Richard H. Scheuermann

Publication Activity (10 Years)

Years Active: 2006-2023
Publications (10 Years): 15

Top Topics

Quality Control

Top Venues

Nucleic Acids Res.

Publications

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)
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) (2023)
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) (2022)
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)
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)
Richard H. Scheuermann
Abstract: Explainable artificial intelligence and single cell genomics to understand the cellular complexity of human brain. BIBM (2021)
Yun Zhang, Brian D. Aevermann, Trygve Bakken, Jeremy A. Miller, Rebecca Hodge, Ed 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)
Disi Ji, Eric T. Nalisnick, Yu Qian, Richard H. Scheuermann, Padhraic Smyth
Bayesian Trees for Automated Cytometry Data Analysis. MLHC (2018)
Trygve Bakken, Lindsay G. Cowell, Brian D. Aevermann, Mark Novotny, Rebecca Hodge, Jeremy A. Miller, Alexandra Lee, Ivan Chang, Jamison M. McCorrison, Bali Pulendran, Yu Qian, Nicholas J. Schork, Roger S. Lasken, Ed Lein, Richard H. Scheuermann
Cell type discovery and representation in the era of high-content single cell phenotyping. BMC Bioinform. 18 (S-17) (2017)
Brian D. Aevermann, Jamison M. McCorrison, Pratap Venepally, Rebecca Hodge, Trygve Bakken, Jeremy A. Miller, Mark Novotny, Danny N. Tran, Francisco Diez-Fuertes, Lena Christiansen, Fan Zhang, Frank Steemers, Roger S. Lasken, Ed 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)
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) (2017)
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) (2017)
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) (2016)
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)
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) (2015)
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 (2013)
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)
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) (2012)
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) (2011)
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) (2011)
Barry Smith, Richard H. Scheuermann
Ontologies for clinical and translational research: Introduction. J. Biomed. Informatics 44 (1) (2011)
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) (2011)
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) (2010)
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) (2010)
Song Zhang, Jing Cao, Y. Megan Kong, Richard H. Scheuermann
GO-Bayes: Gene Ontology-based overrepresentation analysis using a Bayesian approach. Bioinform. 26 (7) (2010)
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)
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)
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)
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)
Feng Luo, Bo Li, Xiu-Feng Wan, Richard H. Scheuermann
Core and periphery structures in protein interaction networks. BMC Bioinform. 10 (S-4) (2009)
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) (2008)
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)
Feng Luo, Yunfeng Yang, Chin-Fu Chen, Roger L. Chang, Jizhong Zhou, Richard H. Scheuermann
Modular organization of protein interaction networks. Bioinform. 23 (2) (2007)
Zhongxue Chen, Monnie McGee, Qingzhong Liu, Richard H. Scheuermann
arrays. Bioinform. 23 (3) (2007)
Feng Luo, Yunfeng Yang, Chin-Fu Chen, Roger L. Chang, Jizhong Zhou, Richard H. Scheuermann
Modular organization of protein interaction networks. Bioinform. 23 (7) (2007)
Alexander D. Diehl, Jamie A. Lee, Richard H. Scheuermann, Judith A. Blake
Ontology development for biological systems: immunology. Bioinform. 23 (7) (2007)
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 (2006)
Feng Luo, Richard H. Scheuermann
Detecting Functional Modules from Protein Interaction Networks. IMSCCS (1) (2006)