Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes [v1; ref status: indexed, http://f1000r.es/4zj]

by Ron Ammar, Tara A. Paton, Dax Torti, Adam Shlien, Gary D. Bader
Published 2015-01-01

Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes [v2; ref status: indexed, http://f1000r.es/5ev]

by Ron Ammar, Tara A. Paton, Dax Torti, Adam Shlien, Gary D. Bader
Published 2015-05-01

A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia cells

by Tony Ly, Yasmeen Ahmad, Adam Shlien, Dominique Soroka, Allie Mills, Michael J Emanuele, Michael R Stratton, Angus I Lamond
Published 2014-03-01

Explosive mutation accumulation triggered by heterozygous human Pol ε proofreading-deficiency is driven by suppression of mismatch repair

by Karl P Hodel, Richard de Borja, Erin E Henninger, Brittany B Campbell, Nathan Ungerleider, Nicholas Light, Tong Wu, Kimberly G LeCompte, A Yasemin Goksenin, Bruce A Bunnell, Uri Tabori, Adam Shlien, Zachary F Pursell
Published 2018-02-01

Principles Governing A-to-I RNA Editing in the Breast Cancer Transcriptome

by Debora Fumagalli, David Gacquer, Françoise Rothé, Anne Lefort, Frederick Libert, David Brown, Naima Kheddoumi, Adam Shlien, Tomasz Konopka, Roberto Salgado, Denis Larsimont, Kornelia Polyak, Karen Willard-Gallo, Christine Desmedt, Martine Piccart, Marc Abramowicz, Peter J. Campbell, Christos Sotiriou, Vincent Detours
Published 2015-10-01

Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden

by Zachary R. Chalmers, Caitlin F. Connelly, David Fabrizio, Laurie Gay, Siraj M. Ali, Riley Ennis, Alexa Schrock, Brittany Campbell, Adam Shlien, Juliann Chmielecki, Franklin Huang, Yuting He, James Sun, Uri Tabori, Mark Kennedy, Daniel S. Lieber, Steven Roels, Jared White, Geoffrey A. Otto, Jeffrey S. Ross, Levi Garraway, Vincent A. Miller, Phillip J. Stephens, Garrett M. Frampton
Published 2017-04-01

Cooperation of cancer drivers with regulatory germline variants shapes clinical outcomes

by Julian Musa, Florencia Cidre-Aranaz, Marie-Ming Aynaud, Martin F. Orth, Maximilian M. L. Knott, Olivier Mirabeau, Gal Mazor, Mor Varon, Tilman L. B. Hölting, Sandrine Grossetête, Moritz Gartlgruber, Didier Surdez, Julia S. Gerke, Shunya Ohmura, Aruna Marchetto, Marlene Dallmayer, Michaela C. Baldauf, Stefanie Stein, Giuseppina Sannino, Jing Li, Laura Romero-Pérez, Frank Westermann, Wolfgang Hartmann, Uta Dirksen, Melissa Gymrek, Nathaniel D. Anderson, Adam Shlien, Barak Rotblat, Thomas Kirchner, Olivier Delattre, Thomas G. P. Grünewald
Published 2019-09-01

The driver landscape of sporadic chordoma

by Patrick S. Tarpey, Sam Behjati, Matthew D. Young, Inigo Martincorena, Ludmil B. Alexandrov, Sarah J. Farndon, Charlotte Guzzo, Claire Hardy, Calli Latimer, Adam P. Butler, Jon W. Teague, Adam Shlien, P. Andrew Futreal, Sohrab Shah, Ali Bashashati, Farzad Jamshidi, Torsten O. Nielsen, David Huntsman, Daniel Baumhoer, Sebastian Brandner, Jay Wunder, Brendan Dickson, Patricia Cogswell, Josh Sommer, Joanna J. Phillips, M. Fernanda Amary, Roberto Tirabosco, Nischalan Pillay, Stephen Yip, Michael R. Stratton, Adrienne M. Flanagan, Peter J. Campbell
Published 2017-10-01

Lineage-defined leiomyosarcoma subtypes emerge years before diagnosis and determine patient survival

by Nathaniel D. Anderson, Yael Babichev, Fabio Fuligni, Federico Comitani, Mehdi Layeghifard, Rosemarie E. Venier, Stefan C. Dentro, Anant Maheshwari, Sheena Guram, Claire Wunker, J. Drew Thompson, Kyoko E. Yuki, Huayun Hou, Matthew Zatzman, Nicholas Light, Marcus Q. Bernardini, Jay S. Wunder, Irene L. Andrulis, Peter Ferguson, Albiruni R. Abdul Razak, Carol J. Swallow, James J. Dowling, Rima S. Al-Awar, Richard Marcellus, Marjan Rouzbahman, Moritz Gerstung, Daniel Durocher, Ludmil B. Alexandrov, Brendan C. Dickson, Rebecca A. Gladdy, Adam Shlien
Published 2021-07-01

