Ali Torkamani

Ali Torkamani

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Ali Torkamani

Publications by authors named "Ali Torkamani"

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Artificial intelligence in clinical and genomic diagnostics.

Genome Med 2019 Nov 19;11(1):70. Epub 2019 Nov 19.

The Scripps Translational Science Institute, The Scripps Research Institute, 3344 North Torrey Pines Court Suite 300, La Jolla, CA, 92037, USA.

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http://dx.doi.org/10.1186/s13073-019-0689-8DOI Listing
November 2019

Ranking of non-coding pathogenic variants and putative essential regions of the human genome.

Nat Commun 2019 Nov 20;10(1):5241. Epub 2019 Nov 20.

Scripps Research Translational Institute, La Jolla, CA, 92037, USA.

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http://dx.doi.org/10.1038/s41467-019-13212-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6868241PMC
November 2019

Polygenic Risk Scores Expand to Obesity.

Cell 2019 Apr;177(3):518-520

Scripps Research Translational Institute, La Jolla, CA 92037, USA; Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674193038
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http://dx.doi.org/10.1016/j.cell.2019.03.051DOI Listing
April 2019

Immunogenetic factors driving formation of ultralong VH CDR3 in Bos taurus antibodies.

Cell Mol Immunol 2019 01 4;16(1):53-64. Epub 2017 Dec 4.

Department of Molecular Medicine, The Scripps Research Institute, 92037, La Jolla, CA, USA.

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http://dx.doi.org/10.1038/cmi.2017.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6318308PMC
January 2019

A primer on deep learning in genomics.

Nat Genet 2019 01 26;51(1):12-18. Epub 2018 Nov 26.

Scripps Research Translational Institute, La Jolla, CA, USA.

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http://www.nature.com/articles/s41588-018-0295-5
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http://dx.doi.org/10.1038/s41588-018-0295-5DOI Listing
January 2019

Physician Communication of Genomic Results in a Diagnostic Odyssey Case Series.

Pediatrics 2019 01;143(Suppl 1):S44-S53

Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA

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http://pediatrics.aappublications.org/lookup/doi/10.1542/ped
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http://dx.doi.org/10.1542/peds.2018-1099IDOI Listing
January 2019

Drilling for Insight: Forecasting Phenotype from Genotype.

Authors:
Ali Torkamani

Trends Genet 2018 11 13;34(11):821-822. Epub 2018 Sep 13.

Scripps Research Translational Institute, La Jolla, California, 92037, USA; Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92037, USA; mygenerank.scripps.edu. Electronic address:

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http://dx.doi.org/10.1016/j.tig.2018.09.001DOI Listing
November 2018

The personal and clinical utility of polygenic risk scores.

Nat Rev Genet 2018 09;19(9):581-590

The Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA, USA.

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http://dx.doi.org/10.1038/s41576-018-0018-xDOI Listing
September 2018

Microdroplet PCR for Highly Multiplexed Targeted Bisulfite Sequencing.

Methods Mol Biol 2018 ;1708:333-348

Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA.

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http://dx.doi.org/10.1007/978-1-4939-7481-8_17DOI Listing
July 2018

When genomics goes digital.

Lancet 2018 06;391(10138):2405

Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1016/S0140-6736(18)31272-8DOI Listing
June 2018

Diverse reprogramming codes for neuronal identity.

Nature 2018 05 9;557(7705):375-380. Epub 2018 May 9.

Department of Molecular and Cellular Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA, USA.

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http://dx.doi.org/10.1038/s41586-018-0103-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6483730PMC
May 2018

Corrigendum: Molecular Autopsy for Sudden Death in the Young: Is Data Aggregation the Key?

Front Cardiovasc Med 2017 24;4:90. Epub 2018 Jan 24.

The Scripps Translational Science Institute, Scripps Health, The Scripps Research Institute, La Jolla, CA, United States.

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http://dx.doi.org/10.3389/fcvm.2017.00090DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5787692PMC
January 2018

Efficacy of the Autoimmune Protocol Diet for Inflammatory Bowel Disease.

