daniel Rosebrock, Thomas J Mitchell, Yulia Rubanova, Pavana Anur, Kaixian Yu, Maxime Tarabichi, Amit Deshwar, Jeff Wintersinger, Kortine Kleinheinz, Ignacio Vázquez-García, Kerstin Haase, Lara Jerman, Subhajit Sengupta, Geoff Macintyre, Salem Malikic, Nilgun Donmez, Dimitri G Livitz, Marek Cmero, Jonas Demeulemeester, Steven Schumacher, Yu Fan, Xiaotong Yao, Juhee Lee, Matthias Schlesner, Paul C Boutros, David D Bowtell, Hongtu Zhu, Gad Getz, Marcin Imielinski, Rameen Beroukhim, S Cenk Sahinalp, Yuan Ji, Martin Peifer, Florian Markowetz, Ville Mustonen, Ke Yuan, Wenyi Wang, Quaid D Morris, PCAWG Evolution & Heterogeneity Working Group, Paul T Spellman, David C Wedge, Peter Van Loo, PCAWG Consortium
Feb 04, 2021
Cancer develops through a process of somatic evolution1,2. Sequencing data from a single biopsy represent a snapshot of this process that can reveal the timing of specific genomic aberrations and the changing influence of...
Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis.
Joana Carlevaro-Fita, Andrés Lanzós, Lars Feuerbach, Chen Hong, David Mas-Ponte, Jakob Skou Pedersen, PCAWG Drivers and Functional Interpretation Group, Rory Johnson, PCAWG Consortium
Feb 17, 2021
Long non-coding RNAs (lncRNAs) are a growing focus of cancer genomics studies, creating the need for a resource of lncRNAs with validated cancer roles. Furthermore, it remains debated whether mutated lncRNAs can drive...
Genomic footprints of activated telomere maintenance mechanisms in cancer.
Lina Sieverling, Chen Hong, Sandra D Koser, Philip Ginsbach, Kortine Kleinheinz, Barbara Hutter, Delia M Braun, Isidro Cortés-Ciriano, Ruibin Xi, Rolf Kabbe, Peter J Park, Roland Eils, Matthias Schlesner, PCAWG-Structural Variation Working Group, Benedikt Brors, Karsten Rippe, David TW Jones, Lars Feuerbach, PCAWG Consortium
Mar 05, 2021
Cancers require telomere maintenance mechanisms for unlimited replicative potential. They achieve this through TERT activation or alternative telomere lengthening associated with ATRX or DAXX loss. Here, as part of the ICGC/TCGA...
Sex differences in oncogenic mutational processes.
Constance H Li, Stephenie D Prokopec, Ren X Sun, Fouad Yousif, Nathaniel Schmitz, PCAWG Tumour Subtypes and Clinical Translation, Paul C Boutros, PCAWG Consortium
Sep 11, 2020
Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have...
A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns.
Wei Jiao, Gurnit Atwal, Paz Polak, Rosa Karlic, Edwin Cuppen, PCAWG Tumor Subtypes and Clinical Translation Working Group, Alexandra Danyi, Jeroen de Ridder, Carla van Herpen, Martijn P Lolkema, Neeltje Steeghs, Gad Getz, Quaid D Morris, Lincoln D Stein, PCAWG Consortium
May 14, 2020
In cancer, the primary tumour's organ of origin and histopathology are the strongest determinants of its clinical behaviour, but in 3% of cases a patient presents with a metastatic tumour and no obvious primary. Here, as part of...
Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer.
Kadir C Akdemir, Victoria T Le, Sahaana Chandran, Yilong Li, Roel G Verhaak, Rameen Beroukhim, Peter J Campbell, Lynda Chin, Jesse R Dixon, P Andrew Futreal, PCAWG Structural Variation Working Group, PCAWG Consortium
Feb 04, 2021
Chromatin is folded into successive layers to organize linear DNA. Genes within the same topologically associating domains (TADs) demonstrate similar expression and histone-modification profiles, and boundaries separating...
High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations.
Yiqun Zhang, Fengju Chen, Nuno A Fonseca, Yao He, Masashi Fujita, Hidewaki Nakagawa, Zemin Zhang, Alvis Brazma, PCAWG Transcriptome Working Group, PCAWG Structural Variation Working Group, Chad J Creighton, PCAWG Consortium
Feb 04, 2021
The impact of somatic structural variants (SVs) on gene expression in cancer is largely unknown. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole-genome sequencing...
Pathway and network analysis of more than 2500 whole cancer genomes.
Matthew A Reyna, David Haan, Marta Paczkowska, Lieven PC 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 MG 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
Feb 04, 2021
The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the past decade. However, non-coding cancer driver mutations are less well-characterized and only a handful of recurrent non-coding...
Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.
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
Oct 12, 2020
The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the...
Patterns of somatic structural variation in human cancer genomes.
Yilong Li, Nicola D Roberts, Jeremiah A Wala, Ofer Shapira, Steven E Schumacher, Kiran Kumar, Ekta Khurana, Sebastian Waszak, Jan O Korbel, James E Haber, Marcin Imielinski, PCAWG Structural Variation Working Group, Joachim Weischenfeldt, Rameen Beroukhim, Peter J Campbell, PCAWG Consortium
Feb 04, 2021
A key mutational process in cancer is structural variation, in which rearrangements delete, amplify or reorder genomic segments that range in size from kilobases to whole chromosomes1-7. Here we develop methods to group...
The repertoire of mutational signatures in human cancer.
