Richard Scheuermann

Title(s)Adjunct Professor, Pathology
SchoolVc-health Sciences-schools
Address9500 Gilman Drive #
La Jolla CA 92093
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    Collapse Biography 
    Collapse Education and Training
    University of California, Berkeley, Berkeley, CAPhD06/1986Molecular Biology
    Massachusetts Institute of Technology, Cambridge, MABS06/1981Life Sciences

    Collapse Overview 
    Collapse Overview
    Richard H. Scheuermann, Ph.D., is the Director of the J. Craig Venter Institute (JCVI) La Jolla Campus, and an Adjunct Professor of Pathology at U.C. San Diego. He received a B.S. in Life Sciences from the Massachusetts Institute of Technology, and a Ph.D. in Molecular Biology from the University of California, Berkeley. Dr. Scheuermann has applied his deep knowledge of molecular immunology and infectious disease to the development of novel computational data mining methods and knowledge representation approaches, including the development of biomedical ontologies and their use in data mining, and the development of novel methods for gene expression, protein network, flow cytometry, and comparative genomics data analysis. These computational methods have been made available through several public database and analysis resources, including the Influenza Research Database (IRD; www.fludb.org), the Virus Pathogen Resource (ViPR; www.viprbrc.org) and the Immunology Database and Analysis Portal (ImmPort; https://immport.niaid.nih.gov/) supported by the U.S. National Institutes of Health. More recently, Dr. Scheuermann have worked to develop computation methods and analytical pipelines incorporating machine learning approaches to process and analyze single cell and single nuclei RNA sequencing data.

    Collapse Research 
    Collapse Research Activities and Funding
    A Community Framework for Data-driven Brain Transcriptomic Cell Type Definition, Ontology, and Nomenclature
    NIH RF1MH123220Sep 4, 2020 - Sep 3, 2022
    Role: Co-Principal Investigator
    Transformative Computational Infrastructures for Cell-Based Biomarker Diagnostics
    NIH U01TR001801Sep 15, 2016 - Jun 30, 2021
    Role: Co-Principal Investigator
    Somatic Mutation in the Etiology of Multiple Sclerosis
    NIH R21AI122100Jul 1, 2016 - Dec 31, 2019
    Role: Principal Investigator
    Bioinformatics Resource Center
    NIH 272200900041C-1-0-1Oct 1, 2009 - Sep 30, 2014
    Role: Principal Investigator
    Bioinformatics Resource Center
    NIH 272200900041C-1-0-9Oct 1, 2009 - Sep 30, 2014
    Role: Principal Investigator
    Bioinformatics Integration Support Contract for Biodefense
    NIH N01AI40076-11-0-1Sep 29, 2004 - Dec 31, 2011
    Role: Principal Investigator
    Bioinformatics Integration Support Contract for Immune-Mediated Diseases
    NIH N01AI40076-11-0-2Sep 29, 2004 - Dec 31, 2011
    Role: Principal Investigator
    Bioinformatics Integration Support Contract for Biodefense
    NIH N01AI40076-10-0-1Sep 29, 2004 - Sep 29, 2010
    Role: Principal Investigator
    BIOINFORMATICS RESOURCE CENTERS
    NIH N01AI40041-11-0-1Jun 30, 2004 - Jun 30, 2013
    Role: Principal Investigator
    BIOINFORMATICS RESOURCE CENTERS FOR BIODEFENSE
    NIH/NIAID N01AI40041Jun 30, 2004 - Jun 29, 2009
    Role: Principal Investigator
    Functional Characterization of BAFF-induced Genes
    NIH R01AI056216Jul 1, 2003 - Dec 31, 2008
    Role: Principal Investigator
    Database development and modeling of signal transduction
    NIH F33CA094654May 2, 2002
    Role: Principal Investigator
    POPULATION STABILITY IN TUMOR DORMANCY
    NIH R01CA078793Aug 1, 1998 - May 31, 2004
    Role: Principal Investigator
    MINIMAL RESIDUAL DISEASE EVALUATION TO GUIDE THERAPY
    NIH R21CA074965Jul 1, 1998 - Jun 30, 2000
    Role: Principal Investigator
    CELL-TYPE SPECIFIC SUPPRESSION OF THE IGH ENHANCER
    NIH R01GM050329Sep 15, 1994 - Feb 28, 2001
    Role: Principal Investigator
    CELL TYPE SPECIFIC SUPPRESSION OF THE IGH ENHANCER
    NIH R55GM050329Sep 15, 1994 - Feb 29, 1996
    Role: Principal Investigator
    Integrative Immunology Training Program
    NIH T32AI005284Jul 1, 1980 - Jun 30, 2025
    Role: Co-Principal Investigator
    DMID CLINICAL RESEARCH OPERATIONS AND MANAGEMENT SUPPORT
    NIH N01AI000000Dec 31, 2022
    Role: Co-Principal Investigator
    Bioinformatics Integration Support Contract for Biodefense
    NIH/NIAID N01AI40076Sep 29, 2010
    Role: Co-Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Standardization of assay representation in the Ontology for Biomedical Investigations. Database (Oxford). 2021 Jul 09; 2021. Vita R, Zheng J, Jackson R, Dooley D, Overton JA, Miller MA, Berrios DC, Scheuermann RH, He Y, McGinty HK, Brochhausen M, Lin AY, Jain SB, Chibucos MC, Judkins J, Giglio MG, Feng IY, Burns G, Brush MH, Peters B, Stoeckert CJ. PMID: 34244718.
      View in: PubMed   Mentions:    Fields:    
    2. Impact of SARS-CoV-2 variants on the total CD4+ and CD8+ T cell reactivity in infected or vaccinated individuals. Cell Rep Med. 2021 Jul 02; 100355. Tarke A, Sidney J, Methot N, Yu ED, Zhang Y, Dan JM, Goodwin B, Rubiro P, Sutherland A, Wang E, Frazier A, Ramirez SI, Rawlings SA, Smith DM, da Silva Antunes R, Peters B, Scheuermann RH, Weiskopf D, Crotty S, Grifoni A, Sette A. PMID: 34230917.
      View in: PubMed   Mentions:
    3. A machine learning method for the discovery of minimum marker gene combinations for cell-type identification from single-cell RNA sequencing. Genome Res. 2021 Jun 04. Aevermann BD, Zhang Y, Novotny M, Keshk M, Bakken TE, Miller JA, Hodge RD, Lelieveldt B, Lein ES, Scheuermann RH. PMID: 34088715.
      View in: PubMed   Mentions: 1     Fields:    
    4. Author Correction: A community-based transcriptomics classification and nomenclature of neocortical cell types. Nat Neurosci. 2021 Apr; 24(4):612. Yuste R, Hawrylycz M, Aalling N, Aguilar-Valles A, Arendt D, Armañanzas R, Ascoli GA, Bielza C, Bokharaie V, Bergmann TB, Bystron I, Capogna M, Chang Y, Clemens A, de Kock CPJ, DeFelipe J, Dos Santos SE, Dunville K, Feldmeyer D, Fiáth R, Fishell GJ, Foggetti A, Gao X, Ghaderi P, Goriounova NA, Güntürkün O, Hagihara K, Hall VJ, Helmstaedter M, Herculano-Houzel S, Hilscher MM, Hirase H, Hjerling-Leffler J, Hodge R, Huang J, Huda R, Khodosevich K, Kiehn O, Koch H, Kuebler ES, Kühnemund M, Larrañaga P, Lelieveldt B, Louth EL, Lui JH, Mansvelder HD, Marin O, Martinez-Trujillo J, Chameh HM, Mohapatra AN, Munguba H, Nedergaard M, Nemec P, Ofer N, Pfisterer UG, Pontes S, Redmond W, Rossier J, Sanes JR, Scheuermann RH, Serrano-Saiz E, Staiger JF, Somogyi P, Tamás G, Tolias AS, Tosches MA, García MT, Wozny C, Wuttke TV, Liu Y, Yuan J, Zeng H, Lein E. PMID: 33742182.
