B. Schwikowski

发表

A network of protein–protein interactions in yeast

B. Schwikowski, P. Uetz, S. Fields, 2000, Nature Biotechnology.

Cytoscape: a software environment for integrated models of biomolecular interaction networks.

P. Shannon, N. Baliga, T. Ideker, 2003, Genome research.

Integration of biological networks and gene expression data using Cytoscape

Michael L. Creech, Gary D Bader, Alexander R. Pico, 2007, Nature Protocols.

Universal DNA tag systems: a combinatorial design scheme

Richard M. Karp, Benno Schwikowski, Zohar Yakhini, 2000, RECOMB '00.

Towards Optimally Multiplexed Applications of Universal Arrays

Roded Sharan, Richard M. Karp, Benno Schwikowski, 2004, J. Comput. Biol..

Discovering regulatory and signalling circuits in molecular interaction networks

Benno Schwikowski, Trey Ideker, Andrew F. Siegel, 2002, ISMB.

ProbIDtree: An automated software program capable of identifying multiple peptides from a single collision‐induced dissociation spectrum collected by a tandem mass spectrometer

R. Aebersold, B. Schwikowski, Xiao-Jun Li, 2005, Proteomics.

ProbID: A probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data

R. Aebersold, B. Schwikowski, Ning Zhang, 2002, Proteomics.

Associations between consumption of dietary fibers and the risk of cardiovascular diseases, cancers, type 2 diabetes, and mortality in the prospective NutriNet-Santé cohort.

B. Schwikowski, S. Shorte, J. Fellay, 2020, The American journal of clinical nutrition.

Better Tree Alignments through Near-optimal Intermediates 1

B. Schwikowski, 2007 .

Host-Viral Infection Maps Reveal Signatures of Severe COVID-19 Patients

I. Amit, B. Schwikowski, Amir Giladi, 2020, Cell.

Single-Cell Analysis of Diverse Pathogen Responses Defines a Molecular Roadmap for Generating Antigen-Specific Immunity.

Johannes U. Mayer, I. Amit, S. Itzkovitz, 2019, Cell systems.

Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis

B. Schwikowski, V. Fromion, E. Klipp, 2012, Science.

Global Network Reorganization During Dynamic Adaptations of Bacillus subtilis Metabolism

Joerg M. Buescher, J. Stelling, U. Sauer, 2012, Science.

Identification of additional proteins in differential proteomics using protein interaction networks

B. Schwikowski, P. Amouyel, H. Drobecq, 2013, Proteomics.

Biomolecular Interaction Networks Cytoscape : A Software Environment for Integrated Models of

Benno Schwikowski, Nada Amin, Trey Ideker, 2003 .

Alignment of LC‐MS images, with applications to biomarker discovery and protein identification

Benno Schwikowski, Tero Aittokallio, Sébastien Li-Thiao-Té, 2008, Proteomics.

Fragmentation‐free LC‐MS can identify hundreds of proteins

P. Clote, B. Schwikowski, D. Goodlett, 2011, Proteomics.

Epithelial Immune Response during Shigella Infection

B. Schwikowski, J. Enninga, Frederik Gwinner, 2015 .

Common and phylogenetically widespread coding for peptides by bacterial small RNAs

B. Schwikowski, Robin C. Friedman, S. Kalkhof, 2017, BMC Genomics.

LGP2 binds to PACT to regulate RIG-I– and MDA5-mediated antiviral responses

B. Schwikowski, Y. Jacob, F. Tangy, 2019, Science Signaling.

Bystander IFN-γ activity promotes widespread and sustained cytokine signaling altering the tumor microenvironment

I. Amit, B. Schwikowski, P. Bousso, 2020, Nature Cancer.

The Restriction Scaffold Problem (Extended Abstract)

R. Karp, R. Shamir, A. Ben-Dor, 2002 .

Deciphering the state of immune silence in fatal COVID-19 patients

I. Amit, B. Schwikowski, M. Iezzi, 2020, Nature Communications.

Immune Profiling Enables Stratification of Patients With Active Tuberculosis Disease or Mycobacterium tuberculosis Infection

B. Schwikowski, S. Shorte, J. Fellay, 2020, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

Democratising Knowledge Representation with BioCypher

Benjamin M. Gyori, Charles Tapley Hoyt, Maximilian T. Strauss, 2022, 2212.13543.