Ludmil B Alexandrov, Jaegil Kim, Nicholas J Haradhvala, Mi Ni Huang, Alvin Wei Tian Ng, Yang Wu, Arnoud Boot, Kyle R Covington, Dmitry A Gordenin, Erik N Bergstrom, SM Ashiqul Islam, Nuria Lopez-Bigas, Leszek J Klimczak, John R McPherson, Sandro Morganella, Radhakrishnan Sabarinathan, David A Wheeler, Ville Mustonen, PCAWG Mutational Signatures Working Group, Gad Getz, Steven G Rozen, Michael R Stratton, PCAWG Consortium
Feb 04, 2021
Somatic mutations in cancer genomes are caused by multiple mutational processes, each of which generates a characteristic mutational signature1. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium2 of...
Genomic basis for RNA alterations in cancer.
PCAWG Transcriptome Core Group, Claudia Calabrese, Natalie R Davidson, Deniz Demircioğlu, Nuno A Fonseca, Yao He, André Kahles, Kjong-Van Lehmann, Fenglin Liu, Yuichi Shiraishi, Cameron M Soulette, Lara Urban, Liliana Greger, Siliang Li, Dongbing Liu, Marc D Perry, Qian Xiang, Fan Zhang, Junjun Zhang, Peter Bailey, Serap Erkek, Katherine A Hoadley, Yong Hou, Matthew R Huska, Helena Kilpinen, Jan O Korbel, Maximillian G Marin, Julia Markowski, Tannistha Nandi, Qiang Pan-Hammarström, Chandra Sekhar Pedamallu, Reiner Siebert, Stefan G Stark, Hong Su, Patrick Tan, Sebastian M Waszak, Christina Yung, Shida Zhu, Philip Awadalla, Chad J Creighton, Matthew Meyerson, BF Francis Ouellette, Kui Wu, Huanming Yang, PCAWG Transcriptome Working Group, Alvis Brazma, Angela N Brooks, Jonathan Göke, Gunnar Rätsch, Roland F Schwarz, Oliver Stegle, Zemin Zhang, PCAWG Consortium
Feb 04, 2021
Transcript alterations often result from somatic changes in cancer genomes1. Various forms of RNA alterations have been described in cancer, including overexpression2, altered splicing3 and gene fusions4; however, it is...
Pan-cancer analysis of whole genomes
Peter J. Campbell, Gad Getz, Jan O. Korbel, Joshua M. Stuart, Jennifer L. Jennings, Lincoln D. Stein, Marc D. Perry, Hardeep K. Nahal-Bose, B. F. Francis Ouellette, Constance H. Li, Esther Rheinbay, G. Petur Nielsen, Dennis C. Sgroi, Chin-Lee Wu, William C. Faquin, Vikram Deshpande, Paul C. Boutros, Alexander J. Lazar, Katherine A. Hoadley, David N. Louis, L. Jonathan Dursi, Christina K. Yung, Matthew H. Bailey, Gordon Saksena, Keiran M. Raine, Ivo Buchhalter, Kortine Kleinheinz, Matthias Schlesner, Junjun Zhang, Wenyi Wang, David A. Wheeler, Li Ding, Jared T. Simpson, Brian D. O’Connor, Sergei Yakneen, Kyle Ellrott, Naoki Miyoshi, Adam P. Butler, Romina Royo, Solomon I. Shorser, Miguel Vazquez, Tobias Rausch, Grace Tiao, Sebastian M. Waszak, Bernardo Rodriguez-Martin, Suyash Shringarpure, Dai-Ying Wu, German M. Demidov, Olivier Delaneau, Shuto Hayashi, Seiya Imoto, Nina Habermann, Ayellet V. Segre, Erik Garrison, Andy Cafferkey, Eva G. Alvarez, José María Heredia-Genestar, Francesc Muyas, Oliver Drechsel, Alicia L. Bruzos, Javier Temes, Jorge Zamora, Adrian Baez-Ortega, Hyung-Lae Kim, R. Jay Mashl, Kai Ye, Anthony DiBiase, Kuan-lin Huang, Ivica Letunic, Michael D. McLellan, Steven J. Newhouse, Tal Shmaya, Sushant Kumar, David C. Wedge, Mark H. Wright, Venkata D. Yellapantula, Mark Gerstein, Ekta Khurana, Tomas Marques-Bonet, Arcadi Navarro, Carlos D. Bustamante, Reiner Siebert, Hidewaki Nakagawa, Douglas F. Easton, Stephan Ossowski, Jose M. C. Tubio, Francisco M. De La Vega, Xavier Estivill, Denis Yuen, George L. Mihaiescu, Larsson Omberg, Vincent Ferretti, Radhakrishnan Sabarinathan, Oriol Pich, Abel Gonzalez-Perez, Amaro Taylor-Weiner, Matthew W. Fittall, Jonas Demeulemeester, Maxime Tarabichi, Nicola D. Roberts, Peter Van Loo, Isidro Cortés-Ciriano, Lara Urban, Peter Park, Bin Zhu, Esa Pitkänen, Yilong Li, Natalie Saini, Leszek J. Klimczak, Joachim Weischenfeldt, Nikos Sidiropoulos, Ludmil B. Alexandrov, Raquel Rabionet, Georgia Escaramis, Mattia Bosio, Aliaksei Z. Holik, Hana Susak, Aparna Prasad, Serap Erkek, Claudia Calabrese, Benjamin Raeder, Eoghan Harrington, Simon Mayes, Daniel Turner, Sissel Juul, Steven