Benno Schwikowski

发表

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

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

Differential levels of IFNα subtypes in autoimmunity and viral infection

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

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

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

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

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

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

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

Mining proteomic data for biomedical research

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

Integration of biological networks and gene expression data using Cytoscape

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

Global Network Reorganization During Dynamic Adaptations of Bacillus subtilis Metabolism

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

An overview of machine learning methods for monotherapy drug response prediction

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

Universal DNA tag systems: a combinatorial design scheme

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

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

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

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

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

Democratising Knowledge Representation with BioCypher

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

Discovering regulatory and signalling circuits in molecular interaction networks

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

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

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

Capturing the dynamics of microbiomes using individual-specific networks

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

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.

A network of protein–protein interactions in yeast

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

Phylogenetic distances are encoded in networks of interacting pathways

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

Common and phylogenetically widespread coding for peptides by bacterial small RNAs

Robin C. Friedman, S. Kalkhof, Olivia Doppelt-Azeroual, 2015, bioRxiv.

Graph-based methods for analysing networks in cell biology

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

Analysis of Time-Resolved Gene Expression Measurements across Individuals

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

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.

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.

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

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

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.

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

Benno Schwikowski, Anavaj Sakuntabhai, Kristel Van Steen, 2015, BMC Genetics.

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

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

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

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

Evolution of metabolic network organization

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

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

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

Signal Maps for Mass Spectrometry-based Comparative Proteomics*

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

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

Benno Schwikowski, Nada Amin, Trey Ideker, 2003 .

Automated phosphopeptide identification using multiple MS/MS fragmentation modes.

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

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

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

Network-based analysis of omics data: the LEAN method

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

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.

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

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

Fragmentation‐free LC‐MS can identify hundreds of proteins

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

A shared disease-associated oligodendrocyte signature among multiple CNS pathologies

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

An Exact Algorithm to Identify Motifs in Orthologous Sequences from Multiple Species

Benno Schwikowski, Mathieu Blanchette, Martin Tompa, 2000, ISMB.

The Cyni framework for network inference in Cytoscape

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

Common and phylogenetically widespread coding for peptides by bacterial small RNAs

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

The Cytoscape Automation app article collection

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

Technical Report: Towards Prediction of Platinum Resistance from Expression Levels of Genes Related to Homologous Recombination

S. Hautaniemi, Kaiyang Zhang, A. Häkkinen, 2019 .

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.

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

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

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

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

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

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

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.

A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection

Thomas Yu, Ka Yee Yeung, Maria K. Jaakkola, 2018, Nature Communications.

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

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

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

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