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Richard Scheuermann

Title(s)Adjunct Professor, Pathology
SchoolHealth Sciences
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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 N01AI40076Sep 29, 2004 - Sep 29, 2010
    Role: Co-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 28, 2001
    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

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    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.
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    1. 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. Differential transcriptome and development of human peripheral plasma cell subsets. JCI Insight. 2019 05 02; 4(9). PMID: 31045577.
      View in: PubMed
    2. Zmasek CM, Knipe DM, Pellett PE, Scheuermann RH. Classification of human Herpesviridae proteins using Domain-architecture Aware Inference of Orthologs (DAIO). Virology. 2019 Mar; 529:29-42. PMID: 30660046.
      View in: PubMed
    3. Zhang Y, Zmasek C, Sun G, Larsen CN, Scheuermann RH. Hepatitis C Virus Database and Bioinformatics Analysis Tools in the Virus Pathogen Resource (ViPR). Methods Mol Biol. 2019; 1911:47-69. PMID: 30593617.
      View in: PubMed
    4. 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. Single-nucleus and single-cell transcriptomes compared in matched cortical cell types. PLoS One. 2018; 13(12):e0209648. PMID: 30586455.
      View in: PubMed
    5. Brown DM, Hixon AM, Oldfield LM, Zhang Y, Novotny M, Wang W, Das SR, Shabman RS, Tyler KL, Scheuermann RH. Contemporary Circulating Enterovirus D68 Strains Have Acquired the Capacity for Viral Entry and Replication in Human Neuronal Cells. MBio. 2018 10 16; 9(5). PMID: 30327438.
      View in: PubMed
    6. 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. Chromosome Y-encoded antigens associate with acute graft-versus-host disease in sex-mismatched stem cell transplant. Blood Adv. 2018 Oct 09; 2(19):2419-2429. PMID: 30262602.
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    7. 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. Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type. Nat Neurosci. 2018 Sep; 21(9):1185-1195. PMID: 30150662.
      View in: PubMed
    8. 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. Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting. Viruses. 2018 May 14; 10(5). PMID: 29757994.
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    9. 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. VDJServer: A Cloud-Based Analysis Portal and Data Commons for Immune Repertoire Sequences and Rearrangements. Front Immunol. 2018; 9:976. PMID: 29867956.
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    10. Aevermann BD, Novotny M, Bakken T, Miller JA, Diehl AD, Osumi-Sutherland D, Lasken RS, Lein ES, Scheuermann RH. Cell type discovery using single-cell transcriptomics: implications for ontological representation. Hum Mol Genet. 2018 05 01; 27(R1):R40-R47. PMID: 29590361.
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    11. Lee AJ, Chang I, Burel JG, Lindestam Arlehamn CS, Mandava A, Weiskopf D, Peters B, Sette A, Scheuermann RH, Qian Y. 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. PMID: 29665244.
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    12. 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. Cell type discovery and representation in the era of high-content single cell phenotyping. BMC Bioinformatics. 2017 12 21; 18(Suppl 17):559. PMID: 29322913.
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    13. Scheuermann RH, Bui J, Wang HY, Qian Y. Automated Analysis of Clinical Flow Cytometry Data: A Chronic Lymphocytic Leukemia Illustration. Clin Lab Med. 2017 12; 37(4):931-944. PMID: 29128077.
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    14. Christley S, Levin MK, Toby IT, Fonner JM, Monson NL, Rounds WH, Rubelt F, Scarborough W, Scheuermann RH, Cowell LG. VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data. BMC Bioinformatics. 2017 Oct 11; 18(1):448. PMID: 29020925.
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    15. 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. 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. PMID: 28798746.
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    16. 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. 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. PMID: 28674023.
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    17. Lee AJ, Bhattacharya R, Scheuermann RH, Pickett BE. Identification of diagnostic peptide regions that distinguish Zika virus from related mosquito-borne Flaviviruses. PLoS One. 2017; 12(5):e0178199. PMID: 28562637.
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    18. 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. Allergen-specific immunotherapy modulates the balance of circulating Tfh and Tfr cells. J Allergy Clin Immunol. 2018 Feb; 141(2):775-777.e6. PMID: 28506846.
