List of works by Richard H. Scheuermann

33 Polymerase chain reaction-based mRNA quantification using an internal standard: Analysis of oncogene expression

scientific article published on 01 January 1993

A Distribution-Free Convolution Model for background correction of oligonucleotide microarray data

scientific article

A Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A Viruses

scientific article

A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway.

scientific article

A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2

scientific article published on 16 March 2020

A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes.

scientific article published on 08 October 2015

A bioinformatics roadmap for the human vaccines project

scientific article

A community-based transcriptomics classification and nomenclature of neocortical cell types

scientific article published on 24 August 2020

A comprehensive collection of systems biology data characterizing the host response to viral infection.

scientific article

A distribution free summarization method for Affymetrix GeneChip(R) arrays

article

A gene selection method for GeneChip array data with small sample sizes

scientific article

A machine learning approach for identifying anatomical locations of actionable findings in radiology reports.

scientific article

A machine learning method for the discovery of minimum marker gene combinations for cell type identification from single-cell RNA sequencing

scientific article published on 04 June 2021

A novel colonic repressor element regulates intestinal gene expression by interacting with Cux/CDP

scientific article published on August 2002

A survey of known immune epitopes in the enteroviruses strains associated with acute flaccid myelitis

scientific article published on 23 August 2019

A unique antibody gene signature is prevalent in the central nervous system of patients with multiple sclerosis

scientific article

Activation of the Syk tyrosine kinase is insufficient for downstream signal transduction in B lymphocytes

scientific article

Allergen-specific immunotherapy modulates the balance of circulating Tfh and Tfr cells

scientific article published on 12 May 2017

An Integrated Workflow To Assess Technical and Biological Variability of Cell Population Frequencies in Human Peripheral Blood by Flow Cytometry

scientific article published on 9 January 2017

An Ontology-Based Framework for Clinical Research Databases

An Ontology-Based Framework for Clinical Research Databases

article

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

scientific article

Analysis of the major patterns of B cell gene expression changes in response to short-term stimulation with 33 single ligands

scientific article published in December 2004

Annexin V staining due to loss of membrane asymmetry can be reversible and precede commitment to apoptotic death

scientific article published in August 1999

Antigen receptor signaling induces differential tyrosine kinase activation and population stability in B-cell lymphoma

scientific article

Application of random matrix theory to biological networks

article

Automated Analysis of Clinical Flow Cytometry Data: A Chronic Lymphocytic Leukemia Illustration

scientific article

Automated Analysis of Flow Cytometry Data to Reduce Inter-Lab Variation in the Detection of Major Histocompatibility Complex Multimer-Binding T Cells.

scientific article published on 26 July 2017

Automated analysis of flow cytometry data comes of age.

scientific article published in January 2016

Bcl-2 Expression in Langerhans' Cell Histiocytosis

scientific article published on 01 May 1998

Benefits and dangers of genetic tests

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

scientific article

Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting.

scientific article

CD19 antigen in leukemia and lymphoma diagnosis and immunotherapy

scientific article

Cancer dormancy. VII. A regulatory role for CD8+ T cells and IFN-gamma in establishing and maintaining the tumor-dormant state

scientific article published on March 1999

Cancer dormancy: from mice to man.

scientific article published on 15 August 2006

Cancer dormancy: isolation and characterization of dormant lymphoma cells

scientific article

Cancer dormancy: opportunities for new therapeutic approaches

scientific article published on May 1997

Cancer dormancy: role of cyclin-dependent kinase inhibitors in induction of cell cycle arrest mediated via membrane IgM.

scientific article

Candidate Targets for Immune Responses to 2019-Novel Coronavirus (nCoV): Sequence Homology- and Bioinformatic-Based Predictions

scientific article published on 25 February 2020

Candidate targets for immune responses to 2019-Novel Coronavirus (nCoV): sequence homology- and bioinformatic-based predictions

scientific article

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

scientific article published on 21 December 2017

Cell type discovery using single-cell transcriptomics: implications for ontological representation.

scientific article published on 24 March 2018

Chromosome Y-encoded antigens associate with acute graft-versus-host disease in sex-mismatched stem cell transplant

scientific article published on 01 October 2018

Classification of human Herpesviridae proteins using Domain-architecture Aware Inference of Orthologs (DAIO)

scientific article published on 06 January 2019

Comparative cellular analysis of motor cortex in human, marmoset and mouse

scientific article published on 06 October 2021

Complete genome sequence of Francisella tularensis subspecies holarctica FTNF002-00

scientific article

Complete genomic characterization of a pathogenic A.II strain of Francisella tularensis subspecies tularensis

scientific article

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

scientific article

Comprehensive Annotation of Mature Peptides and Genotypes for Zika Virus

scientific article (publication date: 26 January 2017)

Connections between signal transduction components and cellular responses initiated by antigen receptor on B lymphocytes

scientific article

Conserved cell types with divergent features in human versus mouse cortex

scientific article published in 2019 in Nature

Contemporary Circulating Enterovirus D68 Strains Have Acquired the Capacity for Viral Entry and Replication in Human Neuronal Cells

scientific article published on 16 October 2018

Contemporary circulating enterovirus D68 strains show differential viral entry and replication in human neuronal cells

