Publications

Our research contributions to computational biology, single-cell analysis, and network biology. Lab members are highlighted in bold in the author lists.

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2010

The Evolution and Structure Prediction of Coiled Coils across All Genomes

Owen Rackham, Martin Madera, Craig T. Armstrong, Thomas L. Vincent, Derek N. Woolfson, Julian Gough

Journal of Molecular Biology (2010) DOI: 10.1016/j.jmb.2010.08.032

network biology

2011

SUPERFAMILY 1.75 including a domain-centric gene ontology method

D. A. de Lima Morais, H. Fang, Owen Rackham, D. Wilson, R. Pethica, C. Chothia, J. Gough

Nucleic Acids Research (2011) DOI: 10.1093/nar/gkq1130

network biology

2012

Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains

Tony E. Lewis, Ian Sillitoe, Antonina Andreeva, Tom L. Blundell, Daniel W.A. Buchan, Cyrus Chothia, Alison Cuff, Jose M. Dana, Ioannis Filippis, Julian Gough, Sarah Hunter, David T. Jones, Lawrence A. Kelley, Gerard J. Kleywegt, Federico Minneci, Alex Mitchell, Alexey G. Murzin, Bernardo Ochoa-Montaño, Owen Rackham, James Smith, Michael J. E. Sternberg, Sameer Velankar, Corin Yeats, Christine Orengo

Nucleic Acids Research (2012) DOI: 10.1093/nar/gks1266

network biology

2013

A daily-updated tree of (sequenced) life as a reference for genome research

Hai Fang, Matt E. Oates, Ralph B. Pethica, Jenny M. Greenwood, Adam J. Sardar, Owen Rackham, Philip C. J. Donoghue, Alexandros Stamatakis, David A. de Lima Morais, Julian Gough

Scientific Reports (2013) DOI: 10.1038/srep02015

network biology

2014

An atlas of active enhancers across human cell types and tissues

The FANTOM Consortium, Robin Andersson, Claudia Gebhard, Irene Miguel-Escalada, Ilka Hoof, Jette Bornholdt, Mette Boyd, Yun Chen, Xiaobei Zhao, Christian Schmidl, Takahiro Suzuki, Evgenia Ntini, Erik Arner, Eivind Valen, Kang Li, Lucia Schwarzfischer, Dagmar Glatz, Johanna Raithel, Berit Lilje, Nicolas Rapin, Frederik Otzen Bagger, Mette Jørgensen, Peter Refsing Andersen, Nicolas Bertin, Owen Rackham, A. Maxwell Burroughs, J. Kenneth Baillie, Yuri Ishizu, Yuri Shimizu, Erina Furuhata, Shiori Maeda, Yutaka Negishi, Christopher J. Mungall, Terrence F. Meehan, Timo Lassmann, Masayoshi Itoh, Hideya Kawaji, Naoto Kondo, Jun Kawai, Andreas Lennartsson, Carsten O. Daub, Peter Heutink, David A. Hume, Torben Heick Jensen, Harukazu Suzuki, Yoshihide Hayashizaki, Ferenc Müller, Alistair R. R. Forrest, Piero Carninci, Michael Rehli, Albin Sandelin

Nature (2014) DOI: 10.1038/nature12787

network biology

A promoter-level mammalian expression atlas

The FANTOM Consortium and the RIKEN PMI and CLST (DGT), Owen Rackham

Nature (2014) DOI: 10.1038/nature13182

network biology

Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation

Hiromasa Morikawa, Naganari Ohkura, Alexis Vandenbon, Masayoshi Itoh, Sayaka Nagao-Sato, Hideya Kawaji, Timo Lassmann, Piero Carninci, Yoshihide Hayashizaki, Alistair R. R. Forrest, Daron M. Standley, Hiroshi Date, Shimon Sakaguchi, the FANTOM Consortium, Alistair R.R. Forrest, Michael Rehli, J. Kenneth Baillie, Michiel J.L. de Hoon, Vanja Haberle, Ivan V. Kulakovskiy, Marina Lizio, Robin Andersson, Christopher J. Mungall, Terrence F. Meehan, Sebastian Schmeier, Nicolas Bertin, Mette Jørgensen, Emmanuel Dimont, Erik Arner, Christian Schmidl, Ulf Schaefer, Yulia A. Medvedeva, Charles Plessy, Morana Vitezic, Jessica Severin, Colin A. Semple, Yuri Ishizu, Margherita Francescatto, Intikhab Alam, Davide Albanese, Gabriel M. Altschuler, John A.C. Archer, Peter Arner, Magda Babina, Sarah Baker, Piotr J. Balwierz, Anthony G. Beckhouse, Swati Pradhan-Bhatt, Judith A. Blake, Antje Blumenthal, Beatrice Bodega, Alessandro Bonetti, James Briggs, Frank Brombacher, A. Maxwell Burroughs, Andrea Califano, Carlo V. Cannistraci, Daniel Carbajo, Yun Chen, Marco Chierici, Yari Ciani, Hans C. Clevers, Emiliano Dalla, Carrie A. Davis, Bart Deplancke, Michael Detmar, Alexander D. Diehl, Taeko Dohi, Finn Drabløs, Albert S.B. Edge, Matthias Edinger, Karl Ekwall, Mitsuhiro Endoh, Hideki Enomoto, Michela Fagiolini, Lynsey Fairbairn, Hai Fang, Mary C. Farach-Carson, Geoffrey J. Faulkner, Alexander V. Favorov, Malcolm E. Fisher, Martin C. Frith, Rie Fujita, Shiro Fukuda, Cesare Furlanello, Masaaki Furuno, Jun-ichi Furusawa, Teunis B. Geijtenbeek, Andrew Gibson, Thomas Gingeras, Daniel Goldowitz, Julian Gough, Sven Guhl, Reto Guler, Stefano Gustincich, Thomas J. Ha, Masahide Hamaguchi, Mitsuko Hara, Matthias Harbers, Jayson Harshbarger, Akira Hasegawa, Yuki Hasegawa, Takehiro Hashimoto, Meenhard Herlyn, Kelly J. Hitchens, Shannan J. Ho Sui, Oliver M. Hofmann, Ilka Hoof, Fumi Hori, Lukasz Huminiecki, Kei Iida, Tomokatsu Ikawa, Boris R. Jankovic, Hui Jia, Anagha Joshi, Giuseppe Jurman, Bogumil Kaczkowski, Chieko Kai, Kaoru Kaida, Ai Kaiho, Kazuhiro Kajiyama, Mutsumi Kanamori-Katayama, Artem S. Kasianov, Takeya Kasukawa, Shintaro Katayama, Sachi Kato, Shuji Kawaguchi, Hiroshi Kawamoto, Yuki I. Kawamura, Tsugumi Kawashima, Judith S. Kempfle, Tony J. Kenna, Juha Kere, Levon M. Khachigian, Toshio Kitamura, S. Peter Klinken, Alan J. Knox, Miki Kojima, Soichi Kojima, Naoto Kondo, Haruhiko Koseki, Shigeo Koyasu, Sarah Krampitz, Atsutaka Kubosaki, Andrew T. Kwon, Jeroen F.J. Laros, Weonju Lee, Andreas Lennartsson, Kang Li, Berit Lilje, Leonard Lipovich, Alan Mackay-sim, Ri-ichiroh Manabe, Jessica C. Mar, Benoit Marchand, Anthony Mathelier, Niklas Mejhert, Alison Meynert, Yosuke Mizuno, David A. de Lima Morais, Mitsuru Morimoto, Kazuyo Moro, Efthymios Motakis, Hozumi Motohashi, Christine L. Mummery, Mitsuyoshi Murata, Yutaka Nakachi, Fumio Nakahara, Toshiyuki Nakamura, Yukio Nakamura, Kenichi Nakazato, Erik van Nimwegen, Noriko Ninomiya, Hiromi Nishiyori, Shohei Noma, Tadasuke Nozaki, Soichi Ogishima, Hiroko Ohmiya, Hiroshi Ohno, Mitsuhiro Ohshima, Mariko Okada-Hatakeyama, Yasushi Okazaki, Valerio Orlando, Dmitry A. Ovchinnikov, Arnab Pain, Robert Passier, Margaret Patrikakis, Helena Persson, Silvano Piazza, James G.D. Prendergast, Owen Rackham, Jordan A. Ramilowski, Mamoon Rashid, Timothy Ravasi, Patrizia Rizzu, Marco Roncador, Sugata Roy, Morten B. Rye, Eri Saijyo, Antti Sajantila, Akiko Saka, Mizuho Sakai, Hiroki Sato, Hironori Satoh, Suzana Savvi, Alka Saxena, Claudio Schneider, Erik A. Schultes, Gundula G. Schulze-Tanzil, Anita Schwegmann, Thierry Sengstag, Guojun Sheng, Hisashi Shimoji, Yishai Shimoni, Jay W. Shin, Christophe Simon, Daisuke Sugiyama, Takaaki Sugiyama, Masanori Suzuki, Rolf K. Swoboda, Peter A.C. 't Hoen, Michihira Tagami, Naoko Takahashi, Jun Takai, Hiroshi Tanaka, Hideki Tatsukawa, Zuotian Tatum, Mark Thompson, Hiroo Toyoda, Tetsuro Toyoda, Eivind Valen, Marc van de Wetering, Linda M. van den Berg, Roberto Verardo, Dipti Vijayan, Ilya E. Vorontsov, Wyeth W. Wasserman, Shoko Watanabe, Christine A. Wells, Louise N. Winteringham, Ernst Wolvetang, Emily J. Wood, Yoko Yamaguchi, Masayuki Yamamoto, Misako Yoneda, Yohei Yonekura, Shigehiro Yoshida, Suzan E. Zabierowski, Peter G. Zhang, Xiaobei Zhao, Silvia Zucchelli, Kim M. Summers, Harukazu Suzuki, Carsten O. Daub, Jun Kawai, Peter Heutink, Winston Hide, Tom C. Freeman, Boris Lenhard, Vladimir B. Bajic, Martin S. Taylor, Vsevolod J. Makeev, Albin Sandelin, David A. Hume

