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List of works by Christophe Dessimoz

A Gene Ontology Tutorial in Python

scientific article

A Transcriptomic-Phylogenomic Analysis of the Evolutionary Relationships of Flatworms ⬇️

scientific article

A dimensionless fit measure for phylogenetic distance trees

scientific article published in December 2005

A generalized Robinson-Foulds distance for labeled trees

scientific article published on 18 November 2020

A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL

scientific article published on 29 October 2019

A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL

scientific article published on 22 July 2020

A putative origin of the insect chemosensory receptor superfamily in the last common eukaryotic ancestor

scientific article published on 04 December 2020

AI and the democratization of knowledge

scientific article published in 2024

ALF--a simulation framework for genome evolution

scientific article

Advances and Applications in the Quest for Orthologs

scientific article published on 01 October 2019

Algorithm of OMA for large-scale orthology inference

scientific article

Algorithm of OMA for large-scale orthology inference

Alignments with Non-overlapping Moves, Inversions and Tandem Duplications in O(n 4) Time

Alignments with non-overlapping moves, inversions and tandem duplications in O(n 4) time

article published in 2007

An expanded evaluation of protein function prediction methods shows an improvement in accuracy ⬇️

scientific article

Approximate Bayesian computation

scientific article published in 2013

Assessing the potential of RAD-sequencing to resolve phylogenetic relationships within species radiations: The fly genus Chiastocheta (Diptera: Anthomyiidae) as a case study.

scientific article published on 20 June 2017

Assigning confidence scores to homoeologs using fuzzy logic

scientific article published in 2019

Base-calling for next-generation sequencing platforms

scientific article published on 18 January 2011

Benchmarking gene ontology function predictions using negative annotations

scientific article published on 01 July 2020

Bidirectional best hits miss many orthologs in duplication-rich clades such as plants and animals

scientific article published on January 2013

Big data and other challenges in the quest for orthologs

scientific article

Bio-SODA UX: enabling natural language question answering over knowledge graphs with user disambiguation

Bio-SODA: Enabling Natural Language Question Answering over Knowledge Graphs without Training Data

scientific article published on 12 August 2021

CAFA and the open world of protein function predictions.

scientific article

Clustering Genes of Common Evolutionary History

scientific article published on 17 February 2016

Comparative genomics approach to detecting split-coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes)

scientific article published on 28 June 2011

Comparative genomics reveals contraction in olfactory receptor genes in bats

scientific article

Compensation of Dosage-Sensitive Genes on the Chicken Z Chromosome

scientific article published on 4 April 2016

Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees

scientific article

Covariance of maximum likelihood evolutionary distances between sequences aligned pairwise

scientific article

Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference.

scientific article

DLIGHT – Lateral Gene Transfer Detection Using Pairwise Evolutionary Distances in a Statistical Framework

article

Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits

scientific article published on 11 July 2006

DrosOMA: the Drosophila Orthologous Matrix browser

scientific article published in 2024

Editorial: Orthology and applications ⬇️

scientific article published on September 1, 2011

Enabling semantic queries across federated bioinformatics databases

scientific article published on 01 January 2019

Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes

scientific article published in December 2008

Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python

scientific article published on 10 January 2019

Fast estimation of the difference between two PAM/JTT evolutionary distances in triplets of homologous sequences

scientific article

GOATOOLS: A Python library for Gene Ontology analyses

scientific article published in Scientific Reports

Gearing up to handle the mosaic nature of life in the quest for orthologs

scientific article published on 30 August 2017

Gene Duplication and Gain in the Trematode Atriophallophorus winterbourni Contributes to Adaptation to Parasitism

scientific article published in 2021

Gene Ontology: Pitfalls, Biases, and Remedies

scientific article published on January 2017

Genomic Encryption of Digital Data Stored in Synthetic DNA

scientific article published on 21 February 2020

Genomic Encryption of Digital Data Stored in Synthetic DNA

scientific article published in 2020

Global regulatory architecture of human, mouse and rat tissue transcriptomes

scientific article

Homoeolog Inference Methods Requiring Bidirectional Best Hits or Synteny Miss Many Pairs

scientific article

Homoeologs: What Are They and How Do We Infer Them?

scientific article

How Much Does GenoGuard Really "Guard"?

scientific article published on 11 November 2019

How to build phylogenetic species trees with OMA

scientific article published in 2020

How to build phylogenetic species trees with OMA

scientific article published in 2022

How to build phylogenetic species trees with OMA [version 2; peer review: 2 approved]

publication published on 01 January 2020

Identifying orthologs with OMA: A primer

scientific article published on 17 January 2020

Inferring Orthology and Paralogy

scientific article published on 01 January 2019

Inferring hierarchical orthologous groups from orthologous gene pairs

scientific article

Inferring horizontal gene transfer

scientific article published in May 2015

Inferring orthology and paralogy

scientific article

Joining forces in the quest for orthologs

scientific article published on 29 September 2009

Lessons Learned: Recommendations for Establishing Critical Periodic Scientific Benchmarking

