All Stories

  1. PhytClust: efficient and optimal node clustering in phylogenetic trees

    Article • December 2025, openRxiv

    Dr Christophe Dessimoz

  2. Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration

    Article • Journal of Molecular Evolution, October 2025, Springer Science + Business Media

    Dr Christophe Dessimoz

  3. Structural phylogenetics unravels the evolutionary diversification of communication systems in gram-positive bacteria and their viruses

    Article • Nature Structural & Molecular Biology, October 2025, Springer Science + Business Media

    Dr Christophe Dessimoz

  4. OrthoXML-Tools: A Toolkit for Manipulating OrthoXML Files for Orthology Data

    Article • Journal of Molecular Evolution, September 2025, Springer Science + Business Media

    Dr Christophe Dessimoz

  5. EdgeHOG: a method for fine-grained ancestral gene order inference at large scale

    Article • Nature Ecology & Evolution, August 2025, Springer Science + Business Media

    Dr Christophe Dessimoz

  6. Unveiling the functional fate of duplicated genes through expression profiling and structural analysis

    Article • Genome Research, August 2025, Cold Spring Harbor Laboratory Press

    Dr Christophe Dessimoz

  7. Invest in data resources to make FAIR a reality

    Article • Nature, July 2025, Springer Science + Business Media

    Dr Christophe Dessimoz

  8. Annotation matters: the effect of structural gene annotation on orthology inference

    Article • Bioinformatics, June 2025, Oxford University Press (OUP)

    Dr Christophe Dessimoz

  9. Federated SPARQL query performance evaluation for exploring disease model mouse: combining gene expression, orthology, and disease knowledge graphs

    Article • BMC Medical Informatics and Decision Making, May 2025, Springer Science + Business Media

    Dr Christophe Dessimoz

  10. Orthology inference at scale with FastOMA

    Article • Nature Chemical Biology, January 2025, Springer Science + Business Media

    Dr Christophe Dessimoz

  11. OMAnnotator: a novel approach to building an annotated consensus genome sequence

    Article • December 2024, Cold Spring Harbor Laboratory Press

    Dr Christophe Dessimoz

  12. Reconstructing the last common ancestor of all eukaryotes

    Article • PLoS Biology, November 2024, PLOS

    Dr Laura Eme, Dr Christophe Dessimoz

  13. When less is more: sketching with minimizers in genomics

    Article • Genome Biology, October 2024, Springer Science + Business Media

    Dr Christophe Dessimoz

  14. Quest for Orthologs in the Era of Biodiversity Genomics

    Article • Genome Biology and Evolution, October 2024, Oxford University Press (OUP)

    Dr Christophe Dessimoz

  15. New developments for the Quest for Orthologs benchmark service

    Article • NAR Genomics and Bioinformatics, September 2024, Oxford University Press (OUP)

    Dr Christophe Dessimoz

  16. EdgeHOG: fine-grained ancestral gene order inference at tree-of-life scale

    Article • August 2024, Cold Spring Harbor Laboratory Press

    Dr Christophe Dessimoz

  17. Matreex: Compact and Interactive Visualization for Scalable Studies of Large Gene Families

    Article • Genome Biology and Evolution, May 2024, Oxford University Press (OUP)

    Dr Christophe Dessimoz

  18. Frequent jumps from human hosts

    Article • Nature Ecology & Evolution, March 2024, Springer Science + Business Media

    Dr Christophe Dessimoz

  19. AI and the democratization of knowledge

    Article • Scientific Data, March 2024, Springer Science + Business Media

    Dr Christophe Dessimoz

  20. Quality assessment of gene repertoire annotations with OMArk

    Article • Nature Biotechnology, February 2024, Springer Science + Business Media

    Dr Christophe Dessimoz

  21. Orthology inference at scale with FastOMA

    Article • January 2024, Cold Spring Harbor Laboratory Press

    Dr Christophe Dessimoz

  22. DrosOMA: the Drosophila Orthologous Matrix browser

    Article • F1000Research, January 2024, Faculty of 1000, Ltd.

