Tyler Alioto

Tyler Alioto

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Tyler Alioto

Tyler Alioto

Publications by authors named "Tyler Alioto"

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31Publications

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Assembly and Annotation of the Larval Transcriptome of Two Spadefoot Toads Widely Divergent in Developmental Rate.

G3 (Bethesda) 2019 08 8;9(8):2647-2655. Epub 2019 Aug 8.

Ecology, Evolution and Development Group, Doñana Biological Station (CSIC), Seville 41092, Spain,

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http://dx.doi.org/10.1534/g3.119.400389DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6686947PMC
August 2019

European sea bass brain DLB-1 cell line is susceptible to nodavirus: A transcriptomic study.

Fish Shellfish Immunol 2019 Mar 11;86:14-24. Epub 2018 Nov 11.

Fish Innate Immune System Group, Department of Cell Biology and Histology, Faculty of Biology, Campus Regional de Excelencia Internacional "Campus Mare Nostrum", University of Murcia, 30100 Murcia, Spain. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10504648183074
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http://dx.doi.org/10.1016/j.fsi.2018.11.024DOI Listing
March 2019

Using geneid to Identify Genes.

Curr Protoc Bioinformatics 2018 12 17;64(1):e56. Epub 2018 Oct 17.

Centre de Regulació Genòmica (CRG), Barcelona, Spain.

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http://dx.doi.org/10.1002/cpbi.56DOI Listing
December 2018

The High-Quality Genome Sequence of the Oceanic Island Endemic Species Drosophila guanche Reveals Signals of Adaptive Evolution in Genes Related to Flight and Genome Stability.

Genome Biol Evol 2018 08 1;10(8):1956-1969. Epub 2018 Aug 1.

Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, i Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain.

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http://dx.doi.org/10.1093/gbe/evy135DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6101566PMC
August 2018

Innate Cell-Mediated Cytotoxic Activity of European Sea Bass Leucocytes Against Nodavirus-Infected Cells: A Functional and RNA-seq Study.

Sci Rep 2017 11 13;7(1):15396. Epub 2017 Nov 13.

Fish Innate Immune System Group, Department of Cell Biology and Histology, Faculty of Biology, Campus Regional de Excelencia Internacional "Campus Mare Nostrum", University of Murcia, 30100, Murcia, Spain.

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http://dx.doi.org/10.1038/s41598-017-15629-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5684396PMC
November 2017

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.

Nat Commun 2015 Dec 9;6:10001. Epub 2015 Dec 9.

CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.

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http://dx.doi.org/10.1038/ncomms10001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4682041PMC
December 2015

ASPic-GeneID: a lightweight pipeline for gene prediction and alternative isoforms detection.

Biomed Res Int 2013 7;2013:502827. Epub 2013 Nov 7.

Centre Nacional d'Anàlisi Genòmica (CNAG), Parc Científic de Barcelona, 08028 Barcelona, Spain.

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http://dx.doi.org/10.1155/2013/502827DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3838850PMC
June 2014

Genome Sequence of Plesiomonas shigelloides Strain 302-73 (Serotype O1).

Genome Announc 2013 Jun 27;1(4). Epub 2013 Jun 27.

Departamento de Microbiología y Parasitología Sanitarias, Facultad de Farmacia, Universitat de Barcelona, Barcelona, Spain.

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http://dx.doi.org/10.1128/genomeA.00404-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3695437PMC
June 2013

Landscape of transcription in human cells.

Nature 2012 Sep;489(7414):101-8

Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain.

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http://dx.doi.org/10.1038/nature11233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3684276PMC
September 2012

Gene prediction.

Authors:
Tyler Alioto

Methods Mol Biol 2012 ;855:175-201

Centro Nacional de Análisis Genómico, Barcelona, Spain.

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http://dx.doi.org/10.1007/978-1-61779-582-4_6DOI Listing
July 2012

The genome of melon (Cucumis melo L.).

Proc Natl Acad Sci U S A 2012 Jul 2;109(29):11872-7. Epub 2012 Jul 2.

Institut de Recerca i Tecnologia Agroalimentàries, Centre for Research in Agricultural Genomics Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona, 08193 Barcelona, Spain.

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http://dx.doi.org/10.1073/pnas.1205415109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3406823PMC
July 2012

The genome sequence of taurine cattle: a window to ruminant biology and evolution.