Inflamm Bowel Dis 2017 11;23(11):2054-2060

*Division of Gastroenterology, Scripps Clinic, La Jolla, California; †Scripps Translational Science Institute, La Jolla, California; ‡Division of Cardiology, Scripps Clinic, La Jolla, California; §Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; ‖School of Exercise and Nutritional Sciences, San Diego State University, San Diego, California; and ¶Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California.

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http://dx.doi.org/10.1097/MIB.0000000000001221DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5647120PMC
November 2017

Molecular Autopsy for Sudden Death in the Young: Is Data Aggregation the Key?

Front Cardiovasc Med 2017 9;4:72. Epub 2017 Nov 9.

The Scripps Translational Science Institute, Scripps Health, The Scripps Research Institute, La Jolla, CA, United States.

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http://dx.doi.org/10.3389/fcvm.2017.00072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5694161PMC
November 2017

Mutation of WIF1: a potential novel cause of a Nail-Patella-like disorder.

Genet Med 2017 10 6;19(10):1179-1183. Epub 2017 Apr 6.

The Scripps Translational Science Institute, La Jolla, California, USA.

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http://dx.doi.org/10.1038/gim.2017.20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5629099PMC
October 2017

Assessment of circulating copy number variant detection for cancer screening.

PLoS One 2017 7;12(7):e0180647. Epub 2017 Jul 7.

The Scripps Translational Science Institute, La Jolla, CA, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0180647PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5501586PMC
October 2017

SG-ADVISER mtDNA: a web server for mitochondrial DNA annotation with data from 200 samples of a healthy aging cohort.

BMC Bioinformatics 2017 Aug 18;18(1):373. Epub 2017 Aug 18.

The Scripps Translational Science Institute, Scripps Health, and The Scripps Research Institute, La Jolla, CA, 92037, USA.

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http://dx.doi.org/10.1186/s12859-017-1778-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5563004PMC
August 2017

High-Definition Medicine.

Cell 2017 Aug;170(5):828-843

The Scripps Translational Science Institute, La Jolla, CA 92037, USA; Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1016/j.cell.2017.08.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5714316PMC
August 2017

Influence of donor age on induced pluripotent stem cells.

Nat Biotechnol 2017 Jan 12;35(1):69-74. Epub 2016 Dec 12.

The Scripps Translational Science Institute, Scripps Health and The Scripps Research Institute, La Jolla, California, USA.

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http://dx.doi.org/10.1038/nbt.3749DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5505172PMC
January 2017

Patient perspectives on whole-genome sequencing for undiagnosed diseases.

Per Med 2017 01 30;14(1):17-25. Epub 2016 Nov 30.

Scripps Translational Science Institute, Scripps Genomic Medicine, Scripps Health, La Jolla, CA, USA.

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http://dx.doi.org/10.2217/pme-2016-0050DOI Listing
January 2017

Liquid Biopsies for Cancer: Coming to a Patient near You.

J Clin Med 2017 Jan 4;6(1). Epub 2017 Jan 4.

Scripps Translational Science Institute/The Scripps Research Institute, 3344 North Torrey Pines Court, Suite 300, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.3390/jcm6010003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5294956PMC
January 2017

Postmortem Genetic Testing for Sudden Unexpected Death-Reply.

Authors:
Ali Torkamani

JAMA 2017 01;317(3):321

Scripps Translational Science Institute, La Jolla, California.

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http://dx.doi.org/10.1001/jama.2016.19277DOI Listing
January 2017

Erratum: Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.

Nat Commun 2016 10 10;7:13205. Epub 2016 Oct 10.

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http://dx.doi.org/10.1038/ncomms13205DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5062501PMC
October 2016

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.

Nat Commun 2016 08 23;7:12460. Epub 2016 Aug 23.

Sage Bionetworks, Seattle, Washington 98115, USA.

