Mario Caccamo

Mario Caccamo

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Mario Caccamo

Mario Caccamo

Publications by authors named "Mario Caccamo"

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Yerba mate (Ilex paraguariensis, A. St.-Hil.) de novo transcriptome assembly based on tissue specific genomic expression profiles.

BMC Genomics 2018 Dec 7;19(1):891. Epub 2018 Dec 7.

Grupo de Investigación en Genética Aplicada (GIGA), Facultad de Ciencias Exactas Químicas y Naturales, Instituto de Biología Subtropical (IBS UNaM-CONICET), Universidad Nacional de Misiones, Jujuy 1745, CP3300, Posadas, Misiones, Argentina.

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http://dx.doi.org/10.1186/s12864-018-5240-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6286616PMC
December 2018

Primula vulgaris (primrose) genome assembly, annotation and gene expression, with comparative genomics on the heterostyly supergene.

Sci Rep 2018 12 18;8(1):17942. Epub 2018 Dec 18.

School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom.

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http://dx.doi.org/10.1038/s41598-018-36304-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6299000PMC
December 2018

Whole-Genome Characteristics and Polymorphic Analysis of Vietnamese Rice Landraces as a Comprehensive Information Resource for Marker-Assisted Selection.

Int J Genomics 2017 7;2017:9272363. Epub 2017 Feb 7.

Department of Genetic Engineering, Agricultural Genetics Institute, Vietnam Academy of Agricultural Sciences, Km2 Pham Van Dong, Tuliem, Hanoi, Vietnam.

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http://dx.doi.org/10.1155/2017/9272363DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5318636PMC
February 2017

Genetic architecture and evolution of the S locus supergene in Primula vulgaris.

Nat Plants 2016 12 2;2(12):16188. Epub 2016 Dec 2.

School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.

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http://dx.doi.org/10.1038/nplants.2016.188DOI Listing
December 2016

gEVAL - a web-based browser for evaluating genome assemblies.

Bioinformatics 2016 08 7;32(16):2508-10. Epub 2016 Apr 7.

Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1093/bioinformatics/btw159DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4978925PMC
August 2016

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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http://dx.doi.org/10.1093/bioinformatics/btv069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4765872PMC
June 2015

New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing.

Plant Sci 2015 Apr 18;233:200-212. Epub 2014 Dec 18.

CERZOS (Centro de Recursos Naturales Renovables de la Zona Semiárida), (CCT-CONICET-Bahía Blanca) and Universidad Nacional del Sur, Bahía Blanca, Buenos Aires, Argentina. Electronic address:

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http://dx.doi.org/10.1016/j.plantsci.2014.12.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4352925PMC
April 2015

NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries.

Bioinformatics 2014 Feb 2;30(4):566-8. Epub 2013 Dec 2.

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

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http://dx.doi.org/10.1093/bioinformatics/btt702DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3928519PMC
February 2014

Turning over a new leaf in plant genomics.

Genome Biol 2013 Jun 27;14(6):403. Epub 2013 Jun 27.

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http://dx.doi.org/10.1186/gb-2013-14-6-403DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3706968PMC
June 2013

The zebrafish reference genome sequence and its relationship to the human genome.

