List of works - Benno Schwikowski

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

scientific article published on 27 February 2018

A clustering approach to Generalized Tree Alignment with application to Alu repeats

A network of protein-protein interactions in yeast

scientific article (publication date: December 2000)

A shared disease-associated oligodendrocyte signature among multiple CNS pathologies

scientific article published in 2022

Algorithms for phylogenetic footprinting

scientific article

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

scientific article

Analysis of time-resolved gene expression measurements across individuals

scientific article (publication date: 2013)

Assessing bias in experiment design for large scale mass spectrometry-based quantitative proteomics

scientific article (publication date: October 2007)

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

scientific article published on 7 January 2015

Automated phosphopeptide identification using multiple MS/MS fragmentation modes

scientific article published on 7 November 2012

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

scientific article

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

scientific article published on 09 March 2020

Common and phylogenetically widespread coding for peptides by bacterial small RNAs

scientific article published on 21 July 2017

Common and phylogenetically widespread coding for peptides by bacterial small RNAs

Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis

scientific article

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

scientific article

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

scientific article published on 5 March 2021

Democratising Knowledge Representation with BioCypher

scientific article published on 27 December 2022

Democratizing knowledge representation with BioCypher

Detecting multi-way epistasis in family-based association studies

scientific article published on 13 May 2016

Discovering regulatory and signalling circuits in molecular interaction networks

scientific article (publication date: 2002)

Discovery of pathways using multiple genome-scale data sets

Evolution of metabolic network organization

scientific article

Feature Detection with Controlled Error Rates in LC/MS Images ⬇️

scientific article published on March 13, 2012

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

scientific article published on 6 February 2015

Fragmentation-free LC-MS can identify hundreds of proteins

scientific article published on 06 December 2010

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

scientific article

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

scientific article

Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism

scientific article published in March 2012

Graph-based methods for analysing networks in cell biology

scientific article published on 30 July 2006

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

scientific article published on 08 May 2020

Identification of additional proteins in differential proteomics using protein interaction networks

scientific article published on April 2013

Indexing and Searching a Mass Spectrometry Database

Integration of biological networks and gene expression data using Cytoscape

scientific article (publication date: 2007)

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

scientific article published on 01 October 2019

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

scientific article published in May 2010

Mining proteomic data for biomedical research

article published in 2011

Network module identification-A widespread theoretical bias and best practices

scientific article

Network-based analysis of omics data: the LEAN method

scientific article

On enumerating all minimal solutions of feedback problems

Phylogenetic distances are encoded in networks of interacting pathways

scientific article published on 26 September 2008

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

scientific article

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

scientific article

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

scientific article published in November 2005

Signal maps for mass spectrometry-based comparative proteomics

scientific article published on 3 November 2005

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

scientific article published on 13 February 2019

TLM-Quant: an open-source pipeline for visualization and quantification of gene expression heterogeneity in growing microbial cells

scientific article

The Cyni framework for network inference in Cytoscape.

scientific article published on 18 December 2014

The Cytoscape Automation app article collection.

scientific article

The Cytoscape app article collection.

scientific article published on July 2014

The deferred path heuristic for the generalized tree alignment problem

scientific article published in January 1997

The deferred path heuristic for the generalized tree alignment problem

The restriction scaffold problem

scientific article

Tools enabling the elucidation of molecular pathways active in human disease: application to Hepatitis C virus infection

scientific article

Towards optimally multiplexed applications of universal DNA tag systems

Towards optimally multiplexed applications of universal arrays

scientific article published in January 2004

Universal DNA tag systems

article

Universal DNA tag systems: a combinatorial design scheme

scientific article published in January 2000

List of works by Benno Schwikowski

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

A clustering approach to Generalized Tree Alignment with application to Alu repeats

A network of protein-protein interactions in yeast

A shared disease-associated oligodendrocyte signature among multiple CNS pathologies

Algorithms for phylogenetic footprinting

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

Analysis of time-resolved gene expression measurements across individuals

Assessing bias in experiment design for large scale mass spectrometry-based quantitative proteomics

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

Automated phosphopeptide identification using multiple MS/MS fragmentation modes

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

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

Common and phylogenetically widespread coding for peptides by bacterial small RNAs

Common and phylogenetically widespread coding for peptides by bacterial small RNAs

Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis

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

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

Democratising Knowledge Representation with BioCypher

Democratizing knowledge representation with BioCypher

Detecting multi-way epistasis in family-based association studies

Discovering regulatory and signalling circuits in molecular interaction networks

Discovery of pathways using multiple genome-scale data sets

Evolution of metabolic network organization

Feature Detection with Controlled Error Rates in LC/MS Images ⬇️

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

Fragmentation-free LC-MS can identify hundreds of proteins

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

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

Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism

Graph-based methods for analysing networks in cell biology

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

Identification of additional proteins in differential proteomics using protein interaction networks

Indexing and Searching a Mass Spectrometry Database

Integration of biological networks and gene expression data using Cytoscape

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

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

Mining proteomic data for biomedical research

Network module identification-A widespread theoretical bias and best practices

Network-based analysis of omics data: the LEAN method

On enumerating all minimal solutions of feedback problems

Phylogenetic distances are encoded in networks of interacting pathways

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

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

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

Signal maps for mass spectrometry-based comparative proteomics

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

TLM-Quant: an open-source pipeline for visualization and quantification of gene expression heterogeneity in growing microbial cells

The Cyni framework for network inference in Cytoscape.

The Cytoscape Automation app article collection.

The Cytoscape app article collection.

The deferred path heuristic for the generalized tree alignment problem

The deferred path heuristic for the generalized tree alignment problem

The restriction scaffold problem

Tools enabling the elucidation of molecular pathways active in human disease: application to Hepatitis C virus infection

Towards optimally multiplexed applications of universal DNA tag systems

Towards optimally multiplexed applications of universal arrays

Universal DNA tag systems

Universal DNA tag systems: a combinatorial design scheme

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