    Dr Christophe Dessimoz

  23. OMA orthology in 2024: improved prokaryote coverage, ancestral and extant GO enrichment, a revamped synteny viewer and more in the OMA Ecosystem

    Article • Nucleic Acids Research, November 2023, Oxford University Press (OUP)

    Dr Christophe Dessimoz

  24. The SIB Swiss Institute of Bioinformatics Semantic Web of data

    Article • Nucleic Acids Research, October 2023, Oxford University Press (OUP)

    Dr Christophe Dessimoz

  25. Structural phylogenetics unravels the evolutionary diversification of communication systems in gram-positive bacteria and their viruses

    Article • October 2023, Springer Science + Business Media

    Dr Christophe Dessimoz

  26. Exploring Disease Model Mouse Using Knowledge Graphs: Combining Gene Expression, Orthology, and Disease Datasets

    Article • August 2023, Cold Spring Harbor Laboratory Press

    Dr Christophe Dessimoz

  27. Protein length distribution is remarkably uniform across the tree of life

    Article • Genome Biology, June 2023, Springer Science + Business Media

    Dr Christophe Dessimoz

  28. Phylogenetic profiling in eukaryotes comes of age

    Article • Proceedings of the National Academy of Sciences, May 2023, Proceedings of the National Academy of Sciences

    Dr Christophe Dessimoz

  29. Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree

    Article • Nature Biotechnology, April 2023, Springer Science + Business Media

    Fritz Sedlazeck, Dr Christophe Dessimoz

  30. Protein S-acylation controls the subcellular localization and biological activity of PHYTOCHROME KINASE SUBSTRATE

    Article • The Plant Cell, March 2023, Oxford University Press (OUP)

    Dr Christophe Dessimoz

  31. Matreex: compact and interactive visualisation for scalable studies of large gene families

    Article • February 2023, Cold Spring Harbor Laboratory Press

    Dr Christophe Dessimoz

  32. Bringing science to the public in the light of evolution

    Article • Biology Methods and Protocols, January 2023, Oxford University Press (OUP)

    Dr Christophe Dessimoz

  33. Multifaceted quality assessment of gene repertoire annotation with OMArk

    Article • November 2022, Cold Spring Harbor Laboratory Press

    Dr Christophe Dessimoz

  34. Reconstructing protein interactions across time using phylogeny-aware graph neural networks

    Article • July 2022, Cold Spring Harbor Laboratory Press

    Dr Christophe Dessimoz

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

    Article • Distributed and Parallel Databases, July 2022, Springer Science + Business Media

    Dr Christophe Dessimoz

  36. Control of PHYTOCHROME KINASE SUBSTRATE subcellular localization and biological activity by protein S-acylation

    Article • July 2022, Cold Spring Harbor Laboratory Press

    Dr Christophe Dessimoz

  37. Discovery of archaeal fusexins homologous to eukaryotic HAP2/GCS1 gamete fusion proteins

    Article • Nature Communications, July 2022, Springer Science + Business Media

    Dr Christophe Dessimoz

  38. ISMB 2022 proceedings

    Article • Bioinformatics, June 2022, Oxford University Press (OUP)

    Dr Christophe Dessimoz

  39. The Quest for Orthologs orthology benchmark service in 2022

    Article • Nucleic Acids Research, May 2022, Oxford University Press (OUP)

    Dr Christophe Dessimoz

  40. Read2Tree: scalable and accurate phylogenetic trees from raw reads

    Article • April 2022, Cold Spring Harbor Laboratory Press

    Fritz Sedlazeck, Dr Christophe Dessimoz

  41. A Linear Time Solution to the Labeled Robinson–Foulds Distance Problem

    Article • Systematic Biology, April 2022, Oxford University Press (OUP)

    Dr Christophe Dessimoz

  42. OMAMO: orthology-based alternative model organism selection

    Article • Bioinformatics, March 2022, Oxford University Press (OUP)

    Dr Christophe Dessimoz

  43. How to build phylogenetic species trees with OMA

    Article • F1000Research, February 2022, Faculty of 1000, Ltd.

