Author details

Full Name

Benjamin M Gyori

Affiliation

Khoury College of Computer Sciences, Northeastern University

ORCID

Career Start Year

2014

Papers

H Index

Expertise

CM4AI Collaborator

Trey Ideker (CM4AI)

PMID	Paper Title	Journal Title	Published Year
37953324	The Human Phenotype Ontology in 2024: phenotypes around the world.	Nucleic Acids Res	2024
36938926	Automated assembly of molecular mechanisms at scale from text mining and curated databases.	Mol Syst Biol	2023
37337100	Democratizing knowledge representation with BioCypher.	Nat Biotechnol	2023
36882166	NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange.	Bioinformatics	2023
36916735	Prediction and curation of missing biomedical identifier mappings with Biomappings.	Bioinformatics	2023
36778477	Nociceptor neuroimmune interactomes reveal cell type- and injury-specific inflammatory pain pathways.	bioRxiv	2023
34986221	STonKGs: a sophisticated transformer trained on biomedical text and knowledge graphs.	Bioinformatics	2022
35616100	A Simple Standard for Sharing Ontological Mappings (SSSOM).	Database (Oxford)	2022
35737447	Integrating multi-omics data reveals function and therapeutic potential of deubiquitinating enzymes.	Elife	2022
36402838	Unifying the identification of biomedical entities with the Bioregistry.	Sci Data	2022
36699362	Gilda: biomedical entity text normalization with machine-learned disambiguation as a service.	Bioinform Adv	2022
36071952	PyBioPAX: biological pathway exchange in Python.	J Open Source Softw	2022
35961013	A roadmap for the functional annotation of protein families: a community perspective.	Database (Oxford)	2022
35238605	Automated Network Assembly of Mechanistic Literature for Informed Evidence Identification to Support Cancer Risk Assessment.	Environ Health Perspect	2022
34664389	COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.	Mol Syst Biol	2021
33558181	Corrigendum to OpenComet: An automated tool for comet assay image analysis [Redox Biol. Volume 2, 2014, Pages 457-465].	Redox Biol	2021
33526072	GeneWalk identifies relevant gene functions for a biological context using network representation learning.	Genome Biol	2021
34860157	Author-sourced capture of pathway knowledge in computable form using Biofactoid.	Elife	2021
34939300	COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.	Mol Syst Biol	2021
32337477	Adeft: Acromine-based Disambiguation of Entities from Text with applications to the biomedical literature.	J Open Source Softw	2020
32365103	Robustness and parameter geography in post-translational modification systems.	PLoS Comput Biol	2020
31070726	INDRA-IPM: interactive pathway modeling using natural language with automated assembly.	Bioinformatics	2019
31225582	Re-curation and rational enrichment of knowledge graphs in Biological Expression Language.	Database (Oxford)	2019
29954318	FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining.	BMC Bioinformatics	2018
29886111	Encoding Growth Factor Identity in the Temporal Dynamics of FOXO3 under the Combinatorial Control of ERK and AKT Kinases.	Cell Syst	2018
29175850	From word models to executable models of signaling networks using automated assembly.	Mol Syst Biol	2017
24624335	OpenComet: an automated tool for comet assay image analysis.	Redox Biol	2014

1 - 27 of 27

Daniel J B Clarke

Icahn School of Medicine at Mount Sinai

Career Start Year 2018

Number of shared co-authors 2

Vasundra Tour??

Norwegian University of Science and Technology (NTNU)

Career Start Year 2016

Number of shared co-authors 20

Kahn Rhrissorrakrai

T.J. Watson Research Center

Career Start Year 2008

Number of shared co-authors 2

Jaewoo Kang

Korea University

Career Start Year 2006

Number of shared co-authors 1

Hai Fang

University of Bristol

Career Start Year 2006

Number of shared co-authors 11

Jan Baumbach

University of Hamburg

Career Start Year 2006

Number of shared co-authors 5

Karin Verspoor

National Centre for Infections in Cancer, 5Peter MacCallum Cancer Centre

Career Start Year 2005

Number of shared co-authors 11

Avi Ma'ayan

Icahn School of Medicine at Mount Sinai

Career Start Year 2005

Number of shared co-authors 3

Anne Niknejad

University of Lausanne

Career Start Year 2004

Number of shared co-authors 14

Wenjin Jim Zheng

University of Texas Health Science Center at Houston

Career Start Year 2004

Number of shared co-authors 3

Benjamin M Good

Lawrence Berkeley National Laboratory

Career Start Year 2003

Number of shared co-authors 25

Jake Y. Chen (CM4AI)