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http://dx.doi.org/10.1038/ncomms12460DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4996969PMC
August 2016

Whole-Genome Sequencing of a Healthy Aging Cohort.

Cell 2016 May 21;165(4):1002-11. Epub 2016 Apr 21.

The Scripps Translational Science Institute, Scripps Health, and The Scripps Research Institute, La Jolla, CA 92037, USA; Cypher Genomics, Inc., San Diego, CA 92121, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.03.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4860090PMC
May 2016

High-performance web services for querying gene and variant annotation.

Genome Biol 2016 05 6;17(1):91. Epub 2016 May 6.

Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.

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http://dx.doi.org/10.1186/s13059-016-0953-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4858870PMC
May 2016

Scripps Genome ADVISER: Annotation and Distributed Variant Interpretation SERver.

PLoS One 2015 23;10(2):e0116815. Epub 2015 Feb 23.

Scripps Health, La Jolla, CA 92037, United States of America; The Scripps Translational Science Institute, La Jolla, CA 92037, United States of America; The Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, United States of America; Cypher Genomics, Inc., La Jolla, CA 92037, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0116815PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4338027PMC
December 2015

ADCY5-related dyskinesia: Broader spectrum and genotype-phenotype correlations.

Neurology 2015 Dec 4;85(23):2026-35. Epub 2015 Nov 4.

From the Departments of Neurology (D.-H.C., E.S.B., M.Y.D., P.D.S., M.W., T.D.B.), Psychiatry and Behavioral Sciences (O.K., W.H.R.), Genome Sciences (H.A.S., E.E.E.), Medicine (F.M.H., L.M.A., W.H.R.), and Pathology (M.O.D.), and Howard Hughes Medical Institute (E.E.E.), University of Washington, Seattle; Inserm (A.M., D. Grabli, M.V., O.T., E.R.), U 1127; CNRS (A.M., D. Grabli, M.V., O.T., E.R.), UMR 7225; Sorbonne Université (A.M., D. Grabli, M.V., O.T., E.R.), UPMC Univ Paris 06, UMR S 1127; Institut du Cerveau et de la Moelle Épinière (A.M., D. Grabli, M.V., O.T., E.R.), ICM; Départements de Neurologie (A.M., B.D., D. Grabli, M.V., O.T., E.R.) et de Génétique (C.M.), Hôpital de la Pitié Salpêtrière, AP-HP, Paris, France; the Departments of Neurosciences and Pediatrics (J.R.F.), University of California, San Diego; Rady Childrens Hospital (J.R.F.), San Diego, CA; Tel-Aviv Brill Community Mental Health Center (A.G.), Tel Aviv Medical School, Israel; Service de Neuropédiatrie (D.D.), Hôpital Trousseau, AP-HP; Centre de Référence Mouvements Anormaux de l'Enfant à l'Adulte (D.D.); Centre des Déficiences Intellectuelles de Causes Rares (C.M.), Paris; Département de Neurologie (M.A., C.T.), Hôpital Civil de Strasbourg; Fédération de Médecine Translationnelle de Strasbourg (FMTS) (M.A., C.T.), Université de Strasbourg; Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) (M.A., C.T.), INSERM-U964/CNRS-UMR7104/Université de Strasbourg, Illkirch, France; Phoenix Children's Hospital (S.B.), AZ; CHU de Bordeaux (N.D.-P.), Explorations Fonctionnelles du Système Nerveux; Service de Neuropédiatrie (D. Gras), Hôpital Robert Debré, AP-HP, Paris, France; Department of Child Neurology (K.M.M.), Lucile Packard Children's Hospital, Stanford University, Palo Alto, CA; Johns Hopkins All Children's Hospital (S.W.), St. Petersburg, FL; The Scripps Translational Science Institute (A.T.), Scripps Health and The Scripps Research Institute, S

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http://dx.doi.org/10.1212/WNL.0000000000002058DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4676753PMC
December 2015

Symptom-driven idiopathic disease gene identification.

