Mr Ricardo H Ramirez-Gonzalez, M.Sc. - The Genome Analysis Centre - PhD Student

Mr Ricardo H Ramirez-Gonzalez

M.Sc.

The Genome Analysis Centre

PhD Student

United Kingdom

ORCID logohttps://orcid.org/0000-0001-5745-7085

Mr Ricardo H Ramirez-Gonzalez, M.Sc. - The Genome Analysis Centre - PhD Student

Mr Ricardo H Ramirez-Gonzalez

M.Sc.

Introduction

Primary Affiliation: The Genome Analysis Centre - United Kingdom

Education

Oct 2012 - Sep 2016
Genome Analysis Centre and John Innes Centre
PhD
Sep 2008 - Sep 2009
University of East Anglia
Bioinformatics
CMP
Aug 2003 - Dec 2007
Instituto Tecnológico y de Estudios Superiores de Monterrey - Campus Ciudad de México
BSc Computer Science and Software Engineering.
Dirección de Ingeniería y Arquitectura

Experience

Feb 2010 - Sep 2012
Genome Analysis Centre
Scientific Programer
Bioinformatics
Aug 2016
John Innes Centre

Crop Genetics

Publications

23Publications

1024Reads

-Profile Views

88PubMed Central Citations

Hotspots in the genomic architecture of field drought responses in wheat as breeding targets.

Funct Integr Genomics 2019 Mar 16;19(2):295-309. Epub 2018 Nov 16.

Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Científicas (CSIC), Alameda del Obispo s/n, 14004, Córdoba, Spain.

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Source
http://link.springer.com/10.1007/s10142-018-0639-3
Publisher Site
http://dx.doi.org/10.1007/s10142-018-0639-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6394720PMC
March 2019
33 Reads
2.480 Impact Factor

Shifting the limits in wheat research and breeding using a fully annotated reference genome.