      View in: PubMed   Mentions:    Fields:    
    5. Publisher Correction: A community-based transcriptomics classification and nomenclature of neocortical cell types. Nat Neurosci. 2021 Apr; 24(4):613. Yuste R, Hawrylycz M, Aalling N, Aguilar-Valles A, Arendt D, Arnedillo RA, Ascoli GA, Bielza C, Bokharaie V, Bergmann TB, Bystron I, Capogna M, Chang Y, Clemens A, de Kock CPJ, DeFelipe J, Dos Santos SE, Dunville K, Feldmeyer D, Fiáth R, Fishell GJ, Foggetti A, Gao X, Ghaderi P, Goriounova NA, Güntürkün O, Hagihara K, Hall VJ, Helmstaedter M, Herculano S, Hilscher MM, Hirase H, Hjerling-Leffler J, Hodge R, Huang J, Huda R, Khodosevich K, Kiehn O, Koch H, Kuebler ES, Kühnemund M, Larrañaga P, Lelieveldt B, Louth EL, Lui JH, Mansvelder HD, Marin O, Martinez-Trujillo J, Moradi Chameh H, Nath A, Nedergaard M, Nemec P, Ofer N, Pfisterer UG, Pontes S, Redmond W, Rossier J, Sanes JR, Scheuermann R, Serrano-Saiz E, Steiger JF, Somogyi P, Tamás G, Tolias AS, Tosches MA, García MT, Vieira HM, Wozny C, Wuttke TV, Yong L, Yuan J, Zeng H, Lein E. PMID: 33277642.
      View in: PubMed   Mentions:    Fields:    
    6. SARS-CoV-2 infection of the oral cavity and saliva. Nat Med. 2021 05; 27(5):892-903. Huang N, Pérez P, Kato T, Mikami Y, Okuda K, Gilmore RC, Conde CD, Gasmi B, Stein S, Beach M, Pelayo E, Maldonado JO, Lafont BA, Jang SI, Nasir N, Padilla RJ, Murrah VA, Maile R, Lovell W, Wallet SM, Bowman NM, Meinig SL, Wolfgang MC, Choudhury SN, Novotny M, Aevermann BD, Scheuermann RH, Cannon G, Anderson CW, Lee RE, Marchesan JT, Bush M, Freire M, Kimple AJ, Herr DL, Rabin J, Grazioli A, Das S, French BN, Pranzatelli T, Chiorini JA, Kleiner DE, Pittaluga S, Hewitt SM, Burbelo PD, Chertow D, NIH COVID-19 Autopsy Consortium , HCA Oral and Craniofacial Biological Network , Frank K, Lee J, Boucher RC, Teichmann SA, Warner BM, Byrd KM. PMID: 33767405.
      View in: PubMed   Mentions: 10     Fields:    Translation:Humans
    7. Systems view of Bordetella pertussis booster vaccination in adults primed with whole-cell vs. acellular vaccine. JCI Insight. 2021 Mar 09. da Silva Antunes R, Soldevila F, Pomaznoy M, Babor M, Bennett J, Tian Y, Khalil NN, Qian Y, Mandava A, Scheuermann RH, Cortese M, Pulendran B, Petro CD, Gilkes AP, Purcell LA, Sette A, Peters B. PMID: 33690224.
      View in: PubMed   Mentions:    Fields:    
    8. Negligible impact of SARS-CoV-2 variants on CD4 + and CD8 + T cell reactivity in COVID-19 exposed donors and vaccinees. bioRxiv. 2021 Mar 01. Tarke A, Sidney J, Methot N, Zhang Y, Dan JM, Goodwin B, Rubiro P, Sutherland A, da Silva Antunes R, Frazier A, Rawlings SA, Smith DM, Peters B, Scheuermann RH, Weiskopf D, Crotty S, Grifoni A, Sette A. PMID: 33688655.
      View in: PubMed   Mentions:
    9. Guidelines for reporting single-cell RNA-seq experiments. Nat Biotechnol. 2020 12; 38(12):1384-1386. Füllgrabe A, George N, Green M, Nejad P, Aronow B, Fexova SK, Fischer C, Freeberg MA, Huerta L, Morrison N, Scheuermann RH, Taylor D, Vasilevsky N, Clarke L, Gehlenborg N, Kent J, Marioni J, Teichmann S, Brazma A, Papatheodorou I. PMID: 33188371.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    10. A community-based transcriptomics classification and nomenclature of neocortical cell types. Nat Neurosci. 2020 12; 23(12):1456-1468. Yuste R, Hawrylycz M, Aalling N, Aguilar-Valles A, Arendt D, Armañanzas R, Ascoli GA, Bielza C, Bokharaie V, Bergmann TB, Bystron I, Capogna M, Chang Y, Clemens A, de Kock CPJ, DeFelipe J, Dos Santos SE, Dunville K, Feldmeyer D, Fiáth R, Fishell GJ, Foggetti A, Gao X, Ghaderi P, Goriounova NA, Güntürkün O, Hagihara K, Hall VJ, Helmstaedter M, Herculano-Houzel S, Hilscher MM, Hirase H, Hjerling-Leffler J, Hodge R, Huang J, Huda R, Khodosevich K, Kiehn O, Koch H, Kuebler ES, Kühnemund M, Larrañaga P, Lelieveldt B, Louth EL, Lui JH, Mansvelder HD, Marin O, Martinez-Trujillo J, Chameh HM, Mohapatra AN, Munguba H, Nedergaard M, Nemec P, Ofer N, Pfisterer UG, Pontes S, Redmond W, Rossier J, Sanes JR, Scheuermann RH, Serrano-Saiz E, Staiger JF, Somogyi P, Tamás G, Tolias AS, Tosches MA, García MT, Wozny C, Wuttke TV, Liu Y, Yuan J, Zeng H, Lein E. PMID: 32839617.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansAnimalsCells
    11. 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. Zhang Y, Aevermann BD, Bakken TE, Miller JA, Hodge RD, Lein ES, Scheuermann RH. PMID: 33249453.
      View in: PubMed   Mentions:    Fields:    
    12. Multi-Omic Data Integration Allows Baseline Immune Signatures to Predict Hepatitis B Vaccine Response in a Small Cohort. Front Immunol. 2020; 11:578801. Shannon CP, Blimkie TM, Ben-Othman R, Gladish N, Amenyogbe N, Drissler S, Edgar RD, Chan Q, Krajden M, Foster LJ, Kobor MS, Mohn WW, Brinkman RR, Le Cao KA, Scheuermann RH, Tebbutt SJ, Hancock REW, Koff WC, Kollmann TR, Sadarangani M, Lee AH. PMID: 33329547.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCellsPHPublic Health
    13. Epidemiology and Sequence-Based Evolutionary Analysis of Circulating Non-Polio Enteroviruses. Microorganisms. 2020 Nov 25; 8(12). Brown DM, Zhang Y, Scheuermann RH. PMID: 33255654.
