Publications by authors named "Nishadi De Silva"

10Publications

Ensembl 2021.

Authors:
Kevin L Howe Premanand Achuthan James Allen Jamie Allen Jorge Alvarez-Jarreta M Ridwan Amode Irina M Armean Andrey G Azov Ruth Bennett Jyothish Bhai Konstantinos Billis Sanjay Boddu Mehrnaz Charkhchi Carla Cummins Luca Da Rin Fioretto Claire Davidson Kamalkumar Dodiya Bilal El Houdaigui Reham Fatima Astrid Gall Carlos Garcia Giron Tiago Grego Cristina Guijarro-Clarke Leanne Haggerty Anmol Hemrom Thibaut Hourlier Osagie G Izuogu Thomas Juettemann Vinay Kaikala Mike Kay Ilias Lavidas Tuan Le Diana Lemos Jose Gonzalez Martinez José Carlos Marugán Thomas Maurel Aoife C McMahon Shamika Mohanan Benjamin Moore Matthieu Muffato Denye N Oheh Dimitrios Paraschas Anne Parker Andrew Parton Irina Prosovetskaia Manoj P Sakthivel Ahamed I Abdul Salam Bianca M Schmitt Helen Schuilenburg Dan Sheppard Emily Steed Michal Szpak Marek Szuba Kieron Taylor Anja Thormann Glen Threadgold Brandon Walts Andrea Winterbottom Marc Chakiachvili Ameya Chaubal Nishadi De Silva Bethany Flint Adam Frankish Sarah E Hunt Garth R IIsley Nick Langridge Jane E Loveland Fergal J Martin Jonathan M Mudge Joanella Morales Emily Perry Magali Ruffier John Tate David Thybert Stephen J Trevanion Fiona Cunningham Andrew D Yates Daniel R Zerbino Paul Flicek

Nucleic Acids Res 2021 01;49(D1):D884-D891

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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January 2021

Collaborative Annotation Redefines Gene Sets for Crucial Phytopathogens.

Authors:
Helder Pedro Andrew D Yates Paul J Kersey Nishadi H De Silva

Front Microbiol 2019 7;10:2477. Epub 2019 Nov 7.

European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom.

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November 2019

PHI-base: the pathogen-host interactions database.

Authors:
Martin Urban Alayne Cuzick James Seager Valerie Wood Kim Rutherford Shilpa Yagwakote Venkatesh Nishadi De Silva Manuel Carbajo Martinez Helder Pedro Andy D Yates Keywan Hassani-Pak Kim E Hammond-Kosack

Nucleic Acids Res 2020 01;48(D1):D613-D620

Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden AL5 2JQ, UK.

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January 2020

Ensembl Genomes 2020-enabling non-vertebrate genomic research.

Authors:
Kevin L Howe Bruno Contreras-Moreira Nishadi De Silva Gareth Maslen Wasiu Akanni James Allen Jorge Alvarez-Jarreta Matthieu Barba Dan M Bolser Lahcen Cambell Manuel Carbajo Marc Chakiachvili Mikkel Christensen Carla Cummins Alayne Cuzick Paul Davis Silvie Fexova Astrid Gall Nancy George Laurent Gil Parul Gupta Kim E Hammond-Kosack Erin Haskell Sarah E Hunt Pankaj Jaiswal Sophie H Janacek Paul J Kersey Nick Langridge Uma Maheswari Thomas Maurel Mark D McDowall Ben Moore Matthieu Muffato Guy Naamati Sushma Naithani Andrew Olson Irene Papatheodorou Mateus Patricio Michael Paulini Helder Pedro Emily Perry Justin Preece Marc Rosello Matthew Russell Vasily Sitnik Daniel M Staines Joshua Stein Marcela K Tello-Ruiz Stephen J Trevanion Martin Urban Sharon Wei Doreen Ware Gary Williams Andrew D Yates Paul Flicek

Nucleic Acids Res 2020 01;48(D1):D689-D695

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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January 2020

Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species.

