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Richard Scheuermann

TitleAdjunct Professor
InstitutionUniversity of California San Diego
DepartmentPathology
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 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

    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.
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    1. 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 R, Zhernakova A, Zwart MP, Schönhuth A, Dutilh BE, Marz M. Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting. Viruses. 2018 05 14; 10(5). PMID: 29757994.
      View in: PubMed
    2. 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 R, Cowell LG. VDJServer: A Cloud-Based Analysis Portal and Data Commons for Immune Repertoire Sequences and Rearrangements. Front Immunol. 2018; 9:976. PMID: 29867956.
      View in: PubMed
    3. Aevermann BD, Novotny M, Bakken T, Miller JA, Diehl AD, Osumi-Sutherland D, Lasken RS, Lein ES, Scheuermann R. Cell type discovery using single-cell transcriptomics: implications for ontological representation. Hum Mol Genet. 2018 May 01; 27(R1):R40-R47. PMID: 29590361.
      View in: PubMed
    4. Lee AJ, Chang I, Burel JG, Lindestam Arlehamn CS, Mandava A, Weiskopf D, Peters B, Sette A, Scheuermann R, 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 Apr 17. PMID: 29665244.
      View in: PubMed
    5. 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 R. Cell type discovery and representation in the era of high-content single cell phenotyping. BMC Bioinformatics. 2017 Dec 21; 18(Suppl 17):559. PMID: 29322913.
      View in: PubMed
    6. Scheuermann R, Bui J, Wang HY, Qian Y. Automated Analysis of Clinical Flow Cytometry Data: A Chronic Lymphocytic Leukemia Illustration. Clin Lab Med. 2017 Dec; 37(4):931-944. PMID: 29128077.
      View in: PubMed
    7. Christley S, Levin MK, Toby IT, Fonner JM, Monson NL, Rounds WH, Rubelt F, Scarborough W, Scheuermann R, Cowell LG. VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data. BMC Bioinformatics. 2017 Oct 11; 18(1):448. PMID: 29020925.
      View in: PubMed
    8. 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 R, 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.
      View in: PubMed
    9. Xie C, Yeo ZX, Wong M, Piper J, Long T, Kirkness EF, Biggs WH, Bloom K, Spellman S, Vierra-Green C, Brady C, Scheuermann R, 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 Jul 25; 114(30):8059-8064. PMID: 28674023.
      View in: PubMed
    10. Lee AJ, Bhattacharya R, Scheuermann R, Pickett BE. Identification of diagnostic peptide regions that distinguish Zika virus from related mosquito-borne Flaviviruses. PLoS One. 2017; 12(5):e0178199. PMID: 28562637.
      View in: PubMed
    11. Schulten V, Tripple V, Seumois G, Qian Y, Scheuermann R, 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.
      View in: PubMed
    12. Scheuermann R, 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.
      View in: PubMed
    13. Sun G, Larsen CN, Baumgarth N, Klem EB, Scheuermann R. Comprehensive Annotation of Mature Peptides and Genotypes for Zika Virus. PLoS One. 2017; 12(1):e0170462. PMID: 28125631.
      View in: PubMed
    14. Burel JG, Qian Y, Lindestam Arlehamn C, Weiskopf D, Zapardiel-Gonzalo J, Taplitz R, Gilman RH, Saito M, de Silva AD, Vijayanand P, Scheuermann R, 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.
      View in: PubMed
    15. 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 R. 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.
      View in: PubMed
    16. Anderson TK, Macken CA, Lewis NS, Scheuermann R, 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.
      View in: PubMed
    17. 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 R, 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.
      View in: PubMed
    18. 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 R. Influenza Research Database: An integrated bioinformatics resource for influenza virus research. Nucleic Acids Res. 2017 Jan 04; 45(D1):D466-D474. PMID: 27679478.
      View in: PubMed
    19. Zhang Y, Cao J, Zhang S, Lee AJ, Sun G, Larsen CN, Zhao H, Gu Z, He S, Klem EB, Scheuermann R. 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.
      View in: PubMed
    20. 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 R, 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; PMCID: PMC4851331.
    21. Scheuermann R. Zika virus: designate standardized names. Nature. 2016 Mar 10; 531(7593):173. PMID: 26961650.
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    22. 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 R, 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.
    23. 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 R, 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.
    24. Brinkman RR, Aghaeepour N, Finak G, Gottardo R, Mosmann T, Scheuermann R. Automated analysis of flow cytometry data comes of age. Cytometry A. 2016 Jan; 89(1):13-5. PMID: 26812230.
      View in: PubMed
    25. 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 R, 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].
