Sam Griffiths-Jones

Sam Griffiths-Jones

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Sam Griffiths-Jones

Sam Griffiths-Jones

Publications by authors named "Sam Griffiths-Jones"

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A guide to naming human non-coding RNA genes.

EMBO J 2020 Feb 24:e103777. Epub 2020 Feb 24.

Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK.

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http://dx.doi.org/10.15252/embj.2019103777DOI Listing
February 2020

miRBase: from microRNA sequences to function.

Nucleic Acids Res 2019 Jan;47(D1):D155-D162

School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK.

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http://dx.doi.org/10.1093/nar/gky1141DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323917PMC
January 2019

Small RNAs: Big Impact on Plant Development.

Trends Plant Sci 2017 12 12;22(12):1056-1068. Epub 2017 Oct 12.

Faculty of Biology, Medicine, and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK. Electronic address:

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http://dx.doi.org/10.1016/j.tplants.2017.09.009DOI Listing
December 2017

Abundant expression of somatic transposon-derived piRNAs throughout Tribolium castaneum embryogenesis.

Genome Biol 2017 09 26;18(1):184. Epub 2017 Sep 26.

Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK.

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http://dx.doi.org/10.1186/s13059-017-1304-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5613491PMC
September 2017

Mutations in SNORD118 cause the cerebral microangiopathy leukoencephalopathy with calcifications and cysts.

Nat Genet 2016 10 29;48(10):1185-92. Epub 2016 Aug 29.

Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Evolution and Genomic Sciences, University of Manchester, Manchester, UK.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5045717PMC
http://dx.doi.org/10.1038/ng.3661DOI Listing
October 2016

Pervasive microRNA Duplication in Chelicerates: Insights from the Embryonic microRNA Repertoire of the Spider Parasteatoda tepidariorum.

Genome Biol Evol 2016 08 3;8(7):2133-44. Epub 2016 Aug 3.

Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, United Kingdom

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http://dx.doi.org/10.1093/gbe/evw143DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987109PMC
August 2016

Conservation and losses of non-coding RNAs in avian genomes.

PLoS One 2015 30;10(3):e0121797. Epub 2015 Mar 30.

Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany; Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany; Fraunhofer Institute for Cell Therapy and Immunology, Perlickstrasse 1, D-04103 Leipzig, Germany; Department of Theoretical Chemistry of the University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria; Center for RNA in Technology and Health, Univ. Copenhagen, Grønnegårdsvej 3, Frederiksberg C, Denmark; Santa Fe Institute, 1399 Hyde Park Road, Santa Fe NM 87501, USA; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Germany.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0121797PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4378963PMC
April 2016

MicroRNA evolution, expression, and function during short germband development in Tribolium castaneum.

Genome Res 2016 Jan 30;26(1):85-96. Epub 2015 Oct 30.

Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, United Kingdom.

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http://dx.doi.org/10.1101/gr.193367.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4691753PMC
January 2016

Natural antisense transcripts and long non-coding RNA in Neurospora crassa.

PLoS One 2014 12;9(3):e91353. Epub 2014 Mar 12.

The Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0091353PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3951366PMC
May 2015

Target repression induced by endogenous microRNAs: large differences, small effects.

PLoS One 2014 20;9(8):e104286. Epub 2014 Aug 20.

Faculty of Life Sciences, The University of Manchester, Manchester, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0104286PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4139194PMC
May 2015

Bias in microRNA functional enrichment analysis.

Bioinformatics 2015 May 20;31(10):1592-8. Epub 2015 Jan 20.

Faculty of Medical and Human Sciences, and Faculty of Life Sciences, University of Manchester, UK.

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http://dx.doi.org/10.1093/bioinformatics/btv023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4426843PMC
May 2015

The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima.

