Publications by authors named "Mark Yandell"

100Publications

A copy number variant is associated with a spectrum of pigmentation patterns in the rock pigeon (Columba livia).

PLoS Genet 2020 05 20;16(5):e1008274. Epub 2020 May 20.

School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1008274DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7239393PMC
May 2020

Discovery of Novel Conotoxin Candidates Using Machine Learning.

Toxins (Basel) 2018 12 1;10(12). Epub 2018 Dec 1.

Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA.

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http://dx.doi.org/10.3390/toxins10120503DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6315676PMC
December 2018

Predicting gene structure changes resulting from genetic variants via exon definition features.

Bioinformatics 2018 11;34(21):3616-3623

Program in Computational Biology and Bioinformatics, Duke University, Durham, NC, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty324DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6198862PMC
November 2018

Mutations Are Associated With Primary Ovarian Insufficiency in Women.

J Endocr Soc 2017 Mar 7;1(3):162-173. Epub 2017 Feb 7.

Division of Endocrinology, Metabolism and Diabetes.

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http://dx.doi.org/10.1210/js.2016-1014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5650244PMC
March 2017

Settling the score: variant prioritization and Mendelian disease.

Nat Rev Genet 2017 10 14;18(10):599-612. Epub 2017 Aug 14.

Department of Human Genetics, Eccles Institute of Human Genetics, School of Medicine, University of Utah, 15 S 2030 E, Salt Lake City, Utah 84112, USA.

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http://dx.doi.org/10.1038/nrg.2017.52DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5935497PMC
October 2017

The Venom Repertoire of Conus gloriamaris (Chemnitz, 1777), the Glory of the Sea.

Mar Drugs 2017 May 20;15(5). Epub 2017 May 20.

Department of Biology, University of Utah, Salt Lake City 84112, UT, USA.

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http://dx.doi.org/10.3390/md15050145DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5450551PMC
May 2017

Emergence of a Viral RNA Polymerase Variant during Gene Copy Number Amplification Promotes Rapid Evolution of Vaccinia Virus.

J Virol 2017 02 31;91(4). Epub 2017 Jan 31.

Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA

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http://dx.doi.org/10.1128/JVI.01428-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5286894PMC
February 2017

VARPRISM: incorporating variant prioritization in tests of de novo mutation association.

Genome Med 2016 08 25;8(1):91. Epub 2016 Aug 25.

Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA.

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http://dx.doi.org/10.1186/s13073-016-0341-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4997702PMC
August 2016

Venom Insulins of Cone Snails Diversify Rapidly and Track Prey Taxa.

Mol Biol Evol 2016 11 14;33(11):2924-2934. Epub 2016 Aug 14.

Department of Biology, University of Utah, Salt Lake City, UT.

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http://dx.doi.org/10.1093/molbev/msw174DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5062327PMC
November 2016

The draft genome sequence and annotation of the desert woodrat Neotoma lepida.

Genom Data 2016 Sep 23;9:58-9. Epub 2016 Jun 23.

Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA.

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http://dx.doi.org/10.1016/j.gdata.2016.06.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4927542PMC
September 2016

Antimicrobial Functions of Lactoferrin Promote Genetic Conflicts in Ancient Primates and Modern Humans.

PLoS Genet 2016 05 20;12(5):e1006063. Epub 2016 May 20.

Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1006063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4874600PMC
May 2016

Unbiased Detection of Respiratory Viruses by Use of RNA Sequencing-Based Metagenomics: a Systematic Comparison to a Commercial PCR Panel.

J Clin Microbiol 2016 Apr 27;54(4):1000-7. Epub 2016 Jan 27.

University of Utah School of Medicine, Department of Pathology, Salt Lake City, Utah, USA ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah, USA

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http://dx.doi.org/10.1128/JCM.03060-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4809917PMC
April 2016

An Introduction to Genome Annotation.

Curr Protoc Bioinformatics 2015 Dec 17;52:4.1.1-4.1.17. Epub 2015 Dec 17.

Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah.

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http://dx.doi.org/10.1002/0471250953.bi0401s52DOI Listing
December 2015

Wham: Identifying Structural Variants of Biological Consequence.

PLoS Comput Biol 2015 Dec 1;11(12):e1004572. Epub 2015 Dec 1.

Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004572DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4666669PMC
December 2015

Hormone-like peptides in the venoms of marine cone snails.

Gen Comp Endocrinol 2017 04 22;244:11-18. Epub 2015 Aug 22.

Department of Biology, University of Utah, Salt Lake City, UT 84112, USA; Department of Biology, Copenhagen Biocenter, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark. Electronic address:

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http://dx.doi.org/10.1016/j.ygcen.2015.07.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4762756PMC
April 2017

Shared Segment Analysis and Next-Generation Sequencing Implicates the Retinoic Acid Signaling Pathway in Total Anomalous Pulmonary Venous Return (TAPVR).

PLoS One 2015 29;10(6):e0131514. Epub 2015 Jun 29.

Department of Pediatrics (Division of Cardiology), University of Utah School of Medicine, Salt Lake City, UT, United States of America; Clinical Genetic Institute, Intermountain Healthcare, Salt Lake City, UT, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0131514PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4485409PMC
March 2016

Muscle stem cells contribute to myofibres in sedentary adult mice.

Nat Commun 2015 May 14;6:7087. Epub 2015 May 14.

Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112 USA.

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http://dx.doi.org/10.1038/ncomms8087DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4435732PMC
May 2015

DisAp-dependent striated fiber elongation is required to organize ciliary arrays.

J Cell Biol 2014 Dec;207(6):705-15

Anschutz Medical Campus, Department of Cell and Developmental Biology, University of Colorado, Aurora, CO 80045

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http://dx.doi.org/10.1083/jcb.201409123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4274257PMC
December 2014

Genome Annotation and Curation Using MAKER and MAKER-P.

Curr Protoc Bioinformatics 2014 Dec 12;48:4.11.1-39. Epub 2014 Dec 12.

Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah.

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http://dx.doi.org/10.1002/0471250953.bi0411s48DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286374PMC
December 2014

Automated update, revision, and quality control of the maize genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes.

Plant Physiol 2015 Jan 10;167(1):25-39. Epub 2014 Nov 10.

The Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.)

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http://dx.doi.org/10.1104/pp.114.245027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4280997PMC
January 2015

Transiently active Wnt/β-catenin signaling is not required but must be silenced for stem cell function during muscle regeneration.

Stem Cell Reports 2014 Sep 31;3(3):475-88. Epub 2014 Jul 31.

Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stemcr.2014.06.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4266007PMC
September 2014

Gibbon genome and the fast karyotype evolution of small apes.

Nature 2014 Sep;513(7517):195-201

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1038/nature13679DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4249732PMC
September 2014

Using VAAST to Identify Disease-Associated Variants in Next-Generation Sequencing Data.

Curr Protoc Hum Genet 2014 Apr 24;81:6.14.1-25. Epub 2014 Apr 24.

Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah; These authors collectively are the first authors of the unit.

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http://dx.doi.org/10.1002/0471142905.hg0614s81DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4137768PMC
April 2014

Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families.

Am J Hum Genet 2014 Apr;94(4):599-610

Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Utah Science, Technology, and Research Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2014.03.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3980410PMC
April 2014

TBX3 regulates splicing in vivo: a novel molecular mechanism for Ulnar-mammary syndrome.

PLoS Genet 2014 Mar 27;10(3):e1004247. Epub 2014 Mar 27.

Department of Pediatrics, University of Utah, Salt Lake City, Utah, United States of America; Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, Utah, United States of America; Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America; Molecular Medicine Program, University of Utah, Salt Lake City, Utah, United States of America; Weis Center for Research, Geisinger Clinic, Danville, Pennsylvania, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1004247DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3967948PMC
March 2014

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.