    Dr Christophe Dessimoz

  44. Citrullination Was Introduced into Animals by Horizontal Gene Transfer from Cyanobacteria

    Article • Molecular Biology and Evolution, November 2021, Oxford University Press (OUP)

    Dr Christophe Dessimoz

  45. Discovery of archaeal Fusexins homologous to eukaryotic HAP2/GCS1 gamete fusion proteins

    Article • October 2021, Cold Spring Harbor Laboratory Press

    Dr Christophe Dessimoz

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

    Article • July 2021, ACM (Association for Computing Machinery)

    Dr Christophe Dessimoz

  47. ISMB/ECCB 2021 proceedings

    Article • Bioinformatics, July 2021, Oxford University Press (OUP)

    Dr Christophe Dessimoz

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

    Article • Genome Biology and Evolution, April 2021, Oxford University Press (OUP)

    Dr Christophe Dessimoz

  49. Ten Years of Collaborative Progress in the Quest for Orthologs

    Article • Molecular Biology and Evolution, April 2021, Oxford University Press (OUP)

    Dr Christophe Dessimoz

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

    Article • Bioinformatics, March 2021, Oxford University Press (OUP)

    Dr Christophe Dessimoz

  51. Want to track pandemic variants faster? Fix the bioinformatics bottleneck

    Article • Nature, March 2021, Springer Science + Business Media

    Dr Christophe Dessimoz

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

    Article • Genome Biology and Evolution, January 2021, Oxford University Press (OUP)

    Dr Christophe Dessimoz

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

    Article • eLife, December 2020, eLife

    Dr Christophe Dessimoz

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

    Article • Frontiers in Microbiology, November 2020, Frontiers

    Dr Christophe Dessimoz, Dr Peter Michael Keller

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

    Article • Nucleic Acids Research, November 2020, Oxford University Press (OUP)

    Dr Christophe Dessimoz

  56. A generalized Robinson-Foulds distance for labeled trees

    Article • BMC Genomics, November 2020, Springer Science + Business Media

    Dr Christophe Dessimoz

  57. Parallel and Scalable Precise Clustering

    Article • September 2020, ACM (Association for Computing Machinery)

    Dr Christophe Dessimoz, James Larus

  58. A Linear Time Solution to the Labeled Robinson-Foulds Distance Problem

    Article • September 2020, Cold Spring Harbor Laboratory Press

    Dr Christophe Dessimoz

  59. A putative origin of insect chemosensory receptors in the last common eukaryotic ancestor

    Article • August 2020, Cold Spring Harbor Laboratory Press

    Dr Christophe Dessimoz

  60. Large scale phylogenetic profiling and investigating gene networks involved in sexual reproduction

    Article • PLoS Computational Biology, July 2020, PLOS

    Dr Christophe Dessimoz, David Moi

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

    Article • F1000Research, July 2020, Faculty of 1000, Ltd.

    Dr Christophe Dessimoz

  62. Benchmarking gene ontology function predictions using negative annotations

    Article • Bioinformatics, July 2020, Oxford University Press (OUP)

    Dr Christophe Dessimoz

  63. Only a Single Taxonomically Restricted Gene Family in the Drosophila melanogaster Subgroup Can Be Identified with High Confidence

    Article • Genome Biology and Evolution, June 2020, Oxford University Press (OUP)

    Joanna Masel, Dr Christophe Dessimoz, Dr Yannick Wurm

  64. Protein citrullination was introduced into animals by horizontal gene transfer from cyanobacteria

    Article • June 2020, Cold Spring Harbor Laboratory Press

    Dr Christophe Dessimoz

  65. How to build phylogenetic species trees with OMA

    Article • F1000Research, June 2020, Faculty of 1000, Ltd.