Authors:
Ariel D Chipman David E K Ferrier Carlo Brena Jiaxin Qu Daniel S T Hughes Reinhard Schröder Montserrat Torres-Oliva Nadia Znassi Huaiyang Jiang Francisca C Almeida Claudio R Alonso Zivkos Apostolou Peshtewani Aqrawi Wallace Arthur Jennifer C J Barna Kerstin P Blankenburg Daniela Brites Salvador Capella-Gutiérrez Marcus Coyle Peter K Dearden Louis Du Pasquier Elizabeth J Duncan Dieter Ebert Cornelius Eibner Galina Erikson Peter D Evans Cassandra G Extavour Liezl Francisco Toni Gabaldón William J Gillis Elizabeth A Goodwin-Horn Jack E Green Sam Griffiths-Jones Cornelis J P Grimmelikhuijzen Sai Gubbala Roderic Guigó Yi Han Frank Hauser Paul Havlak Luke Hayden Sophie Helbing Michael Holder Jerome H L Hui Julia P Hunn Vera S Hunnekuhl LaRonda Jackson Mehwish Javaid Shalini N Jhangiani Francis M Jiggins Tamsin E Jones Tobias S Kaiser Divya Kalra Nathan J Kenny Viktoriya Korchina Christie L Kovar F Bernhard Kraus François Lapraz Sandra L Lee Jie Lv Christigale Mandapat Gerard Manning Marco Mariotti Robert Mata Tittu Mathew Tobias Neumann Irene Newsham Dinh N Ngo Maria Ninova Geoffrey Okwuonu Fiona Ongeri William J Palmer Shobha Patil Pedro Patraquim Christopher Pham Ling-Ling Pu Nicholas H Putman Catherine Rabouille Olivia Mendivil Ramos Adelaide C Rhodes Helen E Robertson Hugh M Robertson Matthew Ronshaugen Julio Rozas Nehad Saada Alejandro Sánchez-Gracia Steven E Scherer Andrew M Schurko Kenneth W Siggens DeNard Simmons Anna Stief Eckart Stolle Maximilian J Telford Kristin Tessmar-Raible Rebecca Thornton Maurijn van der Zee Arndt von Haeseler James M Williams Judith H Willis Yuanqing Wu Xiaoyan Zou Daniel Lawson Donna M Muzny Kim C Worley Richard A Gibbs Michael Akam Stephen Richards

PLoS Biol 2014 Nov 25;12(11):e1002005. Epub 2014 Nov 25.

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1002005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4244043PMC
November 2014

Conserved temporal patterns of microRNA expression in Drosophila support a developmental hourglass model.

Genome Biol Evol 2014 Aug 27;6(9):2459-67. Epub 2014 Aug 27.

Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom

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http://dx.doi.org/10.1093/gbe/evu183DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4202322PMC
August 2014

Sex-biased expression of microRNAs in Schistosoma mansoni.

PLoS Negl Trop Dis 2013 12;7(9):e2402. Epub 2013 Sep 12.

Faculty of Life Sciences, Michael Smith Building, Oxford Road, University of Manchester, Manchester, United Kingdom ; School of Biological Sciences, University of Essex, Colchester, United Kingdom.

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http://dx.doi.org/10.1371/journal.pntd.0002402DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3772069PMC
March 2014

miRBase: annotating high confidence microRNAs using deep sequencing data.

Nucleic Acids Res 2014 Jan 25;42(Database issue):D68-73. Epub 2013 Nov 25.

Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK.

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http://dx.doi.org/10.1093/nar/gkt1181DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965103PMC
January 2014

Clusters of microRNAs emerge by new hairpins in existing transcripts.

Nucleic Acids Res 2013 Sep 17;41(16):7745-52. Epub 2013 Jun 17.

Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK.

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http://dx.doi.org/10.1093/nar/gkt534DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3763532PMC
September 2013

Multiple products from microRNA transcripts.

Biochem Soc Trans 2013 Aug;41(4):850-4

Faculty of Life Sciences, Michael Smith Building, Oxford Road, University of Manchester, Manchester M13 9PT, UK.

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http://dx.doi.org/10.1042/BST20130035DOI Listing
August 2013

Structure, evolution and function of the bi-directionally transcribed iab-4/iab-8 microRNA locus in arthropods.

Nucleic Acids Res 2013 Mar 17;41(5):3352-61. Epub 2013 Jan 17.

School of Life Sciences, Chinese University of Hong Kong, Shatin, Hong Kong, China.

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http://dx.doi.org/10.1093/nar/gks1445DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3597655PMC
March 2013

MicroRNAs from the same precursor have different targeting properties.

Silence 2012 Sep 27;3(1). Epub 2012 Sep 27.

Faculty of Life Sciences, Michael Smith Building, Oxford Road, University of Manchester, Manchester M13 9PT, UK.

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http://dx.doi.org/10.1186/1758-907X-3-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3503882PMC
September 2012

Mitochondrial pseudogenes in the nuclear genomes of Drosophila.

PLoS One 2012 7;7(3):e32593. Epub 2012 Mar 7.

Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0032593PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3296715PMC
August 2012

Reducing ligation bias of small RNAs in libraries for next generation sequencing.

Silence 2012 May 30;3(1). Epub 2012 May 30.

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

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http://dx.doi.org/10.1186/1758-907X-3-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3489589PMC
May 2012

Conserved RNA structures in the non-canonical Hac1/Xbp1 intron.

RNA Biol 2011 Jul-Aug;8(4):552-6. Epub 2011 Jul 1.

Faculty of Life Sciences, University of Manchester, Manchester UK.

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http://www.tandfonline.com/doi/abs/10.4161/rna.8.4.15396
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http://dx.doi.org/10.4161/rna.8.4.15396DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3225973PMC
April 2012

Evolution and function of the extended miR-2 microRNA family.

RNA Biol 2012 Mar 1;9(3):242-8. Epub 2012 Mar 1.

Faculty of Life Sciences, University of Manchester, Manchester, UK.

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http://dx.doi.org/10.4161/rna.19160DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3384581PMC
March 2012

Detection of microRNAs in color space.

Bioinformatics 2012 Feb 9;28(3):318-23. Epub 2011 Dec 9.

University of Manchester, M13 9PT Manchester, UK.

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http://dx.doi.org/10.1093/bioinformatics/btr686DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3268249PMC
February 2012

Functional shifts in insect microRNA evolution.

Genome Biol Evol 2010 3;2:686-96. Epub 2010 Sep 3.

Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.

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http://dx.doi.org/10.1093/gbe/evq053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2956262PMC
February 2011

MicroRNA evolution by arm switching.

EMBO Rep 2011 Feb 7;12(2):172-7. Epub 2011 Jan 7.

Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK.

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http://dx.doi.org/10.1038/embor.2010.191DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3049427PMC
February 2011

miRBase: integrating microRNA annotation and deep-sequencing data.

Nucleic Acids Res 2011 Jan 30;39(Database issue):D152-7. Epub 2010 Oct 30.

Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK.

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http://dx.doi.org/10.1093/nar/gkq1027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013655PMC
January 2011

Rfam: Wikipedia, clans and the "decimal" release.

Nucleic Acids Res 2011 Jan 9;39(Database issue):D141-5. Epub 2010 Nov 9.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA0, USA.

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http://dx.doi.org/10.1093/nar/gkq1129DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013711PMC
January 2011

The evolution of tRNA genes in Drosophila.

Genome Biol Evol 2010 Jul 12;2:467-77. Epub 2010 Jul 12.

Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.

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http://dx.doi.org/10.1093/gbe/evq034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2997554PMC
July 2010

miRBase: microRNA sequences and annotation.

Curr Protoc Bioinformatics 2010 Mar;Chapter 12:Unit 12.9.1-10

University of Manchester, Manchester, United Kingdom.

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http://dx.doi.org/10.1002/0471250953.bi1209s29DOI Listing
March 2010

The role of RNA molecules in cellular biology. Editorial.

Brief Funct Genomic Proteomic 2009 Nov;8(6):405-6

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http://dx.doi.org/10.1093/bfgp/elp044DOI Listing
November 2009

An analysis of structural influences on selection in RNA genes.

Mol Biol Evol 2009 Jan 22;26(1):209-16. Epub 2008 Oct 22.

Department of Statistics, University of Oxford, Oxford, United Kingdom.

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http://dx.doi.org/10.1093/molbev/msn240DOI Listing
January 2009

Rfam: updates to the RNA families database.

Nucleic Acids Res 2009 Jan 25;37(Database issue):D136-40. Epub 2008 Oct 25.

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

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http://dx.doi.org/10.1093/nar/gkn766DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686503PMC
January 2009

Annotation of mammalian primary microRNAs.

BMC Genomics 2008 Nov 27;9:564. Epub 2008 Nov 27.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1186/1471-2164-9-564DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632650PMC
November 2008

Conservation of the H19 noncoding RNA and H19-IGF2 imprinting mechanism in therians.

Nat Genet 2008 Aug 29;40(8):971-6. Epub 2008 Jun 29.

The Babraham Institute, Laboratory of Developmental Genetics and Imprinting, Cambridge CB22 3AT, UK.

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http://dx.doi.org/10.1038/ng.168DOI Listing
August 2008

Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum.

Genome Res 2008 Feb 20;18(2):281-92. Epub 2007 Dec 20.