Core and periphery structures in protein interaction networks

scientific article

Critical assessment of automated flow cytometry data analysis techniques

Critical assessment of automated flow cytometry data analysis techniques

Critical assessment of automated flow cytometry data analysis techniques.

scientific article

Cux/CDP homeoprotein is a component of NF-muNR and represses the immunoglobulin heavy chain intronic enhancer by antagonizing the bright transcription activator

scientific article

DAFi: A Directed Recursive Filtering and Clustering Approach to Data-Driven Identification of Cell Populations from Polychromatic Flow Cytometry Data

DAFi: A directed recursive data filtering and clustering approach for improving and interpreting data clustering identification of cell populations from polychromatic flow cytometry data.

scientific article published on 17 April 2018

Defining the risk of SARS-CoV-2 variants on immune protection

scientific article published on 31 March 2022

Detecting Functional Modules from Protein Interaction Networks

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

scientific article published in January 2010

Development and evaluation of a study design typology for human research

scientific article

Development of real-time PCR assays for the quantitative detection of Epstein-Barr virus and cytomegalovirus, comparison of TaqMan probes, and molecular beacons

scientific article published on February 2003

Differential transcriptome and development of human peripheral plasma cell subsets.

scientific article

Diversifying Selection Analysis Predicts Antigenic Evolution of 2009 Pandemic H1N1 Influenza A Virus in Humans.

scientific article

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

scientific article

Epidemiology and Sequence-Based Evolutionary Analysis of Circulating Non-Polio Enteroviruses

scientific article published on 25 November 2020

Epstein-Barr virus polymerase chain reaction and serology in pediatric post-transplant lymphoproliferative disorder: three-year experience

scientific article

Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse

scientific article published in April 2020

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

Extracting actionable findings of appendicitis from radiology reports using natural language processing

scientific article published on 18 March 2013

FCSTrans: an open source software system for FCS file conversion and data transformation

scientific article

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

scientific article published on 30 November 2020

Fast and accurate HLA typing from short-read next-generation sequence data with xHLA.

scientific article

FuGEFlow: data model and markup language for flow cytometry

scientific article

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

scientific article

GenePattern flow cytometry suite

2013 scientific article

Genetic changes found in a distinct clade of Enterovirus D68 associated with paralysis during the 2014 outbreak.

scientific article

Guidelines for reporting single-cell RNA-seq experiments

scientific article published on 13 November 2020

Hematopoietic cell types: prototype for a revised cell ontology

scientific article

Hepatitis C Virus Database and Bioinformatics Analysis Tools in the Virus Pathogen Resource (ViPR)

scientific article published on 01 January 2019

Human herpesvirus-6 and sudden death in infancy: report of a case and review of the literature.

scientific article

Identification of diagnostic peptide regions that distinguish Zika virus from related mosquito-borne Flaviviruses

scientific article

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

scientific article

Induction of B cell tumor dormancy by anti-idiotypic antibodies

scientific article published in October 1993

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

scientific article published on 26 September 2016

Influenza research database: an integrated bioinformatics resource for influenza research and surveillance.

scientific article

Influenza virus sequence feature variant type analysis: evidence of a role for NS1 in influenza virus host range restriction.

scientific article published on 7 March 2012

Integrated Single-Cell Atlases Reveal an Oral SARS-CoV-2 Infection and Transmission Axis

scientific article published on 27 October 2020

Keeping raw data in context

scientific article published in February 2009

Lymphoid apoptosis and myeloid hyperplasia in CCAAT displacement protein mutant mice

scientific article published on 01 December 2001

Lyn tyrosine kinase signals cell cycle arrest but not apoptosis in B-lineage lymphoma cells

scientific article

Lyn tyrosine kinase signals cell cycle arrest in mouse and human B-cell lymphoma

scientific article published on 01 January 1995

MARs of antigen receptor and co-receptor genes.

scientific article

MIFlowCyt: the minimum information about a Flow Cytometry Experiment

scientific article

Machine Learning of Discriminative Gate Locations for Clinical Diagnosis

scientific article published on 05 November 2019

Machine Learning-Based Single Cell and Integrative Analysis Reveals That Baseline mDC Predisposition Correlates With Hepatitis B Vaccine Antibody Response

scientific article published on 29 October 2021

Mapping cell populations in flow cytometry data for cross-sample comparison using the Friedman-Rafsky test statistic as a distance measure

scientific article

Metadata-driven comparative analysis tool for sequences (meta-CATS): an automated process for identifying significant sequence variations that correlate with virus attributes

scientific article published on 14 September 2013

Minimum Information about a Genotyping Experiment (MIGEN).

scientific article

Modular organization of protein interaction networks

scientific article

Multi-Omic Data Integration Allows Baseline Immune Signatures to Predict Hepatitis B Vaccine Response in a Small Cohort

scientific article published on 30 November 2020

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

scientific article published on October 1995

National Institute of Allergy and Infectious Diseases bioinformatics resource centers: new assets for pathogen informatics

scientific article

Novel sequence feature variant type analysis of the HLA genetic association in systemic sclerosis

scientific article

Nucleic acid testing for viral burden and viral genotyping

scientific article

Ontologies for clinical and translational research: Introduction

scientific article published on 15 January 2011

Ontology development for biological systems: immunology

scientific article

Overview of the Alliance for Cellular Signaling

scientific article

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.