Variability of Primary Sjögren's Syndrome Is Driven by Interferon‐α and Interferon‐α Blood Levels Are Associated With the Class II HLA–DQ Locus

B. Schwikowski, R. Jonsson, J. Fellay, 2022, Arthritis & rheumatology.

Graph-based methods for analysing networks in cell biology

Benno Schwikowski, Tero Aittokallio, B. Schwikowski, 2006, Briefings Bioinform..

Mining proteomic data for biomedical research

Benno Schwikowski, Laura Elo, B. Schwikowski, 2012, WIREs Data Mining Knowl. Discov..

A shared disease-associated oligodendrocyte signature among multiple CNS pathologies

I. Amit, B. Schwikowski, M. Schwartz, 2022, Nature Neuroscience.

Democratising Knowledge Representation with BioCypher

Benjamin M. Gyori, Charles Tapley Hoyt, Maximilian T. Strauss, 2022, 2212.13543.

An overview of machine learning methods for monotherapy drug response prediction

B. Schwikowski, B. Yousefi, Benno Schwikowski, 2021, Briefings Bioinform..

The Cyni framework for network inference in Cytoscape

Benno Schwikowski, Andrea Califano, Frank Rügheimer, 2015, Bioinform..

Early IFNβ secretion determines variable downstream IL-12p70 responses upon TLR4 activation

B. Schwikowski, S. Shorte, F. Rieux-Laucat, 2022, Cell Reports.

Bacterial Internalization, Localization, and Effectors Shape the Epithelial Immune Response during Shigella flexneri Infection

B. Schwikowski, J. Enninga, Frederik Gwinner, 2015, Infection and Immunity.

Network-based analysis of omics data: the LEAN method

Benno Schwikowski, Oriol Guitart-Pla, Iryna Nikolayeva, 2016, Bioinform..

From the exposome to mechanistic understanding of chemical-induced adverse effects.

Benno Schwikowski, Rolf Altenburger, Wibke Busch, 2017, Environment international.

MUDE: a new approach for optimizing sensitivity in the target-decoy search strategy for large-scale peptide/protein identification.

Benno Schwikowski, Christian Baumgartner, Fabio R Cerqueira, 2010, Journal of proteome research.

Analysis of Time-Resolved Gene Expression Measurements across Individuals

Benno Schwikowski, Laura L. Elo, B. Schwikowski, 2013, PloS one.

Differential levels of IFNα subtypes in autoimmunity and viral infection

I. Bruce, B. Schwikowski, D. Isenberg, 2021, bioRxiv.

Consensus gene modules strategy identifies candidate blood-based biomarkers for primary Sjogren's disease

B. Schwikowski, X. Mariette, E. Becht, 2023, medRxiv.

Automated phosphopeptide identification using multiple MS/MS fragmentation modes.

Benno Schwikowski, Heribert Hirt, Véronique Hourdel, 2012, Journal of proteome research.

Signal Maps for Mass Spectrometry-based Comparative Proteomics*

Benno Schwikowski, Jeffrey Whiteaker, Heidi Zhang, 2006, Molecular & Cellular Proteomics.

Version Other version Link to publication record in King ' s Research Portal

B. Schwikowski, J. Hackermüller, J. Kleinjans, 2015 .

Discovery of pathways using multiple genome-scale data sets

Benno Schwikowski, B. Schwikowski, 2005 .

Automated flow cytometric analysis across large numbers of samples and cell types.

Benno Schwikowski, Vincent Rouilly, Milena Hasan, 2015, Clinical immunology.

Weighted sequence graphs: boosting iterated dynamic programming using locally suboptimal solutions

Martin Vingron, Benno Schwikowski, B. Schwikowski, 2003, Discret. Appl. Math..

Filter-free exhaustive odds ratio-based genome-wide interaction approach pinpoints evidence for interaction in the HLA region in psoriasis

B. Schwikowski, A. Sakuntabhai, J. Bureau, 2015, BMC Genetics.

Evolution of metabolic network organization

Danail Bonchev, Aurélien Mazurie, Benno Schwikowski, 2010, BMC Systems Biology.

Autoantibodies neutralizing type I IFNs are present in ~4% of uninfected individuals over 70 years old and account for ~20% of COVID-19 deaths

Mark S. Anderson, P. Gregersen, R. Nussbaum, 2021, Science Immunology.

The Cytoscape Automation app article collection

Benno Schwikowski, Gary D Bader, Trey Ideker, 2018, F1000Research.

Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks

P. Shannon, N. Baliga, T. Ideker, 2003 .

Parallel derivation of isogenic human primed and naive induced pluripotent stem cells

T. Mikkelsen, R. Redon, B. Schwikowski, 2018, Nature Communications.

Assessing Bias in Experiment Design for Large Scale Mass Spectrometry-based Quantitative Proteomics*S

Benno Schwikowski, Heidi Zhang, Ruedi Aebersold, 2007, Molecular & Cellular Proteomics.