Authors:
Rudi Appels Kellye Eversole Catherine Feuillet Beat Keller Jane Rogers Nils Stein Curtis J Pozniak Nils Stein Frédéric Choulet Assaf Distelfeld Kellye Eversole Jesse Poland Jane Rogers Gil Ronen Andrew G Sharpe Curtis Pozniak Gil Ronen Nils Stein Omer Barad Kobi Baruch Frédéric Choulet Gabriel Keeble-Gagnère Martin Mascher Andrew G Sharpe Gil Ben-Zvi Ambre-Aurore Josselin Nils Stein Martin Mascher Axel Himmelbach Frédéric Choulet Gabriel Keeble-Gagnère Martin Mascher Jane Rogers François Balfourier Juan Gutierrez-Gonzalez Matthew Hayden Ambre-Aurore Josselin ChuShin Koh Gary Muehlbauer Raj K Pasam Etienne Paux Curtis J Pozniak Philippe Rigault Andrew G Sharpe Josquin Tibbits Vijay Tiwari Frédéric Choulet Gabriel Keeble-Gagnère Martin Mascher Ambre-Aurore Josselin Jane Rogers Manuel Spannagl Frédéric Choulet Daniel Lang Heidrun Gundlach Georg Haberer Gabriel Keeble-Gagnère Klaus F X Mayer Danara Ormanbekova Etienne Paux Verena Prade Hana Šimková Thomas Wicker Frédéric Choulet Manuel Spannagl David Swarbreck Hélène Rimbert Marius Felder Nicolas Guilhot Heidrun Gundlach Georg Haberer Gemy Kaithakottil Jens Keilwagen Daniel Lang Philippe Leroy Thomas Lux Klaus F X Mayer Sven Twardziok Luca Venturini Rudi Appels Hélène Rimbert Frédéric Choulet Angéla Juhász Gabriel Keeble-Gagnère Frédéric Choulet Manuel Spannagl Daniel Lang Michael Abrouk Georg Haberer Gabriel Keeble-Gagnère Klaus F X Mayer Thomas Wicker Frédéric Choulet Thomas Wicker Heidrun Gundlach Daniel Lang Manuel Spannagl Daniel Lang Manuel Spannagl Rudi Appels Iris Fischer Cristobal Uauy Philippa Borrill Ricardo H Ramirez-Gonzalez Rudi Appels Dominique Arnaud Smahane Chalabi Boulos Chalhoub Frédéric Choulet Aron Cory Raju Datla Mark W Davey Matthew Hayden John Jacobs Daniel Lang Stephen J Robinson Manuel Spannagl Burkhard Steuernagel Josquin Tibbits Vijay Tiwari Fred van Ex Brande B H Wulff Curtis J Pozniak Stephen J Robinson Andrew G Sharpe Aron Cory Moussa Benhamed Etienne Paux Abdelhafid Bendahmane Lorenzo Concia David Latrasse Jane Rogers John Jacobs Michael Alaux Rudi Appels Jan Bartoš Arnaud Bellec Hélène Berges Jaroslav Doležel Catherine Feuillet Zeev Frenkel Bikram Gill Abraham Korol Thomas Letellier Odd-Arne Olsen Hana Šimková Kuldeep Singh Miroslav Valárik Edwin van der Vossen Sonia Vautrin Song Weining Abraham Korol Zeev Frenkel Tzion Fahima Vladimir Glikson Dina Raats Jane Rogers Vijay Tiwari Bikram Gill Etienne Paux Jesse Poland Jaroslav Doležel Jarmila Číhalíková Hana Šimková Helena Toegelová Jan Vrána Pierre Sourdille Benoit Darrier Rudi Appels Manuel Spannagl Daniel Lang Iris Fischer Danara Ormanbekova Verena Prade Delfina Barabaschi Luigi Cattivelli Pilar Hernandez Sergio Galvez Hikmet Budak Burkhard Steuernagel Jonathan D G Jones Kamil Witek Brande B H Wulff Guotai Yu Ian Small Joanna Melonek Ruonan Zhou Angéla Juhász Tatiana Belova Rudi Appels Odd-Arne Olsen Kostya Kanyuka Robert King Kirby Nilsen Sean Walkowiak Curtis J Pozniak Richard Cuthbert Raju Datla Ron Knox Krysta Wiebe Daoquan Xiang Antje Rohde Timothy Golds Jaroslav Doležel Jana Čížková Josquin Tibbits Hikmet Budak Bala Ani Akpinar Sezgi Biyiklioglu Gary Muehlbauer Jesse Poland Liangliang Gao Juan Gutierrez-Gonzalez Amidou N'Daiye Jaroslav Doležel Hana Šimková Jarmila Číhalíková Marie Kubaláková Jan Šafář Jan Vrána Hélène Berges Arnaud Bellec Sonia Vautrin Michael Alaux Françoise Alfama Anne-Françoise Adam-Blondon Raphael Flores Claire Guerche Thomas Letellier Mikaël Loaec Hadi Quesneville Curtis J Pozniak Andrew G Sharpe Sean Walkowiak Hikmet Budak Janet Condie Jennifer Ens ChuShin Koh Ron Maclachlan Yifang Tan Thomas Wicker Frédéric Choulet Etienne Paux Adriana Alberti Jean-Marc Aury François Balfourier Valérie Barbe Arnaud Couloux Corinne Cruaud Karine Labadie Sophie Mangenot Patrick Wincker Bikram Gill Gaganpreet Kaur Mingcheng Luo Sunish Sehgal Kuldeep Singh Parveen Chhuneja Om Prakash Gupta Suruchi Jindal Parampreet Kaur Palvi Malik Priti Sharma Bharat Yadav Nagendra K Singh JitendraP Khurana Chanderkant Chaudhary Paramjit Khurana Vinod Kumar Ajay Mahato Saloni Mathur Amitha Sevanthi Naveen Sharma Ram Sewak Tomar Jane Rogers John Jacobs Michael Alaux Arnaud Bellec Hélène Berges Jaroslav Doležel Catherine Feuillet Zeev Frenkel Bikram Gill Abraham Korol Edwin van der Vossen Sonia Vautrin Bikram Gill Gaganpreet Kaur Mingcheng Luo Sunish Sehgal Jan Bartoš Kateřina Holušová Ondřej Plíhal Matthew D Clark Darren Heavens George Kettleborough Jon Wright Miroslav Valárik Michael Abrouk Barbora Balcárková Kateřina Holušová Yuqin Hu Mingcheng Luo Elena Salina Nikolai Ravin Konstantin Skryabin Alexey Beletsky Vitaly Kadnikov Andrey Mardanov Michail Nesterov Andrey Rakitin Ekaterina Sergeeva Hirokazu Handa Hiroyuki Kanamori Satoshi Katagiri Fuminori Kobayashi Shuhei Nasuda Tsuyoshi Tanaka Jianzhong Wu Rudi Appels Matthew Hayden Gabriel Keeble-Gagnère Philippe Rigault Josquin Tibbits Odd-Arne Olsen Tatiana Belova Federica Cattonaro Min Jiumeng Karl Kugler Klaus F X Mayer Matthias Pfeifer Simen Sandve Xu Xun Bujie Zhan Hana Šimková Michael Abrouk Jacqueline Batley Philipp E Bayer David Edwards Satomi Hayashi Helena Toegelová Zuzana Tulpová Paul Visendi Song Weining Licao Cui Xianghong Du Kewei Feng Xiaojun Nie Wei Tong Le Wang Philippa Borrill Heidrun Gundlach Sergio Galvez Gemy Kaithakottil Daniel Lang Thomas Lux Martin Mascher Danara Ormanbekova Verena Prade Ricardo H Ramirez-Gonzalez Manuel Spannagl Nils Stein Cristobal Uauy Luca Venturini Nils Stein Rudi Appels Kellye Eversole Jane Rogers Philippa Borrill Luigi Cattivelli Frédéric Choulet Pilar Hernandez Kostya Kanyuka Daniel Lang Martin Mascher Kirby Nilsen Etienne Paux Curtis J Pozniak Ricardo H Ramirez-Gonzalez Hana Šimková Ian Small Manuel Spannagl David Swarbreck Cristobal Uauy

