Publications

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  • Ruqian Lyu, Vanessa Tsui, D. McCarthy, Wayne Crismani. Personalized genome structure via single gamete sequencing.. Genome biology, 22, 112 (19pp), 2021. doi: 10.1186/s13059-021-02327-w.

  • Anna SE Cuomo, Daniel D Seaton, D. McCarthy, Iker Martinez, Marc Jan Bonder, Jose Garcia-Bernardo, Shradha Amatya, Pedro Madrigal, Abigail Isaacson, Florian Buettner, Andrew Knights, Kedar Nath Natarajan, Ludovic Vallier, John C Marioni, Mariya Chhatriwala, Oliver Stegle, HipSci Consortium, CA Agu, A Alderton, P Danecek, R Denton, R Durbin, DJ Gaffney, A Goncalves, R Halai, S Harper, CM Kirton, A Kolb-Kokocinski, A Leha, Y Memari, M Patel, E Birney, FP Casale, L Clarke, PW Harrison, H Kilpinen, I Streeter, D Denovi, R Meleckyte, N Moens, FM Watt, WH Ouwehand, AI Lamond, D Bensaddek, P Beales. Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression.. Nature communications, 11, 810 (14pp), 2020. doi: 10.1038/s41467-020-14457-z.

  • David Laehnemann, Johannes Koester, Ewa Szczurek, D. McCarthy, Stephanie C Hicks, Mark D Robinson, Catalina A Vallejos, Kieran R Campbell, Niko Beerenwinkel, Ahmed Mahfouz, Luca Pinello, Pavel Skums, Alexandros Stamatakis, Camille Stephan-Otto Attolini, Samuel Aparicio, Jasmijn Baaijens, Marleen Balvert, Buys de Barbanson, Antonio Cappuccio, Giacomo Corleone, Bas E Dutilh, Maria Florescu, Victor Guryev, Rens Holmer, Katharina Jahn, Thamar Jessurun Lobo, Emma M Keizer, Indu Khatri, Szymon M Kielbasa, Jan O Korbel, Alexey M Kozlov, Tzu-Hao Kuo, Boudewijn PF Lelieveldt, Ion I Mandoiu, John C Marioni, Tobias Marschall, Felix Moelder, Amir Niknejad, Lukasz Raczkowski, Marcel Reinders, Jeroen de Ridder, Antoine-Emmanuel Saliba, Antonios Somarakis, Oliver Stegle, Fabian J Theis, H. Yang, Alex Zelikovsky, Alice C McHardy, Benjamin J Raphael, S. Shah, Alexander Schonhuth, David Lähnemann, Johannes Köster, Felix Mölder, Alexander Schönhuth. Eleven grand challenges in single-cell data science.. Genome biology, 21, 31 (35pp), 2020. doi: 10.1186/s13059-020-1926-6.

  • D. McCarthy, Raghd Rostom, Y. Huang, Daniel J Kunz, Petr Danecek, Marc Jan Bonder, Tzachi Hagai, Ruqian Lyu, HipSci Consortium, Wenyi Wang, Daniel J Gaffney, Benjamin D Simons, Oliver Stegle, Sarah A Teichmann. Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes.. Nature methods, 414-+, 2020. doi: 10.1038/s41592-020-0766-3.

  • ASE Cuomo, DD Seaton, D. McCarthy, I Martinez, MJ Bonder, J Garcia-Bernardo, S Amatya, P Madrigal, A Isaacson, F Buettner, A Knights, KN Natarajan, CA Agu, A Alderton, P Danecek, R Denton, R Durbin, DJ Gaffney, A Goncalves, R Halai, S Harper, CM Kirton, A Kolb-Kokocinski, A Leha, Y Memari, M Patel, E Birney, FP Casale, L Clarke, PW Harrison, H Kilpinen, I Streeter, D Denovi, R Meleckyte, N Moens, FM Watt, WH Ouwehand, AI Lamond, D Bensaddek, P Beales, L Vallier, JC Marioni, M Chhatriwala, O Stegle. Publisher Correction: Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression (Nature Communications, (2020), 11, 1, (810), 10.1038/s41467-020-14457-z). Nature Communications, 11, 1572, 2020. doi: 10.1038/s41467-020-15098-y.

