A new framework for host-pathogen interaction research

Article Immunology

Molnupiravir and Nirmatrelvir-Ritonavir: Oral Coronavirus Disease 2019 Antiviral Drugs

Louis D. Saravolatz et al.

Summary: Molnupiravir and nirmatrelvir-ritonavir are two new oral antiviral drugs for outpatient treatment of mild to moderate COVID-19. Both drugs have shown a reduction in death and hospitalization when started within 5 days of symptom onset.

CLINICAL INFECTIOUS DISEASES (2023)

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Article Medicine, General & Internal

Differential COVID-19 Symptoms Given Pandemic Locations, Time, and Comorbidities During the Early Pandemic

Yang Wang et al.

Summary: Background: The COVID-19 pandemic has caused a global public health disaster. This study used an ontology-based bioinformatics approach to systematically analyze clinical phenotypes and comorbidities in COVID-19 patients during the early stages of the pandemic, aiming to identify new insights and hidden patterns of COVID-19 symptoms. The results revealed differential patterns of symptoms given different locations, time, and comorbidity types, and provided valuable information for future pandemics.

FRONTIERS IN MEDICINE (2022)

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Article Mathematical & Computational Biology

A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology

Yongqun He et al.

Summary: CIDO is an open-source biomedical ontology that integrates heterogeneous coronavirus data, supporting the development of vaccines and drugs and providing insights into coronaviruses and associated diseases. It represents various variants of SARS-CoV-2 viruses, diagnostic kits and methods, host-coronavirus protein-protein interactions (PPIs), and drug-target knowledge. CIDO has been widely used in applications such as term standardization, natural language processing (NLP), and clinical data integration.

JOURNAL OF BIOMEDICAL SEMANTICS (2022)

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Article Zoology

Coevolutionary insights between promoters and transcription factors in the plant and animal kingdoms

Jing-Song Zhang et al.

Summary: The divergence and evolution of plants and animals have contributed to ecological diversity. An extensive analysis of multi-omics sequences in animal and plant species revealed different evolutionary trends in promoter and transcription factor features. Promoters and TFs exhibited antagonistic coevolution in the animal kingdom but mutualistic coevolution in the plant kingdom. These distinct coevolutionary patterns potentially drive the divergence, divergent evolution, and ecological diversity of plants and animals.

ZOOLOGICAL RESEARCH (2022)

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Article Pharmacology & Pharmacy

The tyrosine kinase inhibitor nilotinib inhibits SARS-CoV-2 in vitro

Valeria Cagno et al.

Summary: Since the emergence of SARS-CoV-2 in late 2019, there has been no approved vaccine to combat the infection, highlighting the urgent need for effective treatment for the ongoing COVID-19 pandemic. Drug repurposing offers a rapid antiviral response in such emergencies. Nilotinib shows promising activity against SARS-CoV-2 in vitro, making it a potential candidate for COVID-19 treatment in vivo.

BASIC & CLINICAL PHARMACOLOGY & TOXICOLOGY (2021)

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Review Microbiology

Drug repurposing against SARS-CoV-1, SARS-CoV-2 and MERS-CoV

Sarah Aherfi et al.

Summary: This article reviews drugs with in vitro antiviral activity against SARS-CoV-2, combined with molecular docking data and results from preliminary clinical studies, and proposes 11 potential drug candidates for COVID-19 treatment.

FUTURE MICROBIOLOGY (2021)

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Article Biochemistry & Molecular Biology

The Human Phenotype Ontology in 2021

Sebastian Koehler et al.

Summary: The Human Phenotype Ontology (HPO) serves as a global standard for phenotype exchange, with recent major extensions in neurology, nephrology, immunology, pulmonology, and other fields. Efforts have been made to improve computational definitions of phenotypic abnormalities across HPO and multiple phenotype ontologies for animal disease models, benefiting software accuracy and cross-species phenotype matching. Recent initiatives include translating HPO into indigenous languages and advancing its use in electronic health record systems.

NUCLEIC ACIDS RESEARCH (2021)

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Article Multidisciplinary Sciences

A therapeutic neutralizing antibody targeting receptor binding domain of SARS-CoV-2 spike protein

Cheolmin Kim et al.