A. Roberts, Lei Song, Roelof Koster, Lisa Mirabello, Xing Hua, Tomas J. Tanskanen, Marta Tojo, Jieming Chen, Lauri A. Aaltonen, Gunnar Rätsch, Roland F. Schwarz, Atul J. Butte, Alvis Brazma, Stephen J. Chanock, Nilanjan Chatterjee, Oliver Stegle, Olivier Harismendy, G. Steven Bova, Dmitry A. Gordenin, David Haan, Lina Sieverling, Lars Feuerbach, Don Chalmers, Yann Joly, Bartha Knoppers, Fruzsina Molnár-Gábor, Mark Phillips, Adrian Thorogood, David Townend, Mary Goldman, Nuno A. Fonseca, Qian Xiang, Brian Craft, Elena Piñeiro-Yáñez, Alfonso Muñoz, Robert Petryszak, Anja Füllgrabe, Fatima Al-Shahrour, Maria Keays, David Haussler, John Weinstein, Wolfgang Huber, Alfonso Valencia, Irene Papatheodorou, Jingchun Zhu, Yu Fan, David Torrents, Matthias Bieg, Ken Chen, Zechen Chong, Kristian Cibulskis, Roland Eils, Robert S. Fulton, Josep L. Gelpi, Santiago Gonzalez, Ivo G. Gut, Faraz Hach, Michael Heinold, Taobo Hu, Vincent Huang, Barbara Hutter, Natalie Jäger, Jongsun Jung, Yogesh Kumar, Christopher Lalansingh, Ignaty Leshchiner, Dimitri Livitz, Eric Z. Ma, Yosef E. Maruvka, Ana Milovanovic, Morten Muhlig Nielsen, Nagarajan Paramasivam, Jakob Skou Pedersen, Montserrat Puiggròs, S. Cenk Sahinalp, Iman Sarrafi, Chip Stewart, Miranda D. Stobbe, Jeremiah A. Wala, Jiayin Wang, Michael Wendl, Johannes Werner, Zhenggang Wu, Hong Xue, Takafumi N. Yamaguchi, Venkata Yellapantula, Brandi N. Davis-Dusenbery, Robert L. Grossman, Youngwook Kim, Michael C. Heinold, Jonathan Hinton, David R. Jones, Andrew Menzies, Lucy Stebbings, Julian M. Hess, Mara Rosenberg, Andrew J. Dunford, Manaswi Gupta, Marcin Imielinski, Matthew Meyerson, Rameen Beroukhim, Jüri Reimand, Priyanka Dhingra, Francesco Favero, Stefan Dentro, Jeff Wintersinger, Vasilisa Rudneva, Ji Wan Park, Eun Pyo Hong, Seong Gu Heo, André Kahles, Kjong-Van Lehmann, Cameron M. Soulette, Yuichi Shiraishi, Fenglin Liu, Yao He, Deniz Demircioğlu, Natalie R. Davidson, Liliana Greger, Siliang Li, Dongbing Liu, Stefan G. Stark, Fan Zhang, Samirkumar B. Amin, Peter Bailey, Aurélien Chateigner, Milana Frenkel-Morgenstern, Yong Hou, Matthew R. Huska, Helena Kilpinen, Fabien C. Lamaze, Chang Li, Xiaobo Li, Xinyue Li, Xingmin Liu, Maximillian G. Marin, Julia Markowski, Tannistha Nandi, Akinyemi I. Ojesina, Qiang Pan-Hammarström, Peter J. Park, Chandra Sekhar Pedamallu, Hong Su, Patrick Tan, Bin Tean Teh, Jian Wang, Heng Xiong, Chen Ye, Christina Yung, Xiuqing Zhang, Liangtao Zheng, Shida Zhu, Philip Awadalla, Chad J. Creighton, Kui Wu, Huanming Yang, Jonathan Göke, Zemin Zhang, Angela N. Brooks, Matthew W Fittall, Iñigo Martincorena, Carlota Rubio-Perez, Malene Juul, Steven Schumacher, Ofer Shapira, David Tamborero, Loris Mularoni, Henrik Hornshøj, Jordi Deu-Pons, Ferran Muiños, Johanna Bertl, Qianyun Guo, Wojciech Bazant, Elisabet Barrera, Sultan T. Al-Sedairy, Axel Aretz, Cindy Bell, Miguel Betancourt, Christiane Buchholz, Fabien Calvo, Christine Chomienne, Michael Dunn, Stuart Edmonds, Eric Green, Shailja Gupta, Carolyn M. Hutter, Karine Jegalian, Nic Jones, Youyong Lu, Hitoshi Nakagama, Gerd Nettekoven, Laura Planko, David Scott, Tatsuhiro Shibata, Kiyo Shimizu, Michael R. Stratton, Takashi Yugawa, Giampaolo Tortora, K. VijayRaghavan, Jean C. Zenklusen, Bartha M. Knoppers, Brice Aminou, Javier Bartolome, Keith A. Boroevich, Rich Boyce, Alex Buchanan, Niall J. Byrne, Zhaohong Chen, Sunghoon Cho, Wan Choi, Peter Clapham, Michelle T. Dow, Lewis Jonathan Dursi, Juergen Eils, Claudiu Farcas, Nodirjon Fayzullaev, Paul Flicek, Allison P. Heath, Oliver Hofmann, Jongwhi H. Hong, Thomas J. Hudson, Daniel Hübschmann, Sinisa Ivkovic, Seung-Hyup Jeon, Wei Jiao, Rolf Kabbe, Andre Kahles, Jules N. A. Kerssemakers, Hyunghwan Kim, Jihoon Kim, Michael Koscher, Antonios Koures, Milena Kovacevic, Chris Lawerenz, Jia Liu, Sanja Mijalkovic, Ana Mijalkovic Mijalkovic-Lazic, Satoru Miyano, Mia Nastic, Jonathan Nicholson, David Ocana, Kazuhiro Ohi, Lucila Ohno-Machado, Todd D. Pihl, Manuel Prinz, Petar