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    19. Scheuermann RH, Sinkovits RS, Schenkelberg T, Koff WC. A bioinformatics roadmap for the human vaccines project. Expert Rev Vaccines. 2017 06; 16(6):535-544. PMID: 28434256.
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    20. Sun G, Larsen CN, Baumgarth N, Klem EB, Scheuermann RH. Comprehensive Annotation of Mature Peptides and Genotypes for Zika Virus. PLoS One. 2017; 12(1):e0170462. PMID: 28125631.
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    21. 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. 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. PMID: 28069807.
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    22. 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. 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. PMID: 27897007.
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    23. 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. 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). PMID: 27981236.
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    24. 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. VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements. BMC Bioinformatics. 2016 Oct 06; 17(Suppl 13):333. PMID: 27766961.
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    25. 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. Influenza Research Database: An integrated bioinformatics resource for influenza virus research. Nucleic Acids Res. 2017 01 04; 45(D1):D466-D474. PMID: 27679478.
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    26. Zhang Y, Cao J, Zhang S, Lee AJ, Sun G, Larsen CN, Zhao H, Gu Z, He S, Klem EB, Scheuermann RH. Genetic changes found in a distinct clade of Enterovirus D68 associated with paralysis during the 2014 outbreak. Virus Evol. 2016 Jan; 2(1):vew015. PMID: 28512577.
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    27. 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. The Ontology for Biomedical Investigations. PLoS One. 2016; 11(4):e0154556. PMID: 27128319.
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    28. Scheuermann RH. Zika virus: designate standardized names. Nature. 2016 Mar 10; 531(7593):173. PMID: 26961650.
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    29. 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. Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons. Nat Protoc. 2016 Mar; 11(3):499-524. PMID: 26890679; PMCID: PMC4941947.
    30. 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. Standardizing Flow Cytometry Immunophenotyping Analysis from the Human ImmunoPhenotyping Consortium. Sci Rep. 2016 Feb 10; 6:20686. PMID: 26861911; PMCID: PMC4748244.
    31. Brinkman RR, Aghaeepour N, Finak G, Gottardo R, Mosmann T, Scheuermann RH. Automated analysis of flow cytometry data comes of age. Cytometry A. 2016 Jan; 89(1):13-5. PMID: 26812230.
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    32. 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. A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes. Cytometry A. 2016 Jan; 89(1):16-21. PMID: 26447924; PMCID: PMC4874734 [Available on 01/01/17].
    33. Hsiao C, Liu M, Stanton R, McGee M, Qian Y, Scheuermann RH. 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. PMID: 26274018.
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    34. Zepeda-Orozco D, Kong M, Scheuermann RH. Molecular Profile of Mitochondrial Dysfunction in Kidney Transplant Biopsies Is Associated With Poor Allograft Outcome. Transplant Proc. 2015 Jul-Aug; 47(6):1675-82. PMID: 26293032.
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    35. Brinkman RR, Aghaeepour N, Finak G, Gottardo R, Mosmann T, Scheuermann RH. State-of-the-Art in the Computational Analysis of Cytometry Data. Cytometry A. 2015 Jul; 87(7):591-3. PMID: 26111230.
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    36. 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. Thinking outside the gate: single-cell assessments in multiple dimensions. Immunity. 2015 Apr 21; 42(4):591-2. PMID: 25902473; PMCID: PMC4824634.
    37. Miller MA, Schwartz T, Pickett BE, He S, Klem EB, Scheuermann RH, Passarotti M, Kaufman S, O'Leary MA. A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway. Evol Bioinform Online. 2015; 11:43-8. PMID: 25861210; PMCID: PMC4362911.
    38. Lee AJ, Das SR, Wang W, Fitzgerald T, Pickett BE, Aevermann BD, Topham DJ, Falsey AR, Scheuermann RH. Diversifying Selection Analysis Predicts Antigenic Evolution of 2009 Pandemic H1N1 Influenza A Virus in Humans. J Virol. 2015 May; 89(10):5427-40. PMID: 25741011; PMCID: PMC4442545.
