Richard H. Scheuermann - Publications

Affiliations: 
J. Craig Venter Institute, San Diego, CA, United States 
Website:
https://www.jcvi.org/about/richard-scheuermann

50 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 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, ... ... Scheuermann RH, et al. VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements. Bmc Bioinformatics. 17: 333. PMID 27766961 DOI: 10.1186/S12859-016-1214-3  1
2016 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, ... ... Scheuermann RH, et al. The Ontology for Biomedical Investigations. Plos One. 11: e0154556. PMID 27128319 DOI: 10.1371/Journal.Pone.0154556  1
2016 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, ... ... Scheuermann RH, et al. Standardizing Flow Cytometry Immunophenotyping Analysis from the Human ImmunoPhenotyping Consortium. Scientific Reports. 6: 20686. PMID 26861911 DOI: 10.1038/Srep20686  1
2016 Brinkman RR, Aghaeepour N, Finak G, Gottardo R, Mosmann T, Scheuermann RH. Automated analysis of flow cytometry data comes of age. Cytometry. Part a : the Journal of the International Society For Analytical Cytology. 89: 13-5. PMID 26812230 DOI: 10.1002/Cyto.A.22810  1
2015 Aghaeepour N, Chattopadhyay P, Chikina M, Dhaene T, Van Gassen S, Kursa M, Lambrecht BN, Malek M, Qian Y, Qiu P, Saeys Y, Stanton R, Tong D, Vens C, Walkowiak S, ... ... Scheuermann RH, et al. A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes. Cytometry. Part a : the Journal of the International Society For Analytical Cytology. PMID 26447924 DOI: 10.1002/Cyto.A.22732  1
2015 Brinkman RR, Aghaeepour N, Finak G, Gottardo R, Mosmann T, Scheuermann RH. State-of-the-Art in the Computational Analysis of Cytometry Data. Cytometry. Part a : the Journal of the International Society For Analytical Cytology. 87: 591-3. PMID 26111230 DOI: 10.1002/Cyto.A.22707  1
2015 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, et al. Thinking outside the gate: single-cell assessments in multiple dimensions. Immunity. 42: 591-2. PMID 25902473 DOI: 10.1016/J.Immuni.2015.04.006  1
2015 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. Evolutionary Bioinformatics Online. 11: 43-8. PMID 25861210 DOI: 10.4137/EBO.S21501  1
2015 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. Journal of Virology. 89: 5427-40. PMID 25741011 DOI: 10.1128/JVI.03636-14  1
2015 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 (Oxford, England). 31: 1337-9. PMID 25481008 DOI: 10.1093/Bioinformatics/Btu807  1
2014 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, ... ... Scheuermann RH, et al. A comprehensive collection of systems biology data characterizing the host response to viral infection. Scientific Data. 1: 140033. PMID 25977790 DOI: 10.1038/Sdata.2014.33  1
2014 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, ... ... Scheuermann RH, et al. Standardized metadata for human pathogen/vector genomic sequences. Plos One. 9: e99979. PMID 24936976 DOI: 10.1371/Journal.Pone.0099979  1
2014 Gabriel VA, McClellan EA, Scheuermann RH. Response of human skin to esthetic scarification. Burns : Journal of the International Society For Burn Injuries. 40: 1338-44. PMID 24582755 DOI: 10.1016/J.Burns.2014.01.005  1
2013 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 For Biology and Medicine. 8: 14. PMID 23822732 DOI: 10.1186/1751-0473-8-14  1
2012 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 Part A. 81: 353-356. PMID 22431383 DOI: 10.1002/cyto.a.22037  1
2012 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. Journal of Virology. 86: 5857-66. PMID 22398283 DOI: 10.1128/Jvi.06901-11  1
2011 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). Standards in Genomic Sciences. 5: 224-9. PMID 22180825 DOI: 10.4056/Sigs.1994602  1
2011 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, et al. Hematopoietic cell types: prototype for a revised cell ontology. Journal of Biomedical Informatics. 44: 75-9. PMID 20123131 DOI: 10.1016/J.Jbi.2010.01.006  1
2010 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. 2: 2258-68. PMID 21994619 DOI: 10.3390/v2102258  1
2010 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. International Journal of Computational Biology and Drug Design. 3: 237-57. PMID 21228458 DOI: 10.1504/Ijcbdd.2010.038028  1
2010 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, ... ... Scheuermann RH, et al. 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. Part B, Clinical Cytometry. 78: S69-82. PMID 20839340 DOI: 10.1002/Cyto.B.20554  1
2010 Chang RL, Luo F, Johnson S, Scheuermann RH. Deterministic graph-theoretic algorithm for detecting modules in biological interaction networks. International Journal of Bioinformatics Research and Applications. 6: 101-19. PMID 20223734 DOI: 10.1504/Ijbra.2010.032115  1
2010 Zhang S, Cao J, Kong YM, Scheuermann RH. GO-Bayes: Gene ontology-based overrepresentation analysis using a Bayesian approach Bioinformatics. 26: 905-911. PMID 20176581 DOI: 10.1093/Bioinformatics/Btq059  1
2010 Malin B, Karp D, Scheuermann RH. Technical and policy approaches to balancing patient privacy and data sharing in clinical and translational research. Journal of Investigative Medicine : the Official Publication of the American Federation For Clinical Research. 58: 11-8. PMID 20051768 DOI: 10.2310/Jim.0B013E3181C9B2Ea  1