Summary: A human monoclonal antibody called CT-P59 has been shown to effectively neutralize SARS-CoV-2 and demonstrate significant therapeutic effects in animal models, making it a promising candidate for COVID-19 treatment.

NATURE COMMUNICATIONS (2021)

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Article Multidisciplinary Sciences

Ontological modeling and analysis of experimentally or clinically verified drugs against coronavirus infection

Yingtong Liu et al.

Summary: This study identified chemical drugs and antibodies effective against human coronaviruses and enriched biological processes related to drug targets through Gene Ontology (GO) analysis. The use of Coronavirus Infectious Disease Ontology (CIDO) allowed for representation of various entities related to coronaviruses, and systematic analysis of the knowledgebase provided scientific insights. A proposed Host-coronavirus interaction (HCI) checkpoint cocktail strategy aims to interrupt key checkpoints in the dynamic HCI network for rational drug design, with support from interoperable ontologies.

SCIENTIFIC DATA (2021)

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Editorial Material Medicine, General & Internal

SARS-CoV-2 Viral Variants-Tackling a Moving Target

John R. Mascola et al.

JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION (2021)

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Letter Multidisciplinary Sciences

COVID-19 induces lower levels of IL-8, IL-10, and MCP-1 than other acute CRS-inducing diseasesYY

Liang Cheng et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

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Article Immunology

VaximmutorDB: A Web-Based Vaccine Immune Factor Database and Its Application for Understanding Vaccine-Induced Immune Mechanisms

Kimberly Berke et al.

Summary: Research has shown that vaccines stimulate various immune factors, but a comprehensive picture of vaccine-induced immune factors has not been systematically collected and analyzed. VaximmutorDB is a web-based database system that systematically collects and organizes vaccine immune factors from different host species, providing a better understanding of vaccine immunity.

FRONTIERS IN IMMUNOLOGY (2021)

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Review Biotechnology & Applied Microbiology

Precision omics data integration and analysis with interoperable ontologies and their application for COVID-19 research

Zhigang Wang et al.

Summary: Precision omics, which combines omics technologies with precision medicine, focuses on using standardized and interoperable ontologies to translate large-scale molecular omics data for accurate disease diagnosis, treatment, and prevention. The effectiveness of precision omics is positively correlated with the interoperability of ontologies used for data and knowledge integration, requiring efficient methods for developing and applying interoperable ontologies. Through interoperable omics data and knowledge, precision tools like OmicsViz can be enhanced to identify new knowledge and hypotheses for diseases like COVID-19.

BRIEFINGS IN FUNCTIONAL GENOMICS (2021)

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Article Multidisciplinary Sciences

Towards an engineering theory of evolution

Simeon D. Castle et al.

Summary: Biological technologies are unique in that they involve the evolutionary nature of biology, requiring the application of evolutionary knowledge in the design process. The concept of evotype is proposed by the authors to reason about and shape the evolutionary potential of natural and engineered biosystems. Effective biological engineering necessitates the recognition of evolution and its consideration during the design phase.

NATURE COMMUNICATIONS (2021)

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Article Mathematical & Computational Biology

CIDO ontology updates and secondary analysis of host responses to COVID-19 infection based on ImmPort reports and literature

Anthony Huffman et al.

Summary: With COVID-19 still ongoing, extensive research has been conducted, leading to a vast amount of data and knowledge. The ImmPort database contains studies on molecular immune signatures, epitopes, and sex differences in COVID-19 patients. By using the CIDO as a platform, new knowledge from ImmPort studies was represented and enhanced, contributing to a better understanding of host responses to COVID-19.

JOURNAL OF BIOMEDICAL SEMANTICS (2021)

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Article Mathematical & Computational Biology

The Infectious Disease Ontology in the age of COVID-19

Shane Babcock et al.

Summary: Ontologies provide a powerful tool for data sharing in response to public health emergencies such as COVID-19. Recent developments include extensions like VIDO, CIDO, and IDO-COVID-19, which introduce new terms to differentiate infectious agents and infectious structures. This work showcases a model for ontology building best practices and supports rapid response to current and future public health crises.

JOURNAL OF BIOMEDICAL SEMANTICS (2021)

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Editorial Material Critical Care Medicine

Imatinib in COVID-19: hope and caution

David Bernal-Bello et al.