Genet Med 2015 Nov 15;17(11):859-65. Epub 2015 Jan 15.

Scripps Translational Science Institute, La Jolla, California, USA.

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http://dx.doi.org/10.1038/gim.2014.202DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4861313PMC
November 2015

Protein-protein interaction prediction by combined analysis of genomic and conservation information.

Genes Genet Syst 2014 ;89(6):259-72

Institute of Biochemistry and Biophysics, University of Tehran.

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http://dx.doi.org/10.1266/ggs.89.259DOI Listing
October 2015

SG-ADVISER CNV: copy-number variant annotation and interpretation.

Genet Med 2015 Sep 18;17(9):714-8. Epub 2014 Dec 18.

Scripps Health, La Jolla, California, USA.

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http://dx.doi.org/10.1038/gim.2014.180DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4886732PMC
September 2015

Digital medical tools and sensors.

JAMA 2015 Jan;313(4):353-4

The Scripps Translational Science Institute, La Jolla, California2Scripps Health, La Jolla, California3The Scripps Research Institute, La Jolla, California.

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http://dx.doi.org/10.1001/jama.2014.17125DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4751024PMC
January 2015

Sensitive, multiplex and direct quantification of RNA sequences using a modified RASL assay.

Nucleic Acids Res 2014 Aug 25;42(14):9146-57. Epub 2014 Jul 25.

Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA California Institute for Biomedical Research (Calibr), La Jolla, CA 92307, USA

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http://dx.doi.org/10.1093/nar/gku636DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4132746PMC
August 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

An application and empirical comparison of statistical analysis methods for associating rare variants to a complex phenotype.

Pac Symp Biocomput 2011 :76-87

The Scripps Translational Science Institute, 3344 North Torrey Pines Court, Suite 300, La Jolla, CA 92037, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5017238PMC
http://dx.doi.org/10.1142/9789814335058_0009DOI Listing
November 2013

Deep sequencing of the murine IgH repertoire reveals complex regulation of nonrandom V gene rearrangement frequencies.

J Immunol 2013 Sep 29;191(5):2393-402. Epub 2013 Jul 29.

Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.4049/jimmunol.1301279DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3778908PMC
September 2013

Tcra gene recombination is supported by a Tcra enhancer- and CTCF-dependent chromatin hub.

Proc Natl Acad Sci U S A 2012 Dec 19;109(50):E3493-502. Epub 2012 Nov 19.

Department of Immunology, Duke University Medical Center, Durham, NC 27710, USA.

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http://dx.doi.org/10.1073/pnas.1214131109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3528579PMC
December 2012

Clinical implications of human population differences in genome-wide rates of functional genotypes.

Front Genet 2012 1;3:211. Epub 2012 Nov 1.

The Scripps Translational Science La Jolla, CA, USA ; Scripps Health La Jolla, CA, USA ; Department of Molecular and Experimental Medicine, The Scripps Research Institute La Jolla, CA, USA.

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http://dx.doi.org/10.3389/fgene.2012.00211DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3485509PMC
November 2012

Noncoding transcription within the Igh distal V(H) region at PAIR elements affects the 3D structure of the Igh locus in pro-B cells.

Proc Natl Acad Sci U S A 2012 Oct 1;109(42):17004-9. Epub 2012 Oct 1.

Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1073/pnas.1208398109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3479473PMC
October 2012

Genetic structure of community acquired methicillin-resistant Staphylococcus aureus USA300.

BMC Genomics 2012 Sep 25;13:508. Epub 2012 Sep 25.

Scripps Genomic Medicine, Scripps Translational Science Institute, La Jolla, CA, USA.

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http://dx.doi.org/10.1186/1471-2164-13-508DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3598774PMC
September 2012

Plasma membrane associated transcription of cytoplasmic DNA.

Proc Natl Acad Sci U S A 2012 Jul 18;109(27):10827-31. Epub 2012 Jun 18.

Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1073/pnas.1208716109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390847PMC
July 2012

Skewed primary Igκ repertoire and V-J joining in C57BL/6 mice: implications for recombination accessibility and receptor editing.

J Immunol 2012 Mar 27;188(5):2305-15. Epub 2012 Jan 27.

Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.4049/jimmunol.1103484DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3288532PMC
March 2012

Application of microdroplet PCR for large-scale targeted bisulfite sequencing.

Genome Res 2011 Oct 14;21(10):1738-45. Epub 2011 Jul 14.

Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA.

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http://dx.doi.org/10.1101/gr.116863.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3202290PMC
October 2011

Annotating individual human genomes.

Genomics 2011 Oct 2;98(4):233-41. Epub 2011 Aug 2.

The Scripps Translational Science Institute, USA.

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http://dx.doi.org/10.1016/j.ygeno.2011.07.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4074010PMC
October 2011

Phenotype-information-phenotype cycle for deconvolution of combinatorial antibody libraries selected against complex systems.

Proc Natl Acad Sci U S A 2011 Aug 8;108(33):13456-61. Epub 2011 Aug 8.

Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1073/pnas.1111218108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158238PMC
August 2011

Design and simulation of a neutron source based on an electron linear accelerator for BNCT of skin melanoma.

Appl Radiat Isot 2011 May 18;69(5):749-55. Epub 2011 Feb 18.

Science and Research Branch, Islamic Azad University, Tehran, Iran.

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http://dx.doi.org/10.1016/j.apradiso.2011.01.035DOI Listing
May 2011

Ectopic B-cell clusters that infiltrate transplanted human kidneys are clonal.

Proc Natl Acad Sci U S A 2011 Apr 17;108(14):5560-5. Epub 2011 Mar 17.

Department of Molecular Biology and Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1073/pnas.1101148108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3078383PMC
April 2011

The importance of phase information for human genomics.

Nat Rev Genet 2011 03 8;12(3):215-23. Epub 2011 Feb 8.

The Scripps Translational Science Institute, 3344 North Torrey Pines Road, Suite 300, La Jolla, California 92037, USA.

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http://dx.doi.org/10.1038/nrg2950DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753045PMC
March 2011

Gene profile analysis of CD8(+) ILT3-Fc induced T suppressor cells.

Hum Immunol 2011 Feb 4;72(2):107-14. Epub 2010 Nov 4.

Department of Pathology and Cell Biology, Columbia University, New York, New York, USA.

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http://dx.doi.org/10.1016/j.humimm.2010.10.012DOI Listing
February 2011

BCL6 is required for differentiation of Ig-like transcript 3-Fc-induced CD8+ T suppressor cells.

J Immunol 2010 Nov 8;185(10):5714-22. Epub 2010 Oct 8.

Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA.

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http://dx.doi.org/10.4049/jimmunol.1001732DOI Listing
November 2010

Statistical analysis strategies for association studies involving rare variants.

Nat Rev Genet 2010 Nov 13;11(11):773-85. Epub 2010 Oct 13.

The Scripps Translational Science Institute, 3344 North Torrey Pines Court, Suite 300, La Jolla, California 92037, USA.

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http://dx.doi.org/10.1038/nrg2867DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3743540PMC
November 2010

Regulation of the B cell receptor repertoire and self-reactivity by BAFF.

J Immunol 2010 Oct 3;185(7):4128-36. Epub 2010 Sep 3.

Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.4049/jimmunol.1002176DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3263398PMC
October 2010

Kinase mutations in human disease: interpreting genotype-phenotype relationships.

Nat Rev Genet 2010 Jan;11(1):60-74

Robarts Research Institute and Departments of Medicine and Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario N6A 5C1, Canada.

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http://dx.doi.org/10.1038/nrg2707DOI Listing
January 2010

Pathway and network analysis with high-density allelic association data.

Methods Mol Biol 2009 ;563:289-301

University of California, San Diego, CA, USA.