scientific article published on January 2016

Personalized care, comparative effectiveness research and the electronic health record

scientific article

Polymerase chain reaction amplification of archival material for Epstein-Barr virus, cytomegalovirus, human herpesvirus 6, and parvovirus B19 in children with bone marrow hemophagocytosis

scientific article published on October 1998

Pre-existing immunity against swine-origin H1N1 influenza viruses in the general human population

scientific article

Presence of simian virus 40 DNA sequences in human lymphomas

scientific article published in March 2002

Prevalence and Cellular Reservoir of Latent Human Herpesvirus 6 in Tonsillar Lymphoid Tissue

scientific article published on 01 November 2001

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

scientific article (publication date: August 2008)

Publisher Correction: A community-based transcriptomics classification and nomenclature of neocortical cell types

scientific article published on 04 December 2020

Quantitation of 8 human herpesviruses in peripheral blood of human immunodeficiency virus-infected patients and healthy blood donors by polymerase chain reaction

scientific article published in May 1999

Response of human skin to esthetic scarification

scientific article

Role of antibody signaling in inducing tumor dormancy.

scientific article published on January 1996

SARS-CoV-2 infection of the oral cavity and saliva

SARS-CoV-2 reservoir in post-acute sequelae of COVID-19 (PASC)

scientific article published in 2023

Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable

scientific article published on 07 May 2020

Sequence feature variant type (SFVT) analysis of the HLA genetic association in juvenile idiopathic arthritis.

scientific article

Single-nucleus and single-cell transcriptomes compared in matched cortical cell types

scientific article published in PLoS ONE

Standardization of assay representation in the Ontology for Biomedical Investigations

scientific article published on 16 June 2021

Standardized metadata for human pathogen/vector genomic sequences

scientific article (publication date: 2014)

Standardizing Flow Cytometry Immunophenotyping Analysis from the Human ImmunoPhenotyping Consortium

scientific article

State-of-the-Art in the Computational Analysis of Cytometry Data.

scientific article published in July 2015

Synergies and distinctions between computational disciplines in biomedical research: perspective from the Clinical andTranslational Science Award programs

scientific article

Systems Biology Methods Applied to Blood and Tissue for a Comprehensive Analysis of Immune Response to Hepatitis B Vaccine in Adults

scientific article published on 04 November 2020

Technical and policy approaches to balancing patient privacy and data sharing in clinical and translational research

scientific article (publication date: 2010)

The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration

scientific article published in November 2007

The Ontology for Biomedical Investigations

scientific article

The genome and preliminary single-nuclei transcriptome of Lemna minuta reveals mechanisms of invasiveness ⬇️

scientific article published on 01 February 2022

The human studies database project: federating human studies design data using the ontology of clinical research

scientific article

Thinking outside the gate: single-cell assessments in multiple dimensions

scientific article published on April 2015

Toward a method for tracking virus evolutionary trajectory applied to the pandemic H1N1 2009 influenza virus.

scientific article

Toward an ontological treatment of disease and diagnosis

scientific article

Toward an ontology-based framework for clinical research databases

scientific article

Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop

scientific article

Transcriptional activation by a matrix associating region-binding protein. contextual requirements for the function of bright

scientific article

Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type

scientific article published on 27 August 2018

Transcriptomic evidence that von Economo neurons are regionally specialized extratelencephalic-projecting excitatory neurons

scientific article published on 03 March 2020

Tumor dormancy and cell signaling. II. Antibody as an agonist in inducing dormancy of a B cell lymphoma in SCID mice

scientific article

Tumor dormancy and cell signaling. V. Regrowth of the BCL1 tumor after dormancy is established

scientific article published on 01 June 1997

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

scientific article published on March 1996

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

scientific article published on 01 June 1995

UmuD mutagenesis protein of Escherichia coli: overproduction, purification, and cleavage by RecA.

scientific article

Unbiased analysis of peripheral blood mononuclear cells reveals CD4 T cell response to RSV matrix protein

scientific article published on 21 April 2020

Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons

scientific article

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

2016 scientific article

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

scientific article published on 11 October 2017

VDJServer: A Cloud-Based Analysis Portal and Data Commons for Immune Repertoire Sequences and Rearrangements.

scientific article published on 8 May 2018

VO: Vaccine Ontology

VO: Vaccine Ontology

VO: Vaccine Ontology

VO: Vaccine Ontology

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

scientific article published on 17 October 2011

Virus pathogen database and analysis resource (ViPR): a comprehensive bioinformatics database and analysis resource for the coronavirus research community

scientific article

Zika virus: designate standardized names

scientific article

[Antinuclear antibodies in diagnosis of rheumatic diseases (author's transl)]

scientific article published on 01 March 1981

flowCL: ontology-based cell population labelling in flow cytometry

scientific article

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