Proceedings of the National Academy of Sciences (2014) DOI: 10.1073/pnas.1312717110

network biology

The Evolution of Human Cells in Terms of Protein Innovation

Adam J. Sardar, Matt E. Oates, Hai Fang, Alistair R.R. Forrest, Hideya Kawaji, Julian Gough, Owen Rackham

Molecular Biology and Evolution (2014) DOI: 10.1093/molbev/mst139

network biology

2015

Function-selective domain architecture plasticity potentials in eukaryotic genome evolution

Viktorija Linkeviciute, Owen Rackham, Julian Gough, Matt E. Oates, Hai Fang

Biochimie (2015) DOI: 10.1016/j.biochi.2015.05.003

network biology

The statistical geometry of transcriptome divergence in cell-type evolution and cancer

Cong Liang, the FANTOM Consortium, Alistair R.R. Forrest, Günter P. Wagner, Owen Rackham

Nature Communications (2015) DOI: 10.1038/ncomms7066

network biology

WGBSSuite: simulating whole-genome bisulphite sequencing data and benchmarking differential DNA methylation analysis tools

Owen Rackham, Petros Dellaportas, Enrico Petretto, Leonardo Bottolo

Bioinformatics (2015) DOI: 10.1093/bioinformatics/btv114

network biology

EvoTol: a protein-sequence based evolutionary intolerance framework for disease-gene prioritization

Owen Rackham, Hashem A. Shihab, Michael R. Johnson, Enrico Petretto

Nucleic Acids Research (2015) DOI: 10.1093/nar/gku1322

network biology

The SUPERFAMILY 1.75 database in 2014: a doubling of data

Matt E. Oates, Jonathan Stahlhacke, Dimitrios V. Vavoulis, Ben Smithers, Owen Rackham, Adam J. Sardar, Jan Zaucha, Natalie Thurlby, Hai Fang, Julian Gough

Nucleic Acids Research (2015) DOI: 10.1093/nar/gku1041

network biology

Genome3D: exploiting structure to help users understand their sequences

Tony E. Lewis, Ian Sillitoe, Antonina Andreeva, Tom L. Blundell, Daniel W.A. Buchan, Cyrus Chothia, Domenico Cozzetto, José M. Dana, Ioannis Filippis, Julian Gough, David T. Jones, Lawrence A. Kelley, Gerard J. Kleywegt, Federico Minneci, Jaina Mistry, Alexey G. Murzin, Bernardo Ochoa-Montaño, Matt E. Oates, Marco Punta, Owen Rackham, Jonathan Stahlhacke, Michael J.E. Sternberg, Sameer Velankar, Christine Orengo

Nucleic Acids Research (2015) DOI: 10.1093/nar/gku973

network biology

A <scp>P</scp> roteome <scp>Q</scp> uality <scp>I</scp> ndex

Jan Zaucha, Jonathan Stahlhacke, Matt E. Oates, Natalie Thurlby, Owen Rackham, Hai Fang, Ben Smithers, Julian Gough

Environmental Microbiology (2015) DOI: 10.1111/1462-2920.12622

network biology

Discovery of Molecular Markers to Discriminate Corneal Endothelial Cells in the Human Body

Masahito Yoshihara, Hiroko Ohmiya, Susumu Hara, Satoshi Kawasaki, FANTOM consortium, Yoshihide Hayashizaki, Masayoshi Itoh, Hideya Kawaji, Motokazu Tsujikawa, Kohji Nishida, Owen Rackham

PLOS ONE (2015) DOI: 10.1371/journal.pone.0117581

network biology

2016

A predictive computational framework for direct reprogramming between human cell types

The FANTOM Consortium, Owen Rackham, Jaber Firas, Hai Fang, Matt E Oates, Melissa L Holmes, Anja S Knaupp, Harukazu Suzuki, Christian M Nefzger, Carsten O Daub, Jay W Shin, Enrico Petretto, Alistair R R Forrest, Yoshihide Hayashizaki, Jose M Polo, Julian Gough

Nature Genetics (2016) DOI: 10.1038/ng.3487

network biology

Systems genetics identifies a convergent gene network for cognition and neurodevelopmental disease

Michael R Johnson, Kirill Shkura, Sarah R Langley, Andree Delahaye-Duriez, Prashant Srivastava, W David Hill, Owen Rackham, Gail Davies, Sarah E Harris, Aida Moreno-Moral, Maxime Rotival, Doug Speed, Slavé Petrovski, Anaïs Katz, Caroline Hayward, David J Porteous, Blair H Smith, Sandosh Padmanabhan, Lynne J Hocking, John M Starr, David C Liewald, Alessia Visconti, Mario Falchi, Leonardo Bottolo, Tiziana Rossetti, Bénédicte Danis, Manuela Mazzuferi, Patrik Foerch, Alexander Grote, Christoph Helmstaedter, Albert J Becker, Rafal M Kaminski, Ian J Deary, Enrico Petretto

Nature Neuroscience (2016) DOI: 10.1038/nn.4205

network biology

Computational methods for direct cell conversion

Uma S. Kamaraj, Julian Gough, Jose M. Polo, Enrico Petretto, Owen Rackham

Cell Cycle (2016) DOI: 10.1080/15384101.2016.1238119

network biology

Web-based Gene Pathogenicity Analysis (WGPA): a web platform to interpret gene pathogenicity from personal genome data

Juan J. Diaz-Montana, Owen Rackham, Norberto Diaz-Diaz, Enrico Petretto

Bioinformatics (2016) DOI: 10.1093/bioinformatics/btv598

network biology

A Bayesian approach for analysis of whole-genome bisulphite sequencing data identifies disease-associated changes in DNA methylation

Owen Rackham, Sarah R. Langley, Thomas Oates, Eleni Vradi, Nathan Harmston, Prashant K. Srivastava, Jacques Behmoaras, Petros Dellaportas, Leonardo Bottolo, Enrico Petretto

Preprint (2016) DOI: 10.1101/041715

network biology

2017

Cell Type of Origin Dictates the Route to Pluripotency

Christian M. Nefzger, Fernando J. Rossello, Joseph Chen, Xiaodong Liu, Anja S. Knaupp, Jaber Firas, Jacob M. Paynter, Jahnvi Pflueger, Sam Buckberry, Sue Mei Lim, Brenda Williams, Sara Alaei, Keshav Faye-Chauhan, Enrico Petretto, Susan K. Nilsson, Ryan Lister, Mirana Ramialison, David R. Powell, Owen Rackham, Jose M. Polo

