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ORCIDRichard H. Scheuermann
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Journal Articles
- 2023
[j29]Edgar E. Robles
, Ye Jin, Padhraic Smyth, Richard H. Scheuermann, Jack D. Bui, Huan-You Wang, Jean Oak, Yu Qian:
A cell-level discriminative neural network model for diagnosis of blood cancers. Bioinform. 39(10) (2023)- [j28]Robert D. Olson, Rida Assaf, Thomas S. Brettin, Neal Conrad, Clark Cucinell, James J. Davis, Donald M. Dempsey, Allan Dickerman, Emily M. Dietrich, Ronald W. Kenyon, Mehmet Kuscuoglu, Elliot J. Lefkowitz, Jian Lu, Dustin Machi, Catherine Macken, Chunhong Mao, Anna Maria Niewiadomska, Marcus Nguyen, Gary J. Olsen, Jamie C. Overbeek, Bruce D. Parrello, Victoria Parrello, Jacob s Porter, Gordon D. Pusch, Maulik Shukla, Indresh Singh, Lucy Stewart, Gene Tan, Chris Thomas, Margo VanOeffelen, Veronika Vonstein, Zachary S. Wallace, Andrew S. Warren, Alice R. Wattam, Fangfang Xia, Hyun Seung Yoo, Yun Zhang, Christian M. Zmasek, Richard H. Scheuermann, Rick L. Stevens:
Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR. Nucleic Acids Res. 51(D1): 678-689 (2023) - 2022
- [j27]Yun Zhang, Hao Sun, Aishwarya Mandava, Brian D. Aevermann, Tobias R. Kollmann, Richard H. Scheuermann, Xing Qiu, Yu Qian:
FastMix: a versatile data integration pipeline for cell type-specific biomarker inference. Bioinform. 38(20): 4735-4744 (2022) - [j26]Zachary S. Wallace, James J. Davis, Anna Maria Niewiadomska, Robert D. Olson, Maulik Shukla, Rick Stevens, Yun Zhang, Christian M. Zmasek, Richard H. Scheuermann:
Early detection of emerging SARS-CoV-2 variants of interest for experimental evaluation. Frontiers Bioinform. 2 (2022) - 2021
- [j25]Yun Zhang, Brian D. Aevermann, Trygve E. Bakken, Jeremy A. Miller, Rebecca D. Hodge, Ed S. Lein, Richard H. Scheuermann:
FR-Match: robust matching of cell type clusters from single cell RNA sequencing data using the Friedman-Rafsky non-parametric test. Briefings Bioinform. 22(4) (2021) - [j24]Randi Vita, Jie Zheng, Rebecca C. Jackson, Damion M. Dooley, James A. Overton, Mark A. Miller, Daniel C. Berrios, Richard H. Scheuermann, Yongqun He, Hande Küçük-McGinty, Mathias Brochhausen, Aisyah Yu Lin, Sagar B. Jain, Marcus C. Chibucos, John Judkins, Michelle G. Giglio, Irene Y. Feng, Gully Burns, Matthew H. Brush, Bjoern Peters, Christian J. Stoeckert Jr.:
Standardization of assay representation in the Ontology for Biomedical Investigations. Database J. Biol. Databases Curation 2021 (2021) - 2017
- [j23]Scott Christley, Mikhail K. Levin, Inimary T. Toby, John M. Fonner, Nancy Monson, William Rounds, Florian Rubelt, Walter Scarborough, Richard H. Scheuermann, Lindsay G. Cowell:
VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data. BMC Bioinform. 18(1): 448:1-448:5 (2017) - [j22]Trygve E. Bakken, Lindsay G. Cowell, Brian D. Aevermann, Mark Novotny, Rebecca D. Hodge, Jeremy A. Miller, Alexandra Lee, Ivan Chang, Jamison M. McCorrison, Bali Pulendran, Yu Qian, Nicholas J. Schork, Roger S. Lasken, Ed S. Lein, Richard H. Scheuermann:
Cell type discovery and representation in the era of high-content single cell phenotyping. BMC Bioinform. 18(S-17): 7-16 (2017) - [j21]Yun Zhang, Brian D. Aevermann, Tavis K. Anderson, David F. Burke, Gwenaelle Dauphin, Zhiping Gu, Sherry He, Sanjeev Kumar, Christopher N. Larsen, Alexandra J. Lee, Xiaomei Li, Catherine Macken, Colin Mahaffey, Brett E. Pickett, Brian Reardon, Thomas Smith, Lucy Stewart, Christian Suloway, Guangyu Sun, Lei Tong, Amy L. Vincent, Bryan Walters, Sam Zaremba, Hongtao Zhao, Liwei Zhou, Christian M. Zmasek, Edward B. Klem, Richard H. Scheuermann:
Influenza Research Database: An integrated bioinformatics resource for influenza virus research. Nucleic Acids Res. 45(Database-Issue): D466-D474 (2017) - 2016