Radovic, Charles Short, Heidi J. Sofia, Jonathan Spring, Adam J. Struck, Nebojsa Tijanic, David Vicente, Zhining Wang, Ashley Williams, Youngchoon Woo, Adam J. Wright, Liming Yang, Mark P. Hamilton, Todd A. Johnson, Abdullah Kahraman, Manolis Kellis, Paz Polak, Richard Sallari, Nasa Sinnott-Armstrong, Christian von Mering, Sergi Beltran, Daniela S. Gerhard, Marta Gut, Jean-Rémi Trotta, Justin P. Whalley, Beifang Niu, Shadrielle M. G. Espiritu, Shengjie Gao, Yi Huang, Christopher M. Lalansingh, Jon W. Teague, Michael C. Wendl, Federico Abascal, Gary D. Bader, Pratiti Bandopadhayay, Jonathan Barenboim, Søren Brunak, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin Wing Yiu Chan, Jung Kyoon Choi, Klev Diamanti, J. Lynn Fink, Joan Frigola, Carlo Gambacorti-Passerini, Dale W. Garsed, Nicholas J. Haradhvala, Arif O. Harmanci, Mohamed Helmy, Carl Herrmann, Asger Hobolth, Ermin Hodzic, Chen Hong, Keren Isaev, Jose M. G. Izarzugaza, Rory Johnson, Randi Istrup Juul, Jaegil Kim, Jong K. Kim, Jan Komorowski, Andrés Lanzós, Erik Larsson, Donghoon Lee, Shantao Li, Xiaotong Li, Ziao Lin, Eric Minwei Liu, Lucas Lochovsky, Shaoke Lou, Tobias Madsen, Kathleen Marchal, Alexander Martinez-Fundichely, Patrick D. McGillivray, William Meyerson, Marta Paczkowska, Keunchil Park, Kiejung Park, Tirso Pons, Sergio Pulido-Tamayo, Iker Reyes-Salazar, Matthew A. Reyna, Mark A. Rubin, Leonidas Salichos, Chris Sander, Steven E. Schumacher, Mark Shackleton, Ciyue Shen, Raunak Shrestha, Shimin Shuai, Tatsuhiko Tsunoda, Husen M. Umer, Liis Uusküla-Reimand, Lieven P. C. Verbeke, Claes Wadelius, Lina Wadi, Jonathan Warrell, Guanming Wu, Jun Yu, Jing Zhang, Xuanping Zhang, Yan Zhang, Zhongming Zhao, Lihua Zou, Michael S. Lawrence, Benjamin J. Raphael, Peter J. Bailey, David Craft, Mary J. Goldman, Hiroyuki Aburatani, Hans Binder, Huy Q. Dinh, Simon C. Heath, Steve Hoffmann, Charles David Imbusch, Helene Kretzmer, Peter W. Laird, Jose I. Martin-Subero, Genta Nagae, Hui Shen, Qi Wang, Dieter Weichenhan, Wanding Zhou, Benjamin P. Berman, Benedikt Brors, Christoph Plass, Kadir C. Akdemir, David D. L. Bowtell, Kathleen H. Burns, John Busanovich, Kin Chan, Ana Dueso-Barroso, Paul A. Edwards, Dariush Etemadmoghadam, James E. Haber, David T. W. Jones, Young Seok Ju, Marat D. Kazanov, Youngil Koh, Kiran Kumar, Eunjung Alice Lee, Jake June-Koo Lee, Andy G. Lynch, Geoff Macintyre, Florian Markowetz, Fabio C. P. Navarro, John V. Pearson, Karsten Rippe, Ralph Scully, Izar Villasante, Nicola Waddell, Lixing Yang, Xiaotong Yao, Sung-Soo Yoon, Cheng-Zhong Zhang, Erik N. Bergstrom, Arnoud Boot, Kyle Covington, Akihiro Fujimoto, Mi Ni Huang, S. M. Ashiqul Islam, John R. McPherson, Sandro Morganella, Ville Mustonen, Alvin Wei Tian Ng, Stephenie D. Prokopec, Ignacio Vázquez-García, Yang Wu, Fouad Yousif, Willie Yu, Steven G. Rozen, Vasilisa A. Rudneva, Suyash S. Shringarpure, Daniel J. Turner, Tian Xia, Gurnit Atwal, David K. Chang, Susanna L. Cooke, Bishoy M. Faltas, Syed Haider, Vera B. Kaiser, Rosa Karlić, Mamoru Kato, Kirsten Kübler, Adam Margolin, Sancha Martin, Serena Nik-Zainal, Christine P’ng, Colin A. Semple, Jaclyn Smith, Ren X. Sun, Kevin Thai, Derek W. Wright, Ke Yuan, Andrew V. Biankin, Levi Garraway, Sean M. Grimmond, David J. Adams, Pavana Anur, Shaolong Cao, Elizabeth L. Christie, Marek Cmero, Yupeng Cun, Kevin J. Dawson, Stefan C. Dentro, Amit G. Deshwar, Nilgun Donmez, Ruben M. Drews, Moritz Gerstung, Gavin Ha, Kerstin Haase, Lara Jerman, Yuan Ji, Clemency Jolly, Juhee Lee, Henry Lee-Six, Salem Malikic, Thomas J. Mitchell, Quaid D. Morris, Layla Oesper, Martin Peifer, Myron Peto, Daniel Rosebrock, Yulia Rubanova, Adriana Salcedo, Subhajit Sengupta, Ruian Shi, Seung Jun Shin, Oliver Spiro, Shankar Vembu, Jeffrey A. Wintersinger, Tsun-Po Yang, Kaixian Yu, Hongtu Zhu, Paul T. Spellman, John N. Weinstein, Yiwen Chen, Masashi Fujita, Leng Han, Takanori Hasegawa, Mitsuhiro Komura, Jun Li, Shinichi Mizuno, Eigo Shimizu, Yumeng Wang, Yanxun Xu, Rui Yamaguchi, Fan