      View in: PubMed   Mentions:
    14. Systems Biology Methods Applied to Blood and Tissue for a Comprehensive Analysis of Immune Response to Hepatitis B Vaccine in Adults. Front Immunol. 2020; 11:580373. Ben-Othman R, Cai B, Liu AC, Varankovich N, He D, Blimkie TM, Lee AH, Gill EE, Novotny M, Aevermann B, Drissler S, Shannon CP, McCann S, Marty K, Bjornson G, Edgar RD, Lin DTS, Gladish N, Maclsaac J, Amenyogbe N, Chan Q, Llibre A, Collin J, Landais E, Le K, Reiss SM, Koff WC, Havenar-Daughton C, Heran M, Sangha B, Walt D, Krajden M, Crotty S, Sok D, Briney B, Burton DR, Duffy D, Foster LJ, Mohn WW, Kobor MS, Tebbutt SJ, Brinkman RR, Scheuermann RH, Hancock REW, Kollmann TR, Sadarangani M. PMID: 33250895.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCellsPHPublic HealthCTClinical Trials
    15. Integrated Single-Cell Atlases Reveal an Oral SARS-CoV-2 Infection and Transmission Axis. medRxiv. 2020 Oct 27. Huang N, Perez P, Kato T, Mikami Y, Okuda K, Gilmore RC, Domínguez Conde C, Gasmi B, Stein S, Beach M, Pelayo E, Maldonado J, LaFont B, Padilla R, Murrah V, Maile R, Lovell W, Wallet S, Bowman NM, Meinig SL, Wolfgang MC, Choudhury SN, Novotny M, Aevermann BD, Scheuermann R, Cannon G, Anderson C, Marchesan J, Bush M, Freire M, Kimple A, Herr DL, Rabin J, Grazioli A, French BN, Pranzatelli T, Chiorini JA, Kleiner DE, Pittaluga S, Hewitt S, Burbelo PD, Chertow D, Frank K, Lee J, Boucher RC, Teichmann SA, Warner BM, Byrd KM. PMID: 33140061.
      View in: PubMed   Mentions:
    16. Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable. Proc Natl Acad Sci U S A. 2020 06 09; 117(23):12522-12523. Mavian C, Pond SK, Marini S, Magalis BR, Vandamme AM, Dellicour S, Scarpino SV, Houldcroft C, Villabona-Arenas J, Paisie TK, Trovão NS, Boucher C, Zhang Y, Scheuermann RH, Gascuel O, Lam TT, Suchard MA, Abecasis A, Wilkinson E, de Oliveira T, Bento AI, Schmidt HA, Martin D, Hadfield J, Faria N, Grubaugh ND, Neher RA, Baele G, Lemey P, Stadler T, Albert J, Crandall KA, Leitner T, Stamatakis A, Prosperi M, Salemi M. PMID: 32381734.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansCellsPHPublic Health
    17. Unbiased analysis of peripheral blood mononuclear cells reveals CD4 T cell response to RSV matrix protein. Vaccine X. 2020 Aug 07; 5:100065. Thakar J, Qian Y, Benoodt L, Roumanes D, Qiu X, Laniewski N, Chu C, Slaunwhite C, Wang L, Mandava A, Chang I, Falsey AR, Caserta MT, Mariani TJ, Scheuermann RH, Walsh EE, Topham DJ. PMID: 32529184.
      View in: PubMed   Mentions:
    18. A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2. Cell Host Microbe. 2020 04 08; 27(4):671-680.e2. Grifoni A, Sidney J, Zhang Y, Scheuermann RH, Peters B, Sette A. PMID: 32183941.
      View in: PubMed   Mentions: 285     Fields:    Translation:HumansCellsPHPublic Health
    19. Transcriptomic evidence that von Economo neurons are regionally specialized extratelencephalic-projecting excitatory neurons. Nat Commun. 2020 03 03; 11(1):1172. Hodge RD, Miller JA, Novotny M, Kalmbach BE, Ting JT, Bakken TE, Aevermann BD, Barkan ER, Berkowitz-Cerasano ML, Cobbs C, Diez-Fuertes F, Ding SL, McCorrison J, Schork NJ, Shehata SI, Smith KA, Sunkin SM, Tran DN, Venepally P, Yanny AM, Steemers FJ, Phillips JW, Bernard A, Koch C, Lasken RS, Scheuermann RH, Lein ES. PMID: 32127543.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    20. Candidate Targets for Immune Responses to 2019-Novel Coronavirus (nCoV): Sequence Homology- and Bioinformatic-Based Predictions. SSRN. 2020 Feb 25; 3541361. Grifoni A, Sidney J, Zhang Y, Scheuermann RH, Peters B, Sette A. PMID: 32714104.
      View in: PubMed   Mentions:
    21. Machine Learning of Discriminative Gate Locations for Clinical Diagnosis. Cytometry A. 2020 03; 97(3):296-307. Ji D, Putzel P, Qian Y, Chang I, Mandava A, Scheuermann RH, Bui JD, Wang HY, Smyth P. PMID: 31691488.
      View in: PubMed   Mentions: 1     Fields:    
    22. A survey of known immune epitopes in the enteroviruses strains associated with acute flaccid myelitis. Hum Immunol. 2019 Nov; 80(11):923-929. Grifoni A, Mahajan S, Sidney J, Martini S, Scheuermann RH, Peters B, Sette A. PMID: 31451291.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    23. Conserved cell types with divergent features in human versus mouse cortex. Nature. 2019 09; 573(7772):61-68. Hodge RD, Bakken TE, Miller JA, Smith KA, Barkan ER, Graybuck LT, Close JL, Long B, Johansen N, Penn O, Yao Z, Eggermont J, Höllt T, Levi BP, Shehata SI, Aevermann B, Beller A, Bertagnolli D, Brouner K, Casper T, Cobbs C, Dalley R, Dee N, Ding SL, Ellenbogen RG, Fong O, Garren E, Goldy J, Gwinn RP, Hirschstein D, Keene CD, Keshk M, Ko AL, Lathia K, Mahfouz A, Maltzer Z, McGraw M, Nguyen TN, Nyhus J, Ojemann JG, Oldre A, Parry S, Reynolds S, Rimorin C, Shapovalova NV, Somasundaram S, Szafer A, Thomsen ER, Tieu M, Quon G, Scheuermann RH, Yuste R, Sunkin SM, Lelieveldt B, Feng D, Ng L, Bernard A, Hawrylycz M, Phillips JW, Tasic B, Zeng H, Jones AR, Koch C, Lein ES. PMID: 31435019.
      View in: PubMed   Mentions: 197     Fields:    Translation:HumansAnimalsCells
    24. Differential transcriptome and development of human peripheral plasma cell subsets. JCI Insight. 2019 05 02; 4(9). Garimalla S, Nguyen DC, Halliley JL, Tipton C, Rosenberg AF, Fucile CF, Saney CL, Kyu S, Kaminski D, Qian Y, Scheuermann RH, Gibson G, Sanz I, Lee FE. PMID: 31045577.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCellsPHPublic Health
    25. Classification of human Herpesviridae proteins using Domain-architecture Aware Inference of Orthologs (DAIO). Virology. 2019 03; 529:29-42. Zmasek CM, Knipe DM, Pellett PE, Scheuermann RH. PMID: 30660046.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    26. Hepatitis C Virus Database and Bioinformatics Analysis Tools in the Virus Pathogen Resource (ViPR). Methods Mol Biol. 2019; 1911:47-69. Zhang Y, Zmasek C, Sun G, Larsen CN, Scheuermann RH. PMID: 30593617.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    27. Single-nucleus and single-cell transcriptomes compared in matched cortical cell types. PLoS One. 2018; 13(12):e0209648. Bakken TE, Hodge RD, Miller JA, Yao Z, Nguyen TN, Aevermann B, Barkan E, Bertagnolli D, Casper T, Dee N, Garren E, Goldy J, Graybuck LT, Kroll M, Lasken RS, Lathia K, Parry S, Rimorin C, Scheuermann RH, Schork NJ, Shehata SI, Tieu M, Phillips JW, Bernard A, Smith KA, Zeng H, Lein ES, Tasic B. PMID: 30586455.