Cell Reports (2017) DOI: 10.1016/j.celrep.2017.11.029

network biology

An atlas of human long non-coding RNAs with accurate 5′ ends

Chung-Chau Hon, Jordan A. Ramilowski, Jayson Harshbarger, Nicolas Bertin, Owen Rackham, Julian Gough, Elena Denisenko, Sebastian Schmeier, Thomas M. Poulsen, Jessica Severin, Marina Lizio, Hideya Kawaji, Takeya Kasukawa, Masayoshi Itoh, A. Maxwell Burroughs, Shohei Noma, Sarah Djebali, Tanvir Alam, Yulia A. Medvedeva, Alison C. Testa, Leonard Lipovich, Chi-Wai Yip, Imad Abugessaisa, Mickaël Mendez, Akira Hasegawa, Dave Tang, Timo Lassmann, Peter Heutink, Magda Babina, Christine A. Wells, Soichi Kojima, Yukio Nakamura, Harukazu Suzuki, Carsten O. Daub, Michiel J. L. de Hoon, Erik Arner, Yoshihide Hayashizaki, Piero Carninci, Alistair R. R. Forrest

Nature (2017) DOI: 10.1038/nature21374

network biology

IL-11 is a crucial determinant of cardiovascular fibrosis

Sebastian Schafer, Sivakumar Viswanathan, Anissa A. Widjaja, Wei-Wen Lim, Aida Moreno-Moral, Daniel M. DeLaughter, Benjamin Ng, Giannino Patone, Kingsley Chow, Ester Khin, Jessie Tan, Sonia P. Chothani, Lei Ye, Owen Rackham, Nicole S. J. Ko, Norliza E. Sahib, Chee Jian Pua, Nicole T. G. Zhen, Chen Xie, Mao Wang, Henrike Maatz, Shiqi Lim, Kathrin Saar, Susanne Blachut, Enrico Petretto, Sabine Schmidt, Tracy Putoczki, Nuno Guimarães-Camboa, Hiroko Wakimoto, Sebastiaan van Heesch, Kristmundur Sigmundsson, See L. Lim, Jia L. Soon, Victor T. T. Chao, Yeow L. Chua, Teing E. Tan, Sylvia M. Evans, Yee J. Loh, Muhammad H. Jamal, Kim K. Ong, Kim C. Chua, Boon-Hean Ong, Mathew J. Chakaramakkil, Jonathan G. Seidman, Christine E. Seidman, Norbert Hubner, Kenny Y. K. Sin, Stuart A. Cook

Nature (2017) DOI: 10.1038/nature24676

network biology

Titin-truncating variants affect heart function in disease cohorts and the general population

Sebastian Schafer, Antonio de Marvao, Eleonora Adami, Lorna R Fiedler, Benjamin Ng, Ester Khin, Owen Rackham, Sebastiaan van Heesch, Chee J Pua, Miao Kui, Roddy Walsh, Upasana Tayal, Sanjay K Prasad, Timothy J W Dawes, Nicole S J Ko, David Sim, Laura L H Chan, Calvin W L Chin, Francesco Mazzarotto, Paul J Barton, Franziska Kreuchwig, Dominique P V de Kleijn, Teresa Totman, Carlo Biffi, Nicole Tee, Daniel Rueckert, Valentin Schneider, Allison Faber, Vera Regitz-Zagrosek, Jonathan G Seidman, Christine E Seidman, Wolfgang A Linke, Jean-Paul Kovalik, Declan O'Regan, James S Ware, Norbert Hubner, Stuart A Cook

Nature Genetics (2017) DOI: 10.1038/ng.3719

network biology

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

Marina Lizio, Jayson Harshbarger, Imad Abugessaisa, Shuei Noguchi, Atsushi Kondo, Jessica Severin, Chris Mungall, David Arenillas, Anthony Mathelier, Yulia A. Medvedeva, Andreas Lennartsson, Finn Drabløs, Jordan A. Ramilowski, Owen Rackham, Julian Gough, Robin Andersson, Albin Sandelin, Hans Ienasescu, Hiromasa Ono, Hidemasa Bono, Yoshihide Hayashizaki, Piero Carninci, Alistair R.R. Forrest, Takeya Kasukawa, Hideya Kawaji

Nucleic Acids Research (2017) DOI: 10.1093/nar/gkw995

network biology

Reliable detection of translational regulation with Ribo-seq

Sonia P Chothani, Eleonora Adami, Sivakumar Viswanathan, Norbert Hubner, Stuart Cook, Sebastian Schafer, Owen Rackham

Preprint (2017) DOI: 10.1101/234344

network biology

<scp>RNA</scp> polymerase <scp>II</scp> primes Polycomb‐repressed developmental genes throughout terminal neuronal differentiation

Carmelo Ferrai, Elena Torlai Triglia, Jessica R Risner‐Janiczek, Tiago Rito, Owen Rackham, Inês de Santiago, Alexander Kukalev, Mario Nicodemi, Altuna Akalin, Meng Li, Mark A Ungless, Ana Pombo

Molecular Systems Biology (2017) DOI: 10.15252/msb.20177754

network biology

A Bayesian Approach for Analysis of Whole-Genome Bisulfite Sequencing Data Identifies Disease-Associated Changes in DNA Methylation

Owen Rackham, Sarah R Langley, Thomas Oates, Eleni Vradi, Nathan Harmston, Prashant K Srivastava, Jacques Behmoaras, Petros Dellaportas, Leonardo Bottolo, Enrico Petretto

Genetics (2017) DOI: 10.1534/genetics.116.195008

network biology

2018

Translational control of cardiac fibrosis

Sonia Chothani, Sebastian Schafer, Eleonora Adami, Sivakumar Viswanathan, Anissa A Widjaja, Sarah R Langley, Jessie Tan, Chee Jian Pua, Giuseppe D’Agostino, Sebastiaan van Heesch, Franziska Witte, Leanne E Felkin, Eleni G. Christodoulou, Jinrui Dong, Susanne Blachut, Giannino Patone, Paul JR Barton, Norbert Hubner, Stuart A Cook, Owen Rackham

Preprint (2018) DOI: 10.1101/451666

network biology

2019

Integrated systems‐genetic analyses reveal a network target for delaying glioma progression

Liisi Laaniste, Prashant K. Srivastava, Julianna Stylianou, Nelofer Syed, Silvia Cases‐Cunillera, Kirill Shkura, Qingyu Zeng, Owen Rackham, Sarah R. Langley, Andree Delahaye-Duriez, Kevin O'Neill, Matthew Williams, Albert Becker, Federico Roncaroli, Enrico Petretto, Michael R. Johnson

Annals of Clinical and Translational Neurology (2019) DOI: 10.1002/acn3.50850

network biology

deltaTE: Detection of Translationally Regulated Genes by Integrative Analysis of Ribo‐seq and RNA‐seq Data

Sonia Chothani, Eleonora Adami, John F. Ouyang, Sivakumar Viswanathan, Norbert Hubner, Stuart A. Cook, Sebastian Schafer, Owen Rackham

Current Protocols in Molecular Biology (2019) DOI: 10.1002/cpmb.108

network biology

Molecular Interaction Networks to Select Factors for Cell Conversion

John F. Ouyang, Uma S. Kamaraj, Jose M. Polo, Julian Gough, Owen Rackham

Methods in Molecular Biology (2019) DOI: 10.1007/978-1-4939-9224-9_16

network biology

WWP2 regulates pathological cardiac fibrosis by modulating SMAD2 signaling

Huimei Chen, Aida Moreno-Moral, Francesco Pesce, Nithya Devapragash, Massimiliano Mancini, Ee Ling Heng, Maxime Rotival, Prashant K. Srivastava, Nathan Harmston, Kirill Shkura, Owen Rackham, Wei-Ping Yu, Xi-Ming Sun, Nicole Gui Zhen Tee, Elisabeth Li Sa Tan, Paul J. R. Barton, Leanne E. Felkin, Enrique Lara-Pezzi, Gianni Angelini, Cristina Beltrami, Michal Pravenec, Sebastian Schafer, Leonardo Bottolo, Norbert Hubner, Costanza Emanueli, Stuart A. Cook, Enrico Petretto

