Publications by authors named "Richard H Scheuermann"

100Publications

FR-Match: robust matching of cell type clusters from single cell RNA sequencing data using the Friedman-Rafsky non-parametric test.

Brief Bioinform 2020 Nov 30. Epub 2020 Nov 30.

J. Craig Venter Institute La Jolla Campus, an Adjunct Professor of Pathology at the University of California San Diego, and an Adjunct Professor at the La Jolla Institute for Immunology.

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http://dx.doi.org/10.1093/bib/bbaa339DOI Listing
November 2020

A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2.

Cell Host Microbe 2020 04 16;27(4):671-680.e2. Epub 2020 Mar 16.

Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, University of California, San Diego, San Diego, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.chom.2020.03.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7142693PMC
April 2020

Machine Learning of Discriminative Gate Locations for Clinical Diagnosis.

Cytometry A 2020 03 5;97(3):296-307. Epub 2019 Nov 5.

Department of Computer Science, University of California, Irvine, California.

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http://dx.doi.org/10.1002/cyto.a.23906DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7079150PMC
March 2020

A survey of known immune epitopes in the enteroviruses strains associated with acute flaccid myelitis.

Hum Immunol 2019 Nov 23;80(11):923-929. Epub 2019 Aug 23.

Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, University of California, San Diego, CA 92093, USA.

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http://dx.doi.org/10.1016/j.humimm.2019.08.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6876747PMC
November 2019

Classification of human Herpesviridae proteins using Domain-architecture Aware Inference of Orthologs (DAIO).

Virology 2019 03 6;529:29-42. Epub 2019 Jan 6.

J. Craig Venter Institute, La Jolla, CA 92037, USA; Department of Pathology, University of California, San Diego, CA 92093, USA; Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA. Electronic address:

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http://dx.doi.org/10.1016/j.virol.2019.01.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6502252PMC
March 2019

Automated Analysis of Clinical Flow Cytometry Data: A Chronic Lymphocytic Leukemia Illustration.

Clin Lab Med 2017 12;37(4):931-944

Department of Informatics, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1016/j.cll.2017.07.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5766345PMC
December 2017

A bioinformatics roadmap for the human vaccines project.

Expert Rev Vaccines 2017 06 9;16(6):535-544. Epub 2017 May 9.

c Human Vaccines Project , New York , NY , USA.

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http://dx.doi.org/10.1080/14760584.2017.1322752DOI Listing
June 2017

Zika virus: designate standardized names.

Nature 2016 Mar;531(7593):173

J. Craig Venter Institute, La Jolla, California, USA.

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http://dx.doi.org/10.1038/531173aDOI Listing
March 2016

Automated analysis of flow cytometry data comes of age.

Cytometry A 2016 Jan;89(1):13-5

J. Craig Venter Institute, La Jolla, California.

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http://dx.doi.org/10.1002/cyto.a.22810DOI Listing
January 2016

State-of-the-Art in the Computational Analysis of Cytometry Data.

Cytometry A 2015 Jul;87(7):591-3

J. Craig Venter Institute, La Jolla, California.

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http://dx.doi.org/10.1002/cyto.a.22707DOI Listing
July 2015

A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway.

Evol Bioinform Online 2015 16;11:43-8. Epub 2015 Mar 16.

Department of Anatomical Sciences, Stony Brook University, Stony Brook, NY, USA.

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http://dx.doi.org/10.4137/EBO.S21501DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4362911PMC
April 2015

Diversifying Selection Analysis Predicts Antigenic Evolution of 2009 Pandemic H1N1 Influenza A Virus in Humans.

J Virol 2015 May 4;89(10):5427-40. Epub 2015 Mar 4.

J. Craig Venter Institute, La Jolla, California, USA Department of Pathology, University of California, San Diego, California, USA

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http://dx.doi.org/10.1128/JVI.03636-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4442545PMC
May 2015

flowCL: ontology-based cell population labelling in flow cytometry.

Bioinformatics 2015 Apr 6;31(8):1337-9. Epub 2014 Dec 6.

Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, J. Craig Venter Institute, La Jolla, CA 92037, USA, Department of Pathology, University of California, San Diego, CA 92093, USA.

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http://bioinformatics.oxfordjournals.org/content/early/2015/
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http://bioinformatics.oxfordjournals.org/content/early/2014/
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http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
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http://dx.doi.org/10.1093/bioinformatics/btu807DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393520PMC
April 2015

Toward a method for tracking virus evolutionary trajectory applied to the pandemic H1N1 2009 influenza virus.

Infect Genet Evol 2014 Dec 24;28:351-7. Epub 2014 Jul 24.

Informatics, J. Craig Venter Institute (JCVI), La Jolla, CA, USA; Department of Pathology, University of California San Diego, San Diego, CA, USA.

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http://dx.doi.org/10.1016/j.meegid.2014.07.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4257861PMC
December 2014

Response of human skin to esthetic scarification.

Burns 2014 Nov 28;40(7):1338-44. Epub 2014 Feb 28.

Division of Informatics, J. Craig Venter Institute, San Diego, CA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.burns.2014.01.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4336194PMC
November 2014

Extracting actionable findings of appendicitis from radiology reports using natural language processing.

AMIA Jt Summits Transl Sci Proc 2013 18;2013:221. Epub 2013 Mar 18.

The University of Texas at Dallas, Richardson, TX, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3845763PMC
December 2013

Critical assessment of automated flow cytometry data analysis techniques.

Nat Methods 2013 Mar 10;10(3):228-38. Epub 2013 Feb 10.

Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.

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http://dx.doi.org/10.1038/nmeth.2365DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3906045PMC
March 2013

FCSTrans: an open source software system for FCS file conversion and data transformation.

Cytometry A 2012 May 19;81(5):353-356. Epub 2012 Mar 19.

Division of Biomedical Informatics, Department of Clinical Sciences, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390.

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http://doi.wiley.com/10.1002/cyto.a.22037
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http://dx.doi.org/10.1002/cyto.a.22037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3932304PMC
May 2012

A gene selection method for GeneChip array data with small sample sizes.

BMC Genomics 2011 Dec 23;12 Suppl 5:S7. Epub 2011 Dec 23.

Biostatistics Epidemiology Research Design Core, Center for Clinical and Translational Sciences, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

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http://dx.doi.org/10.1186/1471-2164-12-S5-S7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287503PMC
December 2011

Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop.

Viruses 2010 Oct 13;2(10):2258-68. Epub 2010 Oct 13.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA; E-Mails: (Y.B.); (W.K.); (T.T.).

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http://dx.doi.org/10.3390/v2102258DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3185566PMC
October 2010

Identifying Differentially Expressed Genes based on probe level data for GeneChip arrays.

Int J Comput Biol Drug Des 2010 11;3(3):237-57. Epub 2011 Jan 11.

Biostatistics/Epidemiology/Research Design Core, Center for Clinical and Translational Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

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http://dx.doi.org/10.1504/IJCBDD.2010.038028DOI Listing
March 2011

Toward an ontology-based framework for clinical research databases.

J Biomed Inform 2011 Feb 10;44(1):48-58. Epub 2010 May 10.

Department of Pathology, U.T. Southwestern Medical Center, Dallas, TX 75390-9072, United States.

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http://dx.doi.org/10.1016/j.jbi.2010.05.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2953614PMC
February 2011

Personalized care, comparative effectiveness research and the electronic health record.

Curr Opin Allergy Clin Immunol 2010 Jun;10(3):168-70

Division of Biomedical Informatics and Department of Pathology, U.T. Southwestern Medical Center, Dallas, Texas, USA.

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http://dx.doi.org/10.1097/ACI.0b013e328338c232DOI Listing
June 2010

Deterministic graph-theoretic algorithm for detecting modules in biological interaction networks.

Int J Bioinform Res Appl 2010 ;6(2):101-19

University of California San Diego, La Jolla, San Diego, CA 92093-0412, USA.

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http://dx.doi.org/10.1504/IJBRA.2010.032115DOI Listing
June 2010

GO-Bayes: Gene Ontology-based overrepresentation analysis using a Bayesian approach.