    Dr Christophe Dessimoz, Yannis Nevers

  66. The phylogenetic range of bacterial and viral pathogens of vertebrates

    Article • Molecular Ecology, June 2020, Wiley

    Dr Christophe Dessimoz

  67. Corrigendum: OMA standalone: orthology inference among public and custom genomes and transcriptomes

    Article • Genome Research, June 2020, Cold Spring Harbor Laboratory Press

    Dr Christophe Dessimoz

  68. The Quest for Orthologs benchmark service and consensus calls in 2020

    Article • Nucleic Acids Research, May 2020, Oxford University Press (OUP)

    Dr Christophe Dessimoz

  69. Genomic Encryption of Digital Data Stored in Synthetic DNA

    Article • Angewandte Chemie, March 2020, Wiley

    Dr Christophe Dessimoz

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

    Article • Ecology and Evolution, February 2020, Wiley

    Dr Christophe Dessimoz

  71. Identifying orthologs with OMA: A primer

    Article • F1000Research, January 2020, Faculty of 1000, Ltd.

    Dr Christophe Dessimoz

  72. Scalable Phylogenetic Profiling using MinHash Uncovers Likely Eukaryotic Sexual Reproduction Genes

    Article • November 2019, Cold Spring Harbor Laboratory Press

    Dr Christophe Dessimoz

  73. Structural variant calling: the long and the short of it

    Article • November 2019, Springer Science + Business Media

    Fritz Sedlazeck, Ninon Mounier, Dr Christophe Dessimoz

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

    Article • November 2019, Springer Science + Business Media

    Dr Tunca Dogan, Professor Casey Greene, Dr Christophe Dessimoz

  75. Genomic encryption of digital data stored in synthetic DNA

    Article • November 2019, Cold Spring Harbor Laboratory Press

    Dr Christophe Dessimoz

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

    Article • F1000Research, October 2019, Faculty of 1000, Ltd.

    Dr Christophe Dessimoz

  77. Parallel and Scalable Precise Clustering for Homologous Protein Discovery

    Article • August 2019, Cold Spring Harbor Laboratory Press

    Dr Christophe Dessimoz

  78. Enabling Semantic Queries Across Federated Bioinformatics Databases

    Article • June 2019, Cold Spring Harbor Laboratory Press

    Dr Christophe Dessimoz

  79. Advances and Applications in the Quest for Orthologs

    Article • Molecular Biology and Evolution, June 2019, Oxford University Press (OUP)

    Dr. Yan Wang, Dr Christophe Dessimoz

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

    Article • Genome Research, June 2019, Cold Spring Harbor Laboratory Press

    Dr Christophe Dessimoz

  81. The phylogenetic range of bacterial and viral pathogens of vertebrates

    Article • June 2019, Cold Spring Harbor Laboratory Press

    Dr Christophe Dessimoz

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

    Article • Current Biology, June 2019, Elsevier

    Dr Christophe Dessimoz

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

    Article • May 2019, Cold Spring Harbor Laboratory Press

    Dr Tunca Dogan, Dr Christophe Dessimoz, Professor Casey Greene

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

    Article • F1000Research, March 2019, Faculty of 1000, Ltd.

    Dr Christophe Dessimoz

  85. Assigning confidence scores to homoeologs using fuzzy logic

    Article • PeerJ, January 2019, PeerJ

    Dr Christophe Dessimoz

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

    Article • F1000Research, January 2019, Faculty of 1000, Ltd.

    Dr Christophe Dessimoz

  87. Inferring Orthology and Paralogy

    Article • January 2019, Springer Science + Business Media

    Dr Christophe Dessimoz

  88. Enabling semantic queries across federated bioinformatics databases

    Article • Database, January 2019, Oxford University Press (OUP)

    Dr Christophe Dessimoz

  89. VoIDext: Vocabulary and Patterns for Enhancing Interoperable Datasets with Virtual Links

    Article • January 2019, Springer Science + Business Media

    Dr Christophe Dessimoz

  90. How Much Does GenoGuard Really "Guard"?

    Article • January 2019, ACM (Association for Computing Machinery)

    Dr Christophe Dessimoz

  91. iHam & pyHam: visualizing and processing hierarchical orthologous groups

    Article • Bioinformatics, December 2018, Oxford University Press (OUP)