Nature Communications (2019) DOI: 10.1038/s41467-019-11551-9

network biology

A single-cell atlas of entorhinal cortex from individuals with Alzheimer’s disease reveals cell-type-specific gene expression regulation

Alexandra Grubman, Gabriel Chew, John F. Ouyang, Guizhi Sun, Xin Yi Choo, Catriona McLean, Rebecca K. Simmons, Sam Buckberry, Dulce B. Vargas-Landin, Daniel Poppe, Jahnvi Pflueger, Ryan Lister, Owen Rackham, Enrico Petretto, Jose M. Polo

Nature Neuroscience (2019) DOI: 10.1038/s41593-019-0539-4

network biology

Characterising the loss-of-function impact of 5’ untranslated region variants in whole genome sequence data from 15,708 individuals

Nicola Whiffin, Konrad J Karczewski, Xiaolei Zhang, Sonia Chothani, Miriam J Smith, D Gareth Evans, Angharad M Roberts, Nicholas M Quaife, Sebastian Schafer, Owen Rackham, Jessica Alföldi, Anne H O’Donnell-Luria, Laurent C Francioli, Genome Aggregation Database (gnomAD) Production Team, Irina M. Armean, Eric Banks, Louis Bergelson, Kristian Cibulskis, Ryan L Collins, Kristen M. Connolly, Miguel Covarrubias, Beryl Cummings, Mark J. Daly, Stacey Donnelly, Yossi Farjoun, Steven Ferriera, Laurent Francioli, Stacey Gabriel, Laura D. Gauthier, Jeff Gentry, Namrata Gupta, Thibault Jeandet, Diane Kaplan, Konrad J. Karczewski, Kristen M. Laricchia, Christopher Llanwarne, Eric V. Minikel, Ruchi Munshi, Benjamin M Neale, Sam Novod, Anne H. O’Donnell-Luria, Nikelle Petrillo, Timothy Poterba, David Roazen, Valentin Ruano-Rubio, Andrea Saltzman, Kaitlin E. Samocha, Molly Schleicher, Cotton Seed, Matthew Solomonson, Jose Soto, Grace Tiao, Kathleen Tibbetts, Charlotte Tolonen, Christopher Vittal, Gordon Wade, Arcturus Wang, Qingbo Wang, James S Ware, Nicholas A Watts, Ben Weisburd, Genome Aggregation Database (gnomAD) Consortium, Carlos A Aguilar Salinas, Tariq Ahmad, Christine M. Albert, Diego Ardissino, Gil Atzmon, John Barnard, Laurent Beaugerie, Emelia J. Benjamin, Michael Boehnke, Lori L. Bonnycastle, Erwin P. Bottinger, Donald W Bowden, Matthew J Bown, John C Chambers, Juliana C. Chan, Daniel Chasman, Judy Cho, Mina K. Chung, Bruce Cohen, Adolfo Correa, Dana Dabelea, Dawood Darbar, Ravindranath Duggirala, Josée Dupuis, Patrick T. Ellinor, Roberto Elosua, Jeanette Erdmann, Tõnu Esko, Martti Färkkilä, Jose Florez, Andre Franke, Gad Getz, Benjamin Glaser, Stephen J. Glatt, David Goldstein, Clicerio Gonzalez, Leif Groop, Christopher Haiman, Craig Hanis, Matthew Harms, Mikko Hiltunen, Matti M. Holi, Christina M. Hultman, Mikko Kallela, Jaakko Kaprio, Sekar Kathiresan, Bong-Jo Kim, Young Jin Kim, George Kirov, Jaspal Kooner, Seppo Koskinen, Harlan M. Krumholz, Subra Kugathasan, Soo Heon Kwak, Markku Laakso, Terho Lehtimäki, Ruth J.F. Loos, Steven A. Lubitz, Ronald C.W. Ma, Daniel G. MacArthur, Jaume Marrugat, Kari M. Mattila, Steven McCarroll, Mark I McCarthy, Dermot McGovern, Ruth McPherson, James B. Meigs, Olle Melander, Andres Metspalu, Peter M Nilsson, Michael C O’Donovan, Dost Ongur, Lorena Orozco, Michael J Owen, Colin N.A. Palmer, Aarno Palotie, Kyong Soo Park, Carlos Pato, Ann E. Pulver, Nazneen Rahman, Anne M. Remes, John D. Rioux, Samuli Ripatti, Dan M. Roden, Danish Saleheen, Veikko Salomaa, Nilesh J. Samani, Jeremiah Scharf, Heribert Schunkert, Moore B. Shoemaker, Pamela Sklar, Hilkka Soininen, Harry Soko, Tim Spector, Patrick F. Sullivan, Jaana Suvisaari, E Shyong Tai, Yik Ying Teo, Tuomi Tiinamaija, Ming Tsuang, Dan Turner, Teresa Tusie-Luna, Erkki Vartiainen, Hugh Watkins, Rinse K Weersma, Maija Wessman, James G. Wilson, Ramnik J. Xavier, Stuart A Cook, Paul J R Barton, Daniel G MacArthur

Preprint (2019) DOI: 10.1101/543504

network biology

A single cell brain atlas in human Alzheimer’s disease

Alexandra Grubman, Gabriel Chew, John F. Ouyang, Guizhi Sun, Xin Yi Choo, Catriona McLean, Rebecca Simmons, Sam Buckberry, Dulce Vargas Landin, Jahnvi Pflueger, Ryan Lister, Owen Rackham, Enrico Petretto, Jose M. Polo

Preprint (2019) DOI: 10.1101/628347

network biology

Mouse and human microglial phenotypes in Alzheimer’s disease are controlled by amyloid plaque phagocytosis through Hif1α

Alexandra Grubman, Xin Yi Choo, Gabriel Chew, John F. Ouyang, Guizhi Sun, Nathan P. Croft, Fernando J. Rossello, Rebecca Simmons, Sam Buckberry, Dulce Vargas Landin, Jahnvi Pflueger, Teresa H. Vandekolk, Zehra Abay, Xiaodong Liu, John M. Haynes, Catriona McLean, Sarah Williams, Siew Yeen Chai, Trevor Wilson, Ryan Lister, Colin W. Pouton, Anthony W. Purcell, Owen Rackham, Enrico Petretto, Jose M. Polo

Preprint (2019) DOI: 10.1101/639054

network biology

Identification of drugs for leukaemia differentiation therapy by network pharmacology

Eleni G Christodoulou, Lin Ming Lee, Kian Leong Lee, Tsz Kan Fung, Eric So, Enrico Petretto, S. Tiong Ong, Owen Rackham