Authors:
Paul Julian Kersey James E Allen Alexis Allot Matthieu Barba Sanjay Boddu Bruce J Bolt Denise Carvalho-Silva Mikkel Christensen Paul Davis Christoph Grabmueller Navin Kumar Zicheng Liu Thomas Maurel Ben Moore Mark D McDowall Uma Maheswari Guy Naamati Victoria Newman Chuang Kee Ong Michael Paulini Helder Pedro Emily Perry Matthew Russell Helen Sparrow Electra Tapanari Kieron Taylor Alessandro Vullo Gareth Williams Amonida Zadissia Andrew Olson Joshua Stein Sharon Wei Marcela Tello-Ruiz Doreen Ware Aurelien Luciani Simon Potter Robert D Finn Martin Urban Kim E Hammond-Kosack Dan M Bolser Nishadi De Silva Kevin L Howe Nicholas Langridge Gareth Maslen Daniel Michael Staines Andrew Yates

Nucleic Acids Res 2018 01;46(D1):D802-D808

The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.

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January 2018

Robust high-throughput prokaryote assembly and improvement pipeline for Illumina data.

Authors:
Andrew J Page Nishadi De Silva Martin Hunt Michael A Quail Julian Parkhill Simon R Harris Thomas D Otto Jacqueline A Keane

Microb Genom 2016 08 25;2(8):e000083. Epub 2016 Aug 25.

1​Pathogen Informatics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, Cambridgeshire, UK.

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August 2016

Circlator: automated circularization of genome assemblies using long sequencing reads.

Authors:
Martin Hunt Nishadi De Silva Thomas D Otto Julian Parkhill Jacqueline A Keane Simon R Harris

Genome Biol 2015 Dec 29;16:294. Epub 2015 Dec 29.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK.

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December 2015

The genomes of four tapeworm species reveal adaptations to parasitism.

Authors:
Isheng J Tsai Magdalena Zarowiecki Nancy Holroyd Alejandro Garciarrubio Alejandro Sánchez-Flores Karen L Brooks Alan Tracey Raúl J Bobes Gladis Fragoso Edda Sciutto Martin Aslett Helen Beasley Hayley M Bennett Xuepeng Cai Federico Camicia Richard Clark Marcela Cucher Nishadi De Silva Tim A Day Peter Deplazes Karel Estrada Cecilia Fernández Peter W H Holland Junling Hou Songnian Hu Thomas Huckvale Stacy S Hung Laura Kamenetzky Jacqueline A Keane Ferenc Kiss Uriel Koziol Olivia Lambert Kan Liu Xuenong Luo Yingfeng Luo Natalia Macchiaroli Sarah Nichol Jordi Paps John Parkinson Natasha Pouchkina-Stantcheva Nick Riddiford Mara Rosenzvit Gustavo Salinas James D Wasmuth Mostafa Zamanian Yadong Zheng Jianping Cai Xavier Soberón Peter D Olson Juan P Laclette Klaus Brehm Matthew Berriman

Nature 2013 Apr 13;496(7443):57-63. Epub 2013 Mar 13.

Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

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April 2013

A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni.

Authors:
Anna V Protasio Isheng J Tsai Anne Babbage Sarah Nichol Martin Hunt Martin A Aslett Nishadi De Silva Giles S Velarde Tim J C Anderson Richard C Clark Claire Davidson Gary P Dillon Nancy E Holroyd Philip T LoVerde Christine Lloyd Jacquelline McQuillan Guilherme Oliveira Thomas D Otto Sophia J Parker-Manuel Michael A Quail R Alan Wilson Adhemar Zerlotini David W Dunne Matthew Berriman

PLoS Negl Trop Dis 2012 Jan 10;6(1):e1455. Epub 2012 Jan 10.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom.

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January 2012

GeneDB--an annotation database for pathogens.

Authors:
Flora J Logan-Klumpler Nishadi De Silva Ulrike Boehme Matthew B Rogers Giles Velarde Jacqueline A McQuillan Tim Carver Martin Aslett Christian Olsen Sandhya Subramanian Isabelle Phan Carol Farris Siddhartha Mitra Gowthaman Ramasamy Haiming Wang Adrian Tivey Andrew Jackson Robin Houston Julian Parkhill Matthew Holden Omar S Harb Brian P Brunk Peter J Myler David Roos Mark Carrington Deborah F Smith Christiane Hertz-Fowler Matthew Berriman

Nucleic Acids Res 2012 Jan 23;40(Database issue):D98-108. Epub 2011 Nov 23.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.

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January 2012