James M Sikela

James M Sikela

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James M Sikela

James M Sikela

Publications by authors named "James M Sikela"

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A Third Linear Association Between Olduvai (DUF1220) Copy Number and Severity of the Classic Symptoms of Inherited Autism.

Am J Psychiatry 2019 Aug 15;176(8):643-650. Epub 2019 Feb 15.

The Department of Biochemistry and Molecular Genetics, Human Medical Genetics and Genomics Program and Neuroscience Program, University of Colorado School of Medicine, Aurora (Davis, Heft, Sikela); the McLaughlin Centre and the Department of Molecular Genetics, University of Toronto, and the Centre for Applied Genomics and Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto (Scherer).

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http://dx.doi.org/10.1176/appi.ajp.2018.18080993DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6675654PMC
August 2019

Paired involvement of human-specific Olduvai domains and NOTCH2NL genes in human brain evolution.

Hum Genet 2019 Jul 13;138(7):715-721. Epub 2019 May 13.

Department of Biochemistry and Molecular Genetics, Human Medical Genetics and Genomics Program and Neuroscience Program, University of Colorado School of Medicine, Aurora, CO, 80045, USA.

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http://dx.doi.org/10.1007/s00439-019-02018-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6611739PMC
July 2019

Changing the name of the NBPF/DUF1220 domain to the Olduvai domain.

F1000Res 2017 28;6:2185. Epub 2017 Dec 28.

Department of Biomedical Molecular Biology, Ghent University, Ghent, 9052, Belgium.

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https://f1000research.com/articles/6-2185/v2
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http://dx.doi.org/10.12688/f1000research.13586.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5773923.2PMC
December 2017

High resolution measurement of DUF1220 domain copy number from whole genome sequence data.

BMC Genomics 2017 Aug 14;18(1):614. Epub 2017 Aug 14.

Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA.

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http://dx.doi.org/10.1186/s12864-017-3976-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5556342PMC
August 2017

Human evolutionary genomics and the search for the genes that made us human.

Authors:
James M Sikela

Pac Symp Biocomput 2015 :479-81

Department of Biochemistry and Molecular Genetics, Human Medical Genetics and Neuroscience Programs, University of Colorado School of Medicine, Aurora CO 80045, USA.

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April 2016

DUF1220 copy number is linearly associated with increased cognitive function as measured by total IQ and mathematical aptitude scores.

Hum Genet 2015 Jan 7;134(1):67-75. Epub 2014 Oct 7.

Department of Biochemistry and Molecular Genetics and Human Medical Genetics, Medical Scientist Training and Neuroscience Programs, University of Colorado School of Medicine, Anschutz Medical Campus, RC1-S, L18-10125, 12801 East 17th Ave, Mailstop 8101, P.O. Box 6511, Aurora, CO, 80045, USA.

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http://dx.doi.org/10.1007/s00439-014-1489-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5898241PMC
January 2015

Mode of genetic inheritance modifies the association of head circumference and autism-related symptoms: a cross-sectional study.

PLoS One 2013 18;8(9):e74940. Epub 2013 Sep 18.

Department of Biochemistry and Molecular Genetics & Human Medical Genetics & Neuroscience Programs, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0074940PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3776732PMC
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

Finding and mapping new genes faster than ever: revisited.

Authors:
James M Sikela

Genetics 2014 Aug;197(4):1063-7

Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045-0508

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http://dx.doi.org/10.1534/genetics.114.165373DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4125383PMC
August 2014

The case for DUF1220 domain dosage as a primary contributor to anthropoid brain expansion.

Front Hum Neurosci 2014 24;8:427. Epub 2014 Jun 24.

Department of Biochemistry and Molecular Genetics and Human Medical Genetics and Neuroscience Programs, University of Colorado School of Medicine, Anschutz Medical Campus Aurora, CO, USA.

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http://dx.doi.org/10.3389/fnhum.2014.00427DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4067907PMC
July 2014

Exome sequencing and arrayCGH detection of gene sequence and copy number variation between ILS and ISS mouse strains.

Mamm Genome 2014 Jun 20;25(5-6):235-43. Epub 2014 Feb 20.

Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO, 80045, USA,

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http://dx.doi.org/10.1007/s00335-014-9502-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5512554PMC
June 2014

Finished sequence and assembly of the DUF1220-rich 1q21 region using a haploid human genome.