Membrane Proteins Are Dramatically Less Conserved than Water-Soluble Proteins across the Tree of Life

scientific article published on 08 August 2016

Mitigating Anticipated Effects of Systematic Errors Supports Sister-Group Relationship between Xenacoelomorpha and Ambulacraria

scientific article published on 16 May 2019

NGS-Based <i>S. aureus</i> Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency Test

scientific article published on 24 November 2020

New genome assembly of the barn owl (Tyto alba alba)

scientific article published on 19 February 2020

OMA

method and database for the inference of orthologs among complete genomes

OMA 2011: orthology inference among 1000 complete genomes

scientific article

OMA Browser--exploring orthologous relations across 352 complete genomes

scientific article published in June 2007

OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more

scientific article published on 11 November 2020

OMA standalone: orthology inference among public and custom genomes and transcriptomes

OMA standalone: orthology inference among public and custom genomes and transcriptomes

scientific article published on 24 June 2019

OMA, A Comprehensive, Automated Project for the Identification of Orthologs from Complete Genome Data: Introduction and First Achievements

article

OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches

scientific article published in 2021

Only a single taxonomically restricted gene family in the Drosophila melanogaster subgroup can be identified with high confidence

scientific article published on 26 June 2020

Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference

scientific article

Phylo.io: Interactive Viewing and Comparison of Large Phylogenetic Trees on the Web.

scientific article published on 19 April 2016

Phylogenetic and functional assessment of orthologs inference projects and methods

scientific article

Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome

scientific article published on 01 April 2019

Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome

article

Phylogenetic assessment of alignments reveals neglected tree signal in gaps

scientific article published on 6 April 2010

Phylogenetic profiling in eukaryotes comes of age

scientific article published in 2023

Phylogenetic profiling: how much input data is enough?

scientific article

Preface of Proceedings of GNOME 2014 — Festschrift for Gaston Gonnet

Primer on the Gene Ontology.

scientific article published on January 2017

Prioritising candidate genes causing QTL using hierarchical orthologous groups

article

Quality assessment of gene repertoire annotations with OMArk

scientific article published in 2024

Quality of computationally inferred gene ontology annotations

scientific article

RecPhyloXML: a format for reconciled gene trees

article

Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs ⬇️

scientific article published on May 17, 2012

SWPS3 - fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and x86/SSE2

scientific article

Scalable phylogenetic profiling using MinHash uncovers likely eukaryotic sexual reproduction genes

scientific article published on 22 July 2020

Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks.

scientific article published on 6 January 2015

Speeding up all-against-all protein comparisons while maintaining sensitivity by considering subsequence-level homology

scientific article published on 7 October 2014

Standardized benchmarking in the quest for orthologs

scientific article (publication date: 4 April 2016)

Structural variant calling: the long and the short of it

scientific article published on 20 November 2019

Submit a Topic Page to PLOS Computational Biology and Wikipedia

scientific article

Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes

scientific article published on 3 May 2011

Taxon sampling unequally affects individual nodes in a phylogenetic tree: consequences for model gene tree construction in SwissTree

article

Ten Years of Collaborative Progress in the Quest for Orthologs

scientific article published on 2 April 2021

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

scientific article published on 19 November 2019

The Microbe browser for comparative genomics

scientific article published on 30 April 2009

The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements.

scientific article

The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces.

scientific article

The Quest for Orthologs benchmark service and consensus calls in 2020

scientific article published on 06 May 2020

The SIB Swiss Institute of Bioinformatics Semantic Web of data

scientific article published on 25 October 2023

The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease

scientific article (publication date: December 2014)

The impact of gene duplication, insertion, deletion, lateral gene transfer and sequencing error on orthology inference: a simulation study

scientific article

The phylogenetic range of bacterial and viral pathogens of vertebrates

scientific article published on 10 May 2020

The what, where, how and why of gene ontology--a primer for bioinformaticians

scientific article

Toward community standards in the quest for orthologs ⬇️

scientific article (publication date: 15 March 2012)

Towards practical, high-capacity, low-maintenance information storage in synthesized DNA

scientific article

Transient structural variations alter gene expression and quantitative traits in Schizosaccharomyces pombe

article

Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast

scientific article

Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment.

scientific article

iHam and pyHam: visualizing and processing hierarchical orthologous groups

scientific article published on 01 July 2019

iTRAQ-based analysis of changes in the cassava root proteome reveals pathways associated with post-harvest physiological deterioration

scientific article

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