      View in: PubMed   Mentions: 69     Fields:    Translation:AnimalsCells
    28. Contemporary Circulating Enterovirus D68 Strains Have Acquired the Capacity for Viral Entry and Replication in Human Neuronal Cells. mBio. 2018 10 16; 9(5). Brown DM, Hixon AM, Oldfield LM, Zhang Y, Novotny M, Wang W, Das SR, Shabman RS, Tyler KL, Scheuermann RH. PMID: 30327438.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansAnimalsCells
    29. Chromosome Y-encoded antigens associate with acute graft-versus-host disease in sex-mismatched stem cell transplant. Blood Adv. 2018 10 09; 2(19):2419-2429. Wang W, Huang H, Halagan M, Vierra-Green C, Heuer M, Brelsford JE, Haagenson M, Scheuermann RH, Telenti A, Biggs W, Pearson NM, Udell J, Spellman S, Maiers M, Kennedy CJ. PMID: 30262602.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    30. Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type. Nat Neurosci. 2018 09; 21(9):1185-1195. Boldog E, Bakken TE, Hodge RD, Novotny M, Aevermann BD, Baka J, Bordé S, Close JL, Diez-Fuertes F, Ding SL, Faragó N, Kocsis ÁK, Kovács B, Maltzer Z, McCorrison JM, Miller JA, Molnár G, Oláh G, Ozsvár A, Rózsa M, Shehata SI, Smith KA, Sunkin SM, Tran DN, Venepally P, Wall A, Puskás LG, Barzó P, Steemers FJ, Schork NJ, Scheuermann RH, Lasken RS, Lein ES, Tamás G. PMID: 30150662.
      View in: PubMed   Mentions: 51     Fields:    Translation:HumansCells
    31. Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting. Viruses. 2018 May 14; 10(5). Ibrahim B, Arkhipova K, Andeweg AC, Posada-Céspedes S, Enault F, Gruber A, Koonin EV, Kupczok A, Lemey P, McHardy AC, McMahon DP, Pickett BE, Robertson DL, Scheuermann RH, Zhernakova A, Zwart MP, Schönhuth A, Dutilh BE, Marz M. PMID: 29757994.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    32. VDJServer: A Cloud-Based Analysis Portal and Data Commons for Immune Repertoire Sequences and Rearrangements. Front Immunol. 2018; 9:976. Christley S, Scarborough W, Salinas E, Rounds WH, Toby IT, Fonner JM, Levin MK, Kim M, Mock SA, Jordan C, Ostmeyer J, Buntzman A, Rubelt F, Davila ML, Monson NL, Scheuermann RH, Cowell LG. PMID: 29867956.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansAnimals
    33. Cell type discovery using single-cell transcriptomics: implications for ontological representation. Hum Mol Genet. 2018 05 01; 27(R1):R40-R47. Aevermann BD, Novotny M, Bakken T, Miller JA, Diehl AD, Osumi-Sutherland D, Lasken RS, Lein ES, Scheuermann RH. PMID: 29590361.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCells
    34. DAFi: A directed recursive data filtering and clustering approach for improving and interpreting data clustering identification of cell populations from polychromatic flow cytometry data. Cytometry A. 2018 06; 93(6):597-610. Lee AJ, Chang I, Burel JG, Lindestam Arlehamn CS, Mandava A, Weiskopf D, Peters B, Sette A, Scheuermann RH, Qian Y. PMID: 29665244.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    35. Cell type discovery and representation in the era of high-content single cell phenotyping. BMC Bioinformatics. 2017 12 21; 18(Suppl 17):559. Bakken T, Cowell L, Aevermann BD, Novotny M, Hodge R, Miller JA, Lee A, Chang I, McCorrison J, Pulendran B, Qian Y, Schork NJ, Lasken RS, Lein ES, Scheuermann RH. PMID: 29322913.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansCells
    36. Automated Analysis of Clinical Flow Cytometry Data: A Chronic Lymphocytic Leukemia Illustration. Clin Lab Med. 2017 12; 37(4):931-944. Scheuermann RH, Bui J, Wang HY, Qian Y. PMID: 29128077.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    37. VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data. BMC Bioinformatics. 2017 Oct 11; 18(1):448. Christley S, Levin MK, Toby IT, Fonner JM, Monson NL, Rounds WH, Rubelt F, Scarborough W, Scheuermann RH, Cowell LG. PMID: 29020925.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    38. Automated Analysis of Flow Cytometry Data to Reduce Inter-Lab Variation in the Detection of Major Histocompatibility Complex Multimer-Binding T Cells. Front Immunol. 2017; 8:858. Pedersen NW, Chandran PA, Qian Y, Rebhahn J, Petersen NV, Hoff MD, White S, Lee AJ, Stanton R, Halgreen C, Jakobsen K, Mosmann T, Gouttefangeas C, Chan C, Scheuermann RH, Hadrup SR. PMID: 28798746.
      View in: PubMed   Mentions: 1     Fields:    
    39. Fast and accurate HLA typing from short-read next-generation sequence data with xHLA. Proc Natl Acad Sci U S A. 2017 07 25; 114(30):8059-8064. Xie C, Yeo ZX, Wong M, Piper J, Long T, Kirkness EF, Biggs WH, Bloom K, Spellman S, Vierra-Green C, Brady C, Scheuermann RH, Telenti A, Howard S, Brewerton S, Turpaz Y, Venter JC. PMID: 28674023.
      View in: PubMed   Mentions: 31     Fields:    Translation:Humans
    40. Identification of diagnostic peptide regions that distinguish Zika virus from related mosquito-borne Flaviviruses. PLoS One. 2017; 12(5):e0178199. Lee AJ, Bhattacharya R, Scheuermann RH, Pickett BE. PMID: 28562637.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    41. Allergen-specific immunotherapy modulates the balance of circulating Tfh and Tfr cells. J Allergy Clin Immunol. 2018 02; 141(2):775-777.e6. Schulten V, Tripple V, Seumois G, Qian Y, Scheuermann RH, Fu Z, Locci M, Rosales S, Vijayanand P, Sette A, Alam R, Crotty S, Peters B. PMID: 28506846.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimalsCells
    42. A bioinformatics roadmap for the human vaccines project. Expert Rev Vaccines. 2017 06; 16(6):535-544. Scheuermann RH, Sinkovits RS, Schenkelberg T, Koff WC. PMID: 28434256.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    43. Comprehensive Annotation of Mature Peptides and Genotypes for Zika Virus. PLoS One. 2017; 12(1):e0170462. Sun G, Larsen CN, Baumgarth N, Klem EB, Scheuermann RH. PMID: 28125631.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCellsPHPublic Health
    44. An Integrated Workflow To Assess Technical and Biological Variability of Cell Population Frequencies in Human Peripheral Blood by Flow Cytometry. J Immunol. 2017 02 15; 198(4):1748-1758. Burel JG, Qian Y, Lindestam Arlehamn C, Weiskopf D, Zapardiel-Gonzalo J, Taplitz R, Gilman RH, Saito M, de Silva AD, Vijayanand P, Scheuermann RH, Sette A, Peters B. PMID: 28069807.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansCells
    45. PRODUCTION OF A PRELIMINARY QUALITY CONTROL PIPELINE FOR SINGLE NUCLEI RNA-SEQ AND ITS APPLICATION IN THE ANALYSIS OF CELL TYPE DIVERSITY OF POST-MORTEM HUMAN BRAIN NEOCORTEX. Pac Symp Biocomput. 2017; 22:564-575. Aevermann B, McCorrison J, Venepally P, Hodge R, Bakken T, Miller J, Novotny M, Tran DN, Diezfuertes F, Christiansen L, Zhang F, Steemers F, Lasken RS, Lein ED, Schork N, Scheuermann RH. PMID: 27897007.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    46. A Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A Viruses. mSphere. 2016 Nov-Dec; 1(6). Anderson TK, Macken CA, Lewis NS, Scheuermann RH, Van Reeth K, Brown IH, Swenson SL, Simon G, Saito T, Berhane Y, Ciacci-Zanella J, Pereda A, Davis CT, Donis RO, Webby RJ, Vincent AL. PMID: 27981236.