  • Elisabetta Mereu, Atefeh Lafzi, Catia Moutinho, Christoph Ziegenhain, D. McCarthy, Adrian Alvarez-Varela, Eduard Batlle, Sagar, Dominic Gruen, Julia K Lau, Stephane C Boutet, Chad Sanada, Aik Ooi, Robert C Jones, Kelly Kaihara, Chris Brampton, Yasha Talaga, Yohei Sasagawa, Kaori Tanaka, Tetsutaro Hayashi, Caroline Braeuning, Cornelius Fischer, Sascha Sauers, Timo Trefzer, Christian Conrad, Xian Adiconis, Lan T Nguyen, Aviv Regev, Joshua Z Levin, Swati Parekh, Aleksandar Janjic, Lucas E Wange, Johannes W Bagnoli, Wolfgang Enard, Marta Gut, Rickard Sandberg, Itoshi Nikaido, Oliver Stegle, Holger Heyn, A Álvarez-Varela, D Grün, S Sauer. Benchmarking single-cell RNA-sequencing protocols for cell atlas projects. Nature Biotechnology, 747-+, 2020. doi: 10.1038/s41587-020-0469-4.

  • Tallulah S Andrews, Vladimir Yu Kiselev, D. McCarthy, Martin Hemberg. Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data.. Nature protocols, 1-9, 2020. doi: 10.1038/s41596-020-00409-w.

  • David Jakubosky, Marc Jan Bonder, Craig Smail, Margaret KR Donovan, William W Young Greenwald, Hiroko Matsui, i2QTL Consortium, Oliver Stegle, Erin N Smith, Stephen B Montgomery, Christopher DeBoever, Kelly A Frazer, M D’Antonio, A D’Antonio-Chronowska, N Cai, I Carcamo-Orive, JW Knowles, D. McCarthy, T Quertermous. Properties of structural variants and short tandem repeats associated with gene expression and complex traits.. Nature communications, 11, 2927, 2020. doi: 10.1038/s41467-020-16482-4.

  • David Jakubosky, Erin N Smith, Marc Jan Bonder, William W Young Greenwald, Hiroko Matsui, i2QTL Consortium, Oliver Stegle, Stephen B Montgomery, Christopher DeBoever, Kelly A Frazer, M D’Antonio, A D’Antonio-Chronowska, N Cai, I Carcamo-Orive, JW Knowles, D. McCarthy, BA Mirauta, T Quertermous, DD Seaton, C Smail. Discovery and quality analysis of a comprehensive set of structural variants and short tandem repeats.. Nature communications, 11, 1-15, 2020. doi: 10.1038/s41467-020-16481-5.

  • L Yiangou, RA Grandy, CM Morell, RA Tomaz, A Osnato, J Kadiwala, D Muraro, J Garcia-Bernardo, S Nakanoh, WG Bernard, D Ortmann, D. McCarthy, I Simonic, S Sinha, L Vallier. Method to Synchronize Cell Cycle of Human Pluripotent Stem Cells without Affecting Their Fundamental Characteristics.. Stem cell reports, 12, 165-179, 2019. doi: 10.1016/j.stemcr.2018.11.020.

  • SM Linker, L Urban, SJ Clark, M Chhatriwala, S Amatya, D. McCarthy, I Ebersberger, L Vallier, W Reik, O Stegle, MJ Bonder. Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity.. Genome biology, 20, 30 (14pp), 2019. doi: 10.1186/s13059-019-1644-0.

  • Y. Huang, D. McCarthy, Oliver Stegle. Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference. 598748, Cold Spring Harbor Laboratory, 2019. doi: 10.1101/598748.

  • Y. Huang, D. McCarthy, Oliver Stegle. Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference.. Genome biology, 20, 273 (12pp), 2019. doi: 10.1186/s13059-019-1865-2.

