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Richard Scheuermann

Title(s)Adjunct Professor, Pathology
SchoolHealth Sciences
Address9500 Gilman Drive #0612
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
    Transformative Computational Infrastructures for Cell-Based Biomarker Diagnostics
    NIH/NCATS U01TR001801Sep 15, 2016 - Jun 30, 2021
    Role: Co-Principal Investigator
    Somatic Mutation in the Etiology of Multiple Sclerosis
    NIH/NIAID R21AI122100Jul 1, 2016 - Jun 30, 2018
    Role: Principal Investigator
    Bioinformatics Resource Center
    NIH/NIAID 272200900041C-1-0-1Oct 1, 2009 - Sep 30, 2014
    Role: Principal Investigator
    Bioinformatics Resource Center
    NIH/NIAID 272200900041C-1-0-9Oct 1, 2009 - Sep 30, 2014
    Role: Principal Investigator
    Bioinformatics Integration Support Contract for Biodefense
    NIH/NIAID N01AI40076-11-0-1Sep 29, 2004 - Dec 31, 2011
    Role: Principal Investigator
    Bioinformatics Integration Support Contract for Immune-Mediated Diseases
    NIH/NIAID N01AI40076-11-0-2Sep 29, 2004 - Dec 31, 2011
    Role: Principal Investigator
    Bioinformatics Integration Support Contract for Biodefense
    NIH/NIAID N01AI40076-10-0-1Sep 29, 2004 - Sep 29, 2010
    Role: Principal Investigator
    BIOINFORMATICS RESOURCE CENTERS
    NIH/NIAID 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/NIAID R01AI056216Jul 1, 2003 - Dec 31, 2008
    Role: Principal Investigator
    Database development and modeling of signal transduction
    NIH/NCI F33CA094654May 2, 2002
    Role: Principal Investigator
    POPULATION STABILITY IN TUMOR DORMANCY
    NIH/NCI R01CA078793Aug 1, 1998 - May 31, 2004
    Role: Principal Investigator
    MINIMAL RESIDUAL DISEASE EVALUATION TO GUIDE THERAPY
    NIH/NCI R21CA074965Jul 1, 1998 - Jun 30, 2000
    Role: Principal Investigator
    CELL-TYPE SPECIFIC SUPPRESSION OF THE IGH ENHANCER
    NIH/NIGMS R01GM050329Sep 15, 1994 - Feb 29, 2000
    Role: Principal Investigator
    CELL TYPE SPECIFIC SUPPRESSION OF THE IGH ENHANCER
    NIH/NIGMS R55GM050329Sep 15, 1994 - Feb 29, 1996
    Role: Principal Investigator
    Integrative Immunology Training Program
    NIH/NIAID T32AI005284Jul 1, 1980 - May 31, 2019
    Role: Co-Principal Investigator
    Bioinformatics Integration Support Contract for Biodefense
    NIH/NIAID N01AI40076Sep 29, 2010
    Role: Co-Principal Investigator

    Collapse ORNG Applications 
    Collapse Websites

    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.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    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. Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable. Proc Natl Acad Sci U S A. 2020 May 07. 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: 2     Fields:    Translation:HumansCellsPHPublic Health
    2. 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:
    3. 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: 15     Fields:    Translation:HumansCellsPHPublic Health
    4. 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:    Fields:    Translation:HumansAnimalsCells
    5. Machine Learning of Discriminative Gate Locations for Clinical Diagnosis. Cytometry A. 2020 Mar; 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:    Fields:    
    6. 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:    Fields:    Translation:HumansCells
    7. 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: 9     Fields:    Translation:HumansAnimalsCells
    8. 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: 1     Fields:    
    9. 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:    Fields:    Translation:Cells
    10. 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:    Fields:    Translation:HumansCells
    11. 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: 10     Fields:    Translation:AnimalsCells
    12. 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: 8     Fields:    Translation:HumansAnimalsCells
    13. 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: 2     Fields:    Translation:HumansCells
    14. 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: 13     Fields:    Translation:HumansCells
    15. 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: 1     Fields:    Translation:HumansCells
    16. 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: 5     Fields:    Translation:HumansAnimals
    17. 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: 3     Fields:    Translation:HumansCells