    39. Courtot M, Meskas J, Diehl AD, Droumeva R, Gottardo R, Jalali A, Taghiyar MJ, Maecker HT, McCoy JP, Ruttenberg A, Scheuermann RH, Brinkman RR. flowCL: ontology-based cell population labelling in flow cytometry. Bioinformatics. 2015 Apr 15; 31(8):1337-9. PMID: 25481008; PMCID: PMC4393520.
    40. 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. A comprehensive collection of systems biology data characterizing the host response to viral infection. Sci Data. 2014; 1:140033. PMID: 25977790.
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    41. Squires RB, Pickett BE, Das S, Scheuermann RH. Toward a method for tracking virus evolutionary trajectory applied to the pandemic H1N1 2009 influenza virus. Infect Genet Evol. 2014 Dec; 28:351-7. PMID: 25064525; PMCID: PMC4257861.
    42. 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. Standardized metadata for human pathogen/vector genomic sequences. PLoS One. 2014; 9(6):e99979. PMID: 24936976.
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    43. Gabriel VA, McClellan EA, Scheuermann RH. Response of human skin to esthetic scarification. Burns. 2014 Nov; 40(7):1338-44. PMID: 24582755; PMCID: PMC4336194.
    44. 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. 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. PMID: 24210098.
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    45. 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. GenePattern flow cytometry suite. Source Code Biol Med. 2013 Jul 03; 8(1):14. PMID: 23822732; PMCID: PMC3717030.
    46. Rink B, Roberts K, Harabagiu S, Scheuermann RH, Toomay S, Browning T, Bosler T, Peshock R. Extracting actionable findings of appendicitis from radiology reports using natural language processing. AMIA Jt Summits Transl Sci Proc. 2013; 2013:221. PMID: 24303268; PMCID: PMC3845763.
    47. Aghaeepour N, Finak G, Hoos H, Mosmann TR, Brinkman R, Gottardo R, Scheuermann RH. Critical assessment of automated flow cytometry data analysis techniques. Nat Methods. 2013 Mar; 10(3):228-38. PMID: 23396282.
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    48. Prokscha T, Chow KH, Stilp E, Suter A, Luetkens H, Morenzoni E, Nieuwenhuys GJ, Salman Z, Scheuermann R. Photo-induced persistent inversion of germanium in a 200-nm-deep surface region. Sci Rep. 2013; 3:2569. PMID: 23995307.
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    49. 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. 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. PMID: 23202522.
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    50. Roberts K, Rink B, Harabagiu SM, Scheuermann RH, Toomay S, Browning T, Bosler T, Peshock R. A machine learning approach for identifying anatomical locations of actionable findings in radiology reports. AMIA Annu Symp Proc. 2012; 2012:779-88. PMID: 23304352.
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    51. Qian Y, Liu Y, Campbell J, Thomson E, Kong YM, Scheuermann RH. FCSTrans: an open source software system for FCS file conversion and data transformation. Cytometry A. 2012 May; 81(5):353-356. PMID: 22431383.
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    52. 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. 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. PMID: 22398283; PMCID: PMC3347290.
    53. 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. Influenza research database: an integrated bioinformatics resource for influenza research and surveillance. Influenza Other Respir Viruses. 2012 Nov; 6(6):404-16. PMID: 22260278; PMCID: PMC3345175.
    54. Chen Z, Liu Q, McGee M, Kong M, Huang X, Deng Y, Scheuermann RH. A gene selection method for GeneChip array data with small sample sizes. BMC Genomics. 2011 Dec 23; 12 Suppl 5:S7. PMID: 22369149; PMCID: PMC3287503.
    55. 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. Minimum Information about a Genotyping Experiment (MIGEN). Stand Genomic Sci. 2011 Nov 30; 5(2):224-9. PMID: 22180825; PMCID: PMC3235517.
    56. 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. ViPR: an open bioinformatics database and analysis resource for virology research. Nucleic Acids Res. 2012 Jan; 40(Database issue):D593-8. PMID: 22006842; PMCID: PMC3245011.
    57. Smith B, Scheuermann RH. Ontologies for clinical and translational research: Introduction. J Biomed Inform. 2011 Feb; 44(1):3-7. PMID: 21241822; PMCID: PMC4896064.