Preprint (2019) DOI: 10.1101/676106

network biology

Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping

Jordan A Ramilowski, Chi Wai Yip, Saumya Agrawal, Jen-Chien Chang, Yari Ciani, Ivan V Kulakovskiy, Mickaël Mendez, Jasmine Li Ching Ooi, John F Ouyang, Nick Parkinson, Andreas Petri, Leonie Roos, Jessica Severin, Kayoko Yasuzawa, Imad Abugessaisa, Altuna Akalin, Ivan V Antonov, Erik Arner, Alessandro Bonetti, Hidemasa Bono, Beatrice Borsari, Frank Brombacher, Chris JF Cameron, Carlo Vittorio Cannistraci, Ryan Cardenas, Melissa Cardon, Howard Chang, Josée Dostie, Luca Ducoli, Alexander Favorov, Alexandre Fort, Diego Garrido, Noa Gil, Juliette Gimenez, Reto Guler, Lusy Handoko, Jayson Harshbarger, Akira Hasegawa, Yuki Hasegawa, Kosuke Hashimoto, Norihito Hayatsu, Peter Heutink, Tetsuro Hirose, Eddie L Imada, Masayoshi Itoh, Bogumil Kaczkowski, Aditi Kanhere, Emily Kawabata, Hideya Kawaji, Tsugumi Kawashima, S. Thomas Kelly, Miki Kojima, Naoto Kondo, Haruhiko Koseki, Tsukasa Kouno, Anton Kratz, Mariola Kurowska-Stolarska, Andrew Tae Jun Kwon, Jeffrey Leek, Andreas Lennartsson, Marina Lizio, Fernando López-Redondo, Joachim Luginbühl, Shiori Maeda, Vsevolod J Makeev, Luigi Marchionni, Yulia A Medvedeva, Aki Minoda, Ferenc Müller, Manuel Muñoz-Aguirre, Mitsuyoshi Murata, Hiromi Nishiyori, Kazuhiro R Nitta, Shuhei Noguchi, Yukihiko Noro, Ramil Nurtdinov, Yasushi Okazaki, Valerio Orlando, Denis Paquette, Callum JC Parr, Owen Rackham, Patrizia Rizzu, Diego Fernando Sánchez Martinez, Albin Sandelin, Pillay Sanjana, Colin AM Semple, Youtaro Shibayama, Divya M Sivaraman, Takahiro Suzuki, Suzannah C Szumowski, Michihira Tagami, Martin S Taylor, Chikashi Terao, Malte Thodberg, Supat Thongjuea, Vidisha Tripathi, Igor Ulitsky, Roberto Verardo, Ilya Vorontsov, Chinatsu Yamamoto, Robert S Young, J Kenneth Baillie, Alistair RR Forrest, Roderic Guigó, Michael M Hoffman, Chung Chau Hon, Takeya Kasukawa, Sakari Kauppinen, Juha Kere, Boris Lenhard, Claudio Schneider, Harukazu Suzuki, Ken Yagi, FANTOM consortium, Michiel de Hoon, Jay W Shin, Piero Carninci

Preprint (2019) DOI: 10.1101/700864

network biology

<i>GeneSwitches</i> : Ordering gene-expression and functional events in single-cell experiments

Elaine Y. Cao, John F. Ouyang, Owen Rackham

Preprint (2019) DOI: 10.1101/832626

network biology

Potassium channel dysfunction in human neuronal models of Angelman syndrome

Alfred Xuyang Sun, Qiang Yuan, Masahiro Fukuda, Weonjin Yu, Haidun Yan, Grace Gui Yin Lim, Mui Hoon Nai, Giuseppe Alessandro D’Agostino, Hoang-Dai Tran, Yoko Itahana, Danlei Wang, Hidayat Lokman, Koji Itahana, Stephanie Wai Lin Lim, Jiong Tang, Ya Yin Chang, Menglan Zhang, Stuart A. Cook, Owen Rackham, Chwee Teck Lim, Eng King Tan, Huck Hui Ng, Kah Leong Lim, Yong-Hui Jiang, Hyunsoo Shawn Je

Science (2019) DOI: 10.1126/science.aav5386

network biology

Widespread Translational Control of Fibrosis in the Human Heart by RNA-Binding Proteins

Sonia Chothani, Sebastian Schäfer, Eleonora Adami, Sivakumar Viswanathan, Anissa A. Widjaja, Sarah R. Langley, Jessie Tan, Mao Wang, Nicholas M. Quaife, Chee Jian Pua, Giuseppe D’Agostino, Shamini Guna Shekeran, Benjamin L. George, Stella Lim, Elaine Yiqun Cao, Sebastiaan van Heesch, Franziska Witte, Leanne E. Felkin, Eleni G. Christodoulou, Jinrui Dong, Susanne Blachut, Giannino Patone, Paul J.R. Barton, Norbert Hubner, Stuart A. Cook, Owen Rackham

Circulation (2019) DOI: 10.1161/circulationaha.119.039596

network biology

2020

EpiMogrify Models H3K4me3 Data to Identify Signaling Molecules that Improve Cell Fate Control and Maintenance

Uma S. Kamaraj, Joseph Chen, Khairunnisa Katwadi, John F. Ouyang, Yu Bo Yang Sun, Yu Ming Lim, Xiaodong Liu, Lusy Handoko, Jose M. Polo, Enrico Petretto, Owen Rackham

Cell Systems (2020) DOI: 10.1016/j.cels.2020.09.004

network biology

Clonal myelopoiesis in the UK Biobank cohort: ASXL1 mutations are strongly associated with smoking

Ahmed Dawoud, William J. Tapper, Nicholas C. P. Cross

Leukemia (2020) DOI: 10.1038/s41375-020-0896-8

network biology

Characterising the loss-of-function impact of 5’ untranslated region variants in 15,708 individuals

Nicola Whiffin, Konrad J. Karczewski, Xiaolei Zhang, Sonia Chothani, Miriam J. Smith, D. Gareth Evans, Angharad M. Roberts, Nicholas M. Quaife, Sebastian Schafer, Owen Rackham, Jessica Alföldi, Anne H. O’Donnell-Luria, Laurent C. Francioli, Genome Aggregation Database Production Team, Irina M. Armean, Eric Banks, Louis Bergelson, Kristian Cibulskis, Ryan L. Collins, Kristen M. Connolly, Miguel Covarrubias, Beryl Cummings, Mark J. Daly, Stacey Donnelly, Yossi Farjoun, Steven Ferriera, Stacey Gabriel, Laura D. Gauthier, Jeff Gentry, Namrata Gupta, Thibault Jeandet, Diane Kaplan, Kristen M. Laricchia, Christopher Llanwarne, Eric V. Minikel, Ruchi Munshi, Benjamin M. Neale, Sam Novod, Nikelle Petrillo, Timothy Poterba, David Roazen, Valentin Ruano-Rubio, Andrea Saltzman, Kaitlin E. Samocha, Molly Schleicher, Cotton Seed, Matthew Solomonson, Jose Soto, Grace Tiao, Kathleen Tibbetts, Charlotte Tolonen, Christopher Vittal, Gordon Wade, Arcturus Wang, Qingbo Wang, Nicholas A. Watts, Ben Weisburd, Genome Aggregation Database Consortium, Carlos A. Aguilar Salinas, Tariq Ahmad, Christine M. Albert, Diego Ardissino, Gil Atzmon, John Barnard, Laurent Beaugerie, Emelia J. Benjamin, Michael Boehnke, Lori L. Bonnycastle, Erwin P. Bottinger, Donald W. Bowden, Matthew J. Bown, John C. Chambers, Juliana C. Chan, Daniel Chasman, Judy Cho, Mina K. Chung, Bruce Cohen, Adolfo Correa, Dana Dabelea, Dawood Darbar, Ravindranath Duggirala, Josée Dupuis, Patrick T. Ellinor, Roberto Elosua, Jeanette Erdmann, Tõnu Esko, Martti Färkkilä, Jose Florez, Andre Franke, Gad Getz, Benjamin Glaser, Stephen J. Glatt, David Goldstein, Clicerio Gonzalez, Leif Groop, Christopher Haiman, Craig Hanis, Matthew Harms, Mikko Hiltunen, Matti M. Holi, Christina M. Hultman, Mikko Kallela, Jaakko Kaprio, Sekar Kathiresan, Bong-Jo Kim, Young Jin Kim, George Kirov, Jaspal Kooner, Seppo Koskinen, Harlan M. Krumholz, Subra Kugathasan, Soo Heon Kwak, Markku Laakso, Terho Lehtimäki, Ruth J. F. Loos, Steven A. Lubitz, Ronald C. W. Ma, Jaume Marrugat, Kari M. Mattila, Steven McCarroll, Mark I. McCarthy, Dermot McGovern, Ruth McPherson, James B. Meigs, Olle Melander, Andres Metspalu, Peter M. Nilsson, Michael C. O’Donovan, Dost Ongur, Lorena Orozco, Michael J. Owen, Colin N. A. Palmer, Aarno Palotie, Kyong Soo Park, Carlos Pato, Ann E. Pulver, Nazneen Rahman, Anne M. Remes, John D. Rioux, Samuli Ripatti, Dan M. Roden, Danish Saleheen, Veikko Salomaa, Nilesh J. Samani, Jeremiah Scharf, Heribert Schunkert, Moore B. Shoemaker, Pamela Sklar, Hilkka Soininen, Harry Sokol, Tim Spector, Patrick F. Sullivan, Jaana Suvisaari, E. Shyong Tai, Yik Ying Teo, Tuomi Tiinamaija, Ming Tsuang, Dan Turner, Teresa Tusie-Luna, Erkki Vartiainen, Hugh Watkins, Rinse K. Weersma, Maija Wessman, James G. Wilson, Ramnik J. Xavier, Marquis P. Vawter, Stuart A. Cook, Paul J. R. Barton, Daniel G. MacArthur, James S. Ware