    18. 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: 2     Fields:    Translation:HumansCells
    19. 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: 4     Fields:    Translation:HumansCells
    20. 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:    Fields:    Translation:Humans
    21. 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
    22. 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:    
    23. 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: 12     Fields:    Translation:Humans
    24. 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: 6     Fields:    Translation:AnimalsCells
    25. 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: 3     Fields:    Translation:HumansAnimalsCells
    26. 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:    Fields:    Translation:Humans
    27. 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: 4     Fields:    Translation:HumansCellsPHPublic Health
    28. 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: 3     Fields:    Translation:HumansCells
    29. 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: 1     Fields:    Translation:HumansCells
    30. 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: 14     Fields:    
    31. 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: 6     Fields:    Translation:Humans
    32. 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: 31     Fields:    Translation:Cells
    33. 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:
    34. 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: 24     Fields:    Translation:HumansAnimals
    35. 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
    36. 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: 40     Fields:    Translation:HumansCells
    37. 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: 42     Fields:    Translation:HumansCells
    38. 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: 1     Fields:    Translation:Humans
    39. 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: 11     Fields:    Translation:HumansCells
    40. 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: 5     Fields:    Translation:Humans
    41. Molecular Profile of Mitochondrial Dysfunction in Kidney Transplant Biopsies Is Associated With Poor Allograft Outcome. Transplant Proc. 2015 Jul-Aug; 47(6):1675-82. Zepeda-Orozco D, Kong M, Scheuermann RH. PMID: 26293032.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    42. 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: 1     Fields:    Translation:HumansCells
    43. 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: 14     Fields:    Translation:HumansCells
    44. 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:
    45. 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: 9     Fields:    Translation:HumansCellsPHPublic Health
    46. 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: 5     Fields:    Translation:Humans
    47. 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: 9     Fields:    Translation:HumansAnimalsCells
    48. 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
    49. 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: 13     Fields:    Translation:HumansAnimals
    50. 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
    51. Metadata-driven comparative analysis tool for sequences (meta-CATS): an automated process for identifying significant sequence variations that correlate with virus attributes. Virology. 2013 Dec; 447(1-2):45-51. Pickett BE, Liu M, Sadat EL, Squires RB, Noronha JM, He S, Jen W, Zaremba S, Gu Z, Zhou L, Larsen CN, Bosch I, Gehrke L, McGee M, Klem EB, Scheuermann RH. PMID: 24210098.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    52. 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:
    53. 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:
    54. Critical assessment of automated flow cytometry data analysis techniques. Nat Methods. 2013 Mar; 10(3):228-38. Aghaeepour N, Finak G, Hoos H, Mosmann TR, Brinkman R, Gottardo R, Scheuermann RH. PMID: 23396282.
      View in: PubMed   Mentions: 111     Fields:    Translation:HumansAnimalsCells
    55. Photo-induced persistent inversion of germanium in a 200-nm-deep surface region. Sci Rep. 2013; 3:2569. Prokscha T, Chow KH, Stilp E, Suter A, Luetkens H, Morenzoni E, Nieuwenhuys GJ, Salman Z, Scheuermann R. PMID: 23995307.