  • David Laehnemann, Johannes Köster, Ewa Szczurek, D. McCarthy, Stephanie Hicks, Mark Robinson, Catalina Vallejos, Niko Beerenwinkel, Kieran Campbell, Ahmed Mahfouz, Luca Pinello, Pavel Skums, Alexandros Stamatakis, Camille Stephan-Otto Attolini, Samuel Aparicio, Jasmijn Baaijens, Marleen Balvert, Buys de Barbanson, Antonio Cappuccio, Giacomo Corleone, Bas Dutilh, Maria Florescu, Victor Guryev, Rens Holmer, Katharina Jahn, Thamar Jessurun Lobo, Emma Keizer, Indu Khatri, Szymon KieÅ‚basa, Jan Korbel, Alexey Kozlov, Tzu-Hao Kuo, Boudewijn PF Lelieveldt, Ion Mandoiu, John Marioni, Tobias Marschall, Felix Mölder, Amir Niknejad, Łukasz RÄ…czkowski, Marcel Reinders, Jeroen de Ridder, Antoine-Emmanuel Saliba, Antonios Somarakis, Oliver Stegle, Fabian Theis, H. Yang, Alex Zelikovsky, Alice McHardy, Benjamin Raphael, S. Shah, Alexander Schönhuth. 12 Grand Challenges in Single-Cell Data Science. e27885v3, PeerJ, 2019. doi: 10.7287/peerj.preprints.27885v3.

  • Stephanie Maria Linker, Lara Urban, Stephen Clark, Mariya Chhatriwala, Shradha Amatya, D. McCarthy, Ingo Ebersberger, Ludovic Vallier, Wolf Reik, Oliver Stegle, Marc Jan Bonder. Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity. 328138, 2018. doi: 10.1101/328138.

  • D. McCarthy, Raghd Rostom, Y. Huang, Daniel Kunz, Petr Danecek, Marc Jan Bonder, Tzachi Hagai, Wenyi Wang, Daniel Gaffney, Benjamin Simons, Oliver Stegle, Sarah Teichmann, HipSci Consortium. Cardelino: Integrating whole exomes and single-cell transcriptomes to reveal phenotypic impact of somatic variants. 413047, 2018. doi: 10.1101/413047.

  • Jason Flannick, Christian Fuchsberger, Anubha Mahajan, Tanya M Teslovich, Vineeta Agarwala, Kyle J Gaulton, Lizz Caulkins, Ryan Koesterer, Clement Ma, Loukas Moutsianas, D. McCarthy, Manuel A Rivas, John RB Perry, Xueling Sim, Thomas W Blackwell, Neil R Robertson, N William Rayner, Pablo Cingolani, Adam E Locke, Juan Fernandez Tajes, Heather M Highland, Josee Dupuis, Peter S Chines, Cecilia M Lindgren, Christopher Hartl, Anne U Jackson, Han Chen, Jeroen R Huyghe, Martijn van de Bunt, Richard D Pearson, A. Kumar, Martina Mueller-Nurasyid, Niels Grarup, Heather M Stringham, Eric R Gamazon, Jaehoon Lee, Robert A Scott, Jennifer E Below, Jinyan Huang, Min Jin Go, Michael L Stitzel, Dorota Pasko, Stephen CJ Parker, Tibor V Varga, Todd Green, Nicola L Beer, Aaron G Day-Williams, Teresa Ferreira, Tasha Fingerlin, Momoko Horikoshi, Cheng Hu, Iksoo Huh, Mohammad Kamran Ikram, Bong-Jo Kim, Min-Seok Kwon, Keng-Han Lin, Taylor J Maxwell, Yoshihiko Nagai, Xu Wang, Ryan P Welch, Joon Yoon, Weihua Zhang, Nir Barzilai, Benja. Sequence data and association statistics from 12,940 type 2 diabetes cases and controls (vol 4, 170179, 2017). Scientific data, 5, 180002 (2pp), 2018. doi: 10.1038/sdata.2018.2.

