Peter Van Loo, Silje H Nordgard, Ole Christian Lingjærde, Hege G Russnes, Inga H Rye, Wei Sun, Victor J Weigman, Peter Marynen, Anders Zetterberg, Bjørn Naume, Charles M Perou, Anne-Lise Børresen-Dale, Vessela N Kristensen. Proc Natl Acad Sci U S A 2010
Times Cited: 640
Times Cited: 640
Times Cited
Times Co-cited
Similarity
Absolute quantification of somatic DNA alterations in human cancer.
Scott L Carter, Kristian Cibulskis, Elena Helman, Aaron McKenna, Hui Shen, Travis Zack, Peter W Laird, Robert C Onofrio, Wendy Winckler, Barbara A Weir,[...]. Nat Biotechnol 2012
Scott L Carter, Kristian Cibulskis, Elena Helman, Aaron McKenna, Hui Shen, Travis Zack, Peter W Laird, Robert C Onofrio, Wendy Winckler, Barbara A Weir,[...]. Nat Biotechnol 2012
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The Sequence Alignment/Map format and SAMtools.
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
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Fast and accurate short read alignment with Burrows-Wheeler transform.
Heng Li, Richard Durbin. Bioinformatics 2009
Heng Li, Richard Durbin. Bioinformatics 2009
17
GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers.
Craig H Mermel, Steven E Schumacher, Barbara Hill, Matthew L Meyerson, Rameen Beroukhim, Gad Getz. Genome Biol 2011
Craig H Mermel, Steven E Schumacher, Barbara Hill, Matthew L Meyerson, Rameen Beroukhim, Gad Getz. Genome Biol 2011
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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,[...]. Nature 2020
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,[...]. Nature 2020
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The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.
Aaron McKenna, Matthew Hanna, Eric Banks, Andrey Sivachenko, Kristian Cibulskis, Andrew Kernytsky, Kiran Garimella, David Altshuler, Stacey Gabriel, Mark Daly,[...]. Genome Res 2010
Aaron McKenna, Matthew Hanna, Eric Banks, Andrey Sivachenko, Kristian Cibulskis, Andrew Kernytsky, Kiran Garimella, David Altshuler, Stacey Gabriel, Mark Daly,[...]. Genome Res 2010
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STAR: ultrafast universal RNA-seq aligner.
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
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Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
Aravind Subramanian, Pablo Tamayo, Vamsi K Mootha, Sayan Mukherjee, Benjamin L Ebert, Michael A Gillette, Amanda Paulovich, Scott L Pomeroy, Todd R Golub, Eric S Lander,[...]. Proc Natl Acad Sci U S A 2005
Aravind Subramanian, Pablo Tamayo, Vamsi K Mootha, Sayan Mukherjee, Benjamin L Ebert, Michael A Gillette, Amanda Paulovich, Scott L Pomeroy, Todd R Golub, Eric S Lander,[...]. Proc Natl Acad Sci U S A 2005
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Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples.
Kristian Cibulskis, Michael S Lawrence, Scott L Carter, Andrey Sivachenko, David Jaffe, Carrie Sougnez, Stacey Gabriel, Matthew Meyerson, Eric S Lander, Gad Getz. Nat Biotechnol 2013
Kristian Cibulskis, Michael S Lawrence, Scott L Carter, Andrey Sivachenko, David Jaffe, Carrie Sougnez, Stacey Gabriel, Matthew Meyerson, Eric S Lander, Gad Getz. Nat Biotechnol 2013
14
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
13
ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Kai Wang, Mingyao Li, Hakon Hakonarson. Nucleic Acids Res 2010
Kai Wang, Mingyao Li, Hakon Hakonarson. Nucleic Acids Res 2010
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cgpCaVEManWrapper: Simple Execution of CaVEMan in Order to Detect Somatic Single Nucleotide Variants in NGS Data.
David Jones, Keiran M Raine, Helen Davies, Patrick S Tarpey, Adam P Butler, Jon W Teague, Serena Nik-Zainal, Peter J Campbell. Curr Protoc Bioinformatics 2016
David Jones, Keiran M Raine, Helen Davies, Patrick S Tarpey, Adam P Butler, Jon W Teague, Serena Nik-Zainal, Peter J Campbell. Curr Protoc Bioinformatics 2016
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PyClone: statistical inference of clonal population structure in cancer.