Mutational signatures of ionizing radiation in second malignancies

by Sam Behjati, Gunes Gundem, David C. Wedge, Nicola D. Roberts, Patrick S. Tarpey, Susanna L. Cooke, Peter Van Loo, Ludmil B. Alexandrov, Manasa Ramakrishna, Helen Davies, Serena Nik-Zainal, Claire Hardy, Calli Latimer, Keiran M. Raine, Lucy Stebbings, Andy Menzies, David Jones, Rebecca Shepherd, Adam P. Butler, Jon W. Teague, Mette Jorgensen, Bhavisha Khatri, Nischalan Pillay, Adam Shlien, P. Andrew Futreal, Christophe Badie, ICGC Prostate Group, Ultan McDermott, G. Steven Bova, Andrea L. Richardson, Adrienne M. Flanagan, Michael R. Stratton, Peter J. Campbell
Published 2016-09-01

Recurrent mutation of IGF signalling genes and distinct patterns of genomic rearrangement in osteosarcoma

by Sam Behjati, Patrick S. Tarpey, Kerstin Haase, Hongtao Ye, Matthew D. Young, Ludmil B. Alexandrov, Sarah J. Farndon, Grace Collord, David C. Wedge, Inigo Martincorena, Susanna L. Cooke, Helen Davies, William Mifsud, Mathias Lidgren, Sancha Martin, Calli Latimer, Mark Maddison, Adam P. Butler, Jon W. Teague, Nischalan Pillay, Adam Shlien, Ultan McDermott, P. Andrew Futreal, Daniel Baumhoer, Olga Zaikova, Bodil Bjerkehagen, Ola Myklebost, M. Fernanda Amary, Roberto Tirabosco, Peter Van Loo, Michael R. Stratton, Adrienne M. Flanagan, Peter J. Campbell
Published 2017-06-01

Direct Transcriptional Consequences of Somatic Mutation in Breast Cancer

by Adam Shlien, Keiran Raine, Fabio Fuligni, Roland Arnold, Serena Nik-Zainal, Serge Dronov, Lira Mamanova, Andrej Rosic, Young Seok Ju, Susanna L. Cooke, Manasa Ramakrishna, Elli Papaemmanuil, Helen R. Davies, Patrick S. Tarpey, Peter Van Loo, David C. Wedge, David R. Jones, Sancha Martin, John Marshall, Elizabeth Anderson, Claire Hardy, Violetta Barbashina, Samuel A.J.R. Aparicio, Torill Sauer, Øystein Garred, Anne Vincent-Salomon, Odette Mariani, Sandrine Boyault, Aquila Fatima, Anita Langerød, Åke Borg, Gilles Thomas, Andrea L. Richardson, Anne-Lise Børresen-Dale, Kornelia Polyak, Michael R. Stratton, Peter J. Campbell
Published 2016-08-01

Single cell derived mRNA signals across human kidney tumors

by Matthew D. Young, Thomas J. Mitchell, Lars Custers, Thanasis Margaritis, Francisco Morales-Rodriguez, Kwasi Kwakwa, Eleonora Khabirova, Gerda Kildisiute, Thomas R. W. Oliver, Ronald R. de Krijger, Marry M. van den Heuvel-Eibrink, Federico Comitani, Alice Piapi, Eva Bugallo-Blanco, Christine Thevanesan, Christina Burke, Elena Prigmore, Kirsty Ambridge, Kenny Roberts, Felipe A. Vieira Braga, Tim H. H. Coorens, Ignacio Del Valle, Anna Wilbrey-Clark, Lira Mamanova, Grant D. Stewart, Vincent J. Gnanapragasam, Dyanne Rampling, Neil Sebire, Nicholas Coleman, Liz Hook, Anne Warren, Muzlifah Haniffa, Marcel Kool, Stefan M. Pfister, John C. Achermann, Xiaoling He, Roger A. Barker, Adam Shlien, Omer A. Bayraktar, Sarah A. Teichmann, Frank C. Holstege, Kerstin B. Meyer, Jarno Drost, Karin Straathof, Sam Behjati
Published 2021-06-01

Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer

by Young Seok Ju, Ludmil B Alexandrov, Moritz Gerstung, Inigo Martincorena, Serena Nik-Zainal, Manasa Ramakrishna, Helen R Davies, Elli Papaemmanuil, Gunes Gundem, Adam Shlien, Niccolo Bolli, Sam Behjati, Patrick S Tarpey, Jyoti Nangalia, Charles E Massie, Adam P Butler, Jon W Teague, George S Vassiliou, Anthony R Green, Ming-Qing Du, Ashwin Unnikrishnan, John E Pimanda, Bin Tean Teh, Nikhil Munshi, Mel Greaves, Paresh Vyas, Adel K El-Naggar, Tom Santarius, V Peter Collins, Richard Grundy, Jack A Taylor, D Neil Hayes, David Malkin, ICGC Breast Cancer Group, ICGC Chronic Myeloid Disorders Group, ICGC Prostate Cancer Group, Christopher S Foster, Anne Y Warren, Hayley C Whitaker, Daniel Brewer, Rosalind Eeles, Colin Cooper, David Neal, Tapio Visakorpi, William B Isaacs, G Steven Bova, Adrienne M Flanagan, P Andrew Futreal, Andy G Lynch, Patrick F Chinnery, Ultan McDermott, Michael R Stratton, Peter J Campbell
Published 2014-10-01