  • T Schwerd, RV Bryant, S Pandey, M Capitani, L Meran, J-B Cazier, J Jung, K Mondal, M Parkes, CG Mathew, K Fiedler, D. McCarthy, PB Sullivan, A Rodrigues, SPL Travis, C Moore, J Sambrook, WH Ouwehand, DJ Roberts, J Danesh, RK Russell, DC Wilson, JR Kelsen, R Cornall, LA Denson, S Kugathasan, UG Knaus, EG Serra, CA Anderson, RH Duerr, DPB Mcgovern, J Cho, F Powrie, VSW Li, AM Muise, HH Uhlig, P Donnelly, J Bell, D Bentley, G McVean, P Ratcliffe, J Taylor, AOM Wilkie, J Broxholme, D Buck, L Gregory, G Lunter, I Tomlinson, C Allan, M Attar, A Green, S Humphray, Z Kingsbury, S Lamble, L Lonie, A Pagnamenta, P Piazza, G Polanco, A Trebes, R Copley, S Fiddy, R Grocock, E Hatton, WGS500 Consortium, Oxford IBD cohort study investigators, COLORS in IBD group investigators, UK IBD Genetics Consortium, INTERVAL Study, J Knight, C Holmes, L Hughes, P Humburg, A Kanapin, S Lise, H Martin, L Murray, A Rimmer, N Sahgal, B Wright, C Yau, Carolina Arancibia, Adam Bailey, Ellie Barnes, Beth Bird-Lieberman, Oliver Brain, Ba. NOX1 loss-of-function genetic variants in patients with inflammatory bowel disease.. Mucosal immunology, 11, 562-574, 2018. doi: 10.1038/mi.2017.74.

  • Benedetta Frida Baldi, Susan J Clark, Aaron E Darling, James M Hogan, Sandeep Kaur, Lena Maier-Hein, D. McCarthy, W. Moore, Esther Stenau, Jason R Swedlow, Jenny Vuong, James B Procter. Visualization of Biomedical Data. Annual Review of Biomedical Data Science, 1, 275-304, 2018. doi: 10.1146/annurev-biodatasci-080917-013424.

  • Manuel A Rivas, Brandon E Avila, Jukka Koskela, H. Huang, Christine Stevens, Matti Pirinen, Talin Haritunians, Benjamin M Neale, Mitja Kurki, Andrea Ganna, Daniel Graham, Benjamin Glaser, Inga Peter, Gil Atzmon, Nir Barzilai, Adam P Levine, Elena Schiff, Nikolas Pontikos, Ben Weisburd, Monkol Lek, Konrad J Karczewski, Jonathan Bloom, Eric V Minikel, Britt-Sabina Petersen, Laurent Beaugerie, Philippe Seksik, Jacques Cosnes, Stefan Schreiber, Bernd Bokemeyer, Johannes Bethge, International IBD Genetics Consortium, NIDDK IBD Genetics Consortium, T2D-GENES Consortium, Graham Heap, Tariq Ahmad, Vincent Plagnol, Anthony W Segal, Stephan Targan, Dan Turner, Paivi Saavalainen, Martti Farkkila, Kimmo Kontula, Aarno Palotie, Steven R Brant, Richard H Duerr, Mark S Silverberg, John D Rioux, Rinse K Weersma, Andre Franke, Luke Jostins, Carl A Anderson, Jeffrey C Barrett, Daniel G MacArthur, Chaim Jalas, Harry Sokol, Ramnik J Xavier, Ann Pulver, Judy H Cho, Dermot PB McGovern, Mark J Daly, K Croitoru, C Abraham, JP Ach. Insights into the genetic epidemiology of Crohn's and rare diseases in the Ashkenazi Jewish population.. PLoS genetics, 14, e1007329, 2018. doi: 10.1371/journal.pgen.1007329.