      View in: PubMed   Mentions: 1     Fields:    
    56. 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: 21     Fields:    Translation:HumansCells
    57. 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: 4     Fields:    Translation:Humans
    58. 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
    59. 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: 15     Fields:    Translation:HumansCells
    60. 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: 119     Fields:    Translation:HumansAnimalsCells
    61. 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: 3     Fields:    
    62. 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:
    63. 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: 118     Fields:    Translation:Cells
    64. 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: 4     Fields:    
    65. 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:    
    66. 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: 8     Fields:    
    67. A unique antibody gene signature is prevalent in the central nervous system of patients with multiple sclerosis. J Neuroimmunol. 2010 Sep 14; 226(1-2):192-3. Ligocki AJ, Lovato L, Xiang D, Guidry P, Scheuermann RH, Willis SN, Almendinger S, Racke MK, Frohman EM, Hafler DA, O'Connor KC, Monson NL. PMID: 20655601.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    68. 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
    69. 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: 13     Fields:    
    70. 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:
    71. 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: 12     Fields:    Translation:Humans
    72. 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: 17     Fields:    Translation:HumansAnimalsCells
    73. 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: 70     Fields:    Translation:HumansCellsPHPublic Health
    74. 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: 31     Fields:    Translation:HumansCells
    75. 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: 8     Fields:    Translation:Humans
    76. 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:    
    77. 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: 18     Fields:    Translation:HumansCells
    78. 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: 145     Fields:    Translation:HumansCells
    79. 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
    80. 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: 19     Fields:    Translation:HumansCells
    81. 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: 4     Fields:    
    82. 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. PMID: 19550198.
      View in: PubMed   Mentions: 13     Fields:    Translation:Humans
    83. 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:    
    84. 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
    85. 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:
    86. 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: 18     Fields:    Translation:Cells
    87. 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: 2     Fields:    Translation:Humans
    88. 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, Scheuermann RH, Brinkman RR. PMID: 18752282.
      View in: PubMed   Mentions: 78     Fields:    
    89. 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: 176     Fields:    
    90. 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, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S. PMID: 17989687.
      View in: PubMed   Mentions: 575     Fields:    Translation:Humans
    91. 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: 37     Fields:    Translation:HumansAnimalsCells
    92. 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: 25     Fields:    Translation:HumansCells
    93. 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
    94. 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: 14     Fields:    
    95. 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: 29     Fields:    
    96. 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: 41     Fields:    Translation:AnimalsCells
    97. Cancer dormancy: from mice to man. Cell Cycle. 2006 Aug; 5(16):1772-8. Marches R, Scheuermann R, Uhr J. PMID: 16929181.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
    98. 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. PMID: 16670020.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansCells
    99. 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
    100. 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: 33     Fields:    Translation:AnimalsCells
    101. 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: 13     Fields:    Translation:HumansCells
    102. 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. PMID: 12478301.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansCells
    103. 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
    104. 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
    105. 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: 22     Fields:    Translation:HumansCells
    106. Lymphoid apoptosis and myeloid hyperplasia in CCAAT displacement protein mutant mice. Blood. 2001 Dec 15; 98(13):3658-67. Sinclair AM, Lee JA, Goldstein A, Xing D, Liu S, Ju R, Tucker PW, Neufeld EJ, Scheuermann RH. PMID: 11739170.
      View in: PubMed   Mentions: 41     Fields:    Translation:AnimalsCells
    107. Prevalence and cellular reservoir of latent human herpesvirus 6 in tonsillar lymphoid tissue. Am J Clin Pathol. 2001 Nov; 116(5):648-54. Roush KS, Domiati-Saad RK, Margraf LR, Krisher K, Scheuermann RH, Rogers BB, Dawson DB. PMID: 11710680.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    108. Connection between B lymphocyte and osteoclast differentiation pathways. J Immunol. 2001 Sep 01; 167(5):2625-31. Manabe N, Kawaguchi H, Chikuda H, Miyaura C, Inada M, Nagai R, Nabeshima Y, Nakamura K, Sinclair AM, Scheuermann RH, Kuro-o M. PMID: 11509604.
      View in: PubMed   Mentions: 38     Fields:    Translation:HumansAnimalsCells
    109. Transcriptional activation by a matrix associating region-binding protein. contextual requirements for the function of bright. J Biol Chem. 2001 Jun 15; 276(24):21325-30. Kaplan MH, Zong RT, Herrscher RF, Scheuermann RH, Tucker PW. PMID: 11294836.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCells
    110. Diagnostic applications of quantitative polymerase chain reaction for cytomegalovirus. Methods Mol Med. 2001; 49:337-51. Scheuermann RH, Bai X. PMID: 21370152.