BMC Genomics 2014 May 20;15:387. Epub 2014 May 20.

Department of Biochemistry and Molecular Genetics, Human Medical Genetics and Neuroscience Programs, University of Colorado School of Medicine, 12801 E, 17th Avenue, Aurora, CO 80045, USA.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-15-387DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053653PMC
May 2014

DUF1220 dosage is linearly associated with increasing severity of the three primary symptoms of autism.

PLoS Genet 2014 Mar 20;10(3):e1004241. Epub 2014 Mar 20.

Department of Biochemistry & Molecular Genetics, Human Medical Genetics and Genomics Program & Neuroscience Program, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1004241DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3961203PMC
March 2014

Evolution of genetic and genomic features unique to the human lineage.

Nat Rev Genet 2012 Dec;13(12):853-66

Department of Biochemistry and Molecular Genetics, Human Medical Genetics and Neuroscience Programs, University of Colorado School of Medicine, Aurora, Colorado 80045, USA.

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http://www.nature.com/articles/nrg3336
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http://dx.doi.org/10.1038/nrg3336DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4097811PMC
December 2012

DUF1220-domain copy number implicated in human brain-size pathology and evolution.

Am J Hum Genet 2012 Sep 16;91(3):444-54. Epub 2012 Aug 16.

Department of Biochemistry and Molecular Genetics and Human Medical Genetics and Neuroscience Programs, University of Colorado School of Medicine, Aurora, CO 80045, USA.

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http://dx.doi.org/10.1016/j.ajhg.2012.07.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511999PMC
September 2012

Evolutionary history and genome organization of DUF1220 protein domains.

G3 (Bethesda) 2012 Sep 1;2(9):977-86. Epub 2012 Sep 1.

Department of Biochemistry and Molecular Genetics, Human Medical Genetics Program, University of Colorado School of Medicine, Aurora, Colorado 80045, USA.

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http://dx.doi.org/10.1534/g3.112.003061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3429928PMC
September 2012

The ethics of using transgenic non-human primates to study what makes us human.

Nat Rev Genet 2010 09;11(9):658-62

Department of Psychiatry and Center for Bioethics and Humanities, School of Medicine, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado 80045, USA.

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http://dx.doi.org/10.1038/nrg2864DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2995325PMC
September 2010

A survey of analysis software for array-comparative genomic hybridisation studies to detect copy number variation.

Hum Genomics 2010 Aug;4(6):421-7

Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3525224PMC
August 2010

Hominoid lineage specific amplification of low-copy repeats on 22q11.2 (LCR22s) associated with velo-cardio-facial/digeorge syndrome.

Hum Mol Genet 2007 Nov 3;16(21):2560-71. Epub 2007 Aug 3.

Department of Molecular Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA. mbabcock@aecom

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http://dx.doi.org/10.1093/hmg/ddm197DOI Listing
November 2007

Gene copy number variation spanning 60 million years of human and primate evolution.

Genome Res 2007 Sep 31;17(9):1266-77. Epub 2007 Jul 31.

Human Medical Genetics Program, University of Colorado at Denver and Health Sciences Center, Aurora, Colorado 80045, USA

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http://dx.doi.org/10.1101/gr.6557307DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1950895PMC
September 2007

Evolutionary and biomedical insights from the rhesus macaque genome.