  • D. McCarthy, Kieran R Campbell, Aaron TL Lun, Quin F Wills. Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R.. Bioinformatics (Oxford, England), 33, 1179-1186, 2017. doi: 10.1093/bioinformatics/btw777.

  • Florian Buettner, Naruemon Pratanwanich, D. McCarthy, John C Marioni, Oliver Stegle. f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq.. Genome biology, 18, 212 (13pp), 2017. doi: 10.1186/s13059-017-1334-8.

  • Helena Kilpinen, Angela Goncalves, Andreas Leha, Vackar Afzal, Kaur Alasoo, Sofie Ashford, Sendu Bala, Dalila Bensaddek, Francesco Paolo Casale, Oliver JC Ulley, Petr Danecek, Adam Faulconbridge, Peter W Harrison, Annie Kathuria, D. McCarthy, Ruta Meleckyte, Yasin Memari, Nathalie Moens, Filipa Soares, Alice Mann, Ian Streeter, Chukwuma A Agu, Alex Alderton, Rachel Nelson, Sarah Harper, Minal Patel, Alistair White, Laura Clarke, Reena Halai, Christopher M Kirton, Anja Kolb-Kokocinski, Philip Beales, Ewan Birney, Davide Danovi, Angus I Lamond, Willem H Ouwehand, Ludovic Vallier, Fiona M Watt, Richard Durbin, Oliver Stegle, Daniel J Gaffney, Oliver J Culley. Common genetic variation drives molecular heterogeneity in human iPSCs.. Nature, 546, 370-+, 2017. doi: 10.1038/nature22403.

  • Jason Flannick, Christian Fuchsberger, Anubha Mahajan, Tanya M Teslovich, Vineeta Agarwala, Kyle J Gaulton, Lizz Caulkins, Ryan Koesterer, Clement Ma, Loukas Moutsianas, D. McCarthy, Manuel A Rivas, John RB Perry, Xueling Sim, Thomas W Blackwell, Neil R Robertson, N William Rayner, Pablo Cingolani, Adam E Locke, Juan Fernandez Tajes, Heather M Highland, Josee Dupuis, Peter S Chines, Cecilia M Lindgren, Christopher Hartl, Anne U Jackson, Han Chen, Jeroen R Huyghe, Martijn Van De Bunt, Richard D Pearson, A. Kumar, Martina Muller-Nurasyid, Niels Grarup, Heather M Stringham, Eric R Gamazon, Jaehoon Lee, Robert A Scott, Jennifer E Below, Jinyan Huang, Min Jin Go, Michael L Stitzel, Dorota Pasko, Stephen CJ Parker, Tibor V Varga, Todd Green, Nicola L Beer, Aaron G Day-Williams, Teresa Ferreira, Tasha Fingerlin, Momoko Horikoshi, Cheng Hu, Iksoo Huh, Mohammad Kamran Ikram, Bong-Jo Kim, Min-Seok Kwon, Keng-Han Lin, Taylor J Maxwell, Yoshihiko Nagai, Xu Wang, Ryan P Welch, Joon Yoon, Weihua Zhang, Nir Barzilai, Benjam. Sequence data and association statistics from 12,940 type 2 diabetes cases and controls.. Scientific data, 4, 170179 (20pp), 2017. doi: 10.1038/sdata.2017.179.

  • Helena Kilpinen, Angela Goncalves, Andreas Leha, Vackar Afzal, Kaur Alasoo, Sofie Ashford, Sendu Bala, Dalila Bensaddek, Francesco Paolo Casale, Oliver J Culley, Petr Danecek, Adam Faulconbridge, Peter W Harrison, Annie Kathuria, D. McCarthy, Ruta Meleckyte, Yasin Memari, Nathalie Moens, Filipa Soares, Alice Mann, Ian Streeter, Chukwuma A Agu, Alex Alderton, Rachel Nelson, Sarah Harper, Minal Patel, Alistair White, Laura Clarke, Reena Halai, Christopher M Kirton, Anja Kolb-Kokocinski, Philip Beales, Ewan Birney, Davide Danovi, Angus I Lamond, Willem H Ouwehand, Ludovic Vallier, Fiona M Watt, Richard Durbin, Oliver Stegle, Daniel J Gaffney. Erratum: Corrigendum: Common genetic variation drives molecular heterogeneity in human iPSCs. Nature, 546, 686 (1pp), 2017. doi: 10.1038/nature23012.

