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    Richard Scheuermann

    TitleAdjunct Professor
    SchoolUniversity of California, San Diego
    DepartmentPathology
    Address9500 Gilman Drive #0612
    CA La Jolla 92093
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      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. 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.
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      2. 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 Jan 09. PMID: 28069807.
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      3. 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.
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      4. 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 6; 17(Suppl 13):333. PMID: 27766961.
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      5. 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.
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      6. Valdes G, Scheuermann R, Hung CY, Olszanski A, Bellerive M, Solberg TD. A mathematical framework for virtual IMRT QA using machine learning. Med Phys. 2016 Jul; 43(7):4323. PMID: 27370147.
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      7. 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.
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      8. Scheuermann R. Zika virus: designate standardized names. Nature. 2016 Mar 10; 531(7593):173. PMID: 26961650.
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      9. 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.
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      10. 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; 6:20686. PMID: 26861911.
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      11. 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.
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      12. 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. 2016; 22:564-575. PMID: 27897007.
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      13. 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.
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      14. 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.
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      15. 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.
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      16. Zepeda-Orozco D, Kong M, Scheuermann R. 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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      17. 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.
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      18. 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.
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      19. 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 15; 89(10):5427-40. PMID: 25741011.
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      20. 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.
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      21. 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.
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      22. 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.
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      23. 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.
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      24. Gabriel VA, McClellan EA, Scheuermann R. Response of human skin to esthetic scarification. Burns. 2014 Nov; 40(7):1338-44. PMID: 24582755.
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      25. 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 R. 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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      26. 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; 8(1):14. PMID: 23822732.
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      27. 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 Summits Transl Sci Proc. 2013; 2013:221. PMID: 24303268.
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      28. 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; PMCID: PMC3759057.
      29. 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; 4(11):3209-26. PMID: 23202522.
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      30. 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.
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      31. 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.
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      32. 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.
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      33. 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.
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      34. 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.
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      35. 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.
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      36. Smith B, Scheuermann R. Ontologies for clinical and translational research: Introduction. J Biomed Inform. 2011 Feb; 44(1):3-7. PMID: 21241822.
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      37. 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.
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      38. 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.
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      39. Ligocki AJ, Lovato L, Xiang D, Guidry P, Scheuermann R, 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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      40. 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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      41. 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.
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      42. 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 Summits Transl Sci Proc. 2010; 2010:51-5. PMID: 21347149.
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      43. Zhang S, Cao J, Kong YM, Scheuermann R. GO-Bayes: Gene Ontology-based overrepresentation analysis using a Bayesian approach. Bioinformatics. 2010 Apr 1; 26(7):905-11. PMID: 20176581.
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      44. 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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      45. 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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      46. 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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      47. 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.
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      48. 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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      49. 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.
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      50. 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 1; 106(48):20365-70. PMID: 19918065.
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      51. 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; 2009:81-5. PMID: 20351827.
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      52. 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; 4(9):e7041. PMID: 19756146.
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      53. 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; 10 Suppl 1:S19. PMID: 19594878.
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      54. 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.
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      55. 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; 10:184. PMID: 19531228.
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      56. Luo F, Li B, Wan XF, Scheuermann R. Core and periphery structures in protein interaction networks. BMC Bioinformatics. 2009; 10 Suppl 4:S8. PMID: 19426456.
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      57. Scheuermann R, Ceusters W, Smith B. Toward an ontological treatment of disease and diagnosis. Summit on Translat Bioinforma. 2009; 2009:116-20. PMID: 21347182.
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      58. 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; 10:70. PMID: 19243617.
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      59. Sim I, Chute CG, Lehmann H, Nagarajan R, Nahm M, Scheuermann R. Keeping raw data in context. Science. 2009 Feb 6; 323(5915):713. PMID: 19197039.
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      60. 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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      61. 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.
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      62. 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.
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      63. 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.
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      64. 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; 2(9):e947. PMID: 17895988.
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      65. 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.
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      66. Diehl AD, Lee JA, Scheuermann R, Blake JA. Ontology development for biological systems: immunology. Bioinformatics. 2007 Apr 1; 23(7):913-5. PMID: 17267433.
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      67. Chen Z, McGee M, Liu Q, Scheuermann R. A distribution free summarization method for Affymetrix GeneChip arrays. Bioinformatics. 2007 Feb 1; 23(3):321-7. PMID: 17148508.
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      68. 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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      69. 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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      70. 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; 7:237. PMID: 16670020.
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      71. 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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      72. 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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      73. 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.
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      74. 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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      75. 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 6; 3:16. PMID: 12470302.
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      76. 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.
