Author details

Full Name

Benno Schwikowski

Affiliation

Center for Bioinformatics, Institut Pasteur CNRS

ORCID

Career Start Year

1997

Papers

H Index

Expertise

CM4AI Collaborator

Trey Ideker (CM4AI)

PMID	Paper Title	Journal Title	Published Year
36869684	Identification of new candidate drugs for primary SjÃ¶gren's syndrome using a drug repurposing transcriptomic approach.	Rheumatology (Oxford)	2023
37256048	Capturing the dynamics of microbial interactions through individual-specific networks.	Front Microbiol	2023
37337100	Democratizing knowledge representation with BioCypher.	Nat Biotechnol	2023
36721022	Author Correction: A shared disease-associated oligodendrocyte signature among multiple CNS pathologies.	Nat Neurosci	2023
34619752	An overview of machine learning methods for monotherapy drug response prediction.	Brief Bioinform	2022
35760863	A shared disease-associated oligodendrocyte signature among multiple CNS pathologies.	Nat Neurosci	2022
35726083	Variability of Primary SjÃ¶gren's Syndrome Is Driven by Interferon-Î± and Interferon-Î± Blood Levels Are Associated With the Class II HLA-DQ Locus.	Arthritis Rheumatol	2022
33941444	Differential levels of IFNÎ± subtypes in autoimmunity and viral infection.	Cytokine	2021
33674591	Deciphering the state of immune silence in fatal COVID-19 patients.	Nat Commun	2021
32479746	Host-Viral Infection Maps Reveal Signatures of Severe COVID-19 Patients.	Cell	2020
32803171	Bystander IFN-Î³ activity promotes widespread and sustained cytokine signaling altering the tumor microenvironment.	Nat Cancer	2020
30772378	Single-Cell Analysis of Diverse Pathogen Responses Defines a Molecular Roadmap for Generating Antigen-Specific Immunity.	Cell Syst	2019
31575732	LGP2 binds to PACT to regulate RIG-I- and MDA5-mediated antiviral responses.	Sci Signal	2019
28941788	Network module identification-A widespread theoretical bias and best practices.	Methods	2018
29983926	The Cytoscape Automation app article collection.	F1000Res	2018
29490079	A Blood RNA Signature Detecting Severe Disease in Young Dengue Patients at Hospital Arrival.	J Infect Dis	2018
27178992	Detecting multi-way epistasis in family-based association studies.	Brief Bioinform	2017
28732463	Common and phylogenetically widespread coding for peptides by bacterial small RNAs.	BMC Genomics	2017
27797778	Network-based analysis of omics data: the LEAN method.	Bioinformatics	2017
27939949	From the exposome to mechanistic understanding of chemical-induced adverse effects.	Environ Int	2017
25576660	Automated flow cytometric analysis across large numbers of samples and cell types.	Clin Immunol	2015
26123804	Bacterial Internalization, Localization, and Effectors Shape the Epithelial Immune Response during Shigella flexneri Infection.	Infect Immun	2015
25655172	Filter-free exhaustive odds ratio-based genome-wide interaction approach pinpoints evidence for interaction in the HLA region in psoriasis.	BMC Genet	2015
25527096	The Cyni framework for network inference in Cytoscape.	Bioinformatics	2015
25580224	The Cytoscape app article collection.	F1000Res	2014
23386401	Identification of additional proteins in differential proteomics using protein interaction networks.	Proteomics	2013
24349258	Analysis of time-resolved gene expression measurements across individuals.	PLoS One	2013
23874729	TLM-Quant: an open-source pipeline for visualization and quantification of gene expression heterogeneity in growing microbial cells.	PLoS One	2013
22383848	Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism.	Science	2012
23094866	Automated phosphopeptide identification using multiple MS/MS fragmentation modes.	J Proteome Res	2012
22414152	Feature detection with controlled error rates in LC/MS images.	J Comput Biol	2012
22383849	Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis.	Science	2012
21182191	Fragmentation-free LC-MS can identify hundreds of proteins.	Proteomics	2011
20199108	MUDE: a new approach for optimizing sensitivity in the target-decoy search strategy for large-scale peptide/protein identification.	J Proteome Res	2010
20459825	Evolution of metabolic network organization.	BMC Syst Biol	2010
18297649	Alignment of LC-MS images, with applications to biomarker discovery and protein identification.	Proteomics	2008
18820265	Phylogenetic distances are encoded in networks of interacting pathways.	Bioinformatics	2008
17127678	GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring.	Bioinformatics	2007
17947979	Integration of biological networks and gene expression data using Cytoscape.	Nat Protoc	2007
17617667	Assessing bias in experiment design for large scale mass spectrometry-based quantitative proteomics.	Mol Cell Proteomics	2007
16269421	Signal maps for mass spectrometry-based comparative proteomics.	Mol Cell Proteomics	2006
16880171	Graph-based methods for analysing networks in cell biology.	Brief Bioinform	2006
15967031	Tools enabling the elucidation of molecular pathways active in human disease: application to Hepatitis C virus infection.	BMC Bioinformatics	2005
16196091	ProbIDtree: an automated software program capable of identifying multiple peptides from a single collision-induced dissociation spectrum collected by a tandem mass spectrometer.	Proteomics	2005
15285903	Towards optimally multiplexed applications of universal arrays.	J Comput Biol	2004
15262809	Predicting protein-peptide interactions via a network-based motif sampler.	Bioinformatics	2004
14597658	Cytoscape: a software environment for integrated models of biomolecular interaction networks.	Genome Res	2003
12935335	The restriction scaffold problem.	J Comput Biol	2003
12015878	Algorithms for phylogenetic footprinting.	J Comput Biol	2002
12169552	Discovering regulatory and signalling circuits in molecular interaction networks.	Bioinformatics	2002