A comprehensive assessment of demographic, environmental, and host genetic associations with gut microbiome diversity in healthy individuals

Allyson L. Byrd, B. Schwikowski, S. Shorte, 2019, Microbiome.

Network module identification-A widespread theoretical bias and best practices.

Benno Schwikowski, Iryna Nikolayeva, Oriol Guitart Pla, 2018, Methods.

Identification of new candidate drugs for primary Sjögren's syndrome using a drug repurposing transcriptomic approach.

B. Schwikowski, R. Jonsson, X. Mariette, 2022, Rheumatology.

Phylogenetic distances are encoded in networks of interacting pathways

Danail Bonchev, Aurélien Mazurie, Benno Schwikowski, 2008, Bioinform..

Natural variation in the parameters of innate immune cells is preferentially driven by genetic factors

B. Schwikowski, J. Fellay, A. Cumano, 2018, Nature Immunology.

Predicting protein-peptide interactions via a network-based motif sampler

Benno Schwikowski, David J. Reiss, David J. Reiss, 2004, ISMB/ECCB.

Capturing the dynamics of microbial interactions through individual-specific networks

B. Schwikowski, N. van Best, J. Penders, 2023, Frontiers in Microbiology.

Capturing the dynamics of microbiomes using individual-specific networks

B. Schwikowski, N. van Best, J. Penders, 2023, bioRxiv.

human disease: Application to Hepatitis C virus infection

Benno Schwikowski, David J. Reiss, Vesteinn Thorsson, 2005 .

From the exposome to mechanistic understanding of chemical-induced adverse effects.

B. Schwikowski, J. Hackermüller, J. Kleinjans, 2017, Environment international.

From the exposome to mechanistic understanding of chemical-induced adverse effects

B. Schwikowski, J. Hackermüller, J. Wambaugh, 2016 .

Natural variation in the parameters of innate immune cells is preferentially driven by genetic factors

B. Schwikowski, J. Fellay, A. Cumano, 2018, Nature Immunology.

Towards optimally multiplexed applications of universal DNA tag systems

Roded Sharan, Benno Schwikowski, Tzvika Hartman, 2003, RECOMB '03.

The restriction scaffold problem

Richard M. Karp, Ron Shamir, Benno Schwikowski, 2002, RECOMB '02.

GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring

Benno Schwikowski, Tero Aittokallio, Melissa S. Cline, 2007, Bioinform..

The deferred path heuristic for the generalized tree alignment problem

Martin Vingron, Benno Schwikowski, B. Schwikowski, 1997, RECOMB '97.

A Clustering Approach to Generalized Tree Alignment with Application to Alu Repeats

Martin Vingron, Benno Schwikowski, B. Schwikowski, 1996, German Conference on Bioinformatics - Selected Papers.

Fragmentation‐free LC‐MS can identify hundreds of proteins

P. Clote, B. Schwikowski, D. Goodlett, 2011, Proteomics.

Phylogenetic distances are encoded in networks of interacting pathways

B. Schwikowski, D. Bonchev, Aurélien Mazurie, 2008, Bioinform..

TLM-Quant: An Open-Source Pipeline for Visualization and Quantification of Gene Expression Heterogeneity in Growing Microbial Cells

Benno Schwikowski, Samuel Drulhe, B. Schwikowski, 2013, PloS one.

Feature Detection with Controlled Error Rates in LC/MS Images

Benno Schwikowski, Sébastien Li-Thiao-Té, B. Schwikowski, 2012, J. Comput. Biol..

GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring

B. Schwikowski, T. Aittokallio, M. Cline, 2007, Bioinform..

A Blood RNA Signature Detecting Severe Disease in Young Dengue Patients at Hospital Arrival

B. Schwikowski, K. Bleakley, A. Sakuntabhai, 2018, The Journal of infectious diseases.

Algorithms for Constructing Signal Maps be- tween Mass Spectrometry Experiments

Benno Schwikowski, Heidi Zhang, Amanda G. Paulovich, 2003 .

Predicting protein-peptide interactions via a network-based motif sampler

David J. Reiss, B. Schwikowski, 2004, ISMB/ECCB.

Early IFNβ secretion determines variable downstream IL-12p70 responses upon TLR4 activation

B. Schwikowski, S. Shorte, F. Rieux-Laucat, 2022, Cell Reports.