    Dr Christophe Dessimoz

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

    Article • Bioinformatics, September 2018, Oxford University Press (OUP)

    Dr Christophe Dessimoz

  93. Prioritising candidate genes causing QTL using hierarchical orthologous groups

    Article • Bioinformatics, September 2018, Oxford University Press (OUP)

    Dr Christophe Dessimoz

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

    Article • August 2018, Cold Spring Harbor Laboratory Press

    Dr Christophe Dessimoz

  95. GOATOOLS: A Python library for Gene Ontology analyses

    Article • Scientific Reports, July 2018, Springer Science + Business Media

    Dr Christophe Dessimoz

  96. Submit a Topic Page to PLOS Computational Biology and Wikipedia

    Article • PLoS Computational Biology, May 2018, PLOS

    Dr Christophe Dessimoz

  97. RecPhyloXML - a format for reconciled gene trees

    Article • Bioinformatics, May 2018, Oxford University Press (OUP)

    Dr Christophe Dessimoz

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

    Article • Nucleic Acids Research, November 2017, Oxford University Press (OUP)

    Dr Christophe Dessimoz

  99. Allele-Specific HLA Loss and Immune Escape in Lung Cancer Evolution

    Article • Cell, October 2017, Elsevier

    Dr Christophe Dessimoz

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

    Article • Molecular Phylogenetics and Evolution, September 2017, Elsevier

    Dr Christophe Dessimoz

  101. Lessons Learned: Recommendations for Establishing Critical Periodic Scientific Benchmarking

    Article • August 2017, Cold Spring Harbor Laboratory Press

    Dr Christophe Dessimoz

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

    Article • August 2017, Cold Spring Harbor Laboratory Press

    Dr Christophe Dessimoz

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

    Article • August 2017, Cold Spring Harbor Laboratory Press

    Dr Christophe Dessimoz

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

    Article • Bioinformatics, July 2017, Oxford University Press (OUP)

    Dr Christophe Dessimoz

  105. Tracking the Evolution of Non–Small-Cell Lung Cancer

    Article • The New England Journal of Medicine and Surgery and the Collateral Branches of Science, June 2017, New England Journal of Medicine (NEJM/MMS)

    Dr Christophe Dessimoz

  106. Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution

    Article • Nature, April 2017, Nature

    Dr Christophe Dessimoz

  107. Comparative genomics reveals contraction in olfactory receptor genes in bats

    Article • Scientific Reports, March 2017, Nature

    Dr Christophe Dessimoz

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

    Article • Nature Communications, January 2017, Nature

    Fritz Sedlazeck, Dr Daniel C Jeffares, Dr Christophe Dessimoz, Professor Jurg Bahler

  109. The Gene Ontology Handbook

    Article • January 2017, Springer Science + Business Media

    Dr Christophe Dessimoz

  110. OUP accepted manuscript

    Article • Bioinformatics, January 2017, Oxford University Press (OUP)

    Dr Christophe Dessimoz, Dr. Jose F Parodi

  111. A Gene Ontology Tutorial in Python

    Article • November 2016, Springer Science + Business Media

    Dr Christophe Dessimoz

  112. Gene Ontology: Pitfalls, Biases, and Remedies

    Article • November 2016, Springer Science + Business Media

    Dr Christophe Dessimoz

  113. Primer on the Gene Ontology

    Article • November 2016, Springer Science + Business Media

    Dr Christophe Dessimoz

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

    Article • September 2016, Springer Science + Business Media

    Professor Casey Greene, Dr Christophe Dessimoz, Dr Tunca Dogan, Professor Giorgio Valentini

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

    Article • Molecular Biology and Evolution, August 2016, Oxford University Press (OUP)

    Dr Christophe Dessimoz

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

    Article • Trends in Plant Science, July 2016, Elsevier

    Dr Christophe Dessimoz

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

    Article • Molecular Biology and Evolution, April 2016, Oxford University Press (OUP)

