Fifth International Biannual Evolution and Ecology of Cancer Conference (Cooperation, Conflict and Parasitism) meeting report—Wellcome Genome Campus, Hinxton, UK

by Nynke Raven, Georgina Bramwell, Rodrigo Hamede, Frédéric Thomas, Beata Ujvari
Published 2019-12-01

Common and distinct transcriptional signatures of mammalian embryonic lethality

by John E. Collins, Richard J. White, Nicole Staudt, Ian M. Sealy, Ian Packham, Neha Wali, Catherine Tudor, Cecilia Mazzeo, Angela Green, Emma Siragher, Edward Ryder, Jacqueline K. White, Irene Papatheodoru, Amy Tang, Anja Füllgrabe, Konstantinos Billis, Stefan H. Geyer, Wolfgang J. Weninger, Antonella Galli, Myriam Hemberger, Derek L. Stemple, Elizabeth Robertson, James C. Smith, Timothy Mohun, David J. Adams, Elisabeth M. Busch-Nentwich
Published 2019-06-01

Publisher Correction: Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression

by Anna S. E. Cuomo, Daniel D. Seaton, Davis J. McCarthy, Iker Martinez, Marc Jan Bonder, Jose Garcia-Bernardo, Shradha Amatya, Pedro Madrigal, Abigail Isaacson, Florian Buettner, Andrew Knights, Kedar Nath Natarajan, HipSci Consortium, Ludovic Vallier, John C. Marioni, Mariya Chhatriwala, Oliver Stegle
Published 2020-03-01

Enrichment of low-frequency functional variants revealed by whole-genome sequencing of multiple isolated European populations

by Yali Xue, Massimo Mezzavilla, Marc Haber, Shane McCarthy, Yuan Chen, Vagheesh Narasimhan, Arthur Gilly, Qasim Ayub, Vincenza Colonna, Lorraine Southam, Christopher Finan, Andrea Massaia, Himanshu Chheda, Priit Palta, Graham Ritchie, Jennifer Asimit, George Dedoussis, Paolo Gasparini, Aarno Palotie, Samuli Ripatti, Nicole Soranzo, Daniela Toniolo, James F. Wilson, Richard Durbin, Chris Tyler-Smith, Eleftheria Zeggini
Published 2017-06-01

Single-cell atlas of the first intra-mammalian developmental stage of the human parasite Schistosoma mansoni

by Carmen Lidia Diaz Soria, Jayhun Lee, Tracy Chong, Avril Coghlan, Alan Tracey, Matthew D. Young, Tallulah Andrews, Christopher Hall, Bee Ling Ng, Kate Rawlinson, Stephen R. Doyle, Steven Leonard, Zhigang Lu, Hayley M. Bennett, Gabriel Rinaldi, Phillip A. Newmark, Matthew Berriman
Published 2020-12-01

Minimal genome-wide human CRISPR-Cas9 library

by Emanuel Gonçalves, Mark Thomas, Fiona M. Behan, Gabriele Picco, Clare Pacini, Felicity Allen, Alessandro Vinceti, Mamta Sharma, David A. Jackson, Stacey Price, Charlotte M. Beaver, Oliver Dovey, David Parry-Smith, Francesco Iorio, Leopold Parts, Kosuke Yusa, Mathew J. Garnett
Published 2021-01-01

Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression

by Anna S. E. Cuomo, Daniel D. Seaton, Davis J. McCarthy, Iker Martinez, Marc Jan Bonder, Jose Garcia-Bernardo, Shradha Amatya, Pedro Madrigal, Abigail Isaacson, Florian Buettner, Andrew Knights, Kedar Nath Natarajan, HipSci Consortium, Ludovic Vallier, John C. Marioni, Mariya Chhatriwala, Oliver Stegle
Published 2020-02-01

The contribution of X-linked coding variation to severe developmental disorders

by Hilary C. Martin, Eugene J. Gardner, Kaitlin E. Samocha, Joanna Kaplanis, Nadia Akawi, Alejandro Sifrim, Ruth Y. Eberhardt, Ana Lisa Taylor Tavares, Matthew D. C. Neville, Mari E. K. Niemi, Giuseppe Gallone, Jeremy McRae, Deciphering Developmental Disorders Study, Caroline F. Wright, David R. FitzPatrick, Helen V. Firth, Matthew E. Hurles
Published 2021-01-01

Reproducibility in systems biology modelling

by Krishna Tiwari, Sarubini Kananathan, Matthew G Roberts, Johannes P Meyer, Mohammad Umer Sharif Shohan, Ashley Xavier, Matthieu Maire, Ahmad Zyoud, Jinghao Men, Szeyi Ng, Tung V N Nguyen, Mihai Glont, Henning Hermjakob, Rahuman S Malik‐Sheriff
Published 2021-02-01