  • ATL Lun, D. McCarthy, JC Marioni. A step-by-step workflow for low-level analysis of single-cell RNA-seq data [version 1; referees: 5 approved with reservations]. F1000Research, 5, 2122, 2016. doi: 10.12688/F1000RESEARCH.9501.1.

  • Tomislav Ilicic, Jong Kyoung Kim, Aleksandra A Kolodziejczyk, Frederik Otzen Bagger, D. McCarthy, John C Marioni, Sarah A Teichmann. Classification of low quality cells from single-cell RNA-seq data.. Genome biology, 17, 29 (15pp), 2016. doi: 10.1186/s13059-016-0888-1.

  • Aaron TL Lun, D. McCarthy, John C Marioni. A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor.. F1000Research, 5, 2122, 2016. doi: 10.12688/f1000research.9501.2.

  • Christian Fuchsberger, Jason Flannick, Tanya M Teslovich, Anubha Mahajan, Vineeta Agarwala, Kyle J Gaulton, Clement Ma, Pierre Fontanillas, Loukas Moutsianas, D. McCarthy, Manuel A Rivas, John RB Perry, Xueling Sim, Thomas W Blackwell, Neil R Robertson, N William Rayner, Pablo Cingolani, Adam E Locke, Juan Fernandez Tajes, Heather M Highland, Josee Dupuis, Peter S Chines, Cecilia M Lindgren, Christopher Hartl, Anne U Jackson, Han Chen, Jeroen R Huyghe, Martijn van de Bunt, Richard D Pearson, A. Kumar, Martina Mueller-Nurasyid, Niels Grarup, Heather M Stringham, Eric R Gamazon, Jaehoon Lee, Robert A Scott, Jennifer E Below, Jinyan Huang, Min Jin Go, Michael L Stitzel, Dorota Pasko, Stephen CJ Parker, Tibor V Varga, Todd Green, Nicola L Beer, Aaron G Day-Williams, Teresa Ferreira, Tasha Fingerlin, Momoko Horikoshi, Cheng Hu, Iksoo Huh, Mohammad Kamran Ikram, Bong-Jo Kim, Min-Seok Kwon, Keng-Han Lin, Taylor J Maxwell, Yoshihiko Nagai, Xu Wang, Ryan P Welch, Joon Yoon, Weihua Zhang, Nir Barzilai, Benjamin F Voigh. The genetic architecture of type 2 diabetes.. Nature, 536, 41-+, 2016. doi: 10.1038/nature18642.

  • Bilal N Sheikh, Natalie L Downer, B. Phipson, Hannah K Vanyai, Andrew J Kueh, D. McCarthy, G. Smyth, Tim Thomas, Anne K Voss. MOZ and BMI1 play opposing roles during Hox gene activation in ES cells and in body segment identity specification in vivo. Proceedings of the National Academy of Sciences of the United States of America, 112, 5437-5442, 2015. doi: 10.1073/pnas.1422872112.

  • Pauline A van Schouwenburg, Emma E Davenport, Anne-Kathrin Kienzler, Ishita Marwah, Benjamin Wright, Mary Lucas, Tomas Malinauskas, Hilary C Martin, Helen E Lockstone, Jean-Baptiste Cazier, Helen M Chapel, Julian C Knight, Smita Y Patel, WGS500 Consortium, D. McCarthy. Application of whole genome and RNA sequencing to investigate the genomic landscape of common variable immunodeficiency disorders.. Clinical immunology (Orlando, Fla.), 160, 301-314, 2015. doi: 10.1016/j.clim.2015.05.020.