Andrew Roth, Jaswinder Khattra, Damian Yap, Adrian Wan, Emma Laks, Justina Biele, Gavin Ha, Samuel Aparicio, Alexandre Bouchard-Côté, Sohrab P Shah. Nat Methods 2014
Andrew Roth, Jaswinder Khattra, Damian Yap, Adrian Wan, Emma Laks, Justina Biele, Gavin Ha, Samuel Aparicio, Alexandre Bouchard-Côté, Sohrab P Shah. Nat Methods 2014
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The life history of 21 breast cancers.
Serena Nik-Zainal, Peter Van Loo, David C Wedge, Ludmil B Alexandrov, Christopher D Greenman, King Wai Lau, Keiran Raine, David Jones, John Marshall, Manasa Ramakrishna,[...]. Cell 2012
Serena Nik-Zainal, Peter Van Loo, David C Wedge, Ludmil B Alexandrov, Christopher D Greenman, King Wai Lau, Keiran Raine, David Jones, John Marshall, Manasa Ramakrishna,[...]. Cell 2012
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Landscape of somatic mutations in 560 breast cancer whole-genome sequences.
Serena Nik-Zainal, Helen Davies, Johan Staaf, Manasa Ramakrishna, Dominik Glodzik, Xueqing Zou, Inigo Martincorena, Ludmil B Alexandrov, Sancha Martin, David C Wedge,[...]. Nature 2016
Serena Nik-Zainal, Helen Davies, Johan Staaf, Manasa Ramakrishna, Dominik Glodzik, Xueqing Zou, Inigo Martincorena, Ludmil B Alexandrov, Sancha Martin, David C Wedge,[...]. Nature 2016
11
Signatures of mutational processes in human cancer.
Ludmil B Alexandrov, Serena Nik-Zainal, David C Wedge, Samuel A J R Aparicio, Sam Behjati, Andrew V Biankin, Graham R Bignell, Niccolò Bolli, Ake Borg, Anne-Lise Børresen-Dale,[...]. Nature 2013
Ludmil B Alexandrov, Serena Nik-Zainal, David C Wedge, Samuel A J R Aparicio, Sam Behjati, Andrew V Biankin, Graham R Bignell, Niccolò Bolli, Ake Borg, Anne-Lise Børresen-Dale,[...]. Nature 2013
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Tracking the Evolution of Non-Small-Cell Lung Cancer.
Mariam Jamal-Hanjani, Gareth A Wilson, Nicholas McGranahan, Nicolai J Birkbak, Thomas B K Watkins, Selvaraju Veeriah, Seema Shafi, Diana H Johnson, Richard Mitter, Rachel Rosenthal,[...]. N Engl J Med 2017
Mariam Jamal-Hanjani, Gareth A Wilson, Nicholas McGranahan, Nicolai J Birkbak, Thomas B K Watkins, Selvaraju Veeriah, Seema Shafi, Diana H Johnson, Richard Mitter, Rachel Rosenthal,[...]. N Engl J Med 2017
10
Mutational heterogeneity in cancer and the search for new cancer-associated genes.
Michael S Lawrence, Petar Stojanov, Paz Polak, Gregory V Kryukov, Kristian Cibulskis, Andrey Sivachenko, Scott L Carter, Chip Stewart, Craig H Mermel, Steven A Roberts,[...]. Nature 2013
Michael S Lawrence, Petar Stojanov, Paz Polak, Gregory V Kryukov, Kristian Cibulskis, Andrey Sivachenko, Scott L Carter, Chip Stewart, Craig H Mermel, Steven A Roberts,[...]. Nature 2013
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Pan-cancer patterns of somatic copy number alteration.
Travis I Zack, Stephen E Schumacher, Scott L Carter, Andre D Cherniack, Gordon Saksena, Barbara Tabak, Michael S Lawrence, Cheng-Zhong Zhsng, Jeremiah Wala, Craig H Mermel,[...]. Nat Genet 2013
Travis I Zack, Stephen E Schumacher, Scott L Carter, Andre D Cherniack, Gordon Saksena, Barbara Tabak, Michael S Lawrence, Cheng-Zhong Zhsng, Jeremiah Wala, Craig H Mermel,[...]. Nat Genet 2013
9
FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing.
Ronglai Shen, Venkatraman E Seshan. Nucleic Acids Res 2016
Ronglai Shen, Venkatraman E Seshan. Nucleic Acids Res 2016
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Copynumber: Efficient algorithms for single- and multi-track copy number segmentation.