Authors:
Richard A Gibbs Jeffrey Rogers Michael G Katze Roger Bumgarner George M Weinstock Elaine R Mardis Karin A Remington Robert L Strausberg J Craig Venter Richard K Wilson Mark A Batzer Carlos D Bustamante Evan E Eichler Matthew W Hahn Ross C Hardison Kateryna D Makova Webb Miller Aleksandar Milosavljevic Robert E Palermo Adam Siepel James M Sikela Tony Attaway Stephanie Bell Kelly E Bernard Christian J Buhay Mimi N Chandrabose Marvin Dao Clay Davis Kimberly D Delehaunty Yan Ding Huyen H Dinh Shannon Dugan-Rocha Lucinda A Fulton Ramatu Ayiesha Gabisi Toni T Garner Jennifer Godfrey Alicia C Hawes Judith Hernandez Sandra Hines Michael Holder Jennifer Hume Shalini N Jhangiani Vandita Joshi Ziad Mohid Khan Ewen F Kirkness Andrew Cree R Gerald Fowler Sandra Lee Lora R Lewis Zhangwan Li Yih-Shin Liu Stephanie M Moore Donna Muzny Lynne V Nazareth Dinh Ngoc Ngo Geoffrey O Okwuonu Grace Pai David Parker Heidie A Paul Cynthia Pfannkoch Craig S Pohl Yu-Hui Rogers San Juana Ruiz Aniko Sabo Jireh Santibanez Brian W Schneider Scott M Smith Erica Sodergren Amanda F Svatek Teresa R Utterback Selina Vattathil Wesley Warren Courtney Sherell White Asif T Chinwalla Yucheng Feng Aaron L Halpern Ladeana W Hillier Xiaoqiu Huang Pat Minx Joanne O Nelson Kymberlie H Pepin Xiang Qin Granger G Sutton Eli Venter Brian P Walenz John W Wallis Kim C Worley Shiaw-Pyng Yang Steven M Jones Marco A Marra Mariano Rocchi Jacqueline E Schein Robert Baertsch Laura Clarke Miklós Csürös Jarret Glasscock R Alan Harris Paul Havlak Andrew R Jackson Huaiyang Jiang Yue Liu David N Messina Yufeng Shen Henry Xing-Zhi Song Todd Wylie Lan Zhang Ewan Birney Kyudong Han Miriam K Konkel Jungnam Lee Arian F A Smit Brygg Ullmer Hui Wang Jinchuan Xing Richard Burhans Ze Cheng John E Karro Jian Ma Brian Raney Xinwei She Michael J Cox Jeffery P Demuth Laura J Dumas Sang-Gook Han Janet Hopkins Anis Karimpour-Fard Young H Kim Jonathan R Pollack Tomas Vinar Charles Addo-Quaye Jeremiah Degenhardt Alexandra Denby Melissa J Hubisz Amit Indap Carolin Kosiol Bruce T Lahn Heather A Lawson Alison Marklein Rasmus Nielsen Eric J Vallender Andrew G Clark Betsy Ferguson Ryan D Hernandez Kashif Hirani Hildegard Kehrer-Sawatzki Jessica Kolb Shobha Patil Ling-Ling Pu Yanru Ren David Glenn Smith David A Wheeler Ian Schenck Edward V Ball Rui Chen David N Cooper Belinda Giardine Fan Hsu W James Kent Arthur Lesk David L Nelson William E O'brien Kay Prüfer Peter D Stenson James C Wallace Hui Ke Xiao-Ming Liu Peng Wang Andy Peng Xiang Fan Yang Galt P Barber David Haussler Donna Karolchik Andy D Kern Robert M Kuhn Kayla E Smith Ann S Zwieg

Science 2007 Apr;316(5822):222-34

Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.1126/science.1139247DOI Listing
April 2007

Human lineage-specific amplification, selection, and neuronal expression of DUF1220 domains.

Science 2006 Sep;313(5791):1304-7

Human Medical Genetics, University of Colorado at Denver and Health Sciences Center, Aurora, CO 80045, USA.

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http://dx.doi.org/10.1126/science.1127980DOI Listing
September 2006

The jewels of our genome: the search for the genomic changes underlying the evolutionarily unique capacities of the human brain.

Authors:
James M Sikela

PLoS Genet 2006 May;2(5):e80

Human Medical Genetics Program, Department of Pharmacology, University of Colorado at Denver and Health Sciences Center, USA.

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http://dx.doi.org/10.1371/journal.pgen.0020080DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1464830PMC
May 2006

Expression profiling identifies novel candidate genes for ethanol sensitivity QTLs.

Mamm Genome 2006 Feb 7;17(2):147-56. Epub 2006 Feb 7.

Department of Pharmacology, University of Colorado at Denver and Health Sciences Center, Aurora, Colorado 80045, USA.

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http://dx.doi.org/10.1007/s00335-005-0065-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2677977PMC
February 2006

Norepinephrine transporter: a candidate gene for initial ethanol sensitivity in inbred long-sleep and short-sleep mice.

Alcohol Clin Exp Res 2005 Oct;29(10):1759-68

Department of Pharmacology, University of Colorado Health Sciences Center, Aurora, Colorado, USA.