Science 2018 08 16;361(6403). Epub 2018 Aug 16.

John Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UK.

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http://dx.doi.org/10.1126/science.aar7191DOI Listing
August 2018
207 Reads
8 Citations
31.480 Impact Factor

Host Subtraction, Filtering and Assembly Validations for Novel Viral Discovery Using Next Generation Sequencing Data.

PLoS One 2015 22;10(6):e0129059. Epub 2015 Jun 22.

Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB30ES, United Kingdom.

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Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0129059PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4476701PMC
March 2016
30 Reads
3.234 Impact Factor

bio-samtools 2: a package for analysis and visualization of sequence and alignment data with SAMtools in Ruby.

Bioinformatics 2015 Aug 29;31(15):2565-7. Epub 2015 Mar 29.

The Sainsbury Laboratory and.

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http://dx.doi.org/10.1093/bioinformatics/btv178DOI Listing
August 2015
47 Reads
4.981 Impact Factor

PolyMarker: A fast polyploid primer design pipeline.

Bioinformatics 2015 Jun 2;31(12):2038-9. Epub 2015 Feb 2.

The Genome Analysis Centre (TGAC), Norwich Research Park, Norwich NR4 7UH, UK, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK and National Institute of Agricultural Botany (NIAB), Cambridge CB3 0LE, UK.

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Source
http://dx.doi.org/10.1093/bioinformatics/btv069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4765872PMC
June 2015
3 Reads
4.981 Impact Factor

StatsDB: platform-agnostic storage and understanding of next generation sequencing run metrics.

F1000Res 2013 15;2:248. Epub 2013 Nov 15.

The Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH, UK.

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http://dx.doi.org/10.12688/f1000research.2-248.v2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3938176PMC
March 2014
13 Reads
8 Citations

Analyses of pig genomes provide insight into porcine demography and evolution.