Gro Nilsen, Knut Liestøl, Peter Van Loo, Hans Kristian Moen Vollan, Marianne B Eide, Oscar M Rueda, Suet-Feung Chin, Roslin Russell, Lars O Baumbusch, Carlos Caldas,[...]. BMC Genomics 2012
Gro Nilsen, Knut Liestøl, Peter Van Loo, Hans Kristian Moen Vollan, Marianne B Eide, Oscar M Rueda, Suet-Feung Chin, Roslin Russell, Lars O Baumbusch, Carlos Caldas,[...]. BMC Genomics 2012
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Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data.
F Favero, T Joshi, A M Marquard, N J Birkbak, M Krzystanek, Q Li, Z Szallasi, A C Eklund. Ann Oncol 2015
F Favero, T Joshi, A M Marquard, N J Birkbak, M Krzystanek, Q Li, Z Szallasi, A C Eklund. Ann Oncol 2015
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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,[...]. Nature 2020
Moritz Gerstung, Clemency Jolly, Ignaty Leshchiner, Stefan C Dentro, Santiago Gonzalez, Daniel Rosebrock, Thomas J Mitchell, Yulia Rubanova, Pavana Anur, Kaixian Yu,[...]. Nature 2020
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The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data.
Ethan Cerami, Jianjiong Gao, Ugur Dogrusoz, Benjamin E Gross, Selcuk Onur Sumer, Bülent Arman Aksoy, Anders Jacobsen, Caitlin J Byrne, Michael L Heuer, Erik Larsson,[...]. Cancer Discov 2012
Ethan Cerami, Jianjiong Gao, Ugur Dogrusoz, Benjamin E Gross, Selcuk Onur Sumer, Bülent Arman Aksoy, Anders Jacobsen, Caitlin J Byrne, Michael L Heuer, Erik Larsson,[...]. Cancer Discov 2012
9
Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing.
Emma Laks, Andrew McPherson, Hans Zahn, Daniel Lai, Adi Steif, Jazmine Brimhall, Justina Biele, Beixi Wang, Tehmina Masud, Jerome Ting,[...]. Cell 2019
Emma Laks, Andrew McPherson, Hans Zahn, Daniel Lai, Adi Steif, Jazmine Brimhall, Justina Biele, Beixi Wang, Tehmina Masud, Jerome Ting,[...]. Cell 2019
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Emerging landscape of oncogenic signatures across human cancers.
Giovanni Ciriello, Martin L Miller, Bülent Arman Aksoy, Yasin Senbabaoglu, Nikolaus Schultz, Chris Sander. Nat Genet 2013
Giovanni Ciriello, Martin L Miller, Bülent Arman Aksoy, Yasin Senbabaoglu, Nikolaus Schultz, Chris Sander. Nat Genet 2013
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Genomic and Functional Approaches to Understanding Cancer Aneuploidy.
Alison M Taylor, Juliann Shih, Gavin Ha, Galen F Gao, Xiaoyang Zhang, Ashton C Berger, Steven E Schumacher, Chen Wang, Hai Hu, Jianfang Liu,[...]. Cancer Cell 2018
Alison M Taylor, Juliann Shih, Gavin Ha, Galen F Gao, Xiaoyang Zhang, Ashton C Berger, Steven E Schumacher, Chen Wang, Hai Hu, Jianfang Liu,[...]. Cancer Cell 2018
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Somatic mutant clones colonize the human esophagus with age.
Iñigo Martincorena, Joanna C Fowler, Agnieszka Wabik, Andrew R J Lawson, Federico Abascal, Michael W J Hall, Alex Cagan, Kasumi Murai, Krishnaa Mahbubani, Michael R Stratton,[...]. Science 2018
Iñigo Martincorena, Joanna C Fowler, Agnieszka Wabik, Andrew R J Lawson, Federico Abascal, Michael W J Hall, Alex Cagan, Kasumi Murai, Krishnaa Mahbubani, Michael R Stratton,[...]. Science 2018
8
The mutational landscape of normal human endometrial epithelium.
Luiza Moore, Daniel Leongamornlert, Tim H H Coorens, Mathijs A Sanders, Peter Ellis, Stefan C Dentro, Kevin J Dawson, Tim Butler, Raheleh Rahbari, Thomas J Mitchell,[...]. Nature 2020
Luiza Moore, Daniel Leongamornlert, Tim H H Coorens, Mathijs A Sanders, Peter Ellis, Stefan C Dentro, Kevin J Dawson, Tim Butler, Raheleh Rahbari, Thomas J Mitchell,[...]. Nature 2020
8
The mutational constraint spectrum quantified from variation in 141,456 humans.