    26. Hsiao C, Liu M, Stanton R, McGee M, Qian Y, Scheuermann R. 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.
      View in: PubMed
    27. Brinkman RR, Aghaeepour N, Finak G, Gottardo R, Mosmann T, Scheuermann R. State-of-the-Art in the Computational Analysis of Cytometry Data. Cytometry A. 2015 Jul; 87(7):591-3. PMID: 26111230.
      View in: PubMed
    28. 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 R, 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.
    29. Miller MA, Schwartz T, Pickett BE, He S, Klem EB, Scheuermann R, 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.
    30. Lee AJ, Das SR, Wang W, Fitzgerald T, Pickett BE, Aevermann BD, Topham DJ, Falsey AR, Scheuermann R. 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.
    31. Courtot M, Meskas J, Diehl AD, Droumeva R, Gottardo R, Jalali A, Taghiyar MJ, Maecker HT, McCoy JP, Ruttenberg A, Scheuermann R, Brinkman RR. flowCL: ontology-based cell population labelling in flow cytometry. Bioinformatics. 2015 Apr 15; 31(8):1337-9. PMID: 25481008; PMCID: PMC4393520.
    32. 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 R. A comprehensive collection of systems biology data characterizing the host response to viral infection. Sci Data. 2014; 1:140033. PMID: 25977790.
      View in: PubMed
    33. Squires RB, Pickett BE, Das S, Scheuermann R. 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.
    34. 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 R. Standardized metadata for human pathogen/vector genomic sequences. PLoS One. 2014; 9(6):e99979. PMID: 24936976; PMCID: PMC4061050.
    35. Gabriel VA, McClellan EA, Scheuermann R. Response of human skin to esthetic scarification. Burns. 2014 Nov; 40(7):1338-44. PMID: 24582755; PMCID: PMC4336194.
    36. Spidlen J, Barsky A, Breuer K, Carr P, Nazaire MD, Hill BA, Qian Y, Liefeld T, Reich M, Mesirov JP, Wilkinson P, Scheuermann R, Sekaly RP, Brinkman RR. GenePattern flow cytometry suite. Source Code Biol Med. 2013 Jul 03; 8(1):14. PMID: 23822732; PMCID: PMC3717030.
    37. Rink B, Roberts K, Harabagiu S, Scheuermann R, 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.
    38. Aghaeepour N, Finak G. Critical assessment of automated flow cytometry data analysis techniques. Nat Methods. 2013 Mar; 10(3):228-38. PMID: 23396282.
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    39. 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 R. 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; PMCID: PMC3509690.
    40. Roberts K, Rink B, Harabagiu SM, Scheuermann R, 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; PMCID: PMC3540484.
    41. Qian Y, Liu Y, Campbell J, Thomson E, Kong YM, Scheuermann R. FCSTrans: an open source software system for FCS file conversion and data transformation. Cytometry A. 2012 May; 81(5):353-356. PMID: 22431383.
      View in: PubMed
    42. 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 R. 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.
    43. 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 R. 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.
    44. Chen Z, Liu Q, McGee M, Kong M, Huang X, Deng Y, Scheuermann R. 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.
    45. 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 R. Minimum Information about a Genotyping Experiment (MIGEN). Stand Genomic Sci. 2011 Nov 30; 5(2):224-9. PMID: 22180825; PMCID: PMC3235517.
    46. 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 R. 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.
    47. Smith B, Scheuermann R. Ontologies for clinical and translational research: Introduction. J Biomed Inform. 2011 Feb; 44(1):3-7. PMID: 21241822; PMCID: PMC4896064.
    48. Chen Z, McGee M, Liu Q, Kong YM, Huang X, Yang JY, Scheuermann R. 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.
      View in: PubMed
    49. Brister JR, Bao Y, Kuiken C, Lefkowitz EJ, Le Mercier P, Leplae R, Madupu R, Scheuermann R, 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; PMCID: PMC3185566.
    50. Scheuermann R, 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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    51. Kong YM, Dahlke C, Xiang Q, Qian Y, Karp D, Scheuermann R. Toward an ontology-based framework for clinical research databases. J Biomed Inform. 2011 Feb; 44(1):48-58. PMID: 20460173.
      View in: PubMed
    52. Sim I, Carini S, Tu S, Wynden R, Pollock BH, Mollah SA, Gabriel D, Hagler HK, Scheuermann R, Lehmann HP, Wittkowski KM, Nahm M, Bakken S. The human studies database project: federating human studies design data using the ontology of clinical research. AMIA Jt Summits Transl Sci Proc. 2010 Mar 01; 2010:51-5. PMID: 21347149; PMCID: PMC3041546.