Tumors induce de novo steroid biosynthesis in T cells to evade immunity

by Bidesh Mahata, Jhuma Pramanik, Louise van der Weyden, Krzysztof Polanski, Gozde Kar, Angela Riedel, Xi Chen, Nuno A. Fonseca, Kousik Kundu, Lia S. Campos, Edward Ryder, Graham Duddy, Izabela Walczak, Klaus Okkenhaug, David J. Adams, Jacqueline D. Shields, Sarah A. Teichmann
Published 2020-07-01

Integrated cross-study datasets of genetic dependencies in cancer

by Clare Pacini, Joshua M. Dempster, Isabella Boyle, Emanuel Gonçalves, Hanna Najgebauer, Emre Karakoc, Dieudonne van der Meer, Andrew Barthorpe, Howard Lightfoot, Patricia Jaaks, James M. McFarland, Mathew J. Garnett, Aviad Tsherniak, Francesco Iorio
Published 2021-03-01

A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog

by Joannella Morales, Danielle Welter, Emily H. Bowler, Maria Cerezo, Laura W. Harris, Aoife C. McMahon, Peggy Hall, Heather A. Junkins, Annalisa Milano, Emma Hastings, Cinzia Malangone, Annalisa Buniello, Tony Burdett, Paul Flicek, Helen Parkinson, Fiona Cunningham, Lucia A. Hindorff, Jacqueline A. L. MacArthur
Published 2018-02-01

The genome sequence of the eastern grey squirrel, Sciurus carolinensis Gmelin, 1788 [version 1; peer review: 2 approved]

by Dan Mead, Kathryn Fingland, Rachel Cripps, Roberto Portela Miguez, Michelle Smith, Craig Corton, Karen Oliver, Jason Skelton, Emma Betteridge, Jale Doulcan, Michael A. Quail, Shane A. McCarthy, Kerstin Howe, Ying Sims, James Torrance, Alan Tracey, Richard Challis, Richard Durbin, Mark Blaxter
Published 2020-02-01

CRISPR activation screen in mice identifies novel membrane proteins enhancing pulmonary metastatic colonisation

by Louise van der Weyden, Victoria Harle, Gemma Turner, Victoria Offord, Vivek Iyer, Alastair Droop, Agnieszka Swiatkowska, Roy Rabbie, Andrew D. Campbell, Owen J. Sansom, Mercedes Pardo, Jyoti S. Choudhary, Ingrid Ferreira, Mark Tullett, Mark J. Arends, Anneliese O. Speak, David J. Adams
Published 2021-03-01

Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow

by James C. Wright, Jonathan Mudge, Hendrik Weisser, Mitra P. Barzine, Jose M. Gonzalez, Alvis Brazma, Jyoti S. Choudhary, Jennifer Harrow
Published 2016-06-01

Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets

by Joshua M. Dempster, Clare Pacini, Sasha Pantel, Fiona M. Behan, Thomas Green, John Krill-Burger, Charlotte M. Beaver, Scott T. Younger, Victor Zhivich, Hanna Najgebauer, Felicity Allen, Emanuel Gonçalves, Rebecca Shepherd, John G. Doench, Kosuke Yusa, Francisca Vazquez, Leopold Parts, Jesse S. Boehm, Todd R. Golub, William C. Hahn, David E. Root, Mathew J. Garnett, Aviad Tsherniak, Francesco Iorio
Published 2019-12-01

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells

by Theodoros I. Roumeliotis, Steven P. Williams, Emanuel Gonçalves, Clara Alsinet, Martin Del Castillo Velasco-Herrera, Nanne Aben, Fatemeh Zamanzad Ghavidel, Magali Michaut, Michael Schubert, Stacey Price, James C. Wright, Lu Yu, Mi Yang, Rodrigo Dienstmann, Justin Guinney, Pedro Beltrao, Alvis Brazma, Mercedes Pardo, Oliver Stegle, David J. Adams, Lodewyk Wessels, Julio Saez-Rodriguez, Ultan McDermott, Jyoti S. Choudhary
Published 2017-08-01

The genome sequence of the brown trout, Salmo trutta Linnaeus 1758 [version 1; peer review: 2 approved]

by Tom Hansen, Per Gunnar Fjelldal, Sigbjørn Lien, Michelle Smith, Craig Corton, Karen Oliver, Jason Skelton, Emma Betteridge, Jale Doulcan, Olivier Fedrigo, Jacquelyn Mountcastle, Erich Jarvis, Shane A. McCarthy, William Chow, Kerstin Howe, James Torrance, Jonathan Wood, Ying Sims, Leanne Haggerty, Richard Challis, Jonathan Threlfall, Daniel Mead, Richard Durbin, Mark Blaxter
Published 2021-05-01

Clinically-relevant postzygotic mosaicism in parents and children with developmental disorders in trio exome sequencing data

by C. F. Wright, E. Prigmore, D. Rajan, J. Handsaker, J. McRae, J. Kaplanis, T. W. Fitzgerald, D. R. FitzPatrick, H. V. Firth, M. E. Hurles
Published 2019-07-01

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