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List of works by Christian von Mering

A Family of Interaction-Adjusted Indices of Community Similarity

A comprehensive set of protein complexes in yeast: mining large scale protein-protein interaction screens

scientific article

A family of interaction-adjusted indices of community similarity.

scientific article published on 09 December 2016

A global network of coexisting microbes from environmental and whole-genome sequence data

scientific article

A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation

scientific article

A sentinel protein assay for simultaneously quantifying cellular processes

scientific article published on 7 September 2014

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

scientific article published on 05 February 2020

Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs

scientific article (publication date: July 2004)

Analysis of the Human Kinome and Phosphatome by Mass Cytometry Reveals Overexpression-Induced Effects on Cancer-Related Signaling.

scientific article published on 14 May 2019

Analysis of the human kinome and phosphatome reveals diseased signaling networks induced by overexpression

Arabidopsis female gametophyte gene expression map reveals similarities between plant and animal gametes

scientific article

Assessing systems properties of yeast mitochondria through an interaction map of the organelle

scientific article

Bacterial anoxygenic photosynthesis on plant leaf surfaces

scientific article published on 16 January 2012

Bacterial diversity and composition in the fluid of pitcher plants of the genus Nepenthes

scientific article published on 16 June 2015

Cell-sorting at the A/P boundary in the Drosophila wing primordium: a computational model to consolidate observed non-local effects of Hh signaling

scientific article

Cell-wide analysis of protein thermal unfolding reveals determinants of thermostability.

scientific article

ChromID identifies the protein interactome at chromatin marks

scientific article published on 02 March 2020

Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens

scientific article published on 29 January 2014

Community proteogenomics reveals insights into the physiology of phyllosphere bacteria

scientific article published on 04 September 2009

Comparative analysis of environmental sequences: potential and challenges

scientific article

Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes

scientific article

Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster

scientific article (publication date: 4 October 2002)

Complex genomic rearrangements lead to novel primate gene function

scientific article

Consistency of genome-based methods in measuring Metazoan evolution

scientific article

Cross-Regulation between TDP-43 and Paraspeckles Promotes Pluripotency-Differentiation Transition.

scientific article

Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity

scientific article published on 11 February 2020

Ecological consistency of SSU rRNA-based operational taxonomic units at a global scale

scientific article

Ecologically informed microbial biomarkers and accurate classification of mixed and unmixed samples in an extensive cross-study of human body sites

article

Effects of oral antibiotics and isotretinoin on the murine gut microbiota

scientific article published on 6 July 2017

Environments shape the nucleotide composition of genomes

scientific article

Erratum to: gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens

scientific article published on 21 October 2015

Expression of amino-terminally truncated PrP in the mouse leading to ataxia and specific cerebellar lesions

scientific article published in April 1998

Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper

scientific article published on 29 April 2017

Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper

article

Fermentation Ability of Gut Microbiota of Wild Japanese Macaques in the Highland and Lowland Yakushima: In Vitro Fermentation Assay and Genetic Analyses

scientific article published on 24 April 2020

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support

scientific article

Function prediction and protein networks

scientific article

Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes

scientific article published on December 2004

Genome evolution reveals biochemical networks and functional modules

scientific article

Genome-wide small interfering RNA screens reveal VAMP3 as a novel host factor required for Uukuniemi virus late penetration

scientific article

Global analysis of bacterial transcription factors to predict cellular target processes

scientific article published on March 2004

Growth-restricting effects of siRNA transfections: a largely deterministic combination of off-target binding and hybridization-independent competition

article

HPC-CLUST: distributed hierarchical clustering for large sets of nucleotide sequences

scientific article published on 9 November 2013

High confidence prediction of essential genes in Burkholderia cenocepacia ⬇️

scientific article

High-Resolution RNA Maps Suggest Common Principles of Splicing and Polyadenylation Regulation by TDP-43.

scientific article

IFN-γ Hinders Recovery from Mucosal Inflammation during Antibiotic Therapy for Salmonella Gut Infection

scientific article published on 20 July 2016

Immunity-related genes and gene families in Anopheles gambiae

scientific article published in October 2002

In situ enzyme activity in the dissolved and particulate fraction of the fluid from four pitcher plant species of the genus Nepenthes

scientific article published in 2011

Large-scale functional analysis of the roles of phosphorylation in yeast metabolic pathways

scientific article published on 25 November 2014

Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria

scientific article

Limits to robustness and reproducibility in the demarcation of operational taxonomic units

scientific article

MAPseq: Improved Speed, Accuracy And Consistency In Ribosomal RNA Sequence Analysis

MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis

scientific article published on 14 August 2017

MLTreeMap--accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies

scientific article

Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice

scientific article published on 22 December 2011

Microbial rhodopsins on leaf surfaces of terrestrial plants

scientific article published on September 2011

Microbiota-derived hydrogen fuels Salmonella typhimurium invasion of the gut ecosystem

scientific article published in December 2013

Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat

scientific article published on 3 June 2008

Natural Genetic Variation Differentially Affects the Proteome and Transcriptome in Caenorhabditis elegans.

scientific article published on 4 March 2016

Pathogenic impact of transcript isoform switching in 1,209 cancer samples covering 27 cancer types using an isoform-specific interaction network

scientific article published on 02 September 2020

Pathogens and host immunity in the ancient human oral cavity

scientific article (publication date: April 2014)