    53. Zhang S, Cao J, Kong YM, Scheuermann R. GO-Bayes: Gene Ontology-based overrepresentation analysis using a Bayesian approach. Bioinformatics. 2010 Apr 01; 26(7):905-11. PMID: 20176581; PMCID: PMC2913669.
    54. 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 R, 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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    55. Thomson G, Marthandan N, Hollenbach JA, Mack SJ, Erlich HA, Single RM, Waller MJ, Marsh SG, Guidry PA, Karp DR, Scheuermann R, 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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    56. 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 R. 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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    57. Malin B, Karp D, Scheuermann R. 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.
    58. Chang RL, Luo F, Johnson S, Scheuermann R. 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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    59. 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 R. 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.
    60. Greenbaum JA, Kotturi MF, Kim Y, Oseroff C, Vaughan K, Salimi N, Vita R, Ponomarenko J, Scheuermann R, 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.
    61. Carini S, Pollock BH, Lehmann HP, Bakken S, Barbour EM, Gabriel D, Hagler HK, Harper CR, Mollah SA, Nahm M, Nguyen HH, Scheuermann R, 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.
    62. Barabote RD, Xie G, Brettin TS, Hinrichs SH, Fey PD, Jay JJ, Engle JL, Godbole SD, Noronha JM, Scheuermann R, 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; PMCID: PMC2737636.
    63. Chen Z, McGee M, Liu Q, Kong M, Deng Y, Scheuermann R. 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.
    64. 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 R, 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.
    65. Qian Y, Tchuvatkina O, Spidlen J, Wilkinson P, Gasparetto M, Jones AR, Manion FJ, Scheuermann R, Sekaly RP, Brinkman RR. FuGEFlow: data model and markup language for flow cytometry. BMC Bioinformatics. 2009 Jun 16; 10:184. PMID: 19531228; PMCID: PMC2711079.
    66. Luo F, Li B, Wan XF, Scheuermann R. Core and periphery structures in protein interaction networks. BMC Bioinformatics. 2009 Apr 29; 10 Suppl 4:S8. PMID: 19426456; PMCID: PMC2681073.
    67. Scheuermann R, 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.
    68. Masci AM, Arighi CN, Diehl AD, Lieberman AE, Mungall C, Scheuermann R, 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.
    69. Sim I, Chute CG, Lehmann H, Nagarajan R, Nahm M, Scheuermann R. Keeping raw data in context. Science. 2009 Feb 06; 323(5915):713. PMID: 19197039.
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    70. 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. MIFlowCyt: the minimum information about a Flow Cytometry Experiment. Cytometry A. 2008 Oct; 73(10):926-30. PMID: 18752282.
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    71. 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 R, 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.
    72. Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol. 2007 Nov; 25(11):1251-5. PMID: 17989687; PMCID: PMC2814061.
    73. Squires B, Macken C, Garcia-Sastre A, Godbole S, Noronha J, Hunt V, Chang R, Larsen CN, Klem E, Biersack K, Scheuermann R. 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.
    74. 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 R, 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.
    75. Greene JM, Collins F, Lefkowitz EJ, Roos D, Scheuermann R, 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.
    76. Diehl AD, Lee JA, Scheuermann R, Blake JA. Ontology development for biological systems: immunology. Bioinformatics. 2007 Apr 01; 23(7):913-5. PMID: 17267433.
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    77. Chen Z, McGee M, Liu Q, Scheuermann R. A distribution free summarization method for Affymetrix GeneChip arrays. Bioinformatics. 2007 Feb 01; 23(3):321-7. PMID: 17148508.
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    78. Luo F, Yang Y, Chen CF, Chang R, Zhou J, Scheuermann R. Modular organization of protein interaction networks. Bioinformatics. 2007 Jan 15; 23(2):207-14. PMID: 17092991.
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    79. 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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    80. Lee JA, Sinkovits RS, Mock D, Rab EL, Cai J, Yang P, Saunders B, Hsueh RC, Choi S, Subramaniam S, Scheuermann R. 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; PMCID: PMC1479375.
    81. Domiati-Saad R, Scheuermann R. 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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    82. 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 R, 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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    83. Jebbink J, Bai X, Rogers BB, Dawson DB, Scheuermann R, 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.
    84. 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 R, 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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    85. Hsueh RC, Hammill AM, Lee JA, Uhr JW, Scheuermann R. 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.
    86. Boudreau F, Rings EH, Swain GP, Sinclair AM, Suh ER, Silberg DG, Scheuermann R, 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.
    87. Shivapurkar N, Harada K, Reddy J, Scheuermann R, 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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