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http://dx.doi.org/10.1097/01.alc.0000183009.57805.a6DOI Listing
October 2005

Cerebellar gene expression profiling and eQTL analysis in inbred mouse strains selected for ethanol sensitivity.

Alcohol Clin Exp Res 2005 Sep;29(9):1568-79

Department of Pharmacology, University of Colorado at Denver and Health Sciences Center, Aurora, CO 80045-0508, USA.

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http://dx.doi.org/10.1097/01.alc.0000179376.27331.acDOI Listing
September 2005

Ethanol-responsive brain region expression networks: implications for behavioral responses to acute ethanol in DBA/2J versus C57BL/6J mice.

J Neurosci 2005 Mar;25(9):2255-66

Department of Pharmacology/Toxicology and the Center for Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23298, USA.

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http://dx.doi.org/10.1523/JNEUROSCI.4372-04.2005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6726093PMC
March 2005

The nature and identification of quantitative trait loci: a community's view.

Nat Rev Genet 2003 Nov;4(11):911-6

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http://dx.doi.org/10.1038/nrg1206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063446PMC
November 2003

Genomic approaches to the genetics of alcoholism.

Alcohol Res Health 2002 ;26(3):181-92

Department of Pharmacology, Human Medical Genetics Program, University of Colorado Health Sciences Center, Denver, Colorado, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6683845PMC
September 2003

Investigation of DUSP8 and CALCA in alcohol dependence.

Addict Biol 2003 Sep;8(3):305-12

Department of Preventive Medicine and Biometrics, University of Colorado Health Sciences Center, Denver, Colorado 80262, USA.

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http://dx.doi.org/10.1080/13556210310001602211DOI Listing
September 2003

In silico discovery of gene-coding variants in murine quantitative trait loci using strain-specific genome sequence databases.

Genome Biol 2002 27;3(12):RESEARCH0078. Epub 2002 Nov 27.

Department of Pharmacology and Human Medical Genetics Program, University of Colorado Health Sciences Center, Denver CO 80262, USA.

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http://link.springer.com/content/pdf/10.1186/gb-2002-3-12-re
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC151180PMC
http://dx.doi.org/10.1186/gb-2002-3-12-research0078DOI Listing
June 2003

Variants of kappa-opioid receptor gene and mRNA in alcohol-preferring and alcohol-avoiding mice.

Alcohol 2003 Jan;29(1):39-49

Laboratory of Neurobehavior Genetics, The Nathan S. Kline Institute for Psychiatric Research, 140 Old Orangeburg Road, Orangeburg, NY 10962, USA.

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http://dx.doi.org/10.1016/s0741-8329(02)00322-1DOI Listing
January 2003

Fine mapping of polymorphic alcohol-related quantitative trait loci candidate genes using interval-specific congenic recombinant mice.

Alcohol Clin Exp Res 2002 Nov;26(11):1603-8

Department of Pharmacology and Human Medical Genetics Program, University of Colorado Health Sciences Center, Denver 80262, USA.

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http://dx.doi.org/10.1097/01.ALC.0000036921.33411.67DOI Listing
November 2002

Human alcoholism studies of genes identified through mouse quantitative trait locus analysis.

Addict Biol 2002 Oct;7(4):365-71

Department of Pharmacology and Human Medical Genetics Program, University of Colorado Health Sciences Center, 4200 East Ninth Avenue C236, Denver, CO 80262, USA.

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http://dx.doi.org/10.1080/1355621021000005496DOI Listing
October 2002

Quantitative trait loci affecting initial sensitivity and acute functional tolerance to ethanol-induced ataxia and brain cAMP signaling in BXD recombinant inbred mice.

J Pharmacol Exp Ther 2002 Sep;302(3):1238-45

Department of Pharmacology, University of Colorado Health Sciences Center, 4200 East Ninth Avenue, Denver, CO 80262, USA.

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http://dx.doi.org/10.1124/jpet.302.3.1238DOI Listing
September 2002

Gene coding variant in Cas1 between the C57BL/6J and DBA/2J inbred mouse strains: linkage to a QTL for ethanol-induced locomotor activation.

Alcohol Clin Exp Res 2002 Jan;26(1):1-7

Department of Pharmacology, University of Colorado Health Sciences Center, Denver, Colorado, USA.

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January 2002