Konrad J Karczewski, Laurent C Francioli, Grace Tiao, Beryl B Cummings, Jessica Alföldi, Qingbo Wang, Ryan L Collins, Kristen M Laricchia, Andrea Ganna, Daniel P Birnbaum,[...]. Nature 2020
Konrad J Karczewski, Laurent C Francioli, Grace Tiao, Beryl B Cummings, Jessica Alföldi, Qingbo Wang, Ryan L Collins, Kristen M Laricchia, Andrea Ganna, Daniel P Birnbaum,[...]. Nature 2020
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DeconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution.
Rachel Rosenthal, Nicholas McGranahan, Javier Herrero, Barry S Taylor, Charles Swanton. Genome Biol 2016
Rachel Rosenthal, Nicholas McGranahan, Javier Herrero, Barry S Taylor, Charles Swanton. Genome Biol 2016
8
Systematic pan-cancer analysis of tumour purity.
Dvir Aran, Marina Sirota, Atul J Butte. Nat Commun 2015
Dvir Aran, Marina Sirota, Atul J Butte. Nat Commun 2015
8
Universal Patterns of Selection in Cancer and Somatic Tissues.
Iñigo Martincorena, Keiran M Raine, Moritz Gerstung, Kevin J Dawson, Kerstin Haase, Peter Van Loo, Helen Davies, Michael R Stratton, Peter J Campbell. Cell 2017
Iñigo Martincorena, Keiran M Raine, Moritz Gerstung, Kevin J Dawson, Kerstin Haase, Peter Van Loo, Helen Davies, Michael R Stratton, Peter J Campbell. Cell 2017
8
The Ensembl Variant Effect Predictor.
William McLaren, Laurent Gil, Sarah E Hunt, Harpreet Singh Riat, Graham R S Ritchie, Anja Thormann, Paul Flicek, Fiona Cunningham. Genome Biol 2016
William McLaren, Laurent Gil, Sarah E Hunt, Harpreet Singh Riat, Graham R S Ritchie, Anja Thormann, Paul Flicek, Fiona Cunningham. Genome Biol 2016
8
COSMIC: the Catalogue Of Somatic Mutations In Cancer.
John G Tate, Sally Bamford, Harry C Jubb, Zbyslaw Sondka, David M Beare, Nidhi Bindal, Harry Boutselakis, Charlotte G Cole, Celestino Creatore, Elisabeth Dawson,[...]. Nucleic Acids Res 2019
John G Tate, Sally Bamford, Harry C Jubb, Zbyslaw Sondka, David M Beare, Nidhi Bindal, Harry Boutselakis, Charlotte G Cole, Celestino Creatore, Elisabeth Dawson,[...]. Nucleic Acids Res 2019
8
TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data.
Gavin Ha, Andrew Roth, Jaswinder Khattra, Julie Ho, Damian Yap, Leah M Prentice, Nataliya Melnyk, Andrew McPherson, Ali Bashashati, Emma Laks,[...]. Genome Res 2014
Gavin Ha, Andrew Roth, Jaswinder Khattra, Julie Ho, Damian Yap, Leah M Prentice, Nataliya Melnyk, Andrew McPherson, Ali Bashashati, Emma Laks,[...]. Genome Res 2014
7
Allele-Specific HLA Loss and Immune Escape in Lung Cancer Evolution.
Nicholas McGranahan, Rachel Rosenthal, Crispin T Hiley, Andrew J Rowan, Thomas B K Watkins, Gareth A Wilson, Nicolai J Birkbak, Selvaraju Veeriah, Peter Van Loo, Javier Herrero,[...]. Cell 2017
Nicholas McGranahan, Rachel Rosenthal, Crispin T Hiley, Andrew J Rowan, Thomas B K Watkins, Gareth A Wilson, Nicolai J Birkbak, Selvaraju Veeriah, Peter Van Loo, Javier Herrero,[...]. Cell 2017
7
VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing.