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http://dx.doi.org/10.1007/978-1-60761-175-2_16DOI Listing
October 2009

Sequence and structure signatures of cancer mutation hotspots in protein kinases.

PLoS One 2009 Oct 16;4(10):e7485. Epub 2009 Oct 16.

Graduate Program for Bioinformatics, Center for Bioinformatics, The University of Kansas, Lawrence, Kansas, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2759519PMC
October 2009

Prestige centrality-based functional outlier detection in gene expression analysis.

Bioinformatics 2009 Sep 23;25(17):2222-8. Epub 2009 Jun 23.

The Scripps Translational Science Institute and Scripps Genomic Medicine, Scripps Health and The Scripps Research Institute, 3344 North Torrey Pines Court, Room 306 La Jolla, CA 92037 USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2800353PMC
September 2009

Identification of rare cancer driver mutations by network reconstruction.

Genome Res 2009 Sep 2;19(9):1570-8. Epub 2009 Jul 2.

The Scripps Translational Science Institute and Scripps Genomic Medicine, Scripps Health and The Scripps Research Institute, La Jolla, California 92037, USA.

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http://dx.doi.org/10.1101/gr.092833.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2752121PMC
September 2009

Cancer driver mutations in protein kinase genes.

Cancer Lett 2009 Aug 10;281(2):117-27. Epub 2008 Dec 10.

The Scripps Translational Science Institute and Scripps Genomic Medicine, Scripps Health and The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1016/j.canlet.2008.11.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2905872PMC
August 2009

Pathway analysis of seven common diseases assessed by genome-wide association.

Genomics 2008 Nov 16;92(5):265-72. Epub 2008 Sep 16.

Scripps Genomic Medicine, The Scripps Translational Science Institute, and Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1016/j.ygeno.2008.07.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2602835PMC
November 2008

Identification of ALK as a major familial neuroblastoma predisposition gene.

Nature 2008 Oct 24;455(7215):930-5. Epub 2008 Aug 24.

Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA.

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http://dx.doi.org/10.1038/nature07261DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2672043PMC
October 2008

Predicting functional regulatory polymorphisms.

Bioinformatics 2008 Aug 18;24(16):1787-92. Epub 2008 Jun 18.

Department of Molecular and Experimental Medicine, Scripps Genomic Medicine and the Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn311DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732211PMC
August 2008

Congenital disease SNPs target lineage specific structural elements in protein kinases.

Proc Natl Acad Sci U S A 2008 Jul 25;105(26):9011-6. Epub 2008 Jun 25.

Graduate Program in Biomedical Sciences, University of California, San Diego, CA 92103, USA.

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http://dx.doi.org/10.1073/pnas.0802403105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2449356PMC
July 2008

Prediction of cancer driver mutations in protein kinases.

Cancer Res 2008 Mar;68(6):1675-82

Graduate Program in Biomedical Sciences, Center for Human Genetics and Genomics, University of California, San Diego, CA, USA.

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http://cancerres.aacrjournals.org/cgi/doi/10.1158/0008-5472.
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March 2008

Accurate prediction of deleterious protein kinase polymorphisms.

Bioinformatics 2007 Nov 12;23(21):2918-25. Epub 2007 Sep 12.

Department of Medicine, Center for Human Genetics and Genomics, The Scripps Research Institute, University of California, San Diego, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1093/bioinformatics/btm437DOI Listing
November 2007

Distribution analysis of nonsynonymous polymorphisms within the human kinase gene family.

Genomics 2007 Jul 11;90(1):49-58. Epub 2007 May 11.

Graduate Program in Biomedical Sciences, Department of Medicine, University of California at San Diego, La Jolla, CA 92093, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S088875430700064
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http://dx.doi.org/10.1016/j.ygeno.2007.03.006DOI Listing
July 2007

The clearance of protein-bound solutes by hemofiltration and hemodiafiltration.

Kidney Int 2005 Aug;68(2):867-77

Department of Medicine, VA Palo Alto Health Care Science, Palo Alto, California 94303, USA.

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August 2005