Richard H. Scheuermann

According to our database, Richard H. Scheuermann authored at least 37 papers between 2006 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

A cell-level discriminative neural network model for diagnosis of blood cancers.

Edgar E. Robles, Ye Jin, Padhraic Smyth, Richard H. Scheuermann, Jack D. Bui, Huan-You Wang, Jean Oak, Yu Qian

Bioinform., October, 2023

Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR.

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

Nucleic Acids Res., January, 2023

2022

FastMix: a versatile data integration pipeline for cell type-specific biomarker inference.

Yun Zhang, Hao Sun, Aishwarya Mandava, Brian D. Aevermann, Tobias R. Kollmann, Richard H. Scheuermann, Xing Qiu, Yu Qian

Bioinform., October, 2022

Early detection of emerging SARS-CoV-2 variants of interest for experimental evaluation.

Zachary S. Wallace, James J. Davis, Anna Maria Niewiadomska, Robert D. Olson, Maulik Shukla, Rick Stevens, Yun Zhang, Christian M. Zmasek, Richard H. Scheuermann

Frontiers Bioinform., 2022

2021

FR-Match: robust matching of cell type clusters from single cell RNA sequencing data using the Friedman-Rafsky non-parametric test.

Yun Zhang, Brian D. Aevermann, Trygve E. Bakken, Jeremy A. Miller, Rebecca D. Hodge, Ed S. Lein, Richard H. Scheuermann

Briefings Bioinform., July, 2021

Standardization of assay representation in the Ontology for Biomedical Investigations.

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.

Database J. Biol. Databases Curation, 2021

Abstract: Explainable artificial intelligence and single cell genomics to understand the cellular complexity of human brain.

Richard H. Scheuermann

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021

2018

Bayesian Trees for Automated Cytometry Data Analysis.

Disi Ji, Eric T. Nalisnick, Yu Qian, Richard H. Scheuermann, Padhraic Smyth

Proceedings of the Machine Learning for Healthcare Conference, 2018

2017

Influenza Research Database: An integrated bioinformatics resource for influenza virus research.

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

Nucleic Acids Res., 2017

VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data.

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

BMC Bioinform., 2017

Cell type discovery and representation in the era of high-content single cell phenotyping.

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

BMC Bioinform., 2017

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.

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

Proceedings of the Biocomputing 2017: Proceedings of the Pacific Symposium, 2017

2016

VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements.

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

BMC Bioinform., 2016

2015

flowCL: ontology-based cell population labelling in flow cytometry.

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

Bioinform., 2015

FlowGate: towards extensible and scalable web-based flow cytometry data analysis.

Yu Qian, Hyunsoo Kim, Shweta Purawat, Jianwu Wang, Rick Stanton, Alexandra Lee, Weijia Xu, Ilkay Altintas, Robert S. Sinkovits, Richard H. Scheuermann

Proceedings of the 2015 XSEDE Conference: Scientific Advancements Enabled by Enhanced Cyberinfrastructure, St. Louis, MO, USA, July 26, 2015

2013

GenePattern Flow Cytometry Suite.

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

Source Code Biol. Medicine, 2013

2012

ViPR: an open bioinformatics database and analysis resource for virology research.

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

Nucleic Acids Res., 2012

A Machine Learning Approach for Identifying Anatomical Locations of Actionable Findings in Radiology Reports.

Kirk Roberts, Bryan Rink, Sanda M. Harabagiu, Richard H. Scheuermann, Seth M. Toomay, Travis Browning, Teresa Bosler, Ronald M. Peshock

Proceedings of the AMIA 2012, 2012

2011

Ontologies for clinical and translational research: Introduction.

Barry Smith, Richard H. Scheuermann

J. Biomed. Informatics, 2011

Toward an ontology-based framework for clinical research databases.

Y. Megan Kong, Carl Dahlke, Qun Xiang, Yu Qian, David R. Karp, Richard H. Scheuermann

J. Biomed. Informatics, 2011

Hematopoietic cell types: Prototype for a revised cell ontology.

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

J. Biomed. Informatics, 2011

Overcoming the ontology enrichment bottleneck with Quick Term Templates.

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

Appl. Ontology, 2011

2010

Identifying Differentially Expressed Genes based on probe level data for GeneChip arrays.

Zhongxue Chen, Monnie McGee, Qingzhong Liu, Y. Megan Kong, Xudong Huang, Jack Y. Yang, Richard H. Scheuermann

Int. J. Comput. Biol. Drug Des., 2010

Deterministic graph-theoretic algorithm for detecting modules in biological interaction networks.

Roger L. Chang, Feng Luo, Stuart Johnson, Richard H. Scheuermann

Int. J. Bioinform. Res. Appl., 2010

GO-Bayes: Gene Ontology-based overrepresentation analysis using a Bayesian approach.

Song Zhang, Jing Cao, Y. Megan Kong, Richard H. Scheuermann

Bioinform., 2010

Sequence Feature Variant Type (SFVT) Analysis of the HLA Genetic Association in Juvenile Idiopathic Arthritis.

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

Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

2009

FuGEFlow: data model and markup language for flow cytometry.

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

BMC Bioinform., 2009

An improved ontological representation of dendritic cells as a paradigm for all cell types.

Anna Maria Masci, Cecilia N. Arighi, Alexander D. Diehl, Anne E. Lieberman, Chris Mungall, Richard H. Scheuermann, Barry Smith, Lindsay G. Cowell

BMC Bioinform., 2009

Core and periphery structures in protein interaction networks.

Feng Luo, Bo Li, Xiu-Feng Wan, Richard H. Scheuermann

BMC Bioinform., 2009

Development and Evaluation of a Study Design Typology for Human Research.

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

Proceedings of the AMIA 2009, 2009

2008

BioHealthBase: informatics support in the elucidation of influenza virus host-pathogen interactions and virulence.

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

Nucleic Acids Res., 2008

Exploring Core/Periphery Structures in Protein Interaction Networks Provides Structure-Property Relation Insights.

Thomas Grindinger, Feng Luo, Xiu-Feng Wan, Richard H. Scheuermann

Proceedings of the 2008 IEEE International Conference on Bioinformatics and Biomedicine, 2008

2007

Modular organization of protein interaction networks.

Feng Luo, Yunfeng Yang, Chin-Fu Chen, Roger L. Chang, Jizhong Zhou, Richard H. Scheuermann

Bioinform., 2007

Ontology development for biological systems: immunology.

Alexander D. Diehl, Jamie A. Lee, Richard H. Scheuermann, Judith A. Blake

Bioinform., 2007

A distribution free summarization method for Affymetrix GeneChip^® arrays.

Zhongxue Chen, Monnie McGee, Qingzhong Liu, Richard H. Scheuermann

Bioinform., 2007

2006

Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation.

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

BMC Bioinform., 2006

Detecting Functional Modules from Protein Interaction Networks.

Feng Luo, Richard H. Scheuermann

Proceedings of the Interdisciplinary and Multidisciplinary Research in Computer Science, 2006