Pathway and network analysis of more than 2,500 whole cancer genomes

Pathway and network analysis of more than 2500 whole cancer genomes

scientific article published on 05 February 2020

PaxDb, a database of protein abundance averages across all three domains of life

scientific article

Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast

scientific article

Prediction of effective genome size in metagenomic samples

scientific article published on January 2007

Preventive Trichuris suis ova (TSO) treatment protects immunocompetent rabbits from DSS colitis but may be detrimental under conditions of immunosuppression

scientific article published on 28 November 2017

Protein interaction networks from yeast to human

scientific article (publication date: June 2004)

Protein tyrosine phosphatase non-receptor type 22 modulates colitis in a microbiota-dependent manner

scientific article published on 20 May 2019

Publisher Correction: ChromID identifies the protein interactome at chromatin marks

scientific article published on 01 June 2020

Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments

scientific article (publication date: 23 February 2007)

Quantitative assessment of protein function prediction from metagenomics shotgun sequences

scientific article (publication date: 23 August 2007)

RAIN: RNA-protein Association and Interaction Networks

scientific article published on 10 January 2017

RNAi screen of Salmonella invasion shows role of COPI in membrane targeting of cholesterol and Cdc42 ⬇️

scientific article

Rapid Inference of Direct Interactions in Large-Scale Ecological Networks from Heterogeneous Microbial Sequencing Data

scientific article published on 18 September 2019

Reproducible Propagation of Species-Rich Soil Bacterial Communities Suggests Robust Underlying Deterministic Principles of Community Formation

scientific article published on 30 March 2022

STITCH 2: an interaction network database for small molecules and proteins

scientific article (publication date: 2010)

STITCH 3: zooming in on protein-chemical interactions

scientific article (publication date: 9 November 2011)

STITCH 4: integration of protein-chemical interactions with user data

scientific article

STITCH 5: augmenting protein–chemical interaction networks with tissue and affinity data

scientific article (publication date: 20 November 2015)

STITCH: interaction networks of chemicals and proteins

scientific article

STRING 7--recent developments in the integration and prediction of protein interactions

scientific article

STRING 8--a global view on proteins and their functional interactions in 630 organisms

scientific article

STRING v10: protein-protein interaction networks, integrated over the tree of life

scientific article (publication date: 2015)

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

scientific article published on 22 November 2018

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

scientific article (publication date: 2013)

STRING: a database of predicted functional associations between proteins

scientific article

STRING: known and predicted protein-protein associations, integrated and transferred across organisms

scientific article

SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles

scientific article (publication date: 26 November 2015)

Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota

scientific article

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

scientific article

Sequence-based factors influencing the expression of heterologous genes in the yeast Pichia pastoris--A comparative view on 79 human genes

scientific article published on 28 February 2007

Shared components of protein complexes--versatile building blocks or biochemical artefacts?

scientific article published in December 2004

Shotgun proteomics data from multiple organisms reveals remarkable quantitative conservation of the eukaryotic core proteome

scientific article

Simultaneous analysis of large-scale RNAi screens for pathogen entry

scientific article

Specific genomic regions are differentially affected by copy number alterations across distinct cancer types, in aggregated cytogenetic data.

scientific article

Specific inhibition of diverse pathogens in human cells by synthetic microRNA-like oligonucleotides inferred from RNAi screens

scientific article

Sputum DNA sequencing in cystic fibrosis: non-invasive access to the lung microbiome and to pathogen details.

scientific article published on 10 February 2017

Standardized benchmarking in the quest for orthologs

scientific article (publication date: 4 April 2016)

Teamed up for transcription

scientific article published in Nature

Termites in the woodwork

scientific article (publication date: 2007)

The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data

scientific article (publication date: February 2004)

The HUPO initiative on Model Organism Proteomes, iMOP.

scientific article published in February 2012

The SIB Swiss Institute of Bioinformatics Semantic Web of data

scientific article published on 25 October 2023

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

scientific article (publication date: 4 January 2016)

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

scientific article

The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible

scientific article published on 18 October 2016

The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets

scientific article published on 25 November 2020

The hedgehog signaling pathway: where did it come from?

scientific article

The initiative on Model Organism Proteomes (iMOP) Session September 6, 2011, Geneva, Switzerland

scientific article published in February 2012

The microbiota mediates pathogen clearance from the gut lumen after non-typhoidal Salmonella diarrhea

scientific article (publication date: 2010)

Toward Automatic Reconstruction of a Highly Resolved Tree of Life

scientific article

Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies

scientific article published on 06 May 2019

Unexplored therapeutic opportunities in the human genome

scientific article published on 23 March 2018

Unexplored therapeutic opportunities in the human genome.

scientific article published on 23 February 2018

Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines.

scientific article published on 5 February 2015

Viruses.STRING: A Virus-Host Protein-Protein Interaction Database

scholarly article by Helen Victoria Cook published in September 2018

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

scientific article (publication date: 17 November 2015)

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

scientific article published on 01 January 2019

eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations

scientific article

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

scientific article

eggNOG v4.0: nested orthology inference across 3686 organisms

scientific article (publication date: December 2013)

eggNOG: automated construction and annotation of orthologous groups of genes

scientific article (publication date: 23 December 2007)

gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens

scientific article published on 7 October 2015

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