Authors:
Catherine A Brownstein Alan H Beggs Nils Homer Barry Merriman Timothy W Yu Katherine C Flannery Elizabeth T DeChene Meghan C Towne Sarah K Savage Emily N Price Ingrid A Holm Lovelace J Luquette Elaine Lyon Joseph Majzoub Peter Neupert David McCallie Peter Szolovits Huntington F Willard Nancy J Mendelsohn Renee Temme Richard S Finkel Sabrina W Yum Livija Medne Shamil R Sunyaev Ivan Adzhubey Christopher A Cassa Paul I W de Bakker Hatice Duzkale Piotr Dworzyński William Fairbrother Laurent Francioli Birgit H Funke Monica A Giovanni Robert E Handsaker Kasper Lage Matthew S Lebo Monkol Lek Ignaty Leshchiner Daniel G MacArthur Heather M McLaughlin Michael F Murray Tune H Pers Paz P Polak Soumya Raychaudhuri Heidi L Rehm Rachel Soemedi Nathan O Stitziel Sara Vestecka Jochen Supper Claudia Gugenmus Bernward Klocke Alexander Hahn Max Schubach Mortiz Menzel Saskia Biskup Peter Freisinger Mario Deng Martin Braun Sven Perner Richard J H Smith Janeen L Andorf Jian Huang Kelli Ryckman Val C Sheffield Edwin M Stone Thomas Bair E Ann Black-Ziegelbein Terry A Braun Benjamin Darbro Adam P DeLuca Diana L Kolbe Todd E Scheetz Aiden E Shearer Rama Sompallae Kai Wang Alexander G Bassuk Erik Edens Katherine Mathews Steven A Moore Oleg A Shchelochkov Pamela Trapane Aaron Bossler Colleen A Campbell Jonathan W Heusel Anne Kwitek Tara Maga Karin Panzer Thomas Wassink Douglas Van Daele Hela Azaiez Kevin Booth Nic Meyer Michael M Segal Marc S Williams Gerard Tromp Peter White Donald Corsmeier Sara Fitzgerald-Butt Gail Herman Devon Lamb-Thrush Kim L McBride David Newsom Christopher R Pierson Alexander T Rakowsky Aleš Maver Luca Lovrečić Anja Palandačić Borut Peterlin Ali Torkamani Anna Wedell Mikael Huss Andrey Alexeyenko Jessica M Lindvall Måns Magnusson Daniel Nilsson Henrik Stranneheim Fulya Taylan Christian Gilissen Alexander Hoischen Bregje van Bon Helger Yntema Marcel Nelen Weidong Zhang Jason Sager Lu Zhang Kathryn Blair Deniz Kural Michael Cariaso Greg G Lennon Asif Javed Saloni Agrawal Pauline C Ng Komal S Sandhu Shuba Krishna Vamsi Veeramachaneni Ofer Isakov Eran Halperin Eitan Friedman Noam Shomron Gustavo Glusman Jared C Roach Juan Caballero Hannah C Cox Denise Mauldin Seth A Ament Lee Rowen Daniel R Richards F Anthony San Lucas Manuel L Gonzalez-Garay C Thomas Caskey Yu Bai Ying Huang Fang Fang Yan Zhang Zhengyuan Wang Jorge Barrera Juan M Garcia-Lobo Domingo González-Lamuño Javier Llorca Maria C Rodriguez Ignacio Varela Martin G Reese Francisco M De La Vega Edward Kiruluta Michele Cargill Reece K Hart Jon M Sorenson Gholson J Lyon David A Stevenson Bruce E Bray Barry M Moore Karen Eilbeck Mark Yandell Hongyu Zhao Lin Hou Xiaowei Chen Xiting Yan Mengjie Chen Cong Li Can Yang Murat Gunel Peining Li Yong Kong Austin C Alexander Zayed I Albertyn Kym M Boycott Dennis E Bulman Paul M K Gordon A Micheil Innes Bartha M Knoppers Jacek Majewski Christian R Marshall Jillian S Parboosingh Sarah L Sawyer Mark E Samuels Jeremy Schwartzentruber Isaac S Kohane David M Margulies

Genome Biol 2014 Mar 25;15(3):R53. Epub 2014 Mar 25.

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http://dx.doi.org/10.1186/gb-2014-15-3-r53DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073084PMC
March 2014

Pharmacogenomics of 17-alpha hydroxyprogesterone caproate for recurrent preterm birth prevention.

Am J Obstet Gynecol 2014 Apr 1;210(4):321.e1-321.e21. Epub 2014 Mar 1.

Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT.

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http://dx.doi.org/10.1016/j.ajog.2014.01.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4266558PMC
April 2014

Autoimmunity due to RAG deficiency and estimated disease incidence in RAG1/2 mutations.

J Allergy Clin Immunol 2014 Mar 25;133(3):880-2.e10. Epub 2014 Jan 25.

Division of Immunology and the Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Mass; Pediatric Immunodeficiency Program, Division of Allergy, Massachusetts General Hospital for Children, Boston, Mass.