  • Stephen RF Twigg, Jennifer Forecki, Jacqueline AC Goos, Ivy CA Richardson, A Jeannette M Hoogeboom, Ans MW van den Ouweland, Sigrid MA Swagemakers, Maarten H Lequin, Daniel Van Antwerp, Simon J McGowan, Isabelle Westbury, Kerry A Miller, Steven A Wall, Peter J van der Spek, Irene MJ Mathijssen, Erwin Pauws, Christa S Merzdorf, Andrew OM Wilkie, WGS500 Consortium, Ans MW van den Ouweland, Daniel Van Antwerp, Peter J van der Spek, D. McCarthy. Gain-of-Function Mutations in ZIC1 Are Associated with Coronal Craniosynostosis and Learning Disability.. The American Journal of Human Genetics, 97, 378-388, 2015. doi: 10.1016/j.ajhg.2015.07.007.

  • Jenny C Taylor, Hilary C Martin, Stefano Lise, John Broxholme, Jean-Baptiste Cazier, Andy Rimmer, Alexander Kanapin, Gerton Lunter, Simon Fiddy, Chris Allan, A Radu Aricescu, Moustafa Attar, Christian Babbs, Jennifer Becq, David Beeson, Celeste Bento, Patricia Bignell, Edward Blair, Veronica J Buckle, Katherine Bull, Ondrej Cais, Holger Cario, Helen Chapel, Richard R Copley, Richard Cornall, Jude Craft, Karin Dahan, Emma E Davenport, Calliope Dendrou, Olivier Devuyst, Aimee L Fenwick, Jonathan Flint, Lars Fugger, Rodney D Gilbert, Anne Goriely, Angie Green, Ingo H Greger, Russell Grocock, Anja V Gruszczyk, Robert Hastings, Edouard Hatton, Doug Higgs, Adrian Hill, Chris Holmes, Malcolm Howard, Linda Hughes, Peter Humburg, David Johnson, Fredrik Karpe, Zoya Kingsbury, Usha Kini, Julian C Knight, Jonathan Krohn, Sarah Lamble, Craig Langman, Lorne Lonie, Joshua Luck, D. McCarthy, Simon J McGowan, Mary Frances McMullin, Kerry A Miller, Lisa Murray, Andrea H Nemeth, M Andrew Nesbit, David Nutt, Elizabeth Ormondroyd. Factors influencing success of clinical genome sequencing across a broad spectrum of disorders.. Nature genetics, 47, 717-+, 2015. doi: 10.1038/ng.3304.

  • Nayia Petousi, Richard R Copley, Terence RJ Lappin, Sally E Haggan, Celeste M Bento, Holger Cario, Melanie J Percy, Peter J Ratcliffe, Peter A Robbins, Mary Frances McMullin, WGS Consortium, P Donnelly, J Bell, D Bentley, G McVean, J Taylor, A Wilkie, P Donelly, J Broxholme, D Buck, J.-B Cazier, R Cornall, L Gregory, J Knight, G Lunter, I Tomlinson, C Allan, M Attar, A Green, S Humphray, Z Kingsbury, S Lamble, L Lonie, A Pagnamenta, P Piazza, G Polanco, A Trebes, S Fiddy, R Grocock, E Hatton, C Holmes, L Hughes, P Humburg, A Kanapin, S Lise, H Martin, L Murray, D. McCarthy, A Rimmer, N Sahgal, B Wright, C Yau. Erythrocytosis associated with a novel missense mutation in the BPGM gene.. Haematologica, 99, E201-E204, 2014. doi: 10.3324/haematol.2014.109306.

  • D. McCarthy, Peter Humburg, Alexander Kanapin, Manuel A Rivas, Kyle Gaulton, Jean-Baptiste Cazier, Peter Donnelly. Choice of transcripts and software has a large effect on variant annotation.. Genome medicine, 6, 26 (15pp), 2014. doi: 10.1186/gm543.