    58. Chen Z, McGee M, Liu Q, Kong YM, Huang X, Yang JY, Scheuermann RH. Identifying Differentially Expressed Genes based on probe level data for GeneChip arrays. Int J Comput Biol Drug Des. 2010; 3(3):237-57. PMID: 21228458.
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    59. 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. Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop. Viruses. 2010 Oct; 2(10):2258-68. PMID: 21994619.
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    60. 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. 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. PMID: 20655601.
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    61. Scheuermann RH, Milgrom H. Personalized care, comparative effectiveness research and the electronic health record. Curr Opin Allergy Clin Immunol. 2010 Jun; 10(3):168-70. PMID: 20431366.
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    62. Kong YM, Dahlke C, Xiang Q, Qian Y, Karp D, Scheuermann RH. Toward an ontology-based framework for clinical research databases. J Biomed Inform. 2011 Feb; 44(1):48-58. PMID: 20460173.
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    63. 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. 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. PMID: 21347149.
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    64. Zhang S, Cao J, Kong YM, Scheuermann RH. GO-Bayes: Gene Ontology-based overrepresentation analysis using a Bayesian approach. Bioinformatics. 2010 Apr 01; 26(7):905-11. PMID: 20176581.
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    65. 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. Hematopoietic cell types: prototype for a revised cell ontology. J Biomed Inform. 2011 Feb; 44(1):75-9. PMID: 20123131.
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    66. 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. 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. PMID: 20839340.
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    67. Malin B, Karp D, Scheuermann RH. 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. PMID: 20051768; PMCID: PMC2836827.
    68. 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. Sequence feature variant type (SFVT) analysis of the HLA genetic association in juvenile idiopathic arthritis. Pac Symp Biocomput. 2010; 359-70. PMID: 19908388.
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    69. Chang RL, Luo F, Johnson S, Scheuermann RH. Deterministic graph-theoretic algorithm for detecting modules in biological interaction networks. Int J Bioinform Res Appl. 2010; 6(2):101-19. PMID: 20223734.
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    70. 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. Novel sequence feature variant type analysis of the HLA genetic association in systemic sclerosis. Hum Mol Genet. 2010 Feb 15; 19(4):707-19. PMID: 19933168; PMCID: PMC2807365.
    71. Greenbaum JA, Kotturi MF, Kim Y, Oseroff C, Vaughan K, Salimi N, Vita R, Ponomarenko J, Scheuermann RH, Sette A, Peters B. 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. PMID: 19918065; PMCID: PMC2777968.
    72. 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. Development and evaluation of a study design typology for human research. AMIA Annu Symp Proc. 2009 Nov 14; 2009:81-5. PMID: 20351827; PMCID: PMC2815479.
    73. 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. Complete genome sequence of Francisella tularensis subspecies holarctica FTNF002-00. PLoS One. 2009 Sep 16; 4(9):e7041. PMID: 19756146.
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    74. Chen Z, McGee M, Liu Q, Kong M, Deng Y, Scheuermann RH. A Distribution-Free Convolution Model for background correction of oligonucleotide microarray data. BMC Genomics. 2009 Jul 07; 10 Suppl 1:S19. PMID: 19594878; PMCID: PMC2709262.
    75. 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. 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. PMID: 19550198; PMCID: PMC2884382.
    76. Qian Y, Tchuvatkina O, Spidlen J, Wilkinson P, Gasparetto M, Jones AR, Manion FJ, Scheuermann RH, Sekaly RP, Brinkman RR. FuGEFlow: data model and markup language for flow cytometry. BMC Bioinformatics. 2009 Jun 16; 10:184. PMID: 19531228.
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    77. Luo F, Li B, Wan XF, Scheuermann RH. Core and periphery structures in protein interaction networks. BMC Bioinformatics. 2009 Apr 29; 10 Suppl 4:S8. PMID: 19426456.
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    78. Scheuermann RH, Ceusters W, Smith B. Toward an ontological treatment of disease and diagnosis. Summit Transl Bioinform. 2009 Mar 01; 2009:116-20. PMID: 21347182; PMCID: PMC3041577.
    79. Masci AM, Arighi CN, Diehl AD, Lieberman AE, Mungall C, Scheuermann RH, Smith B, Cowell LG. An improved ontological representation of dendritic cells as a paradigm for all cell types. BMC Bioinformatics. 2009 Feb 25; 10:70. PMID: 19243617; PMCID: PMC2662812.