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http://dx.doi.org/10.1016/j.jaci.2013.11.038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4107635PMC
March 2014

In vivo determination of direct targets of the nonsense-mediated decay pathway in Drosophila.

G3 (Bethesda) 2014 Mar 20;4(3):485-96. Epub 2014 Mar 20.

Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112.

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http://dx.doi.org/10.1534/g3.113.009357DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3962487PMC
March 2014

VAAST 2.0: improved variant classification and disease-gene identification using a conservation-controlled amino acid substitution matrix.

Genet Epidemiol 2013 Sep 8;37(6):622-34. Epub 2013 Jul 8.

Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA.

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http://dx.doi.org/10.1002/gepi.21743DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791556PMC
September 2013

ImagePlane: an automated image analysis pipeline for high-throughput screens using the planarian Schmidtea mediterranea.

J Comput Biol 2013 Aug 3;20(8):583-92. Epub 2013 Jul 3.

Eccles Institute of Human Genetics, University of Utah, and School of Medicine, Salt Lake City, Utah 84112-5330, USA.

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http://dx.doi.org/10.1089/cmb.2013.0025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3728726PMC
August 2013

Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs.

PLoS Genet 2013 Apr 25;9(4):e1003470. Epub 2013 Apr 25.

Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1003470DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3636048PMC
April 2013

The African coelacanth genome provides insights into tetrapod evolution.

Nature 2013 Apr;496(7445):311-6

Molecular Genetics Program, Benaroya Research Institute, Seattle, Washington 98101, USA.

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http://dx.doi.org/10.1038/nature12027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3633110PMC
April 2013

Elucidation of the molecular envenomation strategy of the cone snail Conus geographus through transcriptome sequencing of its venom duct.

BMC Genomics 2012 Jun 28;13:284. Epub 2012 Jun 28.

Eccles institute of Human Genetics, University of Utah, and School of Medicine, Salt Lake City, UT 84112, USA.

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http://dx.doi.org/10.1186/1471-2164-13-284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3441800PMC
June 2012

A beginner's guide to eukaryotic genome annotation.

Nat Rev Genet 2012 Apr 18;13(5):329-42. Epub 2012 Apr 18.

Department of Human Genetics, Eccles Institute of Human Genetics, School of Medicine, University of Utah, Salt Lake City, Utah 84112-5330, USA.

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http://dx.doi.org/10.1038/nrg3174DOI Listing
April 2012

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects.

BMC Bioinformatics 2011 Dec 22;12:491. Epub 2011 Dec 22.

Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-12-491DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3280279PMC
December 2011

A probabilistic disease-gene finder for personal genomes.

Genome Res 2011 Sep 23;21(9):1529-42. Epub 2011 Jun 23.

Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah and School of Medicine, Salt Lake City, UT 84112, USA.

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http://dx.doi.org/10.1101/gr.123158.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166837PMC
September 2011

Characterization of the Conus bullatus genome and its venom-duct transcriptome.

BMC Genomics 2011 Jan 25;12:60. Epub 2011 Jan 25.

Eccles institute of Human Genetics, University of Utah, and School of Medicine, Salt Lake City, UT 84112, USA.

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http://dx.doi.org/10.1186/1471-2164-12-60DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3040727PMC
January 2011

Quantitative measures for the management and comparison of annotated genomes.

BMC Bioinformatics 2009 Feb 23;10:67. Epub 2009 Feb 23.

Department of Human genetics, Eccles Institute of Human Genetics, University of Utah and School of Medicine, Salt Lake City, UT, USA.

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http://dx.doi.org/10.1186/1471-2105-10-67DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2653490PMC
February 2009

Genome-wide analysis of human disease alleles reveals that their locations are correlated in paralogous proteins.

PLoS Comput Biol 2008 Nov 7;4(11):e1000218. Epub 2008 Nov 7.

Eccles Institute of Human Genetics, University of Utah and School of Medicine, Salt Lake City, Utah, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1000218DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2565504PMC
November 2008

Improved repeat identification and masking in Dipterans.

Gene 2007 Mar 12;389(1):1-9. Epub 2006 Oct 12.

Department of Biology, San Francisco State University, San Francisco, CA, United States.

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http://dx.doi.org/10.1016/j.gene.2006.09.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1945102PMC
March 2007