    Dr Christophe Dessimoz

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

    Article • April 2016, Cold Spring Harbor Laboratory Press

    Dr Daniel C Jeffares, Dr Christophe Dessimoz, Fritz Sedlazeck

  119. Standardized benchmarking in the quest for orthologs

    Article • Nature Chemical Biology, April 2016, Nature

    Dr Christophe Dessimoz

  120. Compensation of Dosage-Sensitive Genes on the Chicken Z Chromosome

    Article • Genome Biology and Evolution, April 2016, Oxford University Press (OUP)

    Dr Christophe Dessimoz

  121. Clustering Genes of Common Evolutionary History

    Article • Molecular Biology and Evolution, February 2016, Oxford University Press (OUP)

    Dr Christophe Dessimoz

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

    Article • Systematic Biology, June 2015, Oxford University Press (OUP)

    Dr Christophe Dessimoz

  123. Inferring Horizontal Gene Transfer

    Article • PLoS Computational Biology, May 2015, PLOS

    Dr Christophe Dessimoz

  124. A Transcriptomic-Phylogenomic Analysis of the Evolutionary Relationships of Flatworms

    Article • Current Biology, May 2015, Elsevier

    Dr Christophe Dessimoz

  125. Phylogenetic Profiling: How Much Input Data Is Enough?

    Article • PLOS One, February 2015, PLOS

    Dr Christophe Dessimoz

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

    Article • Proceedings of the National Academy of Sciences, January 2015, Proceedings of the National Academy of Sciences

    Dr Christophe Dessimoz

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

    Article • Nature Biotechnology, November 2014, Springer Science + Business Media

    Dr Christophe Dessimoz

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

    Article • Nucleic Acids Research, November 2014, Oxford University Press (OUP)

    Dr Christophe Dessimoz

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

    Article • PeerJ, October 2014, PeerJ

    Dr Christophe Dessimoz

  130. Big data and other challenges in the quest for orthologs

    Article • Bioinformatics, July 2014, Oxford University Press (OUP)

    Dr Christophe Dessimoz

  131. Preface of Proceedings of GNOME 2014 — Festschrift for Gaston Gonnet

    Article • June 2014, PeerJ

    Dr Christophe Dessimoz

  132. CAFA and the Open World of protein function predictions

    Article • Trends in Genetics, November 2013, Elsevier

    Dr Christophe Dessimoz

  133. Bidirectional Best Hits Miss Many Orthologs in Duplication-Rich Clades such as Plants and Animals

    Article • Genome Biology and Evolution, September 2013, Oxford University Press (OUP)

    Dr Christophe Dessimoz

  134. Who Watches the Watchmen? An Appraisal of Benchmarks for Multiple Sequence Alignment

    Article • August 2013, Springer Science + Business Media

    Dr Christophe Dessimoz

  135. The Impact of Gene Duplication, Insertion, Deletion, Lateral Gene Transfer and Sequencing Error on Orthology Inference: A Simulation Study

    Article • PLOS One, February 2013, PLOS

    Dr Christophe Dessimoz

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

    Article • Nature, January 2013, Nature

    Dr Christophe Dessimoz

  137. Inferring Hierarchical Orthologous Groups from Orthologous Gene Pairs

    Article • PLOS One, January 2013, PLOS

    Dr Christophe Dessimoz

  138. Approximate Bayesian Computation

    Article • PLoS Computational Biology, January 2013, PLOS

    Dr Christophe Dessimoz

  139. Global regulatory architecture of human, mouse and rat tissue transcriptomes

    Article • BMC Genomics, January 2013, Springer Science + Business Media

    Dr Christophe Dessimoz

  140. Quality of Computationally Inferred Gene Ontology Annotations

    Article • PLoS Computational Biology, May 2012, PLOS

    Dr Christophe Dessimoz

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

    Article • PLoS Computational Biology, May 2012, PLOS

    Romain A Studer, Dr Christophe Dessimoz

  142. Toward community standards in the quest for orthologs

    Article • Bioinformatics, February 2012, Oxford University Press (OUP)