    80. Sim I, Chute CG, Lehmann H, Nagarajan R, Nahm M, Scheuermann RH. Keeping raw data in context. Science. 2009 Feb 06; 323(5915):713. PMID: 19197039.
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    81. 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. MIFlowCyt: the minimum information about a Flow Cytometry Experiment. Cytometry A. 2008 Oct; 73(10):926-30. PMID: 18752282.
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    82. 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. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol. 2008 Aug; 26(8):889-96. PMID: 18688244; PMCID: PMC2771753.
    83. 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. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol. 2007 Nov; 25(11):1251-5. PMID: 17989687; PMCID: PMC2814061.
    84. Squires B, Macken C, Garcia-Sastre A, Godbole S, Noronha J, Hunt V, Chang R, Larsen CN, Klem E, Biersack K, Scheuermann RH. BioHealthBase: informatics support in the elucidation of influenza virus host pathogen interactions and virulence. Nucleic Acids Res. 2008 Jan; 36(Database issue):D497-503. PMID: 17965094; PMCID: PMC2238987.
    85. 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. Complete genomic characterization of a pathogenic A.II strain of Francisella tularensis subspecies tularensis. PLoS One. 2007 Sep 26; 2(9):e947. PMID: 17895988; PMCID: PMC1978527.
    86. Greene JM, Collins F, Lefkowitz EJ, Roos D, Scheuermann RH, Sobral B, Stevens R, White O, Di Francesco V. National Institute of Allergy and Infectious Diseases bioinformatics resource centers: new assets for pathogen informatics. Infect Immun. 2007 Jul; 75(7):3212-9. PMID: 17420237; PMCID: PMC1932942.
    87. Diehl AD, Lee JA, Scheuermann RH, Blake JA. Ontology development for biological systems: immunology. Bioinformatics. 2007 Apr 01; 23(7):913-5. PMID: 17267433.
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    88. Chen Z, McGee M, Liu Q, Scheuermann RH. A distribution free summarization method for Affymetrix GeneChip arrays. Bioinformatics. 2007 Feb 01; 23(3):321-7. PMID: 17148508.
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    89. Luo F, Yang Y, Chen CF, Chang R, Zhou J, Scheuermann RH. Modular organization of protein interaction networks. Bioinformatics. 2007 Jan 15; 23(2):207-14. PMID: 17092991.
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    90. Marches R, Scheuermann R, Uhr J. Cancer dormancy: from mice to man. Cell Cycle. 2006 Aug; 5(16):1772-8. PMID: 16929181.
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    91. Lee JA, Sinkovits RS, Mock D, Rab EL, Cai J, Yang P, Saunders B, Hsueh RC, Choi S, Subramaniam S, Scheuermann RH. 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. PMID: 16670020.
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    92. Domiati-Saad R, Scheuermann RH. Nucleic acid testing for viral burden and viral genotyping. Clin Chim Acta. 2006 Jan; 363(1-2):197-205. PMID: 16098959.
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    93. 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. 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. PMID: 15585835.
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    94. Jebbink J, Bai X, Rogers BB, Dawson DB, Scheuermann RH, Domiati-Saad R. 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. PMID: 12552075; PMCID: PMC1907370.
    95. 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. Overview of the Alliance for Cellular Signaling. Nature. 2002 Dec 12; 420(6916):703-6. PMID: 12478301.
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    96. Hsueh RC, Hammill AM, Lee JA, Uhr JW, Scheuermann RH. Activation of the Syk tyrosine kinase is insufficient for downstream signal transduction in B lymphocytes. BMC Immunol. 2002 Dec 06; 3:16. PMID: 12470302; PMCID: PMC139997.
    97. Boudreau F, Rings EH, Swain GP, Sinclair AM, Suh ER, Silberg DG, Scheuermann RH, Traber PG. A novel colonic repressor element regulates intestinal gene expression by interacting with Cux/CDP. Mol Cell Biol. 2002 Aug; 22(15):5467-78. PMID: 12101240; PMCID: PMC133930.