Daniel C Koboldt, Qunyuan Zhang, David E Larson, Dong Shen, Michael D McLellan, Ling Lin, Christopher A Miller, Elaine R Mardis, Li Ding, Richard K Wilson. Genome Res 2012
Daniel C Koboldt, Qunyuan Zhang, David E Larson, Dong Shen, Michael D McLellan, Ling Lin, Christopher A Miller, Elaine R Mardis, Li Ding, Richard K Wilson. Genome Res 2012
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Tumor aneuploidy correlates with markers of immune evasion and with reduced response to immunotherapy.
Teresa Davoli, Hajime Uno, Eric C Wooten, Stephen J Elledge. Science 2017
Teresa Davoli, Hajime Uno, Eric C Wooten, Stephen J Elledge. Science 2017
7
Inferring tumour purity and stromal and immune cell admixture from expression data.
Kosuke Yoshihara, Maria Shahmoradgoli, Emmanuel Martínez, Rahulsimham Vegesna, Hoon Kim, Wandaliz Torres-Garcia, Victor Treviño, Hui Shen, Peter W Laird, Douglas A Levine,[...]. Nat Commun 2013
Kosuke Yoshihara, Maria Shahmoradgoli, Emmanuel Martínez, Rahulsimham Vegesna, Hoon Kim, Wandaliz Torres-Garcia, Victor Treviño, Hui Shen, Peter W Laird, Douglas A Levine,[...]. Nat Commun 2013
7
Tumor evolution. High burden and pervasive positive selection of somatic mutations in normal human skin.
Iñigo Martincorena, Amit Roshan, Moritz Gerstung, Peter Ellis, Peter Van Loo, Stuart McLaren, David C Wedge, Anthony Fullam, Ludmil B Alexandrov, Jose M Tubio,[...]. Science 2015
Iñigo Martincorena, Amit Roshan, Moritz Gerstung, Peter Ellis, Peter Van Loo, Stuart McLaren, David C Wedge, Anthony Fullam, Ludmil B Alexandrov, Jose M Tubio,[...]. Science 2015
7
The landscape of somatic mutation in normal colorectal epithelial cells.
Henry Lee-Six, Sigurgeir Olafsson, Peter Ellis, Robert J Osborne, Mathijs A Sanders, Luiza Moore, Nikitas Georgakopoulos, Franco Torrente, Ayesha Noorani, Martin Goddard,[...]. Nature 2019
Henry Lee-Six, Sigurgeir Olafsson, Peter Ellis, Robert J Osborne, Mathijs A Sanders, Luiza Moore, Nikitas Georgakopoulos, Franco Torrente, Ayesha Noorani, Martin Goddard,[...]. Nature 2019
7
HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures.
Helen Davies, Dominik Glodzik, Sandro Morganella, Lucy R Yates, Johan Staaf, Xueqing Zou, Manasa Ramakrishna, Sancha Martin, Sandrine Boyault, Anieta M Sieuwerts,[...]. Nat Med 2017
Helen Davies, Dominik Glodzik, Sandro Morganella, Lucy R Yates, Johan Staaf, Xueqing Zou, Manasa Ramakrishna, Sancha Martin, Sandrine Boyault, Anieta M Sieuwerts,[...]. Nat Med 2017
7
Pervasive chromosomal instability and karyotype order in tumour evolution.
Thomas B K Watkins, Emilia L Lim, Marina Petkovic, Sergi Elizalde, Nicolai J Birkbak, Gareth A Wilson, David A Moore, Eva Grönroos, Andrew Rowan, Sally M Dewhurst,[...]. Nature 2020
Thomas B K Watkins, Emilia L Lim, Marina Petkovic, Sergi Elizalde, Nicolai J Birkbak, Gareth A Wilson, David A Moore, Eva Grönroos, Andrew Rowan, Sally M Dewhurst,[...]. Nature 2020
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edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
7
The Molecular Signatures Database (MSigDB) hallmark gene set collection.
Arthur Liberzon, Chet Birger, Helga Thorvaldsdóttir, Mahmoud Ghandi, Jill P Mesirov, Pablo Tamayo. Cell Syst 2015
Arthur Liberzon, Chet Birger, Helga Thorvaldsdóttir, Mahmoud Ghandi, Jill P Mesirov, Pablo Tamayo. Cell Syst 2015
7
BEDTools: a flexible suite of utilities for comparing genomic features.
Aaron R Quinlan, Ira M Hall. Bioinformatics 2010
Aaron R Quinlan, Ira M Hall. Bioinformatics 2010
7
Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.