Ancient DNA and Evolution Group, Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark.

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http://dx.doi.org/10.1101/gr.6836108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2203626PMC
February 2008

miRBase: tools for microRNA genomics.

Nucleic Acids Res 2008 Jan 8;36(Database issue):D154-8. Epub 2007 Nov 8.

Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, UK.

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http://dx.doi.org/10.1093/nar/gkm952DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238936PMC
January 2008

Annotating noncoding RNA genes.

Annu Rev Genomics Hum Genet 2007 ;8:279-98

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

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http://dx.doi.org/10.1146/annurev.genom.8.080706.092419DOI Listing
December 2007

Genomic analysis of human microRNA transcripts.

Proc Natl Acad Sci U S A 2007 Nov 26;104(45):17719-24. Epub 2007 Oct 26.

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

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http://dx.doi.org/10.1073/pnas.0703890104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2077053PMC
November 2007

Evolution of genes and genomes on the Drosophila phylogeny.

Authors:
Andrew G Clark Michael B Eisen Douglas R Smith Casey M Bergman Brian Oliver Therese A Markow Thomas C Kaufman Manolis Kellis William Gelbart Venky N Iyer Daniel A Pollard Timothy B Sackton Amanda M Larracuente Nadia D Singh Jose P Abad Dawn N Abt Boris Adryan Montserrat Aguade Hiroshi Akashi Wyatt W Anderson Charles F Aquadro David H Ardell Roman Arguello Carlo G Artieri Daniel A Barbash Daniel Barker Paolo Barsanti Phil Batterham Serafim Batzoglou Dave Begun Arjun Bhutkar Enrico Blanco Stephanie A Bosak Robert K Bradley Adrianne D Brand Michael R Brent Angela N Brooks Randall H Brown Roger K Butlin Corrado Caggese Brian R Calvi A Bernardo de Carvalho Anat Caspi Sergio Castrezana Susan E Celniker Jean L Chang Charles Chapple Sourav Chatterji Asif Chinwalla Alberto Civetta Sandra W Clifton Josep M Comeron James C Costello Jerry A Coyne Jennifer Daub Robert G David Arthur L Delcher Kim Delehaunty Chuong B Do Heather Ebling Kevin Edwards Thomas Eickbush Jay D Evans Alan Filipski Sven Findeiss Eva Freyhult Lucinda Fulton Robert Fulton Ana C L Garcia Anastasia Gardiner David A Garfield Barry E Garvin Greg Gibson Don Gilbert Sante Gnerre Jennifer Godfrey Robert Good Valer Gotea Brenton Gravely Anthony J Greenberg Sam Griffiths-Jones Samuel Gross Roderic Guigo Erik A Gustafson Wilfried Haerty Matthew W Hahn Daniel L Halligan Aaron L Halpern Gillian M Halter Mira V Han Andreas Heger LaDeana Hillier Angie S Hinrichs Ian Holmes Roger A Hoskins Melissa J Hubisz Dan Hultmark Melanie A Huntley David B Jaffe Santosh Jagadeeshan William R Jeck Justin Johnson Corbin D Jones William C Jordan Gary H Karpen Eiko Kataoka Peter D Keightley Pouya Kheradpour Ewen F Kirkness Leonardo B Koerich Karsten Kristiansen Dave Kudrna Rob J Kulathinal Sudhir Kumar Roberta Kwok Eric Lander Charles H Langley Richard Lapoint Brian P Lazzaro So-Jeong Lee Lisa Levesque Ruiqiang Li Chiao-Feng Lin Michael F Lin Kerstin Lindblad-Toh Ana Llopart Manyuan Long Lloyd Low Elena Lozovsky Jian Lu Meizhong Luo Carlos A Machado Wojciech Makalowski Mar Marzo Muneo Matsuda Luciano Matzkin Bryant McAllister Carolyn S McBride Brendan McKernan Kevin McKernan Maria Mendez-Lago Patrick Minx Michael U Mollenhauer Kristi Montooth Stephen M Mount Xu Mu Eugene Myers Barbara Negre Stuart Newfeld Rasmus Nielsen Mohamed A F Noor Patrick O'Grady Lior Pachter Montserrat Papaceit Matthew J Parisi Michael Parisi Leopold Parts Jakob S Pedersen Graziano Pesole Adam M