Bioinformatics 2010 Apr 21;26(7):905-11. Epub 2010 Feb 21.

Department of Clinical Sciences, U.T. Southwestern Medical Center, 5323 Harry Hines Boulevard Dallas, TX 75390-9072, USA.

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http://dx.doi.org/10.1093/bioinformatics/btq059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913669PMC
April 2010

Pre-existing immunity against swine-origin H1N1 influenza viruses in the general human population.

Proc Natl Acad Sci U S A 2009 Dec 16;106(48):20365-70. Epub 2009 Nov 16.

Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1073/pnas.0911580106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2777968PMC
December 2009

A Distribution-Free Convolution Model for background correction of oligonucleotide microarray data.

BMC Genomics 2009 Jul 7;10 Suppl 1:S19. Epub 2009 Jul 7.

Biostatistics Epidemiology Research Design Core, Center for Clinical and Translational Sciences, The University of Texas Health Science Center at Houston, UT Professional Building, Houston, TX 77030, USA.

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http://dx.doi.org/10.1186/1471-2164-10-S1-S19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2709262PMC
July 2009

FuGEFlow: data model and markup language for flow cytometry.

BMC Bioinformatics 2009 Jun 16;10:184. Epub 2009 Jun 16.

Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA.

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http://dx.doi.org/10.1186/1471-2105-10-184DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2711079PMC
June 2009

Core and periphery structures in protein interaction networks.

BMC Bioinformatics 2009 Apr 29;10 Suppl 4:S8. Epub 2009 Apr 29.

School of Computing, Clemson University, Clemson, SC, USA.

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http://dx.doi.org/10.1186/1471-2105-10-S4-S8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2681073PMC
April 2009

An improved ontological representation of dendritic cells as a paradigm for all cell types.

BMC Bioinformatics 2009 Feb 25;10:70. Epub 2009 Feb 25.

Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA.

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http://dx.doi.org/10.1186/1471-2105-10-70DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2662812PMC
February 2009

Toward an ontological treatment of disease and diagnosis.

Summit Transl Bioinform 2009 Mar 1;2009:116-20. Epub 2009 Mar 1.

Department of Pathology and Division of Biomedical Informatics, University of Texas Southwestern Medical Center, Dallas, TX;

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577PMC
March 2009

National Institute of Allergy and Infectious Diseases bioinformatics resource centers: new assets for pathogen informatics.

Infect Immun 2007 Jul 9;75(7):3212-9. Epub 2007 Apr 9.

National Institute of Allergy and Infectious Diseases/NIH, 6610 Rockledge Drive, MSC 6603, Bethesda, MD 20850-6603, USA.

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http://dx.doi.org/10.1128/IAI.00105-07DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1932942PMC
July 2007

Ontology development for biological systems: immunology.

Bioinformatics 2007 Apr 31;23(7):913-5. Epub 2007 Jan 31.

Mouse Genome Informatics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04605, USA.

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http://dx.doi.org/10.1093/bioinformatics/btm029DOI Listing
April 2007

A distribution free summarization method for Affymetrix GeneChip arrays.

Bioinformatics 2007 Feb 5;23(3):321-7. Epub 2006 Dec 5.

Department of Statistical Science, Southern Methodist University, Dallas, TX 75275, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl609DOI Listing
February 2007

Modular organization of protein interaction networks.

Bioinformatics 2007 Jan 8;23(2):207-14. Epub 2006 Nov 8.

Department of Computer Science, 100 McAdams Hall, Clemson University, Clemson, SC 29634-0974, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl562DOI Listing
January 2007

Nucleic acid testing for viral burden and viral genotyping.

Clin Chim Acta 2006 Jan 11;363(1-2):197-205. Epub 2005 Aug 11.

Department of Pathology, Baylor University Medical Center, Dallas, TX 75246, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S000989810500438
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http://dx.doi.org/10.1016/j.cccn.2005.05.049DOI Listing
January 2006

Overview of the Alliance for Cellular Signaling.

Nature 2002 Dec;420(6916):703-6

Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.

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http://dx.doi.org/10.1038/nature01304DOI Listing
December 2002