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      77. 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 9; 359(9309):851-2. PMID: 11897287.
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      78. Sinclair AM, Lee JA, Goldstein A, Xing D, Liu S, Ju R, Tucker PW, Neufeld EJ, Scheuermann R. 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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      79. Roush KS, Domiati-Saad RK, Margraf LR, Krisher K, Scheuermann R, 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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      80. Manabe N, Kawaguchi H, Chikuda H, Miyaura C, Inada M, Nagai R, Nabeshima Y, Nakamura K, Sinclair AM, Scheuermann R, Kuro-o M. Connection between B lymphocyte and osteoclast differentiation pathways. J Immunol. 2001 Sep 1; 167(5):2625-31. PMID: 11509604.
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      81. Kaplan MH, Zong RT, Herrscher RF, Scheuermann R, 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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      82. Scheuermann R, Bai X. Diagnostic applications of quantitative polymerase chain reaction for cytomegalovirus. Methods Mol Med. 2001; 49:337-51. PMID: 21370152.
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      83. Bai X, Rogers BB, Harkins PC, Sommerauer J, Squires R, Rotondo K, Quan A, Dawson DB, Scheuermann R. 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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      84. Hosler GA, Bash R, Scheuermann R. 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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      85. Hsueh RC, Scheuermann R. 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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      86. Hammill AK, Uhr JW, Scheuermann R. 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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      87. Hoang MP, Rogers BB, Dawson DB, Scheuermann R. 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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      88. Hosler GA, Bash RO, Bai X, Jain V, Scheuermann R. 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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      89. Hoang MP, Ross KF, Dawson DB, Scheuermann R, 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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      90. Farrar JD, Katz KH, Windsor J, Thrush G, Scheuermann R, 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 1; 162(5):2842-9. PMID: 10072532.
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      91. Scheuermann R, 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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      92. 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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      93. Hsueh RC, Hammill AK, Marches R, Uhr JW, Scheuermann R. 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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      94. Wang Z, Goldstein A, Zong RT, Lin D, Neufeld EJ, Scheuermann R, 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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      95. Rogers BB, Sommerauer J, Quan A, Timmons CF, Dawson DB, Scheuermann R, 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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      96. Hoang MP, Dawson DB, Rogers ZR, Scheuermann R, 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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      97. Savell VH, Sherman T, Scheuermann R, 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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      98. Scheuermann R, Picker LJ. Benefits and dangers of genetic tests. Nature. 1998 Mar 5; 392(6671):14. PMID: 9510238.
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      99. Marches R, Scheuermann R, 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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      100. Bai X, Hosler G, Rogers BB, Dawson DB, Scheuermann R. 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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      101. Vitetta ES, Tucker TF, Racila E, Huang YW, Marches R, Lane N, Scheuermann R, 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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      102. Uhr JW, Scheuermann R, 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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      103. Broussard-Diehl C, Bauer SR, Scheuermann R. A role for c-myc in the regulation of thymocyte differentiation and possibly positive selection. J Immunol. 1996 May 1; 156(9):3141-50. PMID: 8617934.
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      104. Racila E, Hsueh R, Marches R, Tucker TF, Krammer PH, Scheuermann R, 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 5; 93(5):2165-8. PMID: 8700902.
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      105. Uhr JW, Marches R, Racila E, Tucker TF, Hsueh R, Street NE, Vitetta ES, Scheuermann R. Role of antibody signaling in inducing tumor dormancy. Adv Exp Med Biol. 1996; 406:69-74. PMID: 8910672.
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      106. 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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      107. Zong RT, Scheuermann R. 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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      108. Scheuermann R, Uhr JW. Connections between signal transduction components and cellular responses initiated by antigen receptor on B lymphocytes. J Exp Med. 1995 Oct 1; 182(4):903-6. PMID: 7561692.
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      109. Scheuermann R, 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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      110. Marches R, Racila E, Tucker TF, Picker L, Mongini P, Hsueh R, Vitetta ES, Scheuermann R, 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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      111. Racila E, Scheuermann R, 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 1; 181(4):1539-50. PMID: 7535341.
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      112. Scheuermann R, 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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      113. Scheuermann R, 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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      114. Yefenof E, Picker LJ, Scheuermann R, 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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      115. Yefenof E, Picker LJ, Scheuermann R, Tucker TF, Vitetta ES, Uhr JW. Cancer dormancy: isolation and characterization of dormant lymphoma cells. Proc Natl Acad Sci U S A. 1993 Mar 1; 90(5):1829-33. PMID: 8446596.
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      116. Scheuermann R, 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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      117. Scheuermann R, 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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      118. Chen U, Scheuermann R, 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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