Authors:
Kerstin Howe Matthew D Clark Carlos F Torroja James Torrance Camille Berthelot Matthieu Muffato John E Collins Sean Humphray Karen McLaren Lucy Matthews Stuart McLaren Ian Sealy Mario Caccamo Carol Churcher Carol Scott Jeffrey C Barrett Romke Koch Gerd-Jörg Rauch Simon White William Chow Britt Kilian Leonor T Quintais José A Guerra-Assunção Yi Zhou Yong Gu Jennifer Yen Jan-Hinnerk Vogel Tina Eyre Seth Redmond Ruby Banerjee Jianxiang Chi Beiyuan Fu Elizabeth Langley Sean F Maguire Gavin K Laird David Lloyd Emma Kenyon Sarah Donaldson Harminder Sehra Jeff Almeida-King Jane Loveland Stephen Trevanion Matt Jones Mike Quail Dave Willey Adrienne Hunt John Burton Sarah Sims Kirsten McLay Bob Plumb Joy Davis Chris Clee Karen Oliver Richard Clark Clare Riddle David Elliot David Eliott Glen Threadgold Glenn Harden Darren Ware Sharmin Begum Beverley Mortimore Beverly Mortimer Giselle Kerry Paul Heath Benjamin Phillimore Alan Tracey Nicole Corby Matthew Dunn Christopher Johnson Jonathan Wood Susan Clark Sarah Pelan Guy Griffiths Michelle Smith Rebecca Glithero Philip Howden Nicholas Barker Christine Lloyd Christopher Stevens Joanna Harley Karen Holt Georgios Panagiotidis Jamieson Lovell Helen Beasley Carl Henderson Daria Gordon Katherine Auger Deborah Wright Joanna Collins Claire Raisen Lauren Dyer Kenric Leung Lauren Robertson Kirsty Ambridge Daniel Leongamornlert Sarah McGuire Ruth Gilderthorp Coline Griffiths Deepa Manthravadi Sarah Nichol Gary Barker Siobhan Whitehead Michael Kay Jacqueline Brown Clare Murnane Emma Gray Matthew Humphries Neil Sycamore Darren Barker David Saunders Justene Wallis Anne Babbage Sian Hammond Maryam Mashreghi-Mohammadi Lucy Barr Sancha Martin Paul Wray Andrew Ellington Nicholas Matthews Matthew Ellwood Rebecca Woodmansey Graham Clark James D Cooper James Cooper Anthony Tromans Darren Grafham Carl Skuce Richard Pandian Robert Andrews Elliot Harrison Andrew Kimberley Jane Garnett Nigel Fosker Rebekah Hall Patrick Garner Daniel Kelly Christine Bird Sophie Palmer Ines Gehring Andrea Berger Christopher M Dooley Zübeyde Ersan-Ürün Cigdem Eser Horst Geiger Maria Geisler Lena Karotki Anette Kirn Judith Konantz Martina Konantz Martina Oberländer Silke Rudolph-Geiger Mathias Teucke Christa Lanz Günter Raddatz Kazutoyo Osoegawa Baoli Zhu Amanda Rapp Sara Widaa Cordelia Langford Fengtang Yang Stephan C Schuster Nigel P Carter Jennifer Harrow Zemin Ning Javier Herrero Steve M J Searle Anton Enright Robert Geisler Ronald H A Plasterk Charles Lee Monte Westerfield Pieter J de Jong Leonard I Zon John H Postlethwait Christiane Nüsslein-Volhard Tim J P Hubbard Hugues Roest Crollius Jane Rogers Derek L Stemple

Nature 2013 Apr 17;496(7446):498-503. Epub 2013 Apr 17.

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

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http://dx.doi.org/10.1038/nature12111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3703927PMC
April 2013

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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http://www.umass.edu/vetimm/docs/Groenen_etal_2012.pdf
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http://www.nature.com/doifinder/10.1038/nature11622
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http://dx.doi.org/10.1038/nature11622DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566564PMC
November 2012

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

De novo assembly and genotyping of variants using colored de Bruijn graphs.

Nat Genet 2012 Jan 8;44(2):226-32. Epub 2012 Jan 8.

Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.

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http://www.nature.com/articles/ng.1028
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http://dx.doi.org/10.1038/ng.1028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3272472PMC
January 2012

Advances in bacterial transcriptome and transposon insertion-site profiling using second-generation sequencing.

Trends Biotechnol 2011 Nov 20;29(11):586-94. Epub 2011 Jul 20.

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

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http://dx.doi.org/10.1016/j.tibtech.2011.06.004DOI Listing
November 2011

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

Genome sequence of the vertebrate gut symbiont Lactobacillus reuteri ATCC 53608.

J Bacteriol 2011 Aug 27;193(15):4015-6. Epub 2011 May 27.

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

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http://jb.asm.org/cgi/doi/10.1128/JB.05282-11
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http://dx.doi.org/10.1128/JB.05282-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3147506PMC
August 2011

Draft genome sequence of Streptomyces strain S4, a symbiont of the leaf-cutting ant Acromyrmex octospinosus.

J Bacteriol 2011 Aug 17;193(16):4270-1. Epub 2011 Jun 17.

School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom.

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http://dx.doi.org/10.1128/JB.05275-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3147664PMC
August 2011

Adaptive autoimmunity and Foxp3-based immunoregulation in zebrafish.

PLoS One 2010 Mar 5;5(3):e9478. Epub 2010 Mar 5.

Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0009478PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832694PMC
March 2010

Conservation and divergence of gene families encoding components of innate immune response systems in zebrafish.

Genome Biol 2007 ;8(11):R251

Institute for Genetics, University of Cologne, Zuelpicher Str, 47, 50674 Cologne, Germany.

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http://dx.doi.org/10.1186/gb-2007-8-11-r251DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2258186PMC
August 2008

Control of T(reg) and T(H)17 cell differentiation by the aryl hydrocarbon receptor.

Nature 2008 May 23;453(7191):65-71. Epub 2008 Mar 23.

Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA.

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http://www.nature.com/articles/nature06880
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http://dx.doi.org/10.1038/nature06880DOI Listing
May 2008

ESTGenes: alternative splicing from ESTs in Ensembl.

Genome Res 2004 May;14(5):976-87

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

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http://www.genome.org/cgi/doi/10.1101/gr.1862204
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http://dx.doi.org/10.1101/gr.1862204DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC479129PMC
May 2004

Genome sequence of the Brown Norway rat yields insights into mammalian evolution.