    98. Shivapurkar N, Harada K, Reddy J, Scheuermann RH, Xu Y, McKenna RW, Milchgrub S, Kroft SH, Feng Z, Gazdar AF. Presence of simian virus 40 DNA sequences in human lymphomas. Lancet. 2002 Mar 09; 359(9309):851-2. PMID: 11897287.
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    99. Sinclair AM, Lee JA, Goldstein A, Xing D, Liu S, Ju R, Tucker PW, Neufeld EJ, Scheuermann RH. Lymphoid apoptosis and myeloid hyperplasia in CCAAT displacement protein mutant mice. Blood. 2001 Dec 15; 98(13):3658-67. PMID: 11739170.
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    100. Roush KS, Domiati-Saad RK, Margraf LR, Krisher K, Scheuermann RH, Rogers BB, Dawson DB. Prevalence and cellular reservoir of latent human herpesvirus 6 in tonsillar lymphoid tissue. Am J Clin Pathol. 2001 Nov; 116(5):648-54. PMID: 11710680.
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    101. Manabe N, Kawaguchi H, Chikuda H, Miyaura C, Inada M, Nagai R, Nabeshima Y, Nakamura K, Sinclair AM, Scheuermann RH, Kuro-o M. Connection between B lymphocyte and osteoclast differentiation pathways. J Immunol. 2001 Sep 01; 167(5):2625-31. PMID: 11509604.
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    102. Kaplan MH, Zong RT, Herrscher RF, Scheuermann RH, Tucker PW. 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. PMID: 11294836.
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    103. Scheuermann RH, Bai X. Diagnostic applications of quantitative polymerase chain reaction for cytomegalovirus. Methods Mol Med. 2001; 49:337-51. PMID: 21370152.
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    104. Bai X, Rogers BB, Harkins PC, Sommerauer J, Squires R, Rotondo K, Quan A, Dawson DB, Scheuermann RH. 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. PMID: 11232109.
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    105. Hosler GA, Bash R, Scheuermann RH. 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. PMID: 10914545.
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    106. Hsueh RC, Scheuermann RH. 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. PMID: 10879287.
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    107. Hammill AK, Uhr JW, Scheuermann RH. 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. PMID: 10438567.
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    108. Hoang MP, Rogers BB, Dawson DB, Scheuermann RH. 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. PMID: 10230356.
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    109. Hosler GA, Bash RO, Bai X, Jain V, Scheuermann RH. 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. PMID: 10233841.
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    110. Hoang MP, Ross KF, Dawson DB, Scheuermann RH, Rogers BB. 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. PMID: 10097377.
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    111. Farrar JD, Katz KH, Windsor J, Thrush G, Scheuermann RH, Uhr JW, Street NE. 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. PMID: 10072532.
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    112. Hsueh RC, Hammill AK, Marches R, Uhr JW, Scheuermann RH. 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. PMID: 10396069.
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    113. Wang Z, Goldstein A, Zong RT, Lin D, Neufeld EJ, Scheuermann RH, Tucker PW. 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. PMID: 9858552.
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    114. Scheuermann RH, Garrard WT. MARs of antigen receptor and co-receptor genes. Crit Rev Eukaryot Gene Expr. 1999; 9(3-4):295-310. PMID: 10651246.
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    115. Webb C, Zong RT, Lin D, Wang Z, Kaplan M, Paulin Y, Smith E, Probst L, Bryant J, Goldstein A, Scheuermann R, Tucker P. Differential regulation of immunoglobulin gene transcription via nuclear matrix-associated regions. Cold Spring Harb Symp Quant Biol. 1999; 64:109-18. PMID: 11232275.
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    116. Rogers BB, Sommerauer J, Quan A, Timmons CF, Dawson DB, Scheuermann RH, Krisher K, Atkins C. 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. PMID: 9724334.
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    117. Hoang MP, Dawson DB, Rogers ZR, Scheuermann RH, Rogers BB. 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. PMID: 9781644.
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    118. Savell VH, Sherman T, Scheuermann RH, Siddiqui AM, Margraf LR. Bcl-2 expression in Langerhans' cell histiocytosis. Pediatr Dev Pathol. 1998 May-Jun; 1(3):210-5. PMID: 10463280.