      View in: PubMed   Mentions: 44     Fields:    
    47. VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements. BMC Bioinformatics. 2016 Oct 06; 17(Suppl 13):333. Toby IT, Levin MK, Salinas EA, Christley S, Bhattacharya S, Breden F, Buntzman A, Corrie B, Fonner J, Gupta NT, Hershberg U, Marthandan N, Rosenfeld A, Rounds W, Rubelt F, Scarborough W, Scott JK, Uduman M, Vander Heiden JA, Scheuermann RH, Monson N, Kleinstein SH, Cowell LG. PMID: 27766961.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    48. Influenza Research Database: An integrated bioinformatics resource for influenza virus research. Nucleic Acids Res. 2017 01 04; 45(D1):D466-D474. Zhang Y, Aevermann BD, Anderson TK, Burke DF, Dauphin G, Gu Z, He S, Kumar S, Larsen CN, Lee AJ, Li X, Macken C, Mahaffey C, Pickett BE, Reardon B, Smith T, Stewart L, Suloway C, Sun G, Tong L, Vincent AL, Walters B, Zaremba S, Zhao H, Zhou L, Zmasek C, Klem EB, Scheuermann RH. PMID: 27679478.
      View in: PubMed   Mentions: 83     Fields:    Translation:Cells
    49. Genetic changes found in a distinct clade of Enterovirus D68 associated with paralysis during the 2014 outbreak. Virus Evol. 2016 Jan; 2(1):vew015. Zhang Y, Cao J, Zhang S, Lee AJ, Sun G, Larsen CN, Zhao H, Gu Z, He S, Klem EB, Scheuermann RH. PMID: 28512577.
      View in: PubMed   Mentions:
    50. The Ontology for Biomedical Investigations. PLoS One. 2016; 11(4):e0154556. Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Chibucos MC, Clancy K, Courtot M, Derom D, Dumontier M, Fan L, Fostel J, Fragoso G, Gibson F, Gonzalez-Beltran A, Haendel MA, He Y, Heiskanen M, Hernandez-Boussard T, Jensen M, Lin Y, Lister AL, Lord P, Malone J, Manduchi E, McGee M, Morrison N, Overton JA, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Schober D, Smith B, Soldatova LN, Stoeckert CJ, Taylor CF, Torniai C, Turner JA, Vita R, Whetzel PL, Zheng J. PMID: 27128319.
      View in: PubMed   Mentions: 46     Fields:    Translation:HumansAnimals
    51. Zika virus: designate standardized names. Nature. 2016 Mar 10; 531(7593):173. Scheuermann RH. PMID: 26961650.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCellsPHPublic Health
    52. Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons. Nat Protoc. 2016 Mar; 11(3):499-524. Krishnaswami SR, Grindberg RV, Novotny M, Venepally P, Lacar B, Bhutani K, Linker SB, Pham S, Erwin JA, Miller JA, Hodge R, McCarthy JK, Kelder M, McCorrison J, Aevermann BD, Fuertes FD, Scheuermann RH, Lee J, Lein ES, Schork N, McConnell MJ, Gage FH, Lasken RS. PMID: 26890679.
      View in: PubMed   Mentions: 94     Fields:    Translation:HumansCells
    53. Standardizing Flow Cytometry Immunophenotyping Analysis from the Human ImmunoPhenotyping Consortium. Sci Rep. 2016 Feb 10; 6:20686. Finak G, Langweiler M, Jaimes M, Malek M, Taghiyar J, Korin Y, Raddassi K, Devine L, Obermoser G, Pekalski ML, Pontikos N, Diaz A, Heck S, Villanova F, Terrazzini N, Kern F, Qian Y, Stanton R, Wang K, Brandes A, Ramey J, Aghaeepour N, Mosmann T, Scheuermann RH, Reed E, Palucka K, Pascual V, Blomberg BB, Nestle F, Nussenblatt RB, Brinkman RR, Gottardo R, Maecker H, McCoy JP. PMID: 26861911.
      View in: PubMed   Mentions: 78     Fields:    Translation:HumansCells
    54. Automated analysis of flow cytometry data comes of age. Cytometry A. 2016 Jan; 89(1):13-5. Brinkman RR, Aghaeepour N, Finak G, Gottardo R, Mosmann T, Scheuermann RH. PMID: 26812230.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    55. A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes. Cytometry A. 2016 Jan; 89(1):16-21. Aghaeepour N, Chattopadhyay P, Chikina M, Dhaene T, Van Gassen S, Kursa M, Lambrecht BN, Malek M, McLachlan GJ, Qian Y, Qiu P, Saeys Y, Stanton R, Tong D, Vens C, Walkowiak S, Wang K, Finak G, Gottardo R, Mosmann T, Nolan GP, Scheuermann RH, Brinkman RR. PMID: 26447924.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansCells
    56. Mapping cell populations in flow cytometry data for cross-sample comparison using the Friedman-Rafsky test statistic as a distance measure. Cytometry A. 2016 Jan; 89(1):71-88. Hsiao C, Liu M, Stanton R, McGee M, Qian Y, Scheuermann RH. PMID: 26274018.
      View in: PubMed   Mentions: 11     Fields:    Translation:Humans
    57. State-of-the-Art in the Computational Analysis of Cytometry Data. Cytometry A. 2015 Jul; 87(7):591-3. Brinkman RR, Aghaeepour N, Finak G, Gottardo R, Mosmann T, Scheuermann RH. PMID: 26111230.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    58. Thinking outside the gate: single-cell assessments in multiple dimensions. Immunity. 2015 Apr 21; 42(4):591-2. Kvistborg P, Gouttefangeas C, Aghaeepour N, Cazaly A, Chattopadhyay PK, Chan C, Eckl J, Finak G, Hadrup SR, Maecker HT, Maurer D, Mosmann T, Qiu P, Scheuermann RH, Welters MJ, Ferrari G, Brinkman RR, Britten CM. PMID: 25902473.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansCells
    59. A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway. Evol Bioinform Online. 2015; 11:43-8. Miller MA, Schwartz T, Pickett BE, He S, Klem EB, Scheuermann RH, Passarotti M, Kaufman S, O'Leary MA. PMID: 25861210.