      View in: PubMed   Mentions:    Fields:    
    111. Predictive value of quantitative PCR-based viral burden analysis for eight human herpesviruses in pediatric solid organ transplant patients. J Mol Diagn. 2000 Nov; 2(4):191-201. Bai X, Rogers BB, Harkins PC, Sommerauer J, Squires R, Rotondo K, Quan A, Dawson DB, Scheuermann RH. PMID: 11232109.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    112. Kinetics of early therapeutic response as measured by quantitative PCR predicts survival in a murine xenograft model of human T cell acute lymphoblastic leukemia. Leukemia. 2000 Jul; 14(7):1215-24. Hosler GA, Bash R, Scheuermann RH. PMID: 10914545.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    113. Tyrosine kinase activation in the decision between growth, differentiation, and death responses initiated from the B cell antigen receptor. Adv Immunol. 2000; 75:283-316. Hsueh RC, Scheuermann RH. PMID: 10879287.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansCells
    114. Annexin V staining due to loss of membrane asymmetry can be reversible and precede commitment to apoptotic death. Exp Cell Res. 1999 Aug 25; 251(1):16-21. Hammill AK, Uhr JW, Scheuermann RH. PMID: 10438567.
      View in: PubMed   Mentions: 33     Fields:    Translation:AnimalsCells
    115. Quantitation of 8 human herpesviruses in peripheral blood of human immunodeficiency virus-infected patients and healthy blood donors by polymerase chain reaction. Am J Clin Pathol. 1999 May; 111(5):655-9. Hoang MP, Rogers BB, Dawson DB, Scheuermann RH. PMID: 10230356.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    116. Development and validation of a quantitative polymerase chain reaction assay to evaluate minimal residual disease for T-cell acute lymphoblastic leukemia and follicular lymphoma. Am J Pathol. 1999 Apr; 154(4):1023-35. Hosler GA, Bash RO, Bai X, Jain V, Scheuermann RH. PMID: 10233841.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    117. Human herpesvirus-6 and sudden death in infancy: report of a case and review of the literature. J Forensic Sci. 1999 Mar; 44(2):432-7. Hoang MP, Ross KF, Dawson DB, Scheuermann RH, Rogers BB. PMID: 10097377.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    118. Cancer dormancy. VII. A regulatory role for CD8+ T cells and IFN-gamma in establishing and maintaining the tumor-dormant state. J Immunol. 1999 Mar 01; 162(5):2842-9. Farrar JD, Katz KH, Windsor J, Thrush G, Scheuermann RH, Uhr JW, Street NE. PMID: 10072532.
      View in: PubMed   Mentions: 23     Fields:    Translation:AnimalsCellsPHPublic Health
    119. Antigen receptor signaling induces differential tyrosine kinase activation and population stability in B-cell lymphoma. Curr Top Microbiol Immunol. 1999; 246:299-304; discussion 305. Hsueh RC, Hammill AK, Marches R, Uhr JW, Scheuermann RH. PMID: 10396069.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    120. Cux/CDP homeoprotein is a component of NF-muNR and represses the immunoglobulin heavy chain intronic enhancer by antagonizing the bright transcription activator. Mol Cell Biol. 1999 Jan; 19(1):284-95. Wang Z, Goldstein A, Zong RT, Lin D, Neufeld EJ, Scheuermann RH, Tucker PW. PMID: 9858552.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansAnimalsCells
    121. MARs of antigen receptor and co-receptor genes. Crit Rev Eukaryot Gene Expr. 1999; 9(3-4):295-310. Scheuermann RH, Garrard WT. PMID: 10651246.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