LANCET RESPIRATORY MEDICINE (2021)

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Article Cell Biology

Potential transmission chains of variant B.1.1.7 and co-mutations of SARS-CoV-2

Jingsong Zhang et al.

Summary: The study analyzed the origin and evolution of the SARS-CoV-2 B.1.1.7 variant, suggesting a possible host in the Canidae family and experimental evidence showing that co-mutations significantly reduced viral replication.

CELL DISCOVERY (2021)

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Article Mathematical & Computational Biology

Standardization of assay representation in the Ontology for Biomedical Investigations

Randi Vita et al.

Summary: The Ontology for Biomedical Investigations (OBI) underwent a focused review of assay term annotations to improve and standardize terms, identifying and correcting inconsistencies in W3C Web Ontology Language (OWL) expressions and developing standardized design patterns and maintenance templates. This insightful process provides specific benefits and obstacles for OBI, as well as universal lessons for similar projects.

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2021)

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Article Cell Biology

Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases

Alison Tarke et al.

Summary: By studying T cell responses in 99 convalescent COVID-19 cases, we identified various HLA-restricted epitopes derived from SARS-CoV-2 and observed distinct patterns of immunodominance. The epitopes were combined into megapools to facilitate the identification and quantification of virus-specific CD4(+) and CD8(+) T cells.

CELL REPORTS MEDICINE (2021)

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Review Immunology

Innate Immune Evasion by Human Respiratory RNA Viruses

Marjolein Kikkert

JOURNAL OF INNATE IMMUNITY (2020)

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Article Medicine, General & Internal

Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China

Dawei Wang et al.

JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION (2020)

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Article Biochemistry & Molecular Biology

SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor

Markus Hoffmann et al.

CELL (2020)

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Article Multidisciplinary Sciences

Effective treatment of severe COVID-19 patients with tocilizumab

Xiaoling Xu et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

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Article Immunology

Interferon-Induced Transmembrane Protein 3 Genetic Variant rs12252-C Associated With Disease Severity in Coronavirus Disease 2019

Yonghong Zhang et al.

JOURNAL OF INFECTIOUS DISEASES (2020)

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Article Multidisciplinary Sciences

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing

David E. Gordon et al.

NATURE (2020)

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Article Microbiology

Geographic and Genomic Distribution of SARS-CoV-2 Mutations

Daniele Mercatelli et al.

FRONTIERS IN MICROBIOLOGY (2020)

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Article Immunology

COVID-19 Coronavirus Vaccine Design Using Reverse Vaccinology and Machine Learning

Edison Ong et al.

FRONTIERS IN IMMUNOLOGY (2020)

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Article Multidisciplinary Sciences

CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis

Yongqun He et al.

SCIENTIFIC DATA (2020)

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Review Infectious Diseases

The pathogenesis and treatment of the 'Cytokine Storm' in COVID-19

Qing Ye et al.

JOURNAL OF INFECTION (2020)

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Article Multidisciplinary Sciences

Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity

Donghyuk Shin et al.

NATURE (2020)

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Article Genetics & Heredity

SARS-CoV-2 infections and COVID-19 mortalities strongly correlate with ACE1 I/D genotype

Naoki Yamamoto et al.

GENE (2020)

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Review Medicine, Research & Experimental

The current landscape of coronavirus-host protein-protein interactions

Laure Perrin-Cocon et al.

JOURNAL OF TRANSLATIONAL MEDICINE (2020)

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Review Urology & Nephrology

Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project

Edison Ong et al.

NATURE REVIEWS NEPHROLOGY (2020)

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Article Multidisciplinary Sciences

Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms

David E. Gordon et al.

SCIENCE (2020)

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Article Multidisciplinary Sciences

Antiviral activity of digoxin and ouabain against SARS-CoV-2 infection and its implication for COVID-19

Junhyung Cho et al.

SCIENTIFIC REPORTS (2020)

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Review Biochemistry & Molecular Biology

Receptor-binding domain-specific human neutralizing monoclonal antibodies against SARS-CoV and SARS-CoV-2

Fei Yu et al.

SIGNAL TRANSDUCTION AND TARGETED THERAPY (2020)

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Review Immunology

The trinity of COVID-19: immunity, inflammation and intervention

Matthew Zirui Tay et al.