Authors:
Christine G Elsik Ross L Tellam Kim C Worley Richard A Gibbs Donna M Muzny George M Weinstock David L Adelson Evan E Eichler Laura Elnitski Roderic Guigó Debora L Hamernik Steve M Kappes Harris A Lewin David J Lynn Frank W Nicholas Alexandre Reymond Monique Rijnkels Loren C Skow Evgeny M Zdobnov Lawrence Schook James Womack Tyler Alioto Stylianos E Antonarakis Alex Astashyn Charles E Chapple Hsiu-Chuan Chen Jacqueline Chrast Francisco Câmara Olga Ermolaeva Charlotte N Henrichsen Wratko Hlavina Yuri Kapustin Boris Kiryutin Paul Kitts Felix Kokocinski Melissa Landrum Donna Maglott Kim Pruitt Victor Sapojnikov Stephen M Searle Victor Solovyev Alexandre Souvorov Catherine Ucla Carine Wyss Juan M Anzola Daniel Gerlach Eran Elhaik Dan Graur Justin T Reese Robert C Edgar John C McEwan Gemma M Payne Joy M Raison Thomas Junier Evgenia V Kriventseva Eduardo Eyras Mireya Plass Ravikiran Donthu Denis M Larkin James Reecy Mary Q Yang Lin Chen Ze Cheng Carol G Chitko-McKown George E Liu Lakshmi K Matukumalli Jiuzhou Song Bin Zhu Daniel G Bradley Fiona S L Brinkman Lilian P L Lau Matthew D Whiteside Angela Walker Thomas T Wheeler Theresa Casey J Bruce German Danielle G Lemay Nauman J Maqbool Adrian J Molenaar Seongwon Seo Paul Stothard Cynthia L Baldwin Rebecca Baxter Candice L Brinkmeyer-Langford Wendy C Brown Christopher P Childers Timothy Connelley Shirley A Ellis Krista Fritz Elizabeth J Glass Carolyn T A Herzig Antti Iivanainen Kevin K Lahmers Anna K Bennett C Michael Dickens James G R Gilbert Darren E Hagen Hanni Salih Jan Aerts Alexandre R Caetano Brian Dalrymple Jose Fernando Garcia Clare A Gill Stefan G Hiendleder Erdogan Memili Diane Spurlock John L Williams Lee Alexander Michael J Brownstein Leluo Guan Robert A Holt Steven J M Jones Marco A Marra Richard Moore Stephen S Moore Andy Roberts Masaaki Taniguchi Richard C Waterman Joseph Chacko Mimi M Chandrabose Andy Cree Marvin Diep Dao Huyen H Dinh Ramatu Ayiesha Gabisi Sandra Hines Jennifer Hume Shalini N Jhangiani Vandita Joshi Christie L Kovar Lora R Lewis Yih-Shin Liu John Lopez Margaret B Morgan Ngoc Bich Nguyen Geoffrey O Okwuonu San Juana Ruiz Jireh Santibanez Rita A Wright Christian Buhay Yan Ding Shannon Dugan-Rocha Judith Herdandez Michael Holder Aniko Sabo Amy Egan Jason Goodell Katarzyna Wilczek-Boney Gerald R Fowler Matthew Edward Hitchens Ryan J Lozado Charles Moen David Steffen James T Warren Jingkun Zhang Readman Chiu Jacqueline E Schein K James Durbin Paul Havlak Huaiyang Jiang Yue Liu Xiang Qin Yanru Ren Yufeng Shen Henry Song Stephanie Nicole Bell Clay Davis Angela Jolivet Johnson Sandra Lee Lynne V Nazareth Bella Mayurkumar Patel Ling-Ling Pu Selina Vattathil Rex Lee Williams Stacey Curry Cerissa Hamilton Erica Sodergren David A Wheeler Wes Barris Gary L Bennett André Eggen Ronnie D Green Gregory P Harhay Matthew Hobbs Oliver Jann John W Keele Matthew P Kent Sigbjørn Lien Stephanie D McKay Sean McWilliam Abhirami Ratnakumar Robert D Schnabel Timothy Smith Warren M Snelling Tad S Sonstegard Roger T Stone Yoshikazu Sugimoto Akiko Takasuga Jeremy F Taylor Curtis P Van Tassell Michael D Macneil Antonio R R Abatepaulo Colette A Abbey Virpi Ahola Iassudara G Almeida Ariel F Amadio Elen Anatriello Suria M Bahadue Fernando H Biase Clayton R Boldt Jeffery A Carroll Wanessa A Carvalho Eliane P Cervelatti Elsa Chacko Jennifer E Chapin Ye Cheng Jungwoo Choi Adam J Colley Tatiana A de Campos Marcos De Donato Isabel K F de Miranda Santos Carlo J F de Oliveira Heather Deobald Eve Devinoy Kaitlin E Donohue Peter Dovc Annett Eberlein Carolyn J Fitzsimmons Alessandra M Franzin Gustavo R Garcia Sem Genini Cody J Gladney Jason R Grant Marion L Greaser Jonathan A Green Darryl L Hadsell Hatam A Hakimov Rob Halgren Jennifer L Harrow Elizabeth A Hart Nicola Hastings Marta Hernandez Zhi-Liang Hu Aaron Ingham Terhi Iso-Touru Catherine Jamis Kirsty Jensen Dimos Kapetis Tovah Kerr Sari S Khalil Hasan Khatib Davood Kolbehdari Charu G Kumar Dinesh Kumar Richard Leach Justin C-M Lee Changxi Li Krystin M Logan Roberto Malinverni Elisa Marques William F Martin Natalia F Martins Sandra R Maruyama Raffaele Mazza Kim L McLean Juan F Medrano Barbara T Moreno Daniela D Moré Carl T Muntean Hari P Nandakumar Marcelo F G Nogueira Ingrid Olsaker Sameer D Pant Francesca Panzitta Rosemeire C P Pastor Mario A Poli Nathan Poslusny Satyanarayana Rachagani Shoba Ranganathan Andrej Razpet Penny K Riggs Gonzalo Rincon Nelida Rodriguez-Osorio Sandra L Rodriguez-Zas Natasha E Romero Anne Rosenwald Lillian Sando Sheila M Schmutz Libing Shen Laura Sherman Bruce R Southey Ylva Strandberg Lutzow Jonathan V Sweedler Imke Tammen Bhanu Prakash V L Telugu Jennifer M Urbanski Yuri T Utsunomiya Chris P Verschoor Ashley J Waardenberg Zhiquan Wang Robert Ward Rosemarie Weikard Thomas H Welsh Stephen N White Laurens G Wilming Kris R Wunderlich Jianqi Yang Feng-Qi Zhao