  • J-B Cazier, SR Rao, CM McLean, AL Walker, BJ Wright, EEM Jaeger, C Kartsonaki, L Marsden, C Yau, C Camps, P Kaisaki, J Taylor, JW Catto, IPM Tomlinson, AE Kiltie, FC Hamdy, Oxford-Illumina WGS500 Consortium, D. McCarthy. Whole-genome sequencing of bladder cancers reveals somatic CDKN1A mutations and clinicopathological associations with mutation burden.. Nature communications, 5, 3756 (11pp), 2014. doi: 10.1038/ncomms4756.

  • S Anders, D. McCarthy, Y. Chen, M Okoniewski, G. Smyth, W Huber, MD Robinson. Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nature Protocols, 8, 1765-1786, 2013. doi: 10.1038/nprot.2013.099.

  • Christian Babbs, Nigel A Roberts, Luis Sanchez-Pulido, Simon J McGowan, Momin R Ahmed, Jill M Brown, Mohamed A Sabry, David R Bentley, Gil A McVean, Peter Donnelly, Opher Gileadi, Chris P Ponting, Douglas R Higgs, Veronica J Buckle, WGS500 Consortium, D. McCarthy. Homozygous mutations in a predicted endonuclease are a novel cause of congenital dyserythropoietic anemia type I.. Haematologica, 98, 1383-1387, 2013. doi: 10.3324/haematol.2013.089490.

  • Vikram P Sharma, Aimee L Fenwick, Mia S Brockop, Simon J McGowan, Jacqueline AC Goos, A Jeannette M Hoogeboom, Angela F Brady, Nu Owase Jeelani, Sally Ann Lynch, John B Mulliken, Dylan J Murray, Julie M Phipps, Elizabeth Sweeney, Susan E Tomkins, Louise C Wilson, Sophia Bennett, Richard J Cornall, John Broxholme, Alexander Kanapin, David Johnson, Steven A Wall, Peter J van der Spek, Irene MJ Mathijssen, Robert E Maxson, Stephen RF Twigg, Andrew OM Wilkie, 500 Whole-Genome Sequences (WGS500) Consortium, D. McCarthy. Mutations in TCF12, encoding a basic helix-loop-helix partner of TWIST1, are a frequent cause of coronal craniosynostosis.. Nature genetics, 45, 304-307, 2013. doi: 10.1038/ng.2531.

  • Steven P Lund, Dan Nettleton, D. McCarthy, G. Smyth. Detecting Differential Expression in RNA-sequence Data Using Quasi-likelihood with Shrunken Dispersion Estimates. Statistical Applications in Genetics and Molecular Biology, 11, 2012. doi: 10.1515/1544-6115.1826.

  • D. McCarthy, Y. Chen, G. Smyth. Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Research, 40, 4288-4297, 2012. doi: 10.1093/nar/gks042.

  • M. Young, D. McCarthy, Matthew J Wakefield, G. Smyth, Alicia Oshlack, Mark D Robinson. Differential Expression for RNA Sequencing (RNA-Seq) Data: Mapping, Summarization, Statistical Analysis, and Experimental Design. 169-190, SPRINGER, 2012. doi: 10.1007/978-1-4614-0782-9_10.

  • DJ Campbell, Y. Zhang, D Kelly, RE Gilbert, D. McCarthy, W Shi, G. Smyth. Aliskiren increases bradykinin and tissue kallikrein mRNA levels in the heart. Clinical and Experimental Pharmacology and Physiology, 38, 623-631, 2011. doi: 10.1111/j.1440-1681.2011.05572.x.

  • Mark D Robinson, D. McCarthy, G. Smyth. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.. Bioinformatics (Oxford, England), 26, 139-140, 2010. doi: 10.1093/bioinformatics/btp616.

  • MD Robinson, D. McCarthy, G. Smyth. edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26, 139-140, 2009. doi: 10.1093/bioinformatics/btp616.

  • D. McCarthy, G. Smyth. Testing significance relative to a fold-change threshold is a TREAT. Bioinformatics, 25, 765-771, 2009. doi: 10.1093/bioinformatics/btp053.