    Dr Christophe Dessimoz

  143. Inferring Orthology and Paralogy

    Article • January 2012, Springer Science + Business Media

    Dr Christophe Dessimoz

  144. ALF--A Simulation Framework for Genome Evolution

    Article • Molecular Biology and Evolution, December 2011, Oxford University Press (OUP)

    Dr Christophe Dessimoz

  145. Editorial: Orthology and applications

    Article • Briefings in Bioinformatics, September 2011, Oxford University Press (OUP)

    Dr Christophe Dessimoz

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

    Article • Briefings in Bioinformatics, July 2011, Oxford University Press (OUP)

    Dr Christophe Dessimoz

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

    Article • Briefings in Bioinformatics, June 2011, Oxford University Press (OUP)

    Dr Christophe Dessimoz

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

    Article • The Plant Journal, May 2011, Wiley

    Dr Christophe Dessimoz

  149. Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes

    Article • Systematic Biology, May 2011, Oxford University Press (OUP)

    Dr Christophe Dessimoz

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

    Article • Briefings in Bioinformatics, February 2011, Oxford University Press (OUP)

    Dr Christophe Dessimoz

  151. Base-calling for next-generation sequencing platforms

    Article • Briefings in Bioinformatics, January 2011, Oxford University Press (OUP)

    Dr Christophe Dessimoz

  152. OMA 2011: orthology inference among 1000 complete genomes

    Article • Nucleic Acids Research, November 2010, Oxford University Press (OUP)

    Dr Christophe Dessimoz

  153. Phylogenetic assessment of alignments reveals neglected tree signal in gaps

    Article • Genome Biology, January 2010, Springer Science + Business Media

    Dr Christophe Dessimoz

  154. The Microbe browser for comparative genomics

    Article • Nucleic Acids Research, April 2009, Oxford University Press (OUP)

    Dr Christophe Dessimoz

  155. Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods

    Article • PLoS Computational Biology, January 2009, PLOS

    Jonathan Eisen, Dr Christophe Dessimoz

  156. Algorithm of OMA for large-scale orthology inference

    Article • BMC Bioinformatics, January 2009, Springer Science + Business Media

    Dr Christophe Dessimoz

  157. Joining forces in the quest for orthologs

    Article • Genome Biology, January 2009, Springer Science + Business Media

    Dr Christophe Dessimoz

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

    Article • Philosophical Transactions of the Royal Society B Biological Sciences, December 2008, Royal Society Publishing

    Dr Christophe Dessimoz

  159. Algorithm of OMA for large-scale orthology inference

    Article • BMC Bioinformatics, January 2008, Springer Science + Business Media

    Dr Christophe Dessimoz

  160. Covariance of maximum likelihood evolutionary distances between sequences aligned pairwise

    Article • BMC Evolutionary Biology, January 2008, Springer Science + Business Media

    Dr Christophe Dessimoz

  161. SWPS3 – fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and ×86/SSE2

    Article • BMC Research Notes, January 2008, Springer Science + Business Media

    Dr Christophe Dessimoz

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

    Article • Journal of Combinatorial Optimization, December 2007, Springer Science + Business Media

    Dr Christophe Dessimoz

  163. OMA Browser Exploring orthologous relations across 352 complete genomes

    Article • Bioinformatics, June 2007, Oxford University Press (OUP)

    Dr Christophe Dessimoz

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

    Article • Nucleic Acids Research, June 2006, Oxford University Press (OUP)

    Dr Christophe Dessimoz

  165. Article • BMC Bioinformatics, January 2006, Springer Science + Business Media

    Dr Christophe Dessimoz

  166. A DIMENSIONLESS FIT MEASURE FOR PHYLOGENETIC DISTANCE TREES

    Article • Journal of Bioinformatics and Computational Biology, December 2005, World Scientific Pub Co Pte Lt

    Dr Christophe Dessimoz

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

    Article • January 2005, Springer Science + Business Media

    Dr Christophe Dessimoz, Gina Cannarozzi

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

    Article • Springer Science + Business Media

    Dr Christophe Dessimoz

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