      View in: PubMed   Mentions:
    60. Diversifying Selection Analysis Predicts Antigenic Evolution of 2009 Pandemic H1N1 Influenza A Virus in Humans. J Virol. 2015 May; 89(10):5427-40. Lee AJ, Das SR, Wang W, Fitzgerald T, Pickett BE, Aevermann BD, Topham DJ, Falsey AR, Scheuermann RH. PMID: 25741011.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCellsPHPublic Health
    61. flowCL: ontology-based cell population labelling in flow cytometry. Bioinformatics. 2015 Apr 15; 31(8):1337-9. Courtot M, Meskas J, Diehl AD, Droumeva R, Gottardo R, Jalali A, Taghiyar MJ, Maecker HT, McCoy JP, Ruttenberg A, Scheuermann RH, Brinkman RR. PMID: 25481008.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    62. A comprehensive collection of systems biology data characterizing the host response to viral infection. Sci Data. 2014; 1:140033. Aevermann BD, Pickett BE, Kumar S, Klem EB, Agnihothram S, Askovich PS, Bankhead A, Bolles M, Carter V, Chang J, Clauss TR, Dash P, Diercks AH, Eisfeld AJ, Ellis A, Fan S, Ferris MT, Gralinski LE, Green RR, Gritsenko MA, Hatta M, Heegel RA, Jacobs JM, Jeng S, Josset L, Kaiser SM, Kelly S, Law GL, Li C, Li J, Long C, Luna ML, Matzke M, McDermott J, Menachery V, Metz TO, Mitchell H, Monroe ME, Navarro G, Neumann G, Podyminogin RL, Purvine SO, Rosenberger CM, Sanders CJ, Schepmoes AA, Shukla AK, Sims A, Sova P, Tam VC, Tchitchek N, Thomas PG, Tilton SC, Totura A, Wang J, Webb-Robertson BJ, Wen J, Weiss JM, Yang F, Yount B, Zhang Q, McWeeney S, Smith RD, Waters KM, Kawaoka Y, Baric R, Aderem A, Katze MG, Scheuermann RH. PMID: 25977790.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansAnimalsCells
    63. Toward a method for tracking virus evolutionary trajectory applied to the pandemic H1N1 2009 influenza virus. Infect Genet Evol. 2014 Dec; 28:351-7. Squires RB, Pickett BE, Das S, Scheuermann RH. PMID: 25064525.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCellsPHPublic Health
    64. Standardized metadata for human pathogen/vector genomic sequences. PLoS One. 2014; 9(6):e99979. Dugan VG, Emrich SJ, Giraldo-Calderón GI, Harb OS, Newman RM, Pickett BE, Schriml LM, Stockwell TB, Stoeckert CJ, Sullivan DE, Singh I, Ward DV, Yao A, Zheng J, Barrett T, Birren B, Brinkac L, Bruno VM, Caler E, Chapman S, Collins FH, Cuomo CA, Di Francesco V, Durkin S, Eppinger M, Feldgarden M, Fraser C, Fricke WF, Giovanni M, Henn MR, Hine E, Hotopp JD, Karsch-Mizrachi I, Kissinger JC, Lee EM, Mathur P, Mongodin EF, Murphy CI, Myers G, Neafsey DE, Nelson KE, Nierman WC, Puzak J, Rasko D, Roos DS, Sadzewicz L, Silva JC, Sobral B, Squires RB, Stevens RL, Tallon L, Tettelin H, Wentworth D, White O, Will R, Wortman J, Zhang Y, Scheuermann RH. PMID: 24936976.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansAnimals
    65. Response of human skin to esthetic scarification. Burns. 2014 Nov; 40(7):1338-44. Gabriel VA, McClellan EA, Scheuermann RH. PMID: 24582755.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    66. GenePattern flow cytometry suite. Source Code Biol Med. 2013 Jul 03; 8(1):14. Spidlen J, Barsky A, Breuer K, Carr P, Nazaire MD, Hill BA, Qian Y, Liefeld T, Reich M, Mesirov JP, Wilkinson P, Scheuermann RH, Sekaly RP, Brinkman RR. PMID: 23822732.
      View in: PubMed   Mentions:
    67. Extracting actionable findings of appendicitis from radiology reports using natural language processing. AMIA Jt Summits Transl Sci Proc. 2013; 2013:221. Rink B, Roberts K, Harabagiu S, Scheuermann RH, Toomay S, Browning T, Bosler T, Peshock R. PMID: 24303268.
      View in: PubMed   Mentions:
    68. Critical assessment of automated flow cytometry data analysis techniques. Nat Methods. 2013 Mar; 10(3):228-38. Aghaeepour N, Finak G, FlowCAP Consortium , DREAM Consortium , Hoos H, Mosmann TR, Brinkman R, Gottardo R, Scheuermann RH. PMID: 23396282.
      View in: PubMed   Mentions: 145     Fields:    Translation:HumansAnimalsCells
    69. Virus pathogen database and analysis resource (ViPR): a comprehensive bioinformatics database and analysis resource for the coronavirus research community. Viruses. 2012 Nov 19; 4(11):3209-26. Pickett BE, Greer DS, Zhang Y, Stewart L, Zhou L, Sun G, Gu Z, Kumar S, Zaremba S, Larsen CN, Jen W, Klem EB, Scheuermann RH. PMID: 23202522.
      View in: PubMed   Mentions: 44     Fields:    Translation:HumansCells
    70. A machine learning approach for identifying anatomical locations of actionable findings in radiology reports. AMIA Annu Symp Proc. 2012; 2012:779-88. Roberts K, Rink B, Harabagiu SM, Scheuermann RH, Toomay S, Browning T, Bosler T, Peshock R. PMID: 23304352.
      View in: PubMed   Mentions: 11     Fields:    Translation:Humans
    71. FCSTrans: an open source software system for FCS file conversion and data transformation. Cytometry A. 2012 May; 81(5):353-356. Qian Y, Liu Y, Campbell J, Thomson E, Kong YM, Scheuermann RH. PMID: 22431383.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    72. Influenza virus sequence feature variant type analysis: evidence of a role for NS1 in influenza virus host range restriction. J Virol. 2012 May; 86(10):5857-66. Noronha JM, Liu M, Squires RB, Pickett BE, Hale BG, Air GM, Galloway SE, Takimoto T, Schmolke M, Hunt V, Klem E, García-Sastre A, McGee M, Scheuermann RH. PMID: 22398283.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansCells
    73. Influenza research database: an integrated bioinformatics resource for influenza research and surveillance. Influenza Other Respir Viruses. 2012 Nov; 6(6):404-16. Squires RB, Noronha J, Hunt V, García-Sastre A, Macken C, Baumgarth N, Suarez D, Pickett BE, Zhang Y, Larsen CN, Ramsey A, Zhou L, Zaremba S, Kumar S, Deitrich J, Klem E, Scheuermann RH. PMID: 22260278.
      View in: PubMed   Mentions: 145     Fields:    Translation:HumansAnimalsCells
    74. A gene selection method for GeneChip array data with small sample sizes. BMC Genomics. 2011 Dec 23; 12 Suppl 5:S7. Chen Z, Liu Q, McGee M, Kong M, Huang X, Deng Y, Scheuermann RH. PMID: 22369149.
      View in: PubMed   Mentions: 4     Fields:    
    75. Minimum Information about a Genotyping Experiment (MIGEN). Stand Genomic Sci. 2011 Nov 30; 5(2):224-9. Huang J, Mirel D, Pugh E, Xing C, Robinson PN, Pertsemlidis A, Ding L, Kozlitina J, Maher J, Rios J, Story M, Marthandan N, Scheuermann RH. PMID: 22180825.
      View in: PubMed   Mentions:
    76. ViPR: an open bioinformatics database and analysis resource for virology research. Nucleic Acids Res. 2012 Jan; 40(Database issue):D593-8. Pickett BE, Sadat EL, Zhang Y, Noronha JM, Squires RB, Hunt V, Liu M, Kumar S, Zaremba S, Gu Z, Zhou L, Larson CN, Dietrich J, Klem EB, Scheuermann RH. PMID: 22006842.
      View in: PubMed   Mentions: 223     Fields:    Translation:Cells
    77. Ontologies for clinical and translational research: Introduction. J Biomed Inform. 2011 Feb; 44(1):3-7. Smith B, Scheuermann RH. PMID: 21241822.
      View in: PubMed   Mentions: 6     Fields:    
    78. Identifying Differentially Expressed Genes based on probe level data for GeneChip arrays. Int J Comput Biol Drug Des. 2010; 3(3):237-57. Chen Z, McGee M, Liu Q, Kong YM, Huang X, Yang JY, Scheuermann RH. PMID: 21228458.
      View in: PubMed   Mentions: 3     Fields:    
    79. Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop. Viruses. 2010 Oct; 2(10):2258-68. Brister JR, Bao Y, Kuiken C, Lefkowitz EJ, Le Mercier P, Leplae R, Madupu R, Scheuermann RH, Schobel S, Seto D, Shrivastava S, Sterk P, Zeng Q, Klimke W, Tatusova T. PMID: 21994619.
      View in: PubMed   Mentions: 11     Fields:    
    80. Personalized care, comparative effectiveness research and the electronic health record. Curr Opin Allergy Clin Immunol. 2010 Jun; 10(3):168-70. Scheuermann RH, Milgrom H. PMID: 20431366.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    81. Toward an ontology-based framework for clinical research databases. J Biomed Inform. 2011 Feb; 44(1):48-58. Kong YM, Dahlke C, Xiang Q, Qian Y, Karp D, Scheuermann RH. PMID: 20460173.