Nature Communications (2020) DOI: 10.1038/s41467-019-10717-9

network biology

Reprogramming roadmap reveals route to human induced trophoblast stem cells

Xiaodong Liu, John F. Ouyang, Fernando J. Rossello, Jia Ping Tan, Kathryn C. Davidson, Daniela S. Valdes, Jan Schröder, Yu B. Y. Sun, Joseph Chen, Anja S. Knaupp, Guizhi Sun, Hun S. Chy, Ziyi Huang, Jahnvi Pflueger, Jaber Firas, Vincent Tano, Sam Buckberry, Jacob M. Paynter, Michael R. Larcombe, Daniel Poppe, Xin Yi Choo, Carmel M. O’Brien, William A. Pastor, Di Chen, Anna L. Leichter, Haroon Naeem, Pratibha Tripathi, Partha P. Das, Alexandra Grubman, David R. Powell, Andrew L. Laslett, Laurent David, Susan K. Nilsson, Amander T. Clark, Ryan Lister, Christian M. Nefzger, Luciano G. Martelotto, Owen Rackham, Jose M. Polo

Nature (2020) DOI: 10.1038/s41586-020-2734-6

network biology

GeneSwitches: ordering gene expression and functional events in single-cell experiments

Elaine Y Cao, John F Ouyang, Owen Rackham

Bioinformatics (2020) DOI: 10.1093/bioinformatics/btaa099

network biology

ShinyCell: Simple and sharable visualisation of single-cell gene expression data

John F. Ouyang, Uma S. Kamaraj, Elaine Y. Cao, Owen Rackham

Preprint (2020) DOI: 10.1101/2020.10.25.354100

network biology

Functional annotation of human long noncoding RNAs via molecular phenotyping

Jordan A. Ramilowski, Chi Wai Yip, Saumya Agrawal, Jen-Chien Chang, Yari Ciani, Ivan V. Kulakovskiy, Mickaël Mendez, Jasmine Li Ching Ooi, John F. Ouyang, Nick Parkinson, Andreas Petri, Leonie Roos, Jessica Severin, Kayoko Yasuzawa, Imad Abugessaisa, Altuna Akalin, Ivan V. Antonov, Erik Arner, Alessandro Bonetti, Hidemasa Bono, Beatrice Borsari, Frank Brombacher, Christopher J.F. Cameron, Carlo Vittorio Cannistraci, Ryan Cardenas, Melissa Cardon, Howard Chang, Josée Dostie, Luca Ducoli, Alexander Favorov, Alexandre Fort, Diego Garrido, Noa Gil, Juliette Gimenez, Reto Guler, Lusy Handoko, Jayson Harshbarger, Akira Hasegawa, Yuki Hasegawa, Kosuke Hashimoto, Norihito Hayatsu, Peter Heutink, Tetsuro Hirose, Eddie L. Imada, Masayoshi Itoh, Bogumil Kaczkowski, Aditi Kanhere, Emily Kawabata, Hideya Kawaji, Tsugumi Kawashima, S. Thomas Kelly, Miki Kojima, Naoto Kondo, Haruhiko Koseki, Tsukasa Kouno, Anton Kratz, Mariola Kurowska-Stolarska, Andrew Tae Jun Kwon, Jeffrey Leek, Andreas Lennartsson, Marina Lizio, Fernando López-Redondo, Joachim Luginbühl, Shiori Maeda, Vsevolod J. Makeev, Luigi Marchionni, Yulia A. Medvedeva, Aki Minoda, Ferenc Müller, Manuel Muñoz-Aguirre, Mitsuyoshi Murata, Hiromi Nishiyori, Kazuhiro R. Nitta, Shuhei Noguchi, Yukihiko Noro, Ramil Nurtdinov, Yasushi Okazaki, Valerio Orlando, Denis Paquette, Callum J.C. Parr, Owen Rackham, Patrizia Rizzu, Diego Fernando Sánchez Martinez, Albin Sandelin, Pillay Sanjana, Colin A.M. Semple, Youtaro Shibayama, Divya M. Sivaraman, Takahiro Suzuki, Suzannah C. Szumowski, Michihira Tagami, Martin S. Taylor, Chikashi Terao, Malte Thodberg, Supat Thongjuea, Vidisha Tripathi, Igor Ulitsky, Roberto Verardo, Ilya E. Vorontsov, Chinatsu Yamamoto, Robert S. Young, J. Kenneth Baillie, Alistair R.R. Forrest, Roderic Guigó, Michael M. Hoffman, Chung Chau Hon, Takeya Kasukawa, Sakari Kauppinen, Juha Kere, Boris Lenhard, Claudio Schneider, Harukazu Suzuki, Ken Yagi, Michiel J.L. de Hoon, Jay W. Shin, Piero Carninci

Genome Research (2020) DOI: 10.1101/gr.254219.119

network biology

Whole-Genome Sequencing of Finnish Type 1 Diabetic Siblings Discordant for Kidney Disease Reveals DNA Variants associated with Diabetic Nephropathy

Jing Guo, Owen Rackham, Niina Sandholm, Bing He, Anne-May Österholm, Erkka Valo, Valma Harjutsalo, Carol Forsblom, Iiro Toppila, Maija Parkkonen, Qibin Li, Wenjuan Zhu, Nathan Harmston, Sonia Chothani, Miina K. Öhman, Eudora Eng, Yang Sun, Enrico Petretto, Per-Henrik Groop, Karl Tryggvason

Journal of the American Society of Nephrology (2020) DOI: 10.1681/ASN.2019030289

network biology

2021

Genome-wide association study identifies novel susceptibility loci for KIT D816V positive mastocytosis

Gabriella Galatà, Andrés C. García-Montero, Thomas Kristensen, Ahmed Dawoud, Javier I. Muñoz-González, Manja Meggendorfer, Paola Guglielmelli, Yvette Hoade, Ivan Alvarez-Twose, Christian Gieger, Konstantin Strauch, Luigi Ferrucci, Toshiko Tanaka, Stefania Bandinelli, Theresia M. Schnurr, Torsten Haferlach, Sigurd Broesby-Olsen, Hanne Vestergaard, Michael Boe Møller, Carsten Bindslev-Jensen, Alessandro M. Vannucchi, Alberto Orfao, Deepti Radia, Andreas Reiter, Andrew J. Chase, Nicholas C.P. Cross, William J. Tapper

The American Journal of Human Genetics (2021) DOI: 10.1016/j.ajhg.2020.12.007

network biology

Computational Stem Cell Biology: Open Questions and Guiding Principles

Patrick Cahan, Davide Cacchiarelli, Sara-Jane Dunn, Martin Hemberg, Susana M. Chuva de Sousa Lopes, Samantha A. Morris, Owen Rackham, Antonio del Sol, Christine A. Wells

Cell Stem Cell (2021) DOI: 10.1016/j.stem.2020.12.012

network biology

Challenges for Computational Stem Cell Biology: A Discussion for the Field

Owen Rackham, Patrick Cahan, Nancy Mah, Samantha Morris, John F. Ouyang, Anne L. Plant, Yoshiaki Tanaka, Christine A. Wells

Stem Cell Reports (2021) DOI: 10.1016/j.stemcr.2020.12.015

network biology

Evaluating Capture Sequence Performance for Single-Cell CRISPR Activation Experiments

Xin Yi Choo, Yu Ming Lim, Khairunnisa Katwadi, Lynn Yap, Karl Tryggvason, Alfred Xuyang Sun, Shang Li, Lusy Handoko, John F. Ouyang, Owen Rackham

ACS Synthetic Biology (2021) DOI: 10.1021/acssynbio.0c00499

network biology

Coding and non-coding roles of MOCCI (C15ORF48) coordinate to regulate host inflammation and immunity