NATURE REVIEWS IMMUNOLOGY (2020)

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Review Microbiology

Human Coronavirus: Host-Pathogen Interaction

To Sing Fung et al.

ANNUAL REVIEW OF MICROBIOLOGY, VOL 73 (2019)

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Editorial Material Genetics & Heredity

Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems

Paul D. Thomas et al.

NATURE GENETICS (2019)

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Article Biochemical Research Methods

VIO: ontology classification and study of vaccine responses given various experimental and analytical conditions

Edison Ong et al.

BMC BIOINFORMATICS (2019)

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Article Biochemistry & Molecular Biology

Victors: a web-based knowledge base of virulence factors in human and animal pathogens

Samantha Sayers et al.

NUCLEIC ACIDS RESEARCH (2019)

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Review Microbiology

Candida albicans and Staphylococcus aureus Pathogenicity and Polymicrobial Interactions: Lessons beyond Koch's Postulates

Olivia A. Todd et al.

JOURNAL OF FUNGI (2019)

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Review Mathematical & Computational Biology

The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability

Yongqun He et al.

JOURNAL OF BIOMEDICAL SEMANTICS (2018)

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Review Medicine, General & Internal

Classification, Ontology, and Precision Medicine

Melissa A. Haendel et al.

NEW ENGLAND JOURNAL OF MEDICINE (2018)

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Review Immunology

Immune checkpoint blockade in infectious diseases

Michelle N. Wykes et al.

NATURE REVIEWS IMMUNOLOGY (2018)

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Article Biochemistry & Molecular Biology

Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration

Edison Ong et al.

NUCLEIC ACIDS RESEARCH (2017)

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Review Immunology

Cytokine storm and sepsis disease pathogenesis

Benjamin G. Chousterman et al.

SEMINARS IN IMMUNOPATHOLOGY (2017)

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Article Multidisciplinary Sciences

Ontology-based systematical representation and drug class effect analysis of package insert-reported adverse events associated with cardiovascular drugs used in China

Liwei Wang et al.

SCIENTIFIC REPORTS (2017)

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Article Mathematical & Computational Biology

The Ontology of Biological and Clinical Statistics ( OBCS)-based statistical method standardization and meta-analysis of host responses to yellow fever vaccines

Jie Zheng et al.

QUANTITATIVE BIOLOGY (2017)

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Editorial Material Medicine, Research & Experimental

Causal or not: applying the Bradford Hill aspects of evidence to the association between Zika virus and microcephaly

Christina Frank et al.

EMBO MOLECULAR MEDICINE (2016)

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Article Multidisciplinary Sciences

Statistical and Ontological Analysis of Adverse Events Associated with Monovalent and Combination Vaccines against Hepatitis A and B Diseases

Jiangan Xie et al.

SCIENTIFIC REPORTS (2016)

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Article Plant Sciences

Publishing FAIR Data: An Exemplar Methodology Utilizing PHI-Base

Alejandro Rodriguez-Iglesias et al.

FRONTIERS IN PLANT SCIENCE (2016)

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Article Mathematical & Computational Biology

The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis

Jie Zheng et al.

JOURNAL OF BIOMEDICAL SEMANTICS (2016)

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Article Multidisciplinary Sciences

Comment: The FAIR Guiding Principles for scientific data management and stewardship

Mark D. Wilkinson et al.

SCIENTIFIC DATA (2016)

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Article Multidisciplinary Sciences

The Ontology for Biomedical Investigations

Anita Bandrowski et al.

PLOS ONE (2016)

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Article Biochemical Research Methods

The role of ontologies in biological and biomedical research: a functional perspective

Robert Hoehndorf et al.

BRIEFINGS IN BIOINFORMATICS (2015)

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Article Multidisciplinary Sciences

Tissue-based map of the human proteome

Mathias Uhlen et al.

SCIENCE (2015)

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Article Mathematical & Computational Biology

Ontology application and use at the ENCODE DCC

Venkat S. Malladi et al.

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2015)

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Article Biology

Stringent homology-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions

Hufeng Zhou et al.

BIOLOGY DIRECT (2014)

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Article Biochemical Research Methods

linkedISA: semantic representation of ISA-Tab experimental metadata

Alejandra Gonzalez-Beltran et al.