Yang, Yang Yang, Christopher J. Yoon, Yuan Yuan, Han Liang, Malik Alawi, Ivan Borozan, Daniel S. Brewer, Colin S. Cooper, Nikita Desai, Adam Grundhoff, Murat Iskar, Xiaoping Su, Marc Zapatka, Peter Lichter, Kathryn Alsop, Timothy J. C. Bruxner, Angelika N. Christ, Stephen M. Cordner, Prue A. Cowin, Ronny Drapkin, Sian Fereday, Joshy George, Anne Hamilton, Oliver Holmes, Jillian A. Hung, Karin S. Kassahn, Stephen H. Kazakoff, Catherine J. Kennedy, Conrad R. Leonard, Linda Mileshkin, David K. Miller, Gisela Mir Arnau, Chris Mitchell, Felicity Newell, Katia Nones, Ann-Marie Patch, Michael C. Quinn, Darrin F. Taylor, Heather Thorne, Nadia Traficante, Ravikiran Vedururu, Nick M. Waddell, Paul M. Waring, Scott Wood, Qinying Xu, Anna DeFazio, Matthew J. Anderson, Davide Antonello, Andrew P. Barbour, Claudio Bassi, Samantha Bersani, Ivana Cataldo, Lorraine A. Chantrill, Yoke-Eng Chiew, Angela Chou, Sara Cingarlini, Nicole Cloonan, Vincenzo Corbo, Maria Vittoria Davi, Fraser R. Duthie, Anthony J. Gill, Janet S. Graham, Ivon Harliwong, Nigel B. Jamieson, Amber L. Johns, James G. Kench, Luca Landoni, Rita T. Lawlor, Andrea Mafficini, Neil D. Merrett, Marco Miotto, Elizabeth A. Musgrove, Adnan M. Nagrial, Karin A. Oien, Marina Pajic, Mark Pinese, Alan J. Robertson, Ilse Rooman, Borislav C. Rusev, Jaswinder S. Samra, Maria Scardoni, Christopher J. Scarlett, Aldo Scarpa, Elisabetta Sereni, Katarzyna O. Sikora, Michele Simbolo, Morgan L. Taschuk, Christopher W. Toon, Caterina Vicentini, Jianmin Wu, Nikolajs Zeps, Andreas Behren, Hazel Burke, Jonathan Cebon, Rebecca A. Dagg, Ricardo De Paoli-Iseppi, Ken Dutton-Regester, Matthew A. Field, Anna Fitzgerald, Peter Hersey, Valerie Jakrot, Peter A. Johansson, Hojabr Kakavand, Richard F. Kefford, Loretta M. S. Lau, Georgina V. Long, Hilda A. Pickett, Antonia L. Pritchard, Gulietta M. Pupo, Robyn P. M. Saw, Sarah-Jane Schramm, Catherine A. Shang, Ping Shang, Andrew J. Spillane, Jonathan R. Stretch, Varsha Tembe, John F. Thompson, Ricardo E. Vilain, James S. Wilmott, Jean Y. Yang, Nicholas K. Hayward, Graham J. Mann, Richard A. Scolyer, John Bartlett, Prashant Bavi, Dianne E. Chadwick, Michelle Chan-Seng-Yue, Sean Cleary, Ashton A. Connor, Karolina Czajka, Robert E. Denroche, Neesha C. Dhani, Jenna Eagles, Steven Gallinger, Robert C. Grant, David Hedley, Michael A. Hollingsworth, Gun Ho Jang, Jeremy Johns, Sangeetha Kalimuthu, Sheng-Ben Liang, Ilinca Lungu, Xuemei Luo, Faridah Mbabaali, Treasa A. McPherson, Jessica K. Miller, Malcolm J. Moore, Faiyaz Notta, Danielle Pasternack, Gloria M. Petersen, Michael H. A. Roehrl, Michelle Sam, Iris Selander, Stefano Serra, Sagedeh Shahabi, Sarah P. Thayer, Lee E. Timms, Gavin W. Wilson, Julie M. Wilson, Bradly G. Wouters, John D. McPherson, Timothy A. Beck, Vinayak Bhandari, Colin C. Collins, Neil E. Fleshner, Natalie S. Fox, Michael Fraser, Lawrence E. Heisler, Emilie Lalonde, Julie Livingstone, Alice Meng, Veronica Y. Sabelnykova, Yu-Jia Shiah, Theodorus Van der Kwast, Robert G. Bristow, Shuai Ding, Daiming Fan, Lin Li, Yongzhan Nie, Xiao Xiao, Rui Xing, Shanlin Yang, Yingyan Yu, Yong Zhou, Rosamonde E. Banks, Guillaume Bourque, Paul Brennan, Louis Letourneau, Yasser Riazalhosseini, Ghislaine Scelo, Naveen Vasudev, Juris Viksna, Mark Lathrop, Jörg Tost, Sung-Min Ahn, Samuel Aparicio, Laurent Arnould, M. R. Aure, Shriram G. Bhosle, Ewan Birney, Ake Borg, Sandrine Boyault, Arie B. Brinkman, Jane E. Brock, Annegien Broeks, Anne-Lise Børresen-Dale, Carlos Caldas, Suet-Feung Chin, Helen Davies, Christine Desmedt, Luc Dirix, Serge Dronov, Anna Ehinger, Jorunn E. Eyfjord, Aquila Fatima, John A. Foekens, P. Andrew Futreal, Øystein Garred, Dilip D. Giri, Dominik Glodzik, Dorthe Grabau, Holmfridur Hilmarsdottir, Gerrit K. Hooijer, Jocelyne Jacquemier, Se Jin Jang, Jon G. Jonasson, Jos Jonkers, Hyung-Yong Kim, Tari A. King, Stian Knappskog, Gu Kong, Savitri Krishnamurthy, Sunil R. Lakhani, Anita Langerød, Denis Larsimont, Hee Jin Lee, Jeong-Yeon