Phillippy Chris P Ponting Mihai Pop Damiano Porcelli Jeffrey R Powell Sonja Prohaska Kim Pruitt Marta Puig Hadi Quesneville Kristipati Ravi Ram David Rand Matthew D Rasmussen Laura K Reed Robert Reenan Amy Reily Karin A Remington Tania T Rieger Michael G Ritchie Charles Robin Yu-Hui Rogers Claudia Rohde Julio Rozas Marc J Rubenfield Alfredo Ruiz Susan Russo Steven L Salzberg Alejandro Sanchez-Gracia David J Saranga Hajime Sato Stephen W Schaeffer Michael C Schatz Todd Schlenke Russell Schwartz Carmen Segarra Rama S Singh Laura Sirot Marina Sirota Nicholas B Sisneros Chris D Smith Temple F Smith John Spieth Deborah E Stage Alexander Stark Wolfgang Stephan Robert L Strausberg Sebastian Strempel David Sturgill Granger Sutton Granger G Sutton Wei Tao Sarah Teichmann Yoshiko N Tobari Yoshihiko Tomimura Jason M Tsolas Vera L S Valente Eli Venter J Craig Venter Saverio Vicario Filipe G Vieira Albert J Vilella Alfredo Villasante Brian Walenz Jun Wang Marvin Wasserman Thomas Watts Derek Wilson Richard K Wilson Rod A Wing Mariana F Wolfner Alex Wong Gane Ka-Shu Wong Chung-I Wu Gabriel Wu Daisuke Yamamoto Hsiao-Pei Yang Shiaw-Pyng Yang James A Yorke Kiyohito Yoshida Evgeny Zdobnov Peili Zhang Yu Zhang Aleksey V Zimin Jennifer Baldwin Amr Abdouelleil Jamal Abdulkadir Adal Abebe Brikti Abera Justin Abreu St Christophe Acer Lynne Aftuck Allen Alexander Peter An Erica Anderson Scott Anderson Harindra Arachi Marc Azer Pasang Bachantsang Andrew Barry Tashi Bayul Aaron Berlin Daniel Bessette Toby Bloom Jason Blye Leonid Boguslavskiy Claude Bonnet Boris Boukhgalter Imane Bourzgui Adam Brown Patrick Cahill Sheridon Channer Yama Cheshatsang Lisa Chuda Mieke Citroen Alville Collymore Patrick Cooke Maura Costello Katie D'Aco Riza Daza Georgius De Haan Stuart DeGray Christina DeMaso Norbu Dhargay Kimberly Dooley Erin Dooley Missole Doricent Passang Dorje Kunsang Dorjee Alan Dupes Richard Elong Jill Falk Abderrahim Farina Susan Faro Diallo Ferguson Sheila Fisher Chelsea D Foley Alicia Franke Dennis Friedrich Loryn Gadbois Gary Gearin Christina R Gearin Georgia Giannoukos Tina Goode Joseph Graham Edward Grandbois Sharleen Grewal Kunsang Gyaltsen Nabil Hafez Birhane Hagos Jennifer Hall Charlotte Henson Andrew Hollinger Tracey Honan Monika D Huard Leanne Hughes Brian Hurhula M Erii Husby Asha Kamat Ben Kanga Seva Kashin Dmitry Khazanovich Peter Kisner Krista Lance Marcia Lara William Lee Niall Lennon Frances Letendre Rosie LeVine Alex Lipovsky Xiaohong Liu Jinlei Liu Shangtao Liu Tashi Lokyitsang Yeshi Lokyitsang Rakela Lubonja Annie Lui Pen MacDonald Vasilia Magnisalis Kebede Maru Charles Matthews William McCusker Susan McDonough Teena Mehta James Meldrim Louis Meneus Oana Mihai Atanas Mihalev Tanya Mihova Rachel Mittelman Valentine Mlenga Anna Montmayeur Leonidas Mulrain Adam Navidi Jerome Naylor Tamrat Negash Thu Nguyen Nga Nguyen Robert Nicol Choe Norbu Nyima Norbu Nathaniel Novod Barry O'Neill Sahal Osman Eva Markiewicz Otero L Oyono Christopher Patti Pema Phunkhang Fritz Pierre Margaret Priest Sujaa Raghuraman Filip Rege Rebecca Reyes Cecil Rise Peter Rogov Keenan Ross Elizabeth Ryan Sampath Settipalli Terry Shea Ngawang Sherpa Lu Shi Diana Shih Todd Sparrow Jessica Spaulding John Stalker Nicole Stange-Thomann Sharon Stavropoulos Catherine Stone Christopher Strader Senait Tesfaye Talene Thomson Yama Thoulutsang Dawa Thoulutsang Kerri Topham Ira Topping Tsamla Tsamla Helen Vassiliev Andy Vo Tsering Wangchuk Tsering Wangdi Michael Weiand Jane Wilkinson Adam Wilson Shailendra Yadav Geneva Young Qing Yu Lisa Zembek Danni Zhong Andrew Zimmer Zac Zwirko David B Jaffe Pablo Alvarez Will Brockman Jonathan Butler CheeWhye Chin Sante Gnerre Manfred Grabherr Michael Kleber Evan Mauceli Iain MacCallum