    122. Differential regulation of immunoglobulin gene transcription via nuclear matrix-associated regions. Cold Spring Harb Symp Quant Biol. 1999; 64:109-18. Webb C, Zong RT, Lin D, Wang Z, Kaplan M, Paulin Y, Smith E, Probst L, Bryant J, Goldstein A, Scheuermann R, Tucker P. PMID: 11232275.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansAnimalsCells
    123. Epstein-Barr virus polymerase chain reaction and serology in pediatric post-transplant lymphoproliferative disorder: three-year experience. Pediatr Dev Pathol. 1998 Nov-Dec; 1(6):480-6. Rogers BB, Sommerauer J, Quan A, Timmons CF, Dawson DB, Scheuermann RH, Krisher K, Atkins C. PMID: 9724334.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    124. Polymerase chain reaction amplification of archival material for Epstein-Barr virus, cytomegalovirus, human herpesvirus 6, and parvovirus B19 in children with bone marrow hemophagocytosis. Hum Pathol. 1998 Oct; 29(10):1074-7. Hoang MP, Dawson DB, Rogers ZR, Scheuermann RH, Rogers BB. PMID: 9781644.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    125. Bcl-2 expression in Langerhans' cell histiocytosis. Pediatr Dev Pathol. 1998 May-Jun; 1(3):210-5. Savell VH, Sherman T, Scheuermann RH, Siddiqui AM, Margraf LR. PMID: 10463280.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    126. Benefits and dangers of genetic tests. Nature. 1998 Mar 05; 392(6671):14. Scheuermann RH, Picker LJ. PMID: 9510238.
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    127. Cancer dormancy: role of cyclin-dependent kinase inhibitors in induction of cell cycle arrest mediated via membrane IgM. Cancer Res. 1998 Feb 15; 58(4):691-7. Marches R, Scheuermann RH, Uhr JW. PMID: 9485022.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    128. Quantitative polymerase chain reaction for human herpesvirus diagnosis and measurement of Epstein-Barr virus burden in posttransplant lymphoproliferative disorder. Clin Chem. 1997 Oct; 43(10):1843-9. Bai X, Hosler G, Rogers BB, Dawson DB, Scheuermann RH. PMID: 9342002.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansCells
    129. Tumor dormancy and cell signaling. V. Regrowth of the BCL1 tumor after dormancy is established. Blood. 1997 Jun 15; 89(12):4425-36. Vitetta ES, Tucker TF, Racila E, Huang YW, Marches R, Lane N, Scheuermann RH, Street NE, Watanabe T, Uhr JW. PMID: 9192767.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCellsPHPublic Health
    130. Cancer dormancy: opportunities for new therapeutic approaches. Nat Med. 1997 May; 3(5):505-9. Uhr JW, Scheuermann RH, Street NE, Vitetta ES. PMID: 9142117.
      View in: PubMed   Mentions: 33     Fields:    Translation:HumansAnimals
    131. A role for c-myc in the regulation of thymocyte differentiation and possibly positive selection. J Immunol. 1996 May 01; 156(9):3141-50. Broussard-Diehl C, Bauer SR, Scheuermann RH. PMID: 8617934.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    132. Tumor dormancy and cell signaling: anti-mu-induced apoptosis in human B-lymphoma cells is not caused by an APO-1-APO-1 ligand interaction. Proc Natl Acad Sci U S A. 1996 Mar 05; 93(5):2165-8. Racila E, Hsueh R, Marches R, Tucker TF, Krammer PH, Scheuermann RH, Uhr JW. PMID: 8700902.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    133. Role of antibody signaling in inducing tumor dormancy. Adv Exp Med Biol. 1996; 406:69-74. Uhr JW, Marches R, Racila E, Tucker TF, Hsueh R, Street NE, Vitetta ES, Scheuermann RH. PMID: 8910672.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    134. The immunoglobulin heavy-chain matrix-associating regions are bound by Bright: a B cell-specific trans-activator that describes a new DNA-binding protein family. Genes Dev. 1995 Dec 15; 9(24):3067-82. Herrscher RF, Kaplan MH, Lelsz DL, Das C, Scheuermann R, Tucker PW. PMID: 8543152.