Authors:
Martien A M Groenen Alan L Archibald Hirohide Uenishi Christopher K Tuggle Yasuhiro Takeuchi Max F Rothschild Claire Rogel-Gaillard Chankyu Park Denis Milan Hendrik-Jan Megens Shengting Li Denis M Larkin Heebal Kim Laurent A F Frantz Mario Caccamo Hyeonju Ahn Bronwen L Aken Anna Anselmo Christian Anthon Loretta Auvil Bouabid Badaoui Craig W Beattie Christian Bendixen Daniel Berman Frank Blecha Jonas Blomberg Lars Bolund Mirte Bosse Sara Botti Zhan Bujie Megan Bystrom Boris Capitanu Denise Carvalho-Silva Patrick Chardon Celine Chen Ryan Cheng Sang-Haeng Choi William Chow Richard C Clark Christopher Clee Richard P M A Crooijmans Harry D Dawson Patrice Dehais Fioravante De Sapio Bert Dibbits Nizar Drou Zhi-Qiang Du Kellye Eversole João Fadista Susan Fairley Thomas Faraut Geoffrey J Faulkner Katie E Fowler Merete Fredholm Eric Fritz James G R Gilbert Elisabetta Giuffra Jan Gorodkin Darren K Griffin Jennifer L Harrow Alexander Hayward Kerstin Howe Zhi-Liang Hu Sean J Humphray Toby Hunt Henrik Hornshøj Jin-Tae Jeon Patric Jern Matthew Jones Jerzy Jurka Hiroyuki Kanamori Ronan Kapetanovic Jaebum Kim Jae-Hwan Kim Kyu-Won Kim Tae-Hun Kim Greger Larson Kyooyeol Lee Kyung-Tai Lee Richard Leggett Harris A Lewin Yingrui Li Wansheng Liu Jane E Loveland Yao Lu Joan K Lunney Jian Ma Ole Madsen Katherine Mann Lucy Matthews Stuart McLaren Takeya Morozumi Michael P Murtaugh Jitendra Narayan Dinh Truong Nguyen Peixiang Ni Song-Jung Oh Suneel Onteru Frank Panitz Eung-Woo Park Hong-Seog Park Geraldine Pascal Yogesh Paudel Miguel Perez-Enciso Ricardo Ramirez-Gonzalez James M Reecy Sandra Rodriguez-Zas Gary A Rohrer Lauretta Rund Yongming Sang Kyle Schachtschneider Joshua G Schraiber John Schwartz Linda Scobie Carol Scott Stephen Searle Bertrand Servin Bruce R Southey Goran Sperber Peter Stadler Jonathan V Sweedler Hakim Tafer Bo Thomsen Rashmi Wali Jian Wang Jun Wang Simon White Xun Xu Martine Yerle Guojie Zhang Jianguo Zhang Jie Zhang Shuhong Zhao Jane Rogers Carol Churcher Lawrence B Schook

Nature 2012 Nov;491(7424):393-8

Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands.

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Source
http://www.umass.edu/vetimm/docs/Groenen_etal_2012.pdf
Web Search
http://www.nature.com/doifinder/10.1038/nature11622
Publisher Site
http://dx.doi.org/10.1038/nature11622DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566564PMC
November 2012
82 Reads
42.351 Impact Factor

Evolution of an Eurasian avian-like influenza virus in naïve and vaccinated pigs.

PLoS Pathog 2012 31;8(5):e1002730. Epub 2012 May 31.

Cambridge Infectious Diseases Consortium, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom.

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http://dx.doi.org/10.1371/journal.ppat.1002730DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3364949PMC
October 2012
15 Reads
37 Citations

Bio-samtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments.

Source Code Biol Med 2012 May 28;7(1). Epub 2012 May 28.

The Sainsbury Laboratory, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK.

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http://dx.doi.org/10.1186/1751-0473-7-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3473260PMC
May 2012
33 Reads
11 Citations

Gee Fu: a sequence version and web-services database tool for genomic assembly, genome feature and NGS data.

Bioinformatics 2011 Oct 29;27(19):2754-5. Epub 2011 Jul 29.

The Genome Analysis Centre, Norwich Research Park, Colney Lane, Norwich, UK, NR4 7UH.

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http://dx.doi.org/10.1093/bioinformatics/btr442DOI Listing
October 2011
7 Reads
4.981 Impact Factor

Top co-authors

Frederic Choulet
Frederic Choulet

University Blaise Pascal

13
Cristobal Uauy
Cristobal Uauy

University of California

12
Mario Caccamo
Mario Caccamo

The Genome Analysis Centre (TGAC)

12
Rudi Appels
Rudi Appels

Capital Normal University

11
Manuel Spannagl
Manuel Spannagl

University of Minnesota

10
Jane Rogers
Jane Rogers

The Wellcome Trust Sanger Institute

9
Daniel Lang
Daniel Lang

University of Freiburg

9
Etienne Paux
Etienne Paux

Institute of Plant Biology

7
Martin Mascher
Martin Mascher

Leibniz Institute of Plant Genetics and Crop Plant Research

6