Science 2009 Apr;324(5926):522-8

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http://dx.doi.org/10.1126/science.1169588DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943200PMC
April 2009

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:
Ewan Birney John A Stamatoyannopoulos Anindya Dutta Roderic Guigó Thomas R Gingeras Elliott H Margulies Zhiping Weng Michael Snyder Emmanouil T Dermitzakis Robert E Thurman Michael S Kuehn Christopher M Taylor Shane Neph Christoph M Koch Saurabh Asthana Ankit Malhotra Ivan Adzhubei Jason A Greenbaum Robert M Andrews Paul Flicek Patrick J Boyle Hua Cao Nigel P Carter Gayle K Clelland Sean Davis Nathan Day Pawandeep Dhami Shane C Dillon Michael O Dorschner Heike Fiegler Paul G Giresi Jeff Goldy Michael Hawrylycz Andrew Haydock Richard Humbert Keith D James Brett E Johnson Ericka M Johnson Tristan T Frum Elizabeth R Rosenzweig Neerja Karnani Kirsten Lee Gregory C Lefebvre Patrick A Navas Fidencio Neri Stephen C J Parker Peter J Sabo Richard Sandstrom Anthony Shafer David Vetrie Molly Weaver Sarah Wilcox Man Yu Francis S Collins Job Dekker Jason D Lieb Thomas D Tullius Gregory E Crawford Shamil Sunyaev William S Noble Ian Dunham France Denoeud Alexandre Reymond Philipp Kapranov Joel Rozowsky Deyou Zheng Robert Castelo Adam Frankish Jennifer Harrow Srinka Ghosh Albin Sandelin Ivo L Hofacker Robert Baertsch Damian Keefe Sujit Dike Jill Cheng Heather A Hirsch Edward A Sekinger Julien Lagarde Josep F Abril Atif Shahab Christoph Flamm Claudia Fried Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Missal Andrea Tanzer Stefan Washietl Jan Korbel Olof Emanuelsson Jakob S Pedersen Nancy Holroyd Ruth Taylor David Swarbreck Nicholas Matthews Mark C Dickson Daryl J Thomas Matthew T Weirauch James Gilbert Jorg Drenkow Ian Bell XiaoDong Zhao K G Srinivasan Wing-Kin Sung Hong Sain Ooi Kuo Ping Chiu Sylvain Foissac Tyler Alioto Michael Brent Lior Pachter Michael L Tress Alfonso Valencia Siew Woh Choo Chiou Yu Choo Catherine Ucla Caroline Manzano Carine Wyss Evelyn Cheung Taane G Clark James B Brown Madhavan Ganesh Sandeep Patel Hari Tammana Jacqueline Chrast Charlotte N Henrichsen Chikatoshi Kai Jun Kawai Ugrappa Nagalakshmi Jiaqian Wu Zheng Lian Jin Lian Peter Newburger Xueqing Zhang Peter Bickel John S Mattick Piero Carninci Yoshihide Hayashizaki Sherman Weissman Tim Hubbard Richard M Myers Jane Rogers Peter F Stadler Todd M Lowe Chia-Lin Wei Yijun Ruan Kevin Struhl Mark Gerstein Stylianos E Antonarakis Yutao Fu Eric D Green Ulaş Karaöz Adam Siepel James Taylor Laura A Liefer Kris A Wetterstrand Peter J Good Elise A Feingold Mark S Guyer Gregory M Cooper George Asimenos Colin N Dewey Minmei Hou Sergey Nikolaev Juan I Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham Haiyan Huang Nancy R Zhang Ian Holmes James C Mullikin Abel Ureta-Vidal Benedict Paten Michael Seringhaus Deanna Church Kate Rosenbloom W James Kent Eric A Stone Serafim Batzoglou Nick Goldman Ross C Hardison David Haussler Webb Miller Arend Sidow Nathan D Trinklein Zhengdong D Zhang Leah Barrera Rhona Stuart David C King Adam Ameur Stefan Enroth Mark C Bieda Jonghwan Kim Akshay A Bhinge Nan Jiang Jun Liu Fei Yao Vinsensius B Vega Charlie W H Lee Patrick