- [j20]Inimary T. Toby, Mikhail K. Levin, Edward Salinas, Scott Christley, Sanchita Bhattacharya, Felix Breden, Adam Buntzman, Brian Corrie, John M. Fonner, Namita T. Gupta, Uri Hershberg, Nishanth Marthandan, Aaron M. Rosenfeld, William Rounds, Florian Rubelt, Walter Scarborough, Jamie K. Scott, Mohamed Uduman, Jason A. Vander Heiden, Richard H. Scheuermann, Nancy Monson, Steven H. Kleinstein, Lindsay G. Cowell:
VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements. BMC Bioinform. 17(S-13): 333 (2016) - 2015
- [j19]Mélanie Courtot, Justin Meskas, Alexander D. Diehl, Radina Droumeva, Raphael Gottardo, Adrin Jalali, Mohammad Jafar Taghiyar, Holden T. Maecker, J. Philip McCoy, Alan Ruttenberg, Richard H. Scheuermann, Ryan Remy Brinkman:
flowCL: ontology-based cell population labelling in flow cytometry. Bioinform. 31(8): 1337-1339 (2015) - 2013
- [j18]Josef Spidlen, Aaron Barsky, Karin Breuer, Peter Carr, Marc-Danie Nazaire, Barbara A. Hill, Yu Qian, Ted Liefeld, Michael Reich, Jill P. Mesirov, Peter Wilkinson, Richard H. Scheuermann, Rafick-Pierre Sekaly, Ryan Remy Brinkman:
GenePattern Flow Cytometry Suite. Source Code Biol. Medicine 8: 14 (2013) - 2012
- [j17]Brett E. Pickett, Eva L. Sadat, Yun Zhang, Jyothi Noronha, R. Burke Squires, Victoria Hunt, Mengya Liu, Sanjeev Kumar, Sam Zaremba, Zhiping Gu, Liwei Zhou, Christopher N. Larsen, Jonathan Dietrich, Edward B. Klem, Richard H. Scheuermann:
ViPR: an open bioinformatics database and analysis resource for virology research. Nucleic Acids Res. 40(Database-Issue): 593-598 (2012) - 2011
- [j16]Philippe Rocca-Serra, Alan Ruttenberg, Martin J. O'Connor, Patricia L. Whetzel, Daniel Schober, Jay Greenbaum, Mélanie Courtot, Ryan Remy Brinkman, Susanna-Assunta Sansone, Richard H. Scheuermann, Bjoern Peters:
Overcoming the ontology enrichment bottleneck with Quick Term Templates. Appl. Ontology 6(1): 13-22 (2011) - [j15]Barry Smith, Richard H. Scheuermann:
Ontologies for clinical and translational research: Introduction. J. Biomed. Informatics 44(1): 3-7 (2011) - [j14]Y. Megan Kong, Carl Dahlke, Qun Xiang, Yu Qian, David R. Karp, Richard H. Scheuermann:
Toward an ontology-based framework for clinical research databases. J. Biomed. Informatics 44(1): 48-58 (2011) - [j13]Alexander D. Diehl, Alison Deckhut Augustine, Judith A. Blake, Lindsay G. Cowell, Elizabeth S. Gold, Timothy A. Gondré-Lewis, Anna Maria Masci, Terrence F. Meehan, Penelope A. Morel, Anastasia Nijnik, Bjoern Peters, Bali Pulendran, Richard H. Scheuermann, Q. Alison Yao, Martin S. Zand, Christopher J. Mungall:
Hematopoietic cell types: Prototype for a revised cell ontology. J. Biomed. Informatics 44(1): 75-79 (2011) - 2010
- [j12]Song Zhang, Jing Cao, Y. Megan Kong, Richard H. Scheuermann:
GO-Bayes: Gene Ontology-based overrepresentation analysis using a Bayesian approach. Bioinform. 26(7): 905-911 (2010) - [j11]Roger L. Chang, Feng Luo, Stuart Johnson, Richard H. Scheuermann:
Deterministic graph-theoretic algorithm for detecting modules in biological interaction networks. Int. J. Bioinform. Res. Appl. 6(2): 101-119 (2010) - [j10]Zhongxue Chen, Monnie McGee, Qingzhong Liu, Y. Megan Kong, Xudong Huang, Jack Y. Yang, Richard H. Scheuermann:
Identifying Differentially Expressed Genes based on probe level data for GeneChip arrays. Int. J. Comput. Biol. Drug Des. 3(3): 237-257 (2010) - 2009
- [j9]Feng Luo, Bo Li, Xiu-Feng Wan, Richard H. Scheuermann:
Core and periphery structures in protein interaction networks. BMC Bioinform. 10(S-4) (2009) - [j8]Anna Maria Masci, Cecilia N. Arighi, Alexander D. Diehl, Anne E. Lieberman, Chris Mungall, Richard H. Scheuermann, Barry Smith, Lindsay G. Cowell:
An improved ontological representation of dendritic cells as a paradigm for all cell types. BMC Bioinform. 10 (2009) - [j7]Yu Qian, Olga Tchuvatkina, Josef Spidlen, Peter Wilkinson, Maura Gasparetto, Andrew R. Jones, Frank J. Manion, Richard H. Scheuermann, Rafick-Pierre Sekaly, Ryan Remy Brinkman:
FuGEFlow: data model and markup language for flow cytometry. BMC Bioinform. 10 (2009) - 2008
- [j6]R. Burke Squires, Catherine Macken, Adolfo Garcia-Sastre, Shubhada Godbole, Jyothi Noronha, Victoria Hunt, Roger L. Chang, Christopher N. Larsen, Edward B. Klem, Kevin Biersack, Richard H. Scheuermann:
BioHealthBase: informatics support in the elucidation of influenza virus host-pathogen interactions and virulence. Nucleic Acids Res. 36(Database-Issue): 497-503 (2008) - 2007
- [j5]Feng Luo, Yunfeng Yang, Chin-Fu Chen, Roger L. Chang, Jizhong Zhou, Richard H. Scheuermann:
Modular organization of protein interaction networks. Bioinform. 23(2): 207-214 (2007) - [j4]Zhongxue Chen, Monnie McGee, Qingzhong Liu, Richard H. Scheuermann:
A distribution free summarization method for Affymetrix GeneChip® arrays. Bioinform. 23(3): 321-327 (2007) - [j3]Alexander D. Diehl, Jamie A. Lee, Richard H. Scheuermann, Judith A. Blake:
Ontology development for biological systems: immunology. Bioinform. 23(7): 913-915 (2007) - [j2]Feng Luo, Yunfeng Yang, Chin-Fu Chen, Roger L. Chang, Jizhong Zhou, Richard H. Scheuermann:
Modular organization of protein interaction networks. Bioinform. 23(7): 916 (2007) - 2006
- [j1]Jamie A. Lee, Robert S. Sinkovits, Dennis Mock, Eva L. Rab, Jennifer Cai, Peng Yang, Brian Saunders, Robert C. Hsueh, Sangdun Choi, Shankar Subramaniam, Richard H. Scheuermann:
Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation. BMC Bioinform. 7: 237 (2006)
Conference and Workshop Papers
- 2021
- [c9]Richard H. Scheuermann:
Abstract: Explainable artificial intelligence and single cell genomics to understand the cellular complexity of human brain. BIBM 2021: 4 - 2018
- [c8]Disi Ji, Eric T. Nalisnick, Yu Qian, Richard H. Scheuermann, Padhraic Smyth:
Bayesian Trees for Automated Cytometry Data Analysis. MLHC 2018: 465-483 - 2017
- [c7]Brian D. Aevermann, Jamison M. McCorrison, Pratap Venepally, Rebecca D. Hodge, Trygve E. Bakken, Jeremy A. Miller, Mark Novotny, Danny N. Tran, Francisco Diez-Fuertes, Lena Christiansen, Fan Zhang, Frank Steemers, Roger S. Lasken, Ed S. Lein, Nicholas J. Schork, Richard H. Scheuermann:
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. PSB 2017: 564-575 - 2015
- [c6]Yu Qian, Hyunsoo Kim, Shweta Purawat, Jianwu Wang, Rick Stanton, Alexandra Lee, Weijia Xu, Ilkay Altintas, Robert S. Sinkovits, Richard H. Scheuermann:
FlowGate: towards extensible and scalable web-based flow cytometry data analysis. XSEDE 2015: 5:1-5:8 - 2012
- [c5]Kirk Roberts, Bryan Rink, Sanda M. Harabagiu, Richard H. Scheuermann, Seth M. Toomay, Travis Browning, Teresa Bosler, Ronald M. Peshock:
A Machine Learning Approach for Identifying Anatomical Locations of Actionable Findings in Radiology Reports. AMIA 2012 - 2010
- [c4]Glenys Thomson, Nishanth Marthandan, Jill A. Hollenbach, Steven J. Mack, Henry A. Erlich, Richard M. Single, Matthew J. Waller, Steven G. E. Marsh, Paula A. Guidry, David R. Karp, Richard H. Scheuermann, Susan D. Thompson, David N. Glass, Wolfgang Helmberg:
Sequence Feature Variant Type (SFVT) Analysis of the HLA Genetic Association in Juvenile Idiopathic Arthritis. Pacific Symposium on Biocomputing 2010: 359-370 - 2009
- [c3]Simona Carini, Brad Pollock, Harold P. Lehmann, Suzanne Bakken, Edward M. Barbour, Davera Gabriel, Herbert K. Hagler, Caryn R. Harper, Shamim Mollah, Meredith Nahm, Hien H. Nguyen, Richard H. Scheuermann, Ida Sim:
Development and Evaluation of a Study Design Typology for Human Research. AMIA 2009 - 2008
- [c2]Thomas Grindinger, Feng Luo, Xiu-Feng Wan, Richard H. Scheuermann:
Exploring Core/Periphery Structures in Protein Interaction Networks Provides Structure-Property Relation Insights. BIBM 2008: 179-186 - 2006
- [c1]Feng Luo, Richard H. Scheuermann:
Detecting Functional Modules from Protein Interaction Networks. IMSCCS (1) 2006: 123-130
Coauthor Index
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