Lee, Ming Ta Michael Lee, Ole Christian Lingjaerde, Gaetan MacGrogan, John W. M. Martens, Sarah O’Meara, Iris Pauporté, Sarah Pinder, Xavier Pivot, Elena Provenzano, Colin A. Purdie, Manasa Ramakrishna, Kamna Ramakrishnan, Jorge Reis-Filho, Andrea L. Richardson, Markus Ringnér, Javier Bartolomé Rodriguez, F. Germán Rodríguez-González, Gilles Romieu, Roberto Salgado, Torill Sauer, Rebecca Shepherd, Anieta M. Sieuwerts, Peter T. Simpson, Marcel Smid, Christos Sotiriou, Paul N. Span, Ólafur Andri Stefánsson, Alasdair Stenhouse, Henk G. Stunnenberg, Fred Sweep, Benita Kiat Tee Tan, GIlles Thomas, Alastair M. Thompson, Stefania Tommasi, Isabelle Treilleux, Andrew Tutt, Naoto T. Ueno, Steven Van Laere, Gert G. Van den Eynden, Peter Vermeulen, Alain Viari, Anne Vincent-Salomon, Bernice H. Wong, Lucy Yates, Xueqing Zou, Carolien H. M. van Deurzen, Marc J. van de Vijver, Laura van’t Veer, Ole Ammerpohl, Sietse Aukema, Anke K. Bergmann, Stephan H. Bernhart, Arndt Borkhardt, Christoph Borst, Birgit Burkhardt, Alexander Claviez, Maria Elisabeth Goebler, Andrea Haake, Siegfried Haas, Martin Hansmann, Jessica I. Hoell, Michael Hummel, Dennis Karsch, Wolfram Klapper, Michael Kneba, Markus Kreuz, Dieter Kube, Ralf Küppers, Dido Lenze, Markus Loeffler, Cristina López, Luisa Mantovani-Löffler, Peter Möller, German Ott, Bernhard Radlwimmer, Julia Richter, Marius Rohde, Philip C. Rosenstiel, Andreas Rosenwald, Markus B. Schilhabel, Stefan Schreiber, Peter F. Stadler, Peter Staib, Stephan Stilgenbauer, Stephanie Sungalee, Monika Szczepanowski, Umut H. Toprak, Lorenz H. P. Trümper, Rabea Wagener, Thorsten Zenz, Volker Hovestadt, Christof von Kalle, Marcel Kool, Andrey Korshunov, Pablo Landgraf, Hans Lehrach, Paul A. Northcott, Stefan M. Pfister, Guido Reifenberger, Hans-Jörg Warnatz, Stephan Wolf, Marie-Laure Yaspo, Yassen Assenov, Clarissa Gerhauser, Sarah Minner, Thorsten Schlomm, Ronald Simon, Guido Sauter, Holger Sültmann, Nidhan K. Biswas, Arindam Maitra, Partha P. Majumder, Rajiv Sarin, Stefano Barbi, Giada Bonizzato, Cinzia Cantù, Angelo P. Dei Tos, Matteo Fassan, Sonia Grimaldi, Claudio Luchini, Giuseppe Malleo, Giovanni Marchegiani, Michele Milella, Salvatore Paiella, Antonio Pea, Paolo Pederzoli, Andrea Ruzzenente, Roberto Salvia, Nicola Sperandio, Yasuhito Arai, Natsuko Hama, Nobuyoshi Hiraoka, Fumie Hosoda, Hiromi Nakamura, Hidenori Ojima, Takuji Okusaka, Yasushi Totoki, Tomoko Urushidate, Masashi Fukayama, Shumpei Ishikawa, Hitoshi Katai, Hiroto Katoh, Daisuke Komura, Hirofumi Rokutan, Mihoko Saito-Adachi, Akihiro Suzuki, Hirokazu Taniguchi, Kenji Tatsuno, Tetsuo Ushiku, Shinichi Yachida, Shogo Yamamoto, Hiroshi Aikata, Koji Arihiro, Shun-ichi Ariizumi, Kazuaki Chayama, Mayuko Furuta, Kunihito Gotoh, Shinya Hayami, Satoshi Hirano, Yoshiiku Kawakami, Kazuhiro Maejima, Toru Nakamura, Kaoru Nakano, Hideki Ohdan, Aya Sasaki-Oku, Hiroko Tanaka, Masaki Ueno, Masakazu Yamamoto, Hiroki Yamaue, Su Pin Choo, Ioana Cutcutache, Narong Khuntikeo, Choon Kiat Ong, Chawalit Pairojkul, Irinel Popescu, Keun Soo Ahn, Marta Aymerich, Armando Lopez-Guillermo, Carlos López-Otín, Xose S. Puente, Elias Campo, Fernanda Amary, Daniel Baumhoer, Sam Behjati, Bodil Bjerkehagen, P. A. Futreal, Ola Myklebost, Nischalan Pillay, Patrick Tarpey, Roberto Tirabosco, Olga Zaikova, Adrienne M. Flanagan, Jacqueline Boultwood, David T. Bowen, Mario Cazzola, Anthony R. Green, Eva Hellstrom-Lindberg, Luca Malcovati, Jyoti Nangalia, Elli Papaemmanuil, Paresh Vyas, Yeng Ang, Hugh Barr, Duncan Beardsmore, Matthew Eldridge, James Gossage, Nicola Grehan, George B. Hanna, Stephen J. Hayes, Ted R. Hupp, David Khoo, Jesper Lagergren, Laurence B. Lovat, Shona MacRae, Maria O’Donovan, J. Robert O’Neill, Simon L. Parsons, Shaun R. Preston, Sonia Puig, Tom Roques, Grant Sanders, Sharmila Sothi, Simon Tavaré, Olga Tucker, Richard Turkington, Timothy J. Underwood, Ian Welch, Rebecca C. Fitzgerald, Daniel M. Berney, Johann S. De Bono, Declan Cahill, Niedzica Camacho, Nening