      View in: PubMed   Mentions: 14     Fields:    
    82. The human studies database project: federating human studies design data using the ontology of clinical research. Summit Transl Bioinform. 2010 Mar 01; 2010:51-5. Sim I, Carini S, Tu S, Wynden R, Pollock BH, Mollah SA, Gabriel D, Hagler HK, Scheuermann RH, Lehmann HP, Wittkowski KM, Nahm M, Bakken S. PMID: 21347149.
      View in: PubMed   Mentions:
    83. GO-Bayes: Gene Ontology-based overrepresentation analysis using a Bayesian approach. Bioinformatics. 2010 Apr 01; 26(7):905-11. Zhang S, Cao J, Kong YM, Scheuermann RH. PMID: 20176581.
      View in: PubMed   Mentions: 14     Fields:    Translation:Humans
    84. Hematopoietic cell types: prototype for a revised cell ontology. J Biomed Inform. 2011 Feb; 44(1):75-9. Diehl AD, Augustine AD, Blake JA, Cowell LG, Gold ES, Gondré-Lewis TA, Masci AM, Meehan TF, Morel PA, Nijnik A, Peters B, Pulendran B, Scheuermann RH, Yao QA, Zand MS, Mungall CJ. PMID: 20123131.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansAnimalsCells
    85. Technical and policy approaches to balancing patient privacy and data sharing in clinical and translational research. J Investig Med. 2010 Jan; 58(1):11-8. Malin B, Karp D, Scheuermann RH. PMID: 20051768.
      View in: PubMed   Mentions: 36     Fields:    Translation:HumansCells
    86. Elucidation of seventeen human peripheral blood B-cell subsets and quantification of the tetanus response using a density-based method for the automated identification of cell populations in multidimensional flow cytometry data. Cytometry B Clin Cytom. 2010; 78 Suppl 1:S69-82. Qian Y, Wei C, Eun-Hyung Lee F, Campbell J, Halliley J, Lee JA, Cai J, Kong YM, Sadat E, Thomson E, Dunn P, Seegmiller AC, Karandikar NJ, Tipton CM, Mosmann T, Sanz I, Scheuermann RH. PMID: 20839340.
      View in: PubMed   Mentions: 80     Fields:    Translation:HumansCellsPHPublic Health
    87. Sequence feature variant type (SFVT) analysis of the HLA genetic association in juvenile idiopathic arthritis. Pac Symp Biocomput. 2010; 359-70. Thomson G, Marthandan N, Hollenbach JA, Mack SJ, Erlich HA, Single RM, Waller MJ, Marsh SG, Guidry PA, Karp DR, Scheuermann RH, Thompson SD, Glass DN, Helmberg W. PMID: 19908388.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    88. Deterministic graph-theoretic algorithm for detecting modules in biological interaction networks. Int J Bioinform Res Appl. 2010; 6(2):101-19. Chang RL, Luo F, Johnson S, Scheuermann RH. PMID: 20223734.
      View in: PubMed   Mentions: 2     Fields:    
    89. Novel sequence feature variant type analysis of the HLA genetic association in systemic sclerosis. Hum Mol Genet. 2010 Feb 15; 19(4):707-19. Karp DR, Marthandan N, Marsh SG, Ahn C, Arnett FC, Deluca DS, Diehl AD, Dunivin R, Eilbeck K, Feolo M, Guidry PA, Helmberg W, Lewis S, Mayes MD, Mungall C, Natale DA, Peters B, Petersdorf E, Reveille JD, Smith B, Thomson G, Waller MJ, Scheuermann RH. PMID: 19933168.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansCells
    90. Pre-existing immunity against swine-origin H1N1 influenza viruses in the general human population. Proc Natl Acad Sci U S A. 2009 Dec 01; 106(48):20365-70. Greenbaum JA, Kotturi MF, Kim Y, Oseroff C, Vaughan K, Salimi N, Vita R, Ponomarenko J, Scheuermann RH, Sette A, Peters B. PMID: 19918065.
      View in: PubMed   Mentions: 158     Fields:    Translation:HumansCells
    91. Development and evaluation of a study design typology for human research. AMIA Annu Symp Proc. 2009 Nov 14; 2009:81-5. Carini S, Pollock BH, Lehmann HP, Bakken S, Barbour EM, Gabriel D, Hagler HK, Harper CR, Mollah SA, Nahm M, Nguyen HH, Scheuermann RH, Sim I. PMID: 20351827.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    92. Complete genome sequence of Francisella tularensis subspecies holarctica FTNF002-00. PLoS One. 2009 Sep 16; 4(9):e7041. Barabote RD, Xie G, Brettin TS, Hinrichs SH, Fey PD, Jay JJ, Engle JL, Godbole SD, Noronha JM, Scheuermann RH, Zhou LW, Lion C, Dempsey MP. PMID: 19756146.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansCells
    93. A Distribution-Free Convolution Model for background correction of oligonucleotide microarray data. BMC Genomics. 2009 Jul 07; 10 Suppl 1:S19. Chen Z, McGee M, Liu Q, Kong M, Deng Y, Scheuermann RH. PMID: 19594878.
      View in: PubMed   Mentions: 5     Fields:    
    94. Synergies and distinctions between computational disciplines in biomedical research: perspective from the Clinical andTranslational Science Award programs. Acad Med. 2009 Jul; 84(7):964-70. Bernstam EV, Hersh WR, Johnson SB, Chute CG, Nguyen H, Sim I, Nahm M, Weiner MG, Miller P, DiLaura RP, Overcash M, Lehmann HP, Eichmann D, Athey BD, Scheuermann RH, Anderson N, Starren J, Harris PA, Smith JW, Barbour E, Silverstein JC, Krusch DA, Nagarajan R, Becich MJ, CTSA Biomedical Informatics Key Function Committee . PMID: 19550198.
      View in: PubMed   Mentions: 16     Fields:    Translation:Humans
    95. FuGEFlow: data model and markup language for flow cytometry. BMC Bioinformatics. 2009 Jun 16; 10:184. Qian Y, Tchuvatkina O, Spidlen J, Wilkinson P, Gasparetto M, Jones AR, Manion FJ, Scheuermann RH, Sekaly RP, Brinkman RR. PMID: 19531228.
      View in: PubMed   Mentions: 1     Fields:    
    96. Core and periphery structures in protein interaction networks. BMC Bioinformatics. 2009 Apr 29; 10 Suppl 4:S8. Luo F, Li B, Wan XF, Scheuermann RH. PMID: 19426456.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    97. Toward an ontological treatment of disease and diagnosis. Summit Transl Bioinform. 2009 Mar 01; 2009:116-20. Scheuermann RH, Ceusters W, Smith B. PMID: 21347182.
      View in: PubMed   Mentions:
    98. An improved ontological representation of dendritic cells as a paradigm for all cell types. BMC Bioinformatics. 2009 Feb 25; 10:70. Masci AM, Arighi CN, Diehl AD, Lieberman AE, Mungall C, Scheuermann RH, Smith B, Cowell LG. PMID: 19243617.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells
    99. Keeping raw data in context. Science. 2009 Feb 06; 323(5915):713. Sim I, Chute CG, Lehmann H, Nagarajan R, Nahm M, Scheuermann RH. PMID: 19197039.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    100. MIFlowCyt: the minimum information about a Flow Cytometry Experiment. Cytometry A. 2008 Oct; 73(10):926-30. Lee JA, Spidlen J, Boyce K, Cai J, Crosbie N, Dalphin M, Furlong J, Gasparetto M, Goldberg M, Goralczyk EM, Hyun B, Jansen K, Kollmann T, Kong M, Leif R, McWeeney S, Moloshok TD, Moore W, Nolan G, Nolan J, Nikolich-Zugich J, Parrish D, Purcell B, Qian Y, Selvaraj B, Smith C, Tchuvatkina O, Wertheimer A, Wilkinson P, Wilson C, Wood J, Zigon R, International Society for Advancement of Cytometry Data Standards Task Force , Scheuermann RH, Brinkman RR. PMID: 18752282.