Authors:
Richard A Gibbs George M Weinstock Michael L Metzker Donna M Muzny Erica J Sodergren Steven Scherer Graham Scott David Steffen Kim C Worley Paula E Burch Geoffrey Okwuonu Sandra Hines Lora Lewis Christine DeRamo Oliver Delgado Shannon Dugan-Rocha George Miner Margaret Morgan Alicia Hawes Rachel Gill Celera Robert A Holt Mark D Adams Peter G Amanatides Holly Baden-Tillson Mary Barnstead Soo Chin Cheryl A Evans Steve Ferriera Carl Fosler Anna Glodek Zhiping Gu Don Jennings Cheryl L Kraft Trixie Nguyen Cynthia M Pfannkoch Cynthia Sitter Granger G Sutton J Craig Venter Trevor Woodage Douglas Smith Hong-Mei Lee Erik Gustafson Patrick Cahill Arnold Kana Lynn Doucette-Stamm Keith Weinstock Kim Fechtel Robert B Weiss Diane M Dunn Eric D Green Robert W Blakesley Gerard G Bouffard Pieter J De Jong Kazutoyo Osoegawa Baoli Zhu Marco Marra Jacqueline Schein Ian Bosdet Chris Fjell Steven Jones Martin Krzywinski Carrie Mathewson Asim Siddiqui Natasja Wye John McPherson Shaying Zhao Claire M Fraser Jyoti Shetty Sofiya Shatsman Keita Geer Yixin Chen Sofyia Abramzon William C Nierman Paul H Havlak Rui Chen K James Durbin Amy Egan Yanru Ren Xing-Zhi Song Bingshan Li Yue Liu Xiang Qin Simon Cawley Kim C Worley A J Cooney Lisa M D'Souza Kirt Martin Jia Qian Wu Manuel L Gonzalez-Garay Andrew R Jackson Kenneth J Kalafus Michael P McLeod Aleksandar Milosavljevic Davinder Virk Andrei Volkov David A Wheeler Zhengdong Zhang Jeffrey A Bailey Evan E Eichler Eray Tuzun Ewan Birney Emmanuel Mongin Abel Ureta-Vidal Cara Woodwark Evgeny Zdobnov Peer Bork Mikita Suyama David Torrents Marina Alexandersson Barbara J Trask Janet M Young Hui Huang Huajun Wang Heming Xing Sue Daniels Darryl Gietzen Jeanette Schmidt Kristian Stevens Ursula Vitt Jim Wingrove Francisco Camara M Mar Albà Josep F Abril Roderic Guigo Arian Smit Inna Dubchak Edward M Rubin Olivier Couronne Alexander Poliakov Norbert Hübner Detlev Ganten Claudia Goesele Oliver Hummel Thomas Kreitler Young-Ae Lee Jan Monti Herbert Schulz Heike Zimdahl Heinz Himmelbauer Hans Lehrach Howard J Jacob Susan Bromberg Jo Gullings-Handley Michael I Jensen-Seaman Anne E Kwitek Jozef Lazar Dean Pasko Peter J Tonellato Simon Twigger Chris P Ponting Jose M Duarte Stephen Rice Leo Goodstadt Scott A Beatson Richard D Emes Eitan E Winter Caleb Webber Petra Brandt Gerald Nyakatura Margaret Adetobi Francesca Chiaromonte Laura Elnitski Pallavi Eswara Ross C Hardison Minmei Hou Diana Kolbe Kateryna Makova Webb Miller Anton Nekrutenko Cathy Riemer Scott Schwartz James Taylor Shan Yang Yi Zhang Klaus Lindpaintner T Dan Andrews Mario Caccamo Michele Clamp Laura Clarke Valerie Curwen Richard Durbin Eduardo Eyras Stephen M Searle Gregory M Cooper Serafim Batzoglou Michael Brudno Arend Sidow Eric A Stone J Craig Venter Bret A Payseur Guillaume Bourque Carlos López-Otín Xose S Puente Kushal Chakrabarti Sourav Chatterji Colin Dewey Lior Pachter Nicolas Bray Von Bing Yap Anat Caspi Glenn Tesler Pavel A Pevzner David Haussler Krishna M Roskin Robert Baertsch Hiram Clawson Terrence S Furey Angie S Hinrichs Donna Karolchik William J Kent Kate R Rosenbloom Heather Trumbower Matt Weirauch David N Cooper Peter D Stenson Bin Ma Michael Brent Manimozhiyan Arumugam David Shteynberg Richard R Copley Martin S Taylor Harold Riethman Uma Mudunuri Jane Peterson Mark Guyer Adam Felsenfeld Susan Old Stephen Mockrin Francis Collins

Nature 2004 Apr;428(6982):493-521

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA. http://www.hgsc.bcm.tmc.edu

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http://dx.doi.org/10.1038/nature02426DOI Listing
April 2004