Timeline

Benno Schwikowski

Head of Structure

20 Jun 2022

publication

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.

04 Apr 2022

project

DECIDER: artificial intelligence to improve diagnosis and treatment of ovarian cancer

04 Apr 2022

project

Precision drugs Against Resistance In Subpopulations (PARIS)

17 Jan 2022

publication

An overview of machine learning methods for monotherapy drug response prediction.

08 Nov 2021

project

SLE Map: a consensus map of SLE patients into a low dimensional space

29 Oct 2021

event

Data Analysis for Precision Medicine

01 Aug 2021

publication

Differential levels of IFNα subtypes in autoimmunity and viral infection.

11 Jun 2021

news

DECIDER: artificial intelligence to improve diagnosis and treatment of ovarian cancer

05 Mar 2021

publication

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

25 Jun 2020

publication

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

09 Mar 2020

publication

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

01 Mar 2020

publication

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

01 Oct 2019

publication

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

18 Sep 2019

publication

The Cytoscape platform for network analysis and visualization

10 Sep 2019

project

New clinical endpoints in primary Sjögren’s Syndrome: an interventional trial based on stratifying patients (NECESSITY)

01 Feb 2019

publication

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

24 Oct 2018

publication

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

27 Jul 2018

publication

Human genetic variants and age are the strongest predictors of humoral immune responses to common pathogens and vaccines.

20 Jun 2018

publication

The Cytoscape Automation app article collection

15 Mar 2018

project

Comprehensive characterization and effective combinatorial targeting of high-grade serous ovarian cancer via single-cell analysis (HERCULES)

01 Mar 2018

publication

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

16 Jan 2018

publication

Distinctive roles of age, sex, and genetics in shaping transcriptional variation of human immune responses to microbial challenges.

26 Sep 2017

event

Systems health for precision medicine—Handling Disease Heterogeneity

26 Sep 2017

event

Regulation of gene activity, in 3D and in sequence space

21 Sep 2017

publication

Network module identification-A widespread theoretical bias and best practices

21 Jul 2017

publication

Common and phylogenetically widespread coding for peptides by bacterial small RNAs

01 Mar 2017

publication

Network-based analysis of omics data: the LEAN method

08 Dec 2016

publication

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

14 Nov 2016

software

GRAVITY

10 May 2016

project

Systems biology of cell infection by the bacterial pathogen Listeria monocytogenes

05 Oct 2015

event

Histology informatics: dissecting breast tumour spatial and molecular heterogeneity

29 Jun 2015

publication

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

15 Jun 2015

software

Cytoscape: Visualization and analysis of omics data in interaction networks

11 May 2015

team

Computational Systems Biomedicine

01 Apr 2015

publication

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

06 Feb 2015

publication

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

18 Dec 2014

publication

The Cyni framework for network inference in Cytoscape

01 Jul 2014

publication

The Cytoscape app article collection

09 Dec 2013

publication

Analysis of time-resolved gene expression measurements across individuals

17 Jul 2013

publication

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

01 Apr 2013

publication

Identification of additional proteins in differential proteomics using protein interaction networks

07 Nov 2012

publication

Automated Phosphopeptide Identification Using Multiple MS/MS Fragmentation Modes

13 Mar 2012

publication

Feature detection with controlled error rates in LC/MS images

01 Mar 2012

publication

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

01 Mar 2012

publication

Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism

01 Jan 2012

publication

Mining proteomic data for biomedical research

06 Dec 2010

publication

Fragmentation-free LC-MS can identify hundreds of proteins

11 May 2010

publication

Evolution of metabolic network organization

01 May 2010

publication

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

26 Sep 2008

publication

Phylogenetic distances are encoded in networks of interacting pathways

01 Feb 2008

publication

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

07 Jul 2007

publication

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

01 Jan 2007

publication

Integration of biological networks and gene expression data using Cytoscape

30 Jul 2006

publication

Graph-based methods for analysing networks in cell biology

03 Nov 2005

publication

Signal maps for mass spectrometry-based comparative proteomics

01 Nov 2005

publication

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

20 Jun 2005

publication

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

01 Aug 2004

publication

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

01 Jan 2004

publication

Towards optimally multiplexed applications of universal arrays

01 Nov 2003

publication

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

01 Jan 2003

publication

The restriction scaffold problem

01 Oct 2002

publication

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

01 Jan 2002

publication

Discovering regulatory and signalling circuits in molecular interaction networks

01 Jan 2002

publication

Algorithms for phylogenetic footprinting

01 Dec 2000

publication

A network of protein-protein interactions in yeast

01 Jan 2000

publication

Universal DNA tag systems: a combinatorial design scheme

01 Jan 2000

publication

An exact algorithm to identify motifs in orthologous sequences from multiple species

01 Jan 1997

publication

A little guide for advanced search:

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.

DECIDER: artificial intelligence to improve diagnosis and treatment of ovarian cancer

Precision drugs Against Resistance In Subpopulations (PARIS)

An overview of machine learning methods for monotherapy drug response prediction.

SLE Map: a consensus map of SLE patients into a low dimensional space

Data Analysis for Precision Medicine

Differential levels of IFNα subtypes in autoimmunity and viral infection.

DECIDER: artificial intelligence to improve diagnosis and treatment of ovarian cancer

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

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

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

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

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

The Cytoscape platform for network analysis and visualization

New clinical endpoints in primary Sjögren’s Syndrome: an interventional trial based on stratifying patients (NECESSITY)

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

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

Human genetic variants and age are the strongest predictors of humoral immune responses to common pathogens and vaccines.

The Cytoscape Automation app article collection

Comprehensive characterization and effective combinatorial targeting of high-grade serous ovarian cancer via single-cell analysis (HERCULES)

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

Distinctive roles of age, sex, and genetics in shaping transcriptional variation of human immune responses to microbial challenges.

Systems health for precision medicine—Handling Disease Heterogeneity

Regulation of gene activity, in 3D and in sequence space

Network module identification-A widespread theoretical bias and best practices

Common and phylogenetically widespread coding for peptides by bacterial small RNAs

Network-based analysis of omics data: the LEAN method

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

GRAVITY

Systems biology of cell infection by the bacterial pathogen Listeria monocytogenes

Histology informatics: dissecting breast tumour spatial and molecular heterogeneity

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

Cytoscape: Visualization and analysis of omics data in interaction networks

Computational Systems Biomedicine

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

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

The Cyni framework for network inference in Cytoscape

The Cytoscape app article collection

Analysis of time-resolved gene expression measurements across individuals

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

Identification of additional proteins in differential proteomics using protein interaction networks

Automated Phosphopeptide Identification Using Multiple MS/MS Fragmentation Modes

Feature detection with controlled error rates in LC/MS images

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

Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism

Mining proteomic data for biomedical research

Fragmentation-free LC-MS can identify hundreds of proteins

Evolution of metabolic network organization

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

Phylogenetic distances are encoded in networks of interacting pathways

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

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

Integration of biological networks and gene expression data using Cytoscape

Graph-based methods for analysing networks in cell biology

Signal maps for mass spectrometry-based comparative proteomics

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

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

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

Towards optimally multiplexed applications of universal arrays

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

The restriction scaffold problem

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

Discovering regulatory and signalling circuits in molecular interaction networks

Algorithms for phylogenetic footprinting

A network of protein-protein interactions in yeast

Universal DNA tag systems: a combinatorial design scheme

An exact algorithm to identify motifs in orthologous sequences from multiple species

The deferred path heuristic for the generalized tree alignment problem