M. Dennis, Tim Dudderidge, Sandra E. Edwards, Cyril Fisher, Christopher S. Foster, Mohammed Ghori, Pelvender Gill, Vincent J. Gnanapragasam, Gunes Gundem, Freddie C. Hamdy, Steve Hawkins, Steven Hazell, William Howat, William B. Isaacs, Katalin Karaszi, Jonathan D. Kay, Vincent Khoo, Zsofia Kote-Jarai, Barbara Kremeyer, Pardeep Kumar, Adam Lambert, Daniel A. Leongamornlert, Naomi Livni, Yong-Jie Lu, Hayley J. Luxton, Luke Marsden, Charlie E. Massie, Lucy Matthews, Erik Mayer, Ultan McDermott, Sue Merson, David E. Neal, Anthony Ng, David Nicol, Christopher Ogden, Edward W. Rowe, Nimish C. Shah, Sarah Thomas, Alan Thompson, Clare Verrill, Tapio Visakorpi, Anne Y. Warren, Hayley C. Whitaker, Hongwei Zhang, Nicholas van As, Rosalind A. Eeles, Adam Abeshouse, Nishant Agrawal, Rehan Akbani, Hikmat Al-Ahmadie, Monique Albert, Kenneth Aldape, Adrian Ally, Elizabeth L. Appelbaum, Joshua Armenia, Sylvia Asa, J. Todd Auman, Miruna Balasundaram, Saianand Balu, Jill Barnholtz-Sloan, Oliver F. Bathe, Stephen B. Baylin, Christopher Benz, Andrew Berchuck, Mario Berrios, Darell Bigner, Michael Birrer, Tom Bodenheimer, Lori Boice, Moiz S. Bootwalla, Marcus Bosenberg, Reanne Bowlby, Jeffrey Boyd, Russell R. Broaddus, Malcolm Brock, Denise Brooks, Susan Bullman, Samantha J. Caesar-Johnson, Thomas E. Carey, Rebecca Carlsen, Robert Cerfolio, Vishal S. Chandan, Hsiao-Wei Chen, Andrew D. Cherniack, Jeremy Chien, Juok Cho, Eric Chuah, Carrie Cibulskis, Leslie Cope, Matthew G. Cordes, Erin Curley, Bogdan Czerniak, Ludmila Danilova, Ian J. Davis, Timothy Defreitas, John A. Demchok, Noreen Dhalla, Rajiv Dhir, HarshaVardhan Doddapaneni, Adel El-Naggar, Ina Felau, Martin L. Ferguson, Gaetano Finocchiaro, Kwun M. Fong, Scott Frazer, William Friedman, Catrina C. Fronick, Lucinda A. Fulton, Stacey B. Gabriel, Jianjiong Gao, Nils Gehlenborg, Jeffrey E. Gershenwald, Ronald Ghossein, Nasra H. Giama, Richard A. Gibbs, Carmen Gomez, Ramaswamy Govindan, D. Neil Hayes, Apurva M. Hegde, David I. Heiman, Zachary Heins, Austin J. Hepperla, Andrea Holbrook, Robert A. Holt, Alan P. Hoyle, Ralph H. Hruban, Jianhong Hu, Mei Huang, David Huntsman, Jason Huse, Christine A. Iacobuzio-Donahue, Michael Ittmann, Joy C. Jayaseelan, Stuart R. Jefferys, Corbin D. Jones, Steven J. M. Jones, Hartmut Juhl, Koo Jeong Kang, Beth Karlan, Katayoon Kasaian, Electron Kebebew, Hark Kyun Kim, Viktoriya Korchina, Ritika Kundra, Phillip H. Lai, Eric Lander, Xuan Le, Darlene Lee, Douglas A. Levine, Lora Lewis, Tim Ley, Haiyan Irene Li, Pei Lin, W. M. Linehan, Fei Fei Liu, Yiling Lu, Lisa Lype, Yussanne Ma, Dennis T. Maglinte, Elaine R. Mardis, Jeffrey Marks, Marco A. Marra, Thomas J. Matthew, Michael Mayo, Karen McCune, Samuel R. Meier, Shaowu Meng, Piotr A. Mieczkowski, Tom Mikkelsen, Christopher A. Miller, Gordon B. Mills, Richard A. Moore, Carl Morrison, Lisle E. Mose, Catherine D. Moser, Andrew J. Mungall, Karen Mungall, David Mutch, Donna M. Muzny, Jerome Myers, Yulia Newton, Michael S. Noble, Peter O’Donnell, Brian Patrick O’Neill, Angelica Ochoa, Joong-Won Park, Joel S. Parker, Harvey Pass, Alessandro Pastore, Nathan A. Pennell, Charles M. Perou, Nicholas Petrelli, Olga Potapova, Janet S. Rader, Suresh Ramalingam, W. Kimryn Rathmell, Victor Reuter, Sheila M. Reynolds, Matthew Ringel, Jeffrey Roach, Lewis R. Roberts, A. Gordon Robertson, Sara Sadeghi, Charles Saller, Francisco Sanchez-Vega, Dirk Schadendorf, Jacqueline E. Schein, Heather K. Schmidt, Nikolaus Schultz, Raja Seethala, Yasin Senbabaoglu, Troy Shelton, Yan Shi, Juliann Shih, Ilya Shmulevich, Craig Shriver, Sabina Signoretti, Janae V. Simons, Samuel Singer, Payal Sipahimalani, Tara J. Skelly, Karen Smith-McCune, Nicholas D. Socci, Matthew G. Soloway, Anil K. Sood, Angela Tam, Donghui Tan, Roy Tarnuzzer, Nina Thiessen, R. Houston Thompson, Leigh B. Thorne, Ming Tsao, Christopher Umbricht, David J. Van Den Berg, Erwin G. Van Meir, Umadevi Veluvolu, Douglas Voet, Linghua Wang, Paul Weinberger, Daniel J. Weisenberger, Dennis Wigle, Matthew D. Wilkerson, Richard K. Wilson, Boris Winterhoff, Maciej Wiznerowicz, Tina Wong, Winghing Wong, Liu Xi, Christina Yau, Hailei Zhang, Hongxin Zhang, Jiashan Zhang
