Publications by authors named "Owen J L Rackham"

36Publications

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

Cell Syst 2020 Oct 6. Epub 2020 Oct 6.

Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore (Duke-NUS) Medical School, 8 College Road, 169857 Singapore, Singapore. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cels.2020.09.004DOI Listing
October 2020

Functional annotation of human long noncoding RNAs via molecular phenotyping.

Authors:
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 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 J C Parr Owen J L 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 Res 2020 07 27;30(7):1060-1072. Epub 2020 Jul 27.

RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.254219.119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7397864PMC
July 2020

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

Bioinformatics 2020 May;36(10):3273-3275

Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 169857, Singapore.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btaa099DOI Listing
May 2020

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

Curr Protoc Mol Biol 2019 12;129(1):e108

Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/cpmb.108DOI Listing
December 2019

Correction to: Molecular Interaction Networks to Select Factors for Cell Conversion.

Methods Mol Biol 2019 ;1975:C1

Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-4939-9224-9_20DOI Listing
January 2019

Molecular Interaction Networks to Select Factors for Cell Conversion.

Methods Mol Biol 2019 ;1975:333-361

Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-4939-9224-9_16DOI Listing
September 2019

Cell Type of Origin Dictates the Route to Pluripotency.

Cell Rep 2017 Dec;21(10):2649-2660

Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.celrep.2017.11.029DOI Listing
December 2017

Computational methods for direct cell conversion.

Cell Cycle 2016 Dec 13;15(24):3343-3354. Epub 2016 Oct 13.

a Cardiovascular and Metabolic Disorders, Duke-NUS Medical School , Singapore.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1080/15384101.2016.1238119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5224461PMC
December 2016

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

Bioinformatics 2016 Feb 21;32(4):635-7. Epub 2015 Oct 21.

Duke-NUS Graduate Medical School Singapore, Singapore, 169857 Singapore.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btv598DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4743624PMC
February 2016

Function-selective domain architecture plasticity potentials in eukaryotic genome evolution.

Biochimie 2015 Dec 15;119:269-77. Epub 2015 May 15.

Computational Genomics Group, Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, UK; Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.biochi.2015.05.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4679076PMC
December 2015

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

Nucleic Acids Res 2015 Mar 29;43(5):e33. Epub 2014 Dec 29.

Medical Research Council (MRC) Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gku1322DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4357693PMC
March 2015

The SUPERFAMILY 1.75 database in 2014: a doubling of data.

Nucleic Acids Res 2015 Jan 20;43(Database issue):D227-33. Epub 2014 Nov 20.

Computer Science, University of Bristol, Bristol, BS8 1UB, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gku1041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383889PMC
January 2015

A proteome quality index.

Environ Microbiol 2015 Jan 22;17(1):4-9. Epub 2014 Oct 22.

Department of Computer Science, University of Bristol, Bristol, UK; Bristol Centre for Complexity Sciences, University of Bristol, Bristol, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/1462-2920.12622DOI Listing
January 2015

The evolution of human cells in terms of protein innovation.

Mol Biol Evol 2014 Jun 1;31(6):1364-74. Epub 2014 Apr 1.

Department of Computer Science, University of Bristol, Bristol, United KingdomMedical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, United Kingdom

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/molbev/mst139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4032124PMC
June 2014

A promoter-level mammalian expression atlas.

Authors:
Alistair R R Forrest Hideya Kawaji Michael Rehli J Kenneth Baillie Michiel J L de Hoon Vanja Haberle Timo Lassmann Ivan V Kulakovskiy Marina Lizio Masayoshi Itoh 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 Robert S Young Margherita Francescatto Intikhab Alam Davide Albanese Gabriel M Altschuler Takahiro Arakawa John A C Archer Peter Arner Magda Babina Sarah Rennie 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 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 Furino Jun-ichi Furusawa Teunis B Geijtenbeek Andrew P 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 Furni 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 Hiromasa Morikawa Mitsuru Morimoto Kazuyo Moro Efthymios Motakis Hozumi Motohashi Christine L Mummery Mitsuyoshi Murata Sayaka Nagao-Sato Yutaka Nakachi Fumio Nakahara Toshiyuki Nakamura Yukio Nakamura Kenichi Nakazato Erik van Nimwegen Noriko Ninomiya Hiromi Nishiyori Shohei Noma Shohei Noma Tadasuke Noazaki Soichi Ogishima Naganari Ohkura Hiroko Ohimiya 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 J L Rackham Jordan A Ramilowski Mamoon Rashid Timothy Ravasi Patrizia Rizzu Marco Roncador Sugata Roy Morten B Rye Eri Saijyo Antti Sajantila Akiko Saka Shimon Sakaguchi Mizuho Sakai Hiroki Sato 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 Takaai Sugiyama Masanori Suzuki Naoko Suzuki Rolf K Swoboda Peter A C 't Hoen Michihira Tagami Naoko Takahashi Jun Takai Hiroshi Tanaka Hideki Tatsukawa Zuotian Tatum Mark Thompson Hiroo Toyodo Tetsuro Toyoda Elvind Valen Marc van de Wetering Linda M van den Berg Roberto Verado 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 Susan 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 Piero Carninci Yoshihide Hayashizaki

Nature 2014 Mar;507(7493):462-70

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature13182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4529748PMC
March 2014

SUPERFAMILY 1.75 including a domain-centric gene ontology method.

Nucleic Acids Res 2011 Jan 9;39(Database issue):D427-34. Epub 2010 Nov 9.

Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkq1130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013712PMC
January 2011

The evolution and structure prediction of coiled coils across all genomes.

J Mol Biol 2010 Oct 9;403(3):480-93. Epub 2010 Sep 9.

Department of Computer Science, University of Bristol, Bristol BS8 1UB, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jmb.2010.08.032DOI Listing
October 2010

A Ca-Based Computational Model for NMDA Receptor-Dependent Synaptic Plasticity at Individual Post-Synaptic Spines in the Hippocampus.

Front Synaptic Neurosci 2010 21;2:31. Epub 2010 Jul 21.

Department of Engineering Mathematics, Bristol Centre for Complexity Sciences, University of Bristol, University Walk Bristol, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3389/fnsyn.2010.00031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3059685PMC
July 2011