Ng Atif Shahab Annie Yang Zarmik Moqtaderi Zhou Zhu Xiaoqin Xu Sharon Squazzo Matthew J Oberley David Inman Michael A Singer Todd A Richmond Kyle J Munn Alvaro Rada-Iglesias Ola Wallerman Jan Komorowski Joanna C Fowler Phillippe Couttet Alexander W Bruce Oliver M Dovey Peter D Ellis Cordelia F Langford David A Nix Ghia Euskirchen Stephen Hartman Alexander E Urban Peter Kraus Sara Van Calcar Nate Heintzman Tae Hoon Kim Kun Wang Chunxu Qu Gary Hon Rosa Luna Christopher K Glass M Geoff Rosenfeld Shelley Force Aldred Sara J Cooper Anason Halees Jane M Lin Hennady P Shulha Xiaoling Zhang Mousheng Xu Jaafar N S Haidar Yong Yu Yijun Ruan Vishwanath R Iyer Roland D Green Claes Wadelius Peggy J Farnham Bing Ren Rachel A Harte Angie S Hinrichs Heather Trumbower Hiram Clawson Jennifer Hillman-Jackson Ann S Zweig Kayla Smith Archana Thakkapallayil Galt Barber Robert M Kuhn Donna Karolchik Lluis Armengol Christine P Bird Paul I W de Bakker Andrew D Kern Nuria Lopez-Bigas Joel D Martin Barbara E Stranger Abigail Woodroffe Eugene Davydov Antigone Dimas Eduardo Eyras Ingileif B Hallgrímsdóttir Julian Huppert Michael C Zody Gonçalo R Abecasis Xavier Estivill Gerard G Bouffard Xiaobin Guan Nancy F Hansen Jacquelyn R Idol Valerie V B Maduro Baishali Maskeri Jennifer C McDowell Morgan Park Pamela J Thomas Alice C Young Robert W Blakesley Donna M Muzny Erica Sodergren David A Wheeler Kim C Worley Huaiyang Jiang George M Weinstock Richard A Gibbs Tina Graves Robert Fulton Elaine R Mardis Richard K Wilson Michele Clamp James Cuff Sante Gnerre David B Jaffe Jean L Chang Kerstin Lindblad-Toh Eric S Lander Maxim Koriabine Mikhail Nefedov Kazutoyo Osoegawa Yuko Yoshinaga Baoli Zhu Pieter J de Jong
June 2007

U12DB: a database of orthologous U12-type spliceosomal introns.

Authors:
Tyler S Alioto

Nucleic Acids Res 2007 Jan 1;35(Database issue):D110-5. Epub 2006 Nov 1.

Genome Bioinformatics Laboratory, Center for Genomic Regulation, Doctor Aiguader 88, 08003 Barcelona, Spain.

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http://dx.doi.org/10.1093/nar/gkl796DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635337PMC
January 2007

The repertoire of olfactory C family G protein-coupled receptors in zebrafish: candidate chemosensory receptors for amino acids.

BMC Genomics 2006 Dec 8;7:309. Epub 2006 Dec 8.

Department of Molecular and Cell Biology, Functional Genomics Laboratory, and Helen Wills Neuroscience Institute, University of California, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1186/1471-2164-7-309DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1764893PMC
December 2006

The odorant receptor repertoire of teleost fish.

BMC Genomics 2005 Dec 6;6:173. Epub 2005 Dec 6.

Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, University of California, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1186/1471-2164-6-173DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1325023PMC
December 2005

Septin 3 gene polymorphism in Alzheimer's disease.

Gene Expr 2004 ;11(5-6):263-70

Laboratory of Molecular Clinical Chemistry, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5991150PMC
http://dx.doi.org/10.3727/000000003783992243DOI Listing
January 2005