Feb 04, 2021
Abstract: Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658...
The evolution of complex multicellularity in animals
Abstract The transition to multicellularity is perhaps the best-studied of the “major evolutionary transitions”. It has occurred independently multiple times within the eukaryotes alone, and...
A Nejad Kourki
Oct 30, 2022
Major transitions in human evolution.
Evolutionary problems are often considered in terms of 'origins', and research in human evolution seen as a search for human origins. However, evolution, including human evolution, is a process of transitions from one state to...
CML
A retrospective view of the design and evolution of Chemical Markup Language (CML) is presented by its original authors.
The evolution of complex multicellularity in animals
Abstract The transition to multicellularity is perhaps the best-studied of the “major evolutionary transitions”. It has occurred independently multiple times within the eukaryotes alone, and...
A Nejad Kourki
Sep 12, 2022
The evolution and co-evolution of a primary care cancer research network
Debbie Vermond, Esther de Groot, Valerie A Sills, Georgios Lyratzopoulos, Fiona M Walter, Niek J de Wit, Greg Rubin
Jul 29, 2022
Academic networks are expected to enhance scientific collaboration and thereby increase research outputs. However, little is known about whether and how the initial steps of getting to know other researchers translates into...
Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition.
Bernardo Rodriguez-Martin, Eva G Alvarez, Adrian Baez-Ortega, Jorge Zamora, Fran Supek, Jonas Demeulemeester, Martin Santamarina, Young Seok Ju, Javier Temes, Daniel Garcia-Souto, Harald Detering, Yilong Li, Jorge Rodriguez-Castro, Ana Dueso-Barroso, Alicia L Bruzos, Stefan C Dentro, Miguel G Blanco, Gianmarco Contino, Daniel Ardeljan, Marta Tojo, Nicola D Roberts, Sonia Zumalave, Paul A Edwards, Joachim Weischenfeldt, Montserrat Puiggròs, Zechen Chong, Ken Chen, Eunjung Alice Lee, Jeremiah A Wala, Keiran M Raine, Adam Butler, Sebastian M Waszak, Fabio CP Navarro, Steven E Schumacher, Jean Monlong, Francesco Maura, Niccolo Bolli, Guillaume Bourque, Mark Gerstein, Peter J Park, David C Wedge, Rameen Beroukhim, David Torrents, Jan O Korbel, Iñigo Martincorena, Rebecca C Fitzgerald, Peter Van Loo, Haig H Kazazian, Kathleen H Burns, PCAWG Structural Variation Working Group, Peter J Campbell, Jose MC Tubio, PCAWG Consortium
Jan 14, 2019
About half of all cancers have somatic integrations of retrotransposons. Here, to characterize their role in oncogenesis, we analyzed the patterns and mechanisms of somatic retrotransposition in 2,954 cancer genomes from...
Modelling the evolution of novelty
Evolution has been an inventive process since its inception, about 4 billion years ago. It has generated an astounding diversity of novel mechanisms and structures for adaptation to the environment, for competition and...
Pan-cancer analysis of whole genomes.
Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of...
Cell Proliferation Cellular Senescence Chromothripsis Cloud Computing DNA Mutational Analysis evolution Molecular Female Genome Human Genomics Germ-Line Mutation High-Throughput Nucleotide Sequencing Humans Information Dissemination Male Mutagenesis Mutation Neoplasms Oncogenes Promoter Regions Genetic RNA Splicing Reproducibility of Results Telomerase Telomere
Analyzing the Evolution of Interdisciplinary Areas
Won Lee
Jan 01, 2022
Recently, various new areas of research have been of great interest to researchers. As these areas are highly based on academic and industrial needs, it is necessary to examine the change and evolution in research. This study...
Published by: IGI Global Scientific Publishing
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