      View in: PubMed   Mentions: 93     Fields:    Translation:Cells
    135. Mutually exclusive interaction of a novel matrix attachment region binding protein and the NF-muNR enhancer repressor. Implications for regulation of immunoglobulin heavy chain expression. J Biol Chem. 1995 Oct 13; 270(41):24010-8. Zong RT, Scheuermann RH. PMID: 7592598.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
    136. Connections between signal transduction components and cellular responses initiated by antigen receptor on B lymphocytes. J Exp Med. 1995 Oct 01; 182(4):903-6. Scheuermann RH, Uhr JW. PMID: 7561692.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    137. CD19 antigen in leukemia and lymphoma diagnosis and immunotherapy. Leuk Lymphoma. 1995 Aug; 18(5-6):385-97. Scheuermann RH, Racila E. PMID: 8528044.
      View in: PubMed   Mentions: 54     Fields:    Translation:HumansCells
    138. Tumour dormancy and cell signalling--III: Role of hypercrosslinking of IgM and CD40 on the induction of cell cycle arrest and apoptosis in B lymphoma cells. Ther Immunol. 1995 Jun; 2(3):125-36. Marches R, Racila E, Tucker TF, Picker L, Mongini P, Hsueh R, Vitetta ES, Scheuermann RH, Uhr JW. PMID: 8885131.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    139. Tumor dormancy and cell signaling. II. Antibody as an agonist in inducing dormancy of a B cell lymphoma in SCID mice. J Exp Med. 1995 Apr 01; 181(4):1539-50. Racila E, Scheuermann RH, Picker LJ, Yefenof E, Tucker T, Chang W, Marches R, Street NE, Vitetta ES, Uhr JW. PMID: 7535341.
      View in: PubMed   Mentions: 15     Fields:    Translation:AnimalsCells
    140. Lyn tyrosine kinase signals cell cycle arrest in mouse and human B-cell lymphoma. Curr Top Microbiol Immunol. 1995; 194:313-21. Scheuermann RH, Racila E, Uhr JW. PMID: 7895504.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCellsPHPublic Health
    141. Lyn tyrosine kinase signals cell cycle arrest but not apoptosis in B-lineage lymphoma cells. Proc Natl Acad Sci U S A. 1994 Apr 26; 91(9):4048-52. Scheuermann RH, Racila E, Tucker T, Yefenof E, Street NE, Vitetta ES, Picker LJ, Uhr JW. PMID: 7513431.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansAnimalsCells
    142. Induction of B cell tumor dormancy by anti-idiotypic antibodies. Curr Opin Immunol. 1993 Oct; 5(5):740-4. Yefenof E, Picker LJ, Scheuermann RH, Vitetta ES, Street NE, Tucker TF, Uhr JW. PMID: 8240736.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsPHPublic Health
    143. Cancer dormancy: isolation and characterization of dormant lymphoma cells. Proc Natl Acad Sci U S A. 1993 Mar 01; 90(5):1829-33. Yefenof E, Picker LJ, Scheuermann RH, Tucker TF, Vitetta ES, Uhr JW. PMID: 8446596.
      View in: PubMed   Mentions: 17     Fields:    Translation:Animals
    144. Polymerase chain reaction-based mRNA quantification using an internal standard: analysis of oncogene expression. Methods Enzymol. 1993; 218:446-73. Scheuermann RH, Bauer SR. PMID: 7685470.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    145. Loss of p53 expression in Myc-induced B lineage tumors. Curr Top Microbiol Immunol. 1992; 182:493-9. Scheuermann RH, Bauer SR. PMID: 1490390.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    146. Anti-IgM antibodies down modulate mu-enhancer activity and OTF2 levels in LPS-stimulated mouse splenic B-cells. Nucleic Acids Res. 1991 Nov 11; 19(21):5981-9. Chen U, Scheuermann RH, Wirth T, Gerster T, Roeder RG, Harshman K, Berger C. PMID: 1658749.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
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