2010 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, ... ... Scheuermann RH, et al. Novel sequence feature variant type analysis of the HLA genetic association in systemic sclerosis. Human Molecular Genetics. 19: 707-19. PMID 19933168 DOI: 10.1093/Hmg/Ddp521  1
2010 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. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 359-70. PMID 19908388  1
2009 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 ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 2009: 81-5. PMID 20351827  1
2009 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. Proceedings of the National Academy of Sciences of the United States of America. 106: 20365-70. PMID 19918065 DOI: 10.1073/pnas.0911580106  1
2009 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. 4: e7041. PMID 19756146 DOI: 10.1371/journal.pone.0007041  1
2009 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, et al. Synergies and distinctions between computational disciplines in biomedical research: perspective from the Clinical andTranslational Science Award programs. Academic Medicine : Journal of the Association of American Medical Colleges. 84: 964-70. PMID 19550198 DOI: 10.1097/Acm.0B013E3181A8144D  1
2009 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. 10: 184. PMID 19531228 DOI: 10.1186/1471-2105-10-184  1
2009 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. 10: 70. PMID 19243617 DOI: 10.1186/1471-2105-10-70  1
2009 Sim I, Chute CG, Lehmann H, Nagarajan R, Nahm M, Scheuermann RH. Keeping raw data in context. Science (New York, N.Y.). 323: 713. PMID 19197039 DOI: 10.1126/Science.323.5915.713A  1
2008 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, ... ... Scheuermann RH, et al. MIFlowCyt: the minimum information about a Flow Cytometry Experiment. Cytometry. Part a : the Journal of the International Society For Analytical Cytology. 73: 926-30. PMID 18752282 DOI: 10.1002/Cyto.A.20623  1
2008 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, ... ... Scheuermann RH, et al. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nature Biotechnology. 26: 889-96. PMID 18688244 DOI: 10.1038/Nbt.1411  1
2007 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, et al. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnology. 25: 1251-5. PMID 17989687 DOI: 10.1038/Nbt1346  1
2007 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, et al. Complete genomic characterization of a pathogenic A.II strain of Francisella tularensis subspecies tularensis. Plos One. 2: e947. PMID 17895988 DOI: 10.1371/Journal.Pone.0000947  1
2007 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. Infection and Immunity. 75: 3212-9. PMID 17420237 DOI: 10.1128/Iai.00105-07  1
2007 Diehl AD, Lee JA, Scheuermann RH, Blake JA. Ontology development for biological systems: immunology. Bioinformatics (Oxford, England). 23: 913-5. PMID 17267433 DOI: 10.1093/bioinformatics/btm029  1
2006 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. 7: 237. PMID 16670020 DOI: 10.1186/1471-2105-7-237  1
2004 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, et al. Analysis of the major patterns of B cell gene expression changes in response to short-term stimulation with 33 single ligands. Journal of Immunology (Baltimore, Md. : 1950). 173: 7141-9. PMID 15585835 DOI: 10.4049/Jimmunol.173.12.7141  1
2002 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, ... ... Scheuermann RH, et al. Overview of the Alliance for Cellular Signaling. Nature. 420: 703-6. PMID 12478301 DOI: 10.1038/Nature01304  1
2002 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 Immunology. 3: 16. PMID 12470302 DOI: 10.1186/1471-2172-3-16  1
2002 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. Molecular and Cellular Biology. 22: 5467-78. PMID 12101240 DOI: 10.1128/MCB.22.15.5467-5478.2002  1
1999 Hammill AK, Uhr JW, Scheuermann RH. Annexin V staining due to loss of membrane asymmetry can be reversible and precede commitment to apoptotic death. Experimental Cell Research. 251: 16-21. PMID 10438567 DOI: 10.1006/excr.1999.4581  1
1999 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. Current Topics in Microbiology and Immunology. 246: 299-304; discussion . PMID 10396069 DOI: 10.1007/978-3-642-60162-0_37  1
1988 Burckhardt SE, Woodgate R, Scheuermann RH, Echols H. UmuD mutagenesis protein of Escherichia coli: overproduction, purification, and cleavage by RecA. Proceedings of the National Academy of Sciences of the United States of America. 85: 1811-5. PMID 3279417 DOI: 10.1073/pnas.85.6.1811  1
1986 Lu C, Scheuermann RH, Echols H. Capacity of RecA protein to bind preferentially to UV lesions and inhibit the editing subunit (epsilon) of DNA polymerase III: a possible mechanism for SOS-induced targeted mutagenesis. Proceedings of the National Academy of Sciences of the United States of America. 83: 619-23. PMID 3456159  1
1984 Scheuermann RH, Echols H. A separate editing exonuclease for DNA replication: the epsilon subunit of Escherichia coli DNA polymerase III holoenzyme. Proceedings of the National Academy of Sciences of the United States of America. 81: 7747-51. PMID 6393125  1
1983 Scheuermann R, Tam S, Burgers PMJ. Identification of the ε-subunit of Escherichia coli DNA polymerase III holoenzyme as the dnaQ gene product: A fidelity subunit for DNA replication Proceedings of the National Academy of Sciences of the United States of America. 80: 7085-7089. PMID 6359162  1
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