Cheryl Q. E. Lee, Baptiste Kerouanton, Sonia Chothani, Shan Zhang, Ying Chen, Chinmay Kumar Mantri, Daniella Helena Hock, Radiance Lim, Rhea Nadkarni, Vinh Thang Huynh, Daryl Lim, Wei Leong Chew, Franklin L. Zhong, David Arthur Stroud, Sebastian Schafer, Vinay Tergaonkar, Ashley L. St John, Owen Rackham, Lena Ho

Nature Communications (2021) DOI: 10.1038/s41467-021-22397-5

network biology

Modelling human blastocysts by reprogramming fibroblasts into iBlastoids

Xiaodong Liu, Jia Ping Tan, Jan Schröder, Asma Aberkane, John F. Ouyang, Monika Mohenska, Sue Mei Lim, Yu B. Y. Sun, Joseph Chen, Guizhi Sun, Yichen Zhou, Daniel Poppe, Ryan Lister, Amander T. Clark, Owen Rackham, Jennifer Zenker, Jose M. Polo

Nature (2021) DOI: 10.1038/s41586-021-03372-y

network biology

ShinyCell: simple and sharable visualization of single-cell gene expression data

John F Ouyang, Uma S Kamaraj, Elaine Y Cao, Owen Rackham

Bioinformatics (2021) DOI: 10.1093/bioinformatics/btab209

network biology

Cardiomyocyte BRAF and type 1 RAF inhibitors promote cardiomyocyte and cardiac hypertrophy in mice <i>in vivo</i>

A Clerk, DN Meijles, MA Hardyman, SJ Fuller, SP Chothani, JJ Cull, STE Cooper, HO Alharbi, K Vanezis, LE Felkin, T Markou, SJ Leonard, SW Shaw, Owen Rackham, SA Cook, PE Glennon, MN Sheppard, JC Sembrat, M Rojas, CF McTiernan, PJ Barton, PH Sugden

Preprint (2021) DOI: 10.1101/2021.08.14.455637

network biology

CLIPreg: Constructing translational regulatory networks from CLIP-, Ribo- and RNA-seq

Baptiste Kerouanton, Sebastian Schäfer, Lena Ho, Sonia Chothani, Owen Rackham

Preprint (2021) DOI: 10.1101/2021.12.06.470871

network biology

Synthetic biology: at the crossroads of genetic engineering and human therapeutics—a Keystone Symposia report

Jennifer Cable, Joshua N. Leonard, Timothy K. Lu, Zhen Xie, Matthew Wook Chang, Luis Ángel Fernández, José M. Lora, Howard L. Kaufman, Francisco J. Quintana, Roger Geiger, Cammie F. Lesser, Jason P. Lynch, David L. Hava, Virginia W. Cornish, Gary K. Lee, Breanna DiAndreth, Michael Fero, Rajkamal Srivastava, Tim De Coster, Kole T. Roybal, Owen Rackham, Samira Kiani, Iowis Zhu, Rogelio A. Hernandez‐Lopez, Tingxi Guo, William C. W. Chen

Annals of the New York Academy of Sciences (2021) DOI: 10.1111/nyas.14710

network biology

2022

A high-resolution map of human RNA translation

Sonia P. Chothani, Eleonora Adami, Anissa A. Widjaja, Sarah R. Langley, Sivakumar Viswanathan, Chee Jian Pua, Nevin Tham Zhihao, Nathan Harmston, Giuseppe D’Agostino, Nicola Whiffin, Wang Mao, John F. Ouyang, Wei Wen Lim, Shiqi Lim, Cheryl Q.E. Lee, Alexandra Grubman, Joseph Chen, J.P. Kovalik, Karl Tryggvason, Jose M. Polo, Lena Ho, Stuart A. Cook, Owen Rackham, Sebastian Schafer

Molecular Cell (2022) DOI: 10.1016/j.molcel.2022.06.023

network biology

Clonal myelopoiesis promotes adverse outcomes in chronic kidney disease

Ahmed Dawoud, Rodney D. Gilbert, William J. Tapper, Nicholas C. P. Cross

Leukemia (2022) DOI: 10.1038/s41375-021-01382-3

network biology

A novel network pharmacology approach for leukaemia differentiation therapy using Mogrify®

Lin Ming Lee, Eleni G. Christodoulou, Pavithra Shyamsunder, Bei Jun Chen, Kian Leong Lee, Tsz Kan Fung, Chi Wai Eric So, Gee Chuan Wong, Enrico Petretto, Owen Rackham, S. Tiong Ong

Oncogene (2022) DOI: 10.1038/s41388-022-02505-5

network biology

Intestinal stem cell aging signature reveals a reprogramming strategy to enhance regenerative potential

Christian M. Nefzger, Thierry Jardé, Akanksha Srivastava, Jan Schroeder, Fernando J. Rossello, Katja Horvay, Mirsada Prasko, Jacob M. Paynter, Joseph Chen, Chen-Fang Weng, Yu B. Y. Sun, Xiaodong Liu, Eva Chan, Nikita Deshpande, Xiaoli Chen, Y. Jinhua Li, Jahnvi Pflueger, Rebekah M. Engel, Anja S. Knaupp, Kirill Tsyganov, Susan K. Nilsson, Ryan Lister, Owen Rackham, Helen E. Abud, Jose M. Polo

npj Regenerative Medicine (2022) DOI: 10.1038/s41536-022-00226-7

network biology

CLIPreg: constructing translational regulatory networks from CLIP-, Ribo- and RNA-seq

Baptiste Kerouanton, Sebastian Schäfer, Lena Ho, Sonia Chothani, Owen Rackham

Bioinformatics (2022) DOI: 10.1093/bioinformatics/btac363

network biology

2023

LINC01013 Is a Determinant of Fibroblast Activation and Encodes a Novel Fibroblast-Activating Micropeptide

N. M. Quaife, S. Chothani, J. F. Schulz, E. L. Lindberg, K. Vanezis, E. Adami, K. O’Fee, J. Greiner, M. Litviňuková, S. van Heesch, N. Whiffin, N. Hubner, S. Schafer, Owen Rackham, S. A. Cook, P. J. R. Barton

Journal of Cardiovascular Translational Research (2023) DOI: 10.1007/s12265-022-10288-z

network biology

Deep learning models will shape the future of stem cell research

John F. Ouyang, Sonia Chothani, Owen Rackham

Stem Cell Reports (2023) DOI: 10.1016/j.stemcr.2022.11.007

network biology

DNA methylation is associated with codon degeneracy in a species of bumblebee

H. Marshall, Moi Taiga Nicholas, J. S. van Zweden, F. Wäckers, L. Ross, T. Wenseleers, E. B. Mallon

Heredity (2023) DOI: 10.1038/s41437-023-00591-z

network biology

Single cell analysis in head and neck cancer reveals potential immune evasion mechanisms during early metastasis

Hong Sheng Quah, Elaine Yiqun Cao, Lisda Suteja, Constance H. Li, Hui Sun Leong, Fui Teen Chong, Shilpi Gupta, Camille Arcinas, John F. Ouyang, Vivian Ang, Teja Celhar, Yunqian Zhao, Hui Chen Tay, Jerry Chan, Takeshi Takahashi, Daniel S. W. Tan, Subhra K. Biswas, Owen Rackham, N. Gopalakrishna Iyer

Nature Communications (2023) DOI: 10.1038/s41467-023-37379-y

network biology

Transient naive reprogramming corrects hiPS cells functionally and epigenetically

Sam Buckberry, Xiaodong Liu, Daniel Poppe, Jia Ping Tan, Guizhi Sun, Joseph Chen, Trung Viet Nguyen, Alex de Mendoza, Jahnvi Pflueger, Thomas Frazer, Dulce B. Vargas-Landín, Jacob M. Paynter, Nathan Smits, Ning Liu, John F. Ouyang, Fernando J. Rossello, Hun S. Chy, Owen Rackham, Andrew L. Laslett, James Breen, Geoffrey J. Faulkner, Christian M. Nefzger, Jose M. Polo, Ryan Lister