University of Alabama at Birmingham

Career Start Year 2003

Number of shared co-authors 1

Dietrich Rebholz-Schuhmann

University of Cologne

Career Start Year 2003

Number of shared co-authors 9

Gil Alterovitz

Brigham and Women's Hospital

Career Start Year 2002

Number of shared co-authors 14

Esther E Schmidt

NYU Grossman School of Medicine

Career Start Year 2002

Number of shared co-authors 16

Andrew I Su

The Scripps Research Institute

Career Start Year 2001

Number of shared co-authors 15

Chun-Nan Hsu

University of California, C.N.H.) and Veterans Affairs San Diego Healthcare System

Career Start Year 2001

Number of shared co-authors 2

Georgios V Gkoutos

Institute of Cancer and Genomic Sciences, University of Birmingham

Career Start Year 2000

Number of shared co-authors 14

Igor Jurisica

Schroeder Arthritis Institute

Career Start Year 1998

Number of shared co-authors 4

Lars Juhl Jensen

Novo Nordisk Foundation Center for Protein Research, University of Copenhagen

Career Start Year 1998

Number of shared co-authors 9

Michel Dumontier

Institute of Data Science, Maastricht University

Career Start Year 1998

Number of shared co-authors 35

Fabien Campagne

Weill Cornell Medical College

Career Start Year 1998

Number of shared co-authors 1

Andra Waagmeester

Maastricht University

Career Start Year 1998

Number of shared co-authors 12

J Lynn Fink

The University of Queensland Diamantina Institute, The University of Queensland

Career Start Year 1997

Number of shared co-authors 4

Nick Juty

University of Manchester

Career Start Year 1997

Number of shared co-authors 20

Ioannis Xenarios

University of Lausanne

Career Start Year 1994

Number of shared co-authors 30

Lawrence E Hunter

University of Colorado School of Medicine

Career Start Year 1993

Number of shared co-authors 9

Warren A Kibbe

Duke Clinical Research Institute, Duke University

Career Start Year 1987

Number of shared co-authors 20

Russ B Altman

Stanford University

Career Start Year 1982

Number of shared co-authors 7

Yves A Lussier

Center for Biomedical Informatics and Biostatistics, University of Arizona

Career Start Year 1971

Number of shared co-authors 0

row(s) 1 - 30 of 30

Charles Tapley Hoyt

Harvard Medical School

Co-authored papers 9

Peter K Sorger

Co-authored papers 8

Christopher J Mungall

International Society for Biocuration, Lawrence Berkeley National Laboratory, University of Edinburgh, University of Edinburgh School of Biological Sciences

Co-authored papers 4

Julie A McMurry

University of Colorado - Anschutz Medical Campus

Co-authored papers 3

Chris T Evelo

Maastricht University

Co-authored papers 3

Julio Saez-Rodriguez

Institute of Computational Biomedicine, Heidelberg University

Co-authored papers 3

Emek Demir

Knight Cancer Institute, Oregon Health & Science University

Co-authored papers 3

D??nes T??rei

Heidelberg University

Co-authored papers 3

Anita de Waard

Co-authored papers 3

Daniel Domingo-Fern??ndez

Fraunhofer Institute for Algorithms and Scientific Computing (SCAI)

Co-authored papers 3

Augustin Luna

Harvard Medical School

Co-authored papers 3

Chris Sander

Broad Institute of MIT and Harvard

Co-authored papers 3

Ozgun Babur

Houston Methodist Research Institute

Co-authored papers 3

Melissa A Haendel

American Medical Informatics Association, Oregon Health and Science University, Oregon State University, University of Colorado Anschutz Medical Campus, University of North Carolina at Chapel Hill, University of Wisconsin-Madison

Co-authored papers 3

Karen Rothfels

Co-authored papers 2

Bertrand De Meulder

European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL-INSERM

Co-authored papers 2

Laurence Calzone

Institut Curie, Universite PSL

Co-authored papers 2

Lisa Matthews

NYU Grossman School of Medicine

Co-authored papers 2