1 - 50 of 55

Gergely Csaba

Ludwig-Maximilians-Universitat Munchen

Career Start Year 2007

Number of shared co-authors 0

Stefan R Maetschke

Institute for Molecular Bioscience and ARC Centre of Excellence in Bioinformatics

Career Start Year 2007

Number of shared co-authors 0

Jan Baumbach

University of Hamburg

Career Start Year 2006

Number of shared co-authors 6

Alberto Paccanaro

University of London

Career Start Year 2005

Number of shared co-authors 1

Dongxiao Zhu

Wayne State University

Career Start Year 2005

Number of shared co-authors 0

Arnaud Droit

Centre de Recherche du CHU de Quebec-Universite, Universite Laval

Career Start Year 2005

Number of shared co-authors 3

Veit Schw??mmle

University of Southern Denmark

Career Start Year 2003

Number of shared co-authors 1

Roland Krause

University of Luxembourg

Career Start Year 2002

Number of shared co-authors 3

Bobbie-Jo M Webb-Robertson

Pacific Northwest National Laboratory

Career Start Year 2002

Number of shared co-authors 0

Johan Rung

Uppsala University

Career Start Year 2001

Number of shared co-authors 1

Oliver Kohlbacher

Max Planck Institute for Developmental Biology

Career Start Year 2000

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 3

Ralf Zimmer

Ludwig-Maximilians-Universitat Munchen

Career Start Year 1995

Number of shared co-authors 2

Ioannis Xenarios

University of Lausanne

Career Start Year 1994

Number of shared co-authors 10

Bonnie Berger

Massachusetts Institute of Technology

Career Start Year 1994

Number of shared co-authors 7

Simon Kasif

Boston University

Career Start Year 1993

Number of shared co-authors 2

Jason E McDermott

Pacific Northwest National Laboratory

Career Start Year 1993

Number of shared co-authors 1

Edward M Marcotte

University of Texas

Career Start Year 1993

Number of shared co-authors 5

Erik L L Sonnhammer

Stockholm University

Career Start Year 1992

Number of shared co-authors 1

Robert Gentleman

Center for Computational Biomedicine, Harvard Medical School

Career Start Year 1991

Number of shared co-authors 2

Andreas Beyer

University of Cologne

Career Start Year 1991

Number of shared co-authors 8

Mark Gerstein

Yale University

Career Start Year 1991

Number of shared co-authors 7

Miguel A Andrade-Navarro

Institute of Organismic and Molecular Evolution, Johannes Gutenberg University

Career Start Year 1991

Number of shared co-authors 2

Andrew Emili

Boston University School of Medicine, Boston University

Career Start Year 1991

Number of shared co-authors 6

Shankar Subramaniam

University of California

Career Start Year 1989

Number of shared co-authors 1

David Feny??

Institute for Systems Genetics, NYU Grossman School of Medicine

Career Start Year 1989

Number of shared co-authors 0

S??ren Brunak

Novo Nordisk Foundation Center for Protein Research, University of Copenhagen

Career Start Year 1988

Number of shared co-authors 5

Michal Linial

Institute of Life Sciences, The Hebrew University of Jerusalem

Career Start Year 1986

Number of shared co-authors 2

Joaqu??n Dopazo

Andalusian Public Foundation Progress and Health-FPS

Career Start Year 1977

Number of shared co-authors 9

Yves Moreau

KU Leuven - University of Leuven

Career Start Year 1967

Number of shared co-authors 4

row(s) 1 - 30 of 30

Ido Amit

Weizmann Institute of Science

Co-authored papers 6

Trey Ideker (CM4AI)

University of California San Diego

Co-authored papers 5

Ruedi Aebersold

Institute of Molecular Systems Biology, ETH Zurich

Co-authored papers 4

Oriol Guitart-Pla

Institut Pasteur

Co-authored papers 4

John H Morris

University of California san francisco

Co-authored papers 3

Richard M Karp

University of California at Berkeley and International Computer Science Institute

Co-authored papers 3

Keiichiro Ono

university of california san diego

Co-authored papers 3

Gary D Bader

University of Toronto

Co-authored papers 3

Tero Aittokallio

Institute for Molecular Medicine Finland (FIMM), University of Helsinki

Co-authored papers 3

Alexander R Pico

Institute of Data Science and Biotechnology, Gladstone Institutes

Co-authored papers 3

Co-authored papers 2

Christian Lopes

University of Toronto

Co-authored papers 2

Mathias Vandenbogaert

Co-authored papers 2

Martin Tompa

Co-authored papers 2

Samad Lotia

Gladstone Institutes

Co-authored papers 2

Christopher J Lessard

Co-authored papers 2

Gregory A Buck

Virginia Commonwealth University.

Co-authored papers 2

David R Goodlett

University of Victoria

Co-authored papers 2

Piet Molenaar

Academic Medical Center

Co-authored papers 2

Owen Ozier

Co-authored papers 2

Bernd Bodenmiller

University of Zurich

Co-authored papers 2

Barry Demchak

University of California

Co-authored papers 2

Amanda G Paulovich

Co-authored papers 2

Melissa S Cline

Genomics Institute, University of California Santa Cruz

Co-authored papers 2

William J R Longabaugh

Institute for Systems Biology

Co-authored papers 2

Jeffrey R Whiteaker

Co-authored papers 2

Iliana Avila-Campillo

New York University

Co-authored papers 2

Pengliang Wang

Sun Yat-sen Memorial Hospital, Sun Yat-sen University

Co-authored papers 1

Nitin S Baliga

Institute for Systems Biology

Co-authored papers 1

Ruth Isserlin

University of Toronto

Co-authored papers 1

1 - 30

Author Details

Column Actions

Recommended Authors

Collaborators