Nature 2007 Nov;450(7167):203-18

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.

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http://dx.doi.org/10.1038/nature06341DOI Listing
November 2007

miRBase: the microRNA sequence database.

Methods Mol Biol 2006 ;342:129-38

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.

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http://dx.doi.org/10.1385/1-59745-123-1:129DOI Listing
September 2006

miRBase: microRNA sequences, targets and gene nomenclature.

Nucleic Acids Res 2006 Jan;34(Database issue):D140-4

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

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http://dx.doi.org/10.1093/nar/gkj112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347474PMC
January 2006

Pfam: clans, web tools and services.

Nucleic Acids Res 2006 Jan;34(Database issue):D247-51

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

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http://dx.doi.org/10.1093/nar/gkj149DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347511PMC
January 2006

C. elegans noncoding RNA genes.

WormBook 2005 Jun 25:1-7. Epub 2005 Jun 25.

Howard Hughes Medical Institute and Department of Genetics, Washington University, St. Louis, MO 63108, USA.

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http://www.wormbook.org/chapters/www_noncodingRNA/noncodingR
Publisher Site
http://dx.doi.org/10.1895/wormbook.1.1.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4781554PMC
June 2005

Annotating non-coding RNAs with Rfam.

Curr Protoc Bioinformatics 2005 Apr;Chapter 12:Unit 12.5

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

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April 2005

RALEE--RNA ALignment editor in Emacs.

Bioinformatics 2005 Jan 17;21(2):257-9. Epub 2004 Sep 17.

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

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http://dx.doi.org/10.1093/bioinformatics/bth489DOI Listing
January 2005

Rfam: annotating non-coding RNAs in complete genomes.

Nucleic Acids Res 2005 Jan;33(Database issue):D121-4

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

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http://dx.doi.org/10.1093/nar/gki081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC540035PMC
January 2005

Structural relatedness of plant food allergens with specific reference to cross-reactive allergens: an in silico analysis.

J Allergy Clin Immunol 2005 Jan;115(1):163-70

Institute of Food Research, Norwich, Cambridge, United Kingdom.

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http://dx.doi.org/10.1016/j.jaci.2004.10.026DOI Listing
January 2005

Identification of mammalian microRNA host genes and transcription units.

Genome Res 2004 Oct 13;14(10A):1902-10. Epub 2004 Sep 13.

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

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http://dx.doi.org/10.1101/gr.2722704DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC524413PMC
October 2004

The microRNA Registry.

Nucleic Acids Res 2004 Jan;32(Database issue):D109-11

The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 9SA, UK.

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http://dx.doi.org/10.1093/nar/gkh023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC308757PMC
January 2004

The Pfam protein families database.

Nucleic Acids Res 2004 Jan;32(Database issue):D138-41

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

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http://dx.doi.org/10.1093/nar/gkh121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC308855PMC
January 2004

Identifying protein domains with the Pfam database.

Curr Protoc Bioinformatics 2003 May;Chapter 2:Unit 2.5

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

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http://dx.doi.org/10.1002/0471250953.bi0205s01DOI Listing
May 2003

Rfam: an RNA family database.

Nucleic Acids Res 2003 Jan;31(1):439-41

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

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http://dx.doi.org/10.1093/nar/gkg006DOI Listing
January 2003

The use of structure information to increase alignment accuracy does not aid homologue detection with profile HMMs.

Bioinformatics 2002 Sep;18(9):1243-9

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

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September 2002

The Pfam protein families database.

Nucleic Acids Res 2002 Jan;30(1):276-80

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

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http://dx.doi.org/10.1093/nar/30.1.276DOI Listing
January 2002