      View in: PubMed   Mentions: 110     Fields:    
    101. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol. 2008 Aug; 26(8):889-96. Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T, Brazma A, Brinkman RR, Michael Clark A, Deutsch EW, Fiehn O, Fostel J, Ghazal P, Gibson F, Gray T, Grimes G, Hancock JM, Hardy NW, Hermjakob H, Julian RK, Kane M, Kettner C, Kinsinger C, Kolker E, Kuiper M, Le Novère N, Leebens-Mack J, Lewis SE, Lord P, Mallon AM, Marthandan N, Masuya H, McNally R, Mehrle A, Morrison N, Orchard S, Quackenbush J, Reecy JM, Robertson DG, Rocca-Serra P, Rodriguez H, Rosenfelder H, Santoyo-Lopez J, Scheuermann RH, Schober D, Smith B, Snape J, Stoeckert CJ, Tipton K, Sterk P, Untergasser A, Vandesompele J, Wiemann S. PMID: 18688244.
      View in: PubMed   Mentions: 202     Fields:    
    102. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol. 2007 Nov; 25(11):1251-5. Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, OBI Consortium , Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S. PMID: 17989687.
      View in: PubMed   Mentions: 654     Fields:    Translation:Humans
    103. BioHealthBase: informatics support in the elucidation of influenza virus host pathogen interactions and virulence. Nucleic Acids Res. 2008 Jan; 36(Database issue):D497-503. Squires B, Macken C, Garcia-Sastre A, Godbole S, Noronha J, Hunt V, Chang R, Larsen CN, Klem E, Biersack K, Scheuermann RH. PMID: 17965094.
      View in: PubMed   Mentions: 38     Fields:    Translation:HumansAnimalsCells
    104. Complete genomic characterization of a pathogenic A.II strain of Francisella tularensis subspecies tularensis. PLoS One. 2007 Sep 26; 2(9):e947. Beckstrom-Sternberg SM, Auerbach RK, Godbole S, Pearson JV, Beckstrom-Sternberg JS, Deng Z, Munk C, Kubota K, Zhou Y, Bruce D, Noronha J, Scheuermann RH, Wang A, Wei X, Wang J, Hao J, Wagner DM, Brettin TS, Brown N, Gilna P, Keim PS. PMID: 17895988.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansCells
    105. National Institute of Allergy and Infectious Diseases bioinformatics resource centers: new assets for pathogen informatics. Infect Immun. 2007 Jul; 75(7):3212-9. Greene JM, Collins F, Lefkowitz EJ, Roos D, Scheuermann RH, Sobral B, Stevens R, White O, Di Francesco V. PMID: 17420237.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    106. Ontology development for biological systems: immunology. Bioinformatics. 2007 Apr 01; 23(7):913-5. Diehl AD, Lee JA, Scheuermann RH, Blake JA. PMID: 17267433.
      View in: PubMed   Mentions: 16     Fields:    
    107. A distribution free summarization method for Affymetrix GeneChip arrays. Bioinformatics. 2007 Feb 01; 23(3):321-7. Chen Z, McGee M, Liu Q, Scheuermann RH. PMID: 17148508.
      View in: PubMed   Mentions: 32     Fields:    
    108. Modular organization of protein interaction networks. Bioinformatics. 2007 Jan 15; 23(2):207-14. Luo F, Yang Y, Chen CF, Chang R, Zhou J, Scheuermann RH. PMID: 17092991.
      View in: PubMed   Mentions: 42     Fields:    Translation:AnimalsCells
    109. Cancer dormancy: from mice to man. . 2006 Aug; 5(16):1772-8. Marches R, Scheuermann R, Uhr J. PMID: 16929181.
      View in: PubMed   Mentions:
    110. Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation. BMC Bioinformatics. 2006 May 02; 7:237. Lee JA, Sinkovits RS, Mock D, Rab EL, Cai J, Yang P, Saunders B, Hsueh RC, Choi S, Subramaniam S, Scheuermann RH, Alliance for Cellular Signaling . PMID: 16670020.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansCells
    111. Nucleic acid testing for viral burden and viral genotyping. Clin Chim Acta. 2006 Jan; 363(1-2):197-205. Domiati-Saad R, Scheuermann RH. PMID: 16098959.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    112. Analysis of the major patterns of B cell gene expression changes in response to short-term stimulation with 33 single ligands. J Immunol. 2004 Dec 15; 173(12):7141-9. Zhu X, Hart R, Chang MS, Kim JW, Lee SY, Cao YA, Mock D, Ke E, Saunders B, Alexander A, Grossoehme J, Lin KM, Yan Z, Hsueh R, Lee J, Scheuermann RH, Fruman DA, Seaman W, Subramaniam S, Sternweis P, Simon MI, Choi S. PMID: 15585835.
      View in: PubMed   Mentions: 34     Fields:    Translation:AnimalsCells
    113. Development of real-time PCR assays for the quantitative detection of Epstein-Barr virus and cytomegalovirus, comparison of TaqMan probes, and molecular beacons. J Mol Diagn. 2003 Feb; 5(1):15-20. Jebbink J, Bai X, Rogers BB, Dawson DB, Scheuermann RH, Domiati-Saad R. PMID: 12552075.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansCells
    114. Overview of the Alliance for Cellular Signaling. Nature. 2002 Dec 12; 420(6916):703-6. Gilman AG, Simon MI, Bourne HR, Harris BA, Long R, Ross EM, Stull JT, Taussig R, Bourne HR, Arkin AP, Cobb MH, Cyster JG, Devreotes PN, Ferrell JE, Fruman D, Gold M, Weiss A, Stull JT, Berridge MJ, Cantley LC, Catterall WA, Coughlin SR, Olson EN, Smith TF, Brugge JS, Botstein D, Dixon JE, Hunter T, Lefkowitz RJ, Pawson AJ, Sternberg PW, Varmus H, Subramaniam S, Sinkovits RS, Li J, Mock D, Ning Y, Saunders B, Sternweis PC, Hilgemann D, Scheuermann RH, DeCamp D, Hsueh R, Lin KM, Ni Y, Seaman WE, Simpson PC, O'Connell TD, Roach T, Simon MI, Choi S, Eversole-Cire P, Fraser I, Mumby MC, Zhao Y, Brekken D, Shu H, Meyer T, Chandy G, Heo WD, Liou J, O'Rourke N, Verghese M, Mumby SM, Han H, Brown HA, Forrester JS, Ivanova P, Milne SB, Casey PJ, Harden TK, Arkin AP, Doyle J, Gray ML, Meyer T, Michnick S, Schmidt MA, Toner M, Tsien RY, Natarajan M, Ranganathan R, Sambrano GR, Participating investigators and scientists of the Alliance for Cellular Signaling . PMID: 12478301.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansCells
    115. Activation of the Syk tyrosine kinase is insufficient for downstream signal transduction in B lymphocytes. BMC Immunol. 2002 Dec 06; 3:16. Hsueh RC, Hammill AM, Lee JA, Uhr JW, Scheuermann RH. PMID: 12470302.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    116. A novel colonic repressor element regulates intestinal gene expression by interacting with Cux/CDP. Mol Cell Biol. 2002 Aug; 22(15):5467-78. Boudreau F, Rings EH, Swain GP, Sinclair AM, Suh ER, Silberg DG, Scheuermann RH, Traber PG. PMID: 12101240.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    117. Presence of simian virus 40 DNA sequences in human lymphomas. Lancet. 2002 Mar 09; 359(9309):851-2. Shivapurkar N, Harada K, Reddy J, Scheuermann RH, Xu Y, McKenna RW, Milchgrub S, Kroft SH, Feng Z, Gazdar AF. PMID: 11897287.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansCells
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