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    119. Scheuermann RH, Picker LJ. Benefits and dangers of genetic tests. Nature. 1998 Mar 05; 392(6671):14. PMID: 9510238.
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    120. Marches R, Scheuermann RH, Uhr JW. 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. PMID: 9485022.
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    121. Bai X, Hosler G, Rogers BB, Dawson DB, Scheuermann RH. 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. PMID: 9342002.
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    122. Vitetta ES, Tucker TF, Racila E, Huang YW, Marches R, Lane N, Scheuermann RH, Street NE, Watanabe T, Uhr JW. Tumor dormancy and cell signaling. V. Regrowth of the BCL1 tumor after dormancy is established. Blood. 1997 Jun 15; 89(12):4425-36. PMID: 9192767.
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    123. Uhr JW, Scheuermann RH, Street NE, Vitetta ES. Cancer dormancy: opportunities for new therapeutic approaches. Nat Med. 1997 May; 3(5):505-9. PMID: 9142117.
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    124. Broussard-Diehl C, Bauer SR, Scheuermann RH. A role for c-myc in the regulation of thymocyte differentiation and possibly positive selection. J Immunol. 1996 May 01; 156(9):3141-50. PMID: 8617934.
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    125. Racila E, Hsueh R, Marches R, Tucker TF, Krammer PH, Scheuermann RH, Uhr JW. 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. PMID: 8700902.
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    126. Uhr JW, Marches R, Racila E, Tucker TF, Hsueh R, Street NE, Vitetta ES, Scheuermann RH. Role of antibody signaling in inducing tumor dormancy. Adv Exp Med Biol. 1996; 406:69-74. PMID: 8910672.
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    127. Herrscher RF, Kaplan MH, Lelsz DL, Das C, Scheuermann R, Tucker PW. 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. PMID: 8543152.
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    128. Zong RT, Scheuermann RH. 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. PMID: 7592598.
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    129. Scheuermann RH, Uhr JW. 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. PMID: 7561692.
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    130. Scheuermann RH, Racila E. CD19 antigen in leukemia and lymphoma diagnosis and immunotherapy. Leuk Lymphoma. 1995 Aug; 18(5-6):385-97. PMID: 8528044.
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    131. Marches R, Racila E, Tucker TF, Picker L, Mongini P, Hsueh R, Vitetta ES, Scheuermann RH, Uhr JW. 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. PMID: 8885131.
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    132. Racila E, Scheuermann RH, Picker LJ, Yefenof E, Tucker T, Chang W, Marches R, Street NE, Vitetta ES, Uhr JW. 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. PMID: 7535341.
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    133. Scheuermann RH, Racila E, Uhr JW. Lyn tyrosine kinase signals cell cycle arrest in mouse and human B-cell lymphoma. Curr Top Microbiol Immunol. 1995; 194:313-21. PMID: 7895504.
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    134. Scheuermann RH, Racila E, Tucker T, Yefenof E, Street NE, Vitetta ES, Picker LJ, Uhr JW. 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. PMID: 7513431.
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    135. Yefenof E, Picker LJ, Scheuermann RH, Vitetta ES, Street NE, Tucker TF, Uhr JW. Induction of B cell tumor dormancy by anti-idiotypic antibodies. Curr Opin Immunol. 1993 Oct; 5(5):740-4. PMID: 8240736.
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    136. Yefenof E, Picker LJ, Scheuermann RH, Tucker TF, Vitetta ES, Uhr JW. Cancer dormancy: isolation and characterization of dormant lymphoma cells. Proc Natl Acad Sci U S A. 1993 Mar 01; 90(5):1829-33. PMID: 8446596.
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    137. Scheuermann RH, Bauer SR. Polymerase chain reaction-based mRNA quantification using an internal standard: analysis of oncogene expression. Methods Enzymol. 1993; 218:446-73. PMID: 7685470.
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    138. Scheuermann RH, Bauer SR. Loss of p53 expression in Myc-induced B lineage tumors. Curr Top Microbiol Immunol. 1992; 182:493-9. PMID: 1490390.
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    139. Chen U, Scheuermann RH, Wirth T, Gerster T, Roeder RG, Harshman K, Berger C. 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. PMID: 1658749.
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