Nature (2023) DOI: 10.1038/s41586-023-06424-7

network biology

Discovering microproteins: making the most of ribosome profiling data

Sonia Chothani, Lena Ho, Sebastian Schafer, Owen Rackham

RNA Biology (2023) DOI: 10.1080/15476286.2023.2279845

network biology

Differences in 5’untranslated regions highlight the importance of translational regulation of dosage sensitive genes

Nechama Wieder, Elston N. D’Souza, Alexandra C. Martin-Geary, Frederik H. Lassen, Jonathan Talbot-Martin, Maria Fernandes, Sonia P. Chothani, Owen Rackham, Sebastian Schafer, Julie L. Aspden, Daniel G. MacArthur, Robert W. Davies, Nicola Whiffin

Preprint (2023) DOI: 10.1101/2023.05.15.540809

network biology

Striatin plays a major role in angiotensin II-induced cardiomyocyte and cardiac hypertrophy in mice <i>in vivo</i>

JJ Cull, STE Cooper, HO Alharbi, SP Chothani, Owen Rackham, DN Meijles, PR Dash, Risto Kerkelä, N Ruparelia, PH Sugden, A Clerk

Preprint (2023) DOI: 10.1101/2023.10.21.563397

network biology

A Single-cell Atlas Identifies Pretreatment Features of Primary Imatinib Resistance in Chronic Myeloid Leukemia

Vaidehi Krishnan, Florian Schmidt, Zahid Nawaz, Prasanna Nori Venkatesh, Kian Leong Lee, Xi Ren, Zhu En Chan, Mengge Yu, Meera Makheja, Nirmala Arul Rayan, Michelle Gek Liang Lim, Alice Man Sze Cheung, Sudipto Bari, Wee Joo Chng, Hein Than, John Ouyang, Owen Rackham, Tuan Zea Tan, William Ying Khee Hwang, Charles Chuah, Shyam Prabhakar, S. Tiong Ong

Blood (2023) DOI: 10.1182/blood.2022017295

network biology

2024

Striatin plays a major role in angiotensin II-induced cardiomyocyte and cardiac hypertrophy in mice <i>in vivo</i>

Joshua J. Cull, Susanna T.E. Cooper, Hajed O. Alharbi, Sonia P. Chothani, Owen Rackham, Daniel N. Meijles, Philip R. Dash, Risto Kerkelä, Neil Ruparelia, Peter H. Sugden, Angela Clerk

Clinical Science (2024) DOI: 10.1042/cs20240496

network biology

Differences in 5'untranslated regions highlight the importance of translational regulation of dosage sensitive genes

Nechama Wieder, Elston N. D’Souza, Alexandra C. Martin-Geary, Frederik H. Lassen, Jonathan Talbot-Martin, Maria Fernandes, Sonia P. Chothani, Owen Rackham, Sebastian Schafer, Julie L. Aspden, Daniel G. MacArthur, Robert W. Davies, Nicola Whiffin

Genome Biology (2024) DOI: 10.1186/s13059-024-03248-0

network biology

2025

Global analysis of ligand-gated ion channel conservation across Platyhelminthes

Víctor Hugo Caña-Bozada, Ahmed Dawoud, Ivana Ramos-de la Cruz, Lizeth C. Flores-Méndez, Josué Barrera-Redondo, Jesús Briones-Mendoza, Luis A. Yañez-Guerra

General and Comparative Endocrinology (2025) DOI: 10.1016/j.ygcen.2025.114718

network biology

High-Capacity Optical Fingerprinting Using Dual-Peak Photoluminescence of Quantum Dots

Syeda Ramsha Ali, Stephen V. Kershaw, Yinglong Zhu, Ahmed Dawoud, Yueyu Guo, Kees De Groot, Nema M. Abdelazim

ACS Applied Materials &amp; Interfaces (2025) DOI: 10.1021/acsami.5c19508

network biology

Microprotein SMIM26 drives oxidative metabolism via serine-responsive mitochondrial translation

Jiemin Nah, Sreya Mahendran, Baptiste Kerouanton, Liang Cui, Daniella H. Hock, Alfredo Cabrera-Orefice, Kyle Dunlap, David Robinson, Desmond W.H. Tung, Sze Huey Leong, Kiat-Yi Tan, Sonia P. Chothani, Jingjing Sun, Agnieszka Dziegowska, Grazyna Leszczynska, Owen Rackham, Ilka Wittig, Peter Dedon, Gregory S. Ducker, David A. Stroud, Lena Ho

Molecular Cell (2025) DOI: 10.1016/j.molcel.2025.05.033

network biology

Personalized uncertainty quantification in artificial intelligence

Tapabrata Chakraborti, Christopher R. S. Banerji, Ariane Marandon, Vicky Hellon, Robin Mitra, Brieuc Lehmann, Leandra Bräuninger, Sarah McGough, Cagatay Turkay, Alejandro F. Frangi, Ginestra Bianconi, Weizi Li, Owen Rackham, Deepak Parashar, Chris Harbron, Ben MacArthur

Nature Machine Intelligence (2025) DOI: 10.1038/s42256-025-01024-8

network biology

taxMyPhage: Automated Taxonomy of dsDNA Phage Genomes at the Genus and Species Level

Andrew Millard, Rémi Denise, Maria Lestido, Moi Taiga Nicholas, Deven Webster, Dann Turner, Thomas Sicheritz-Pontén

PHAGE: Therapy, Applications, and Research (2025) DOI: 10.1089/phage.2024.0050

network biology

ShinyCell2: An extended library for simple and sharable visualisation of spatial, peak-based and multi-omic single-cell data

Bei Jun Chen, Yi Yang Lim, Xinyi Yang, Lijin Wang, Owen Rackham, John F Ouyang

Preprint (2025) DOI: 10.1101/2025.04.22.650045

network biology

Loss of chromosome Y shapes the immune cell fate with aging in men

Ahmed Dawoud, Luke Green, Owen Rackham

Preprint (2025) DOI: 10.1101/2025.06.01.25328624

network biology

Genome-wide analysis defines genetic determinants of MPN subtypes and identifies a sex-specific association at <i>CDH22</i> / <i>CD40</i>

William J. Tapper, Ahmed Dawoud, Joannah Score, Andrew J. Chase, E. Joanna Baxter, Joanne Ewing, Louise Wallis, Paola Guglielmelli, Dolors Colomer, Beatriz Bellosillo, Montse Gomez, Juan Carlos Hernández-Boluda, Carlos Besses, Francisco Cervantes, Steffen Koschmieder, Anthony R. Green, Andreas Reiter, Alessandro Vannucchi, Claire Harrison, Nicholas C. P. Cross

Blood (2025) DOI: 10.1182/blood.2025028489

network biology

2026

Genome-scale Identification of Microprotein Regulators of Mitochondrial Metabolism

Baptiste Kerouanton, Shree Pooja Sridharan, Jiemin Nah, Alanna Wong, Sreya Mahendran, Liang Chao, Long Gao, Matthew Hirschey, Sonia Chothani, Owen Rackham, Lena Ho

Preprint (2026) DOI: 10.2139/ssrn.6460221

network biology

PathPinpointR: Predicting the progression of sc-RNAseq samples through reference trajectories.

Moi Taiga Nicholas, Disha Mehta, John Ouyang, Ahmed Dawoud, Charlotte Ellison, Juri Westendorf, Luke Green, Paul Skipp, Owen Rackham

TBC (2026) DOI: TBC

Abstract

Single-cell RNA sequencing (scRNA-seq) has transformed our ability to analyse cellular heterogeneity, enabling detailed mapping of cellular progression. Trajectory inference tools construct trajectories from scRNA-seq data, facilitating the tracing of cellular progression through developmental pathways. PathPinpointR (PPR) is a lightweight and user-friendly R package developed to predict and compare the positions of scRNA-seq samples along reference biological trajectories, such as those created from large cell atlas projects. PPR utilises sets of switching-gene events from reference trajectories as indicators of cellular progression. By applying these positional indicators to query datasets, each cell can be accurately assigned a pseudo-time value, providing predictive insight into its position along a trajectory. This information can be used to stage cells within an established developmental process, or to evaluate how different patient samples compare when mapped onto reference disease or drug response trajectories.

single cell-biologydata tools Featured