BMC BIOINFORMATICS (2014)

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Article Biochemistry & Molecular Biology

Updates on the web-based VIOLIN vaccine database and analysis system

Yongqun He et al.

NUCLEIC ACIDS RESEARCH (2014)

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Article Biochemistry & Molecular Biology

3did: a catalog of domain-based interactions of known three-dimensional structure

Roberto Mosca et al.

NUCLEIC ACIDS RESEARCH (2014)

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Article Multidisciplinary Sciences

Standardized Metadata for Human Pathogen/Vector Genomic Sequences

Vivien G. Dugan et al.

PLOS ONE (2014)

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Article Mathematical & Computational Biology

Interdisciplinary perspectives on the development, integration, and application of cognitive ontologies

Janna Hastings et al.

FRONTIERS IN NEUROINFORMATICS (2014)

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Article Mathematical & Computational Biology

Stringent DDI-based Prediction of H. sapiens-M. tuberculosis H37Rv Protein-Protein Interactions

Hufeng Zhou et al.

BMC SYSTEMS BIOLOGY (2013)

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Article Multidisciplinary Sciences

Toward Reproducible Computational Research: An Empirical Analysis of Data and Code Policy Adoption by Journals

Victoria Stodden et al.

PLOS ONE (2013)

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Article Multidisciplinary Sciences

Epstein-Barr virus nuclear antigen leader protein localizes to promoters and enhancers with cell transcription factors and EBNA2

Daniel Portal et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

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Review Biochemical Research Methods

PROGRESS IN COMPUTATIONAL STUDIES OF HOST-PATHOGEN INTERACTIONS

Hufeng Zhou et al.

JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY (2013)

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Article Computer Science, Artificial Intelligence

BioPortal as a dataset of linked biomedical ontologies and terminologies in RDF

Manuel Salvadores et al.

SEMANTIC WEB (2013)

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Review Medical Informatics

From Concept Representations to Ontologies: A Paradigm Shift in Health Informatics?

Stefan Schulz et al.

HEALTHCARE INFORMATICS RESEARCH (2013)

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Article Biochemistry & Molecular Biology

The NCBI Taxonomy database

Scott Federhen

NUCLEIC ACIDS RESEARCH (2012)

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Article Mathematical & Computational Biology

Modeling biomedical experimental processes with OBI

Ryan R Brinkman et al.

Journal of Biomedical Semantics (2012)

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Article Biotechnology & Applied Microbiology

Comparative analysis and assessment of M. tuberculosis H37Rv protein-protein interaction datasets

Hufeng Zhou et al.

BMC GENOMICS (2011)

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Article Computer Science, Interdisciplinary Applications

Towards an ontological representation of resistance: The case of MRSA

Albert Goldfain et al.

JOURNAL OF BIOMEDICAL INFORMATICS (2011)

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Review Biochemical Research Methods

Network analyses in systems pharmacology

Seth I. Berger et al.

BIOINFORMATICS (2009)

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Article Biochemical Research Methods

FPPI: Fusarium graminearum Protein-Protein Interaction Database

Xing-Ming Zhao et al.

JOURNAL OF PROTEOME RESEARCH (2009)

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Article Biochemistry & Molecular Biology

Host-pathogen protein interactions predicted by comparative modeling

Fred P. Davis et al.

PROTEIN SCIENCE (2007)

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Article Biotechnology & Applied Microbiology

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

Barry Smith et al.

NATURE BIOTECHNOLOGY (2007)

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Review Medicine, General & Internal

HIV/AIDS epidemiology, pathogenesis, prevention, and treatment

Viviana Simon et al.

LANCET (2006)

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Article Biochemical Research Methods

iPfam:: visualization of protein-protein interactions in PDB at domain and amino acid resolutions

RD Finn et al.

BIOINFORMATICS (2005)

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Article Biology

The aetiology of SARS: Koch's postulates fulfilled

ADME Osterhaus et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY OF LONDON SERIES B-BIOLOGICAL SCIENCES (2004)

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Review Microbiology

The damage-response framework of microbial pathogenesis

A Casadevall et al.

NATURE REVIEWS MICROBIOLOGY (2003)

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Article Multidisciplinary Sciences

Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins

T Ito et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2000)

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A new framework for host-pathogen interaction research

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