All Stories

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

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

    Dr Christophe Dessimoz

  2. Parallel and Scalable Precise Clustering

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

    Dr Christophe Dessimoz, James Larus

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

    Article • PLoS Computational Biology, July 2020, PLOS

    Dr Christophe Dessimoz, David Moi

  4. How to build phylogenetic species trees with OMA

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

    Dr Christophe Dessimoz, Yannis Nevers

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

    Article • Ecology and Evolution, February 2020, Wiley

    Dr Christophe Dessimoz

  6. Identifying orthologs with OMA: A primer

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

    Dr Christophe Dessimoz

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

    Article • November 2019, Cold Spring Harbor Laboratory Press

    Dr Christophe Dessimoz

  8. Genomic encryption of digital data stored in synthetic DNA

    Article • November 2019, Cold Spring Harbor Laboratory Press

    Dr Christophe Dessimoz

  9. 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

  10. Parallel and Scalable Precise Clustering for Homologous Protein Discovery

    Article • August 2019, Cold Spring Harbor Laboratory Press

    Dr Christophe Dessimoz

  11. Enabling Semantic Queries Across Federated Bioinformatics Databases

    Article • June 2019, Cold Spring Harbor Laboratory Press

    Dr Christophe Dessimoz

  12. 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

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

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

    Dr Christophe Dessimoz

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

    Article • June 2019, Cold Spring Harbor Laboratory Press

    Dr Christophe Dessimoz

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

    Article • Current Biology, June 2019, Elsevier

    Dr Christophe Dessimoz

  16. 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

  17. 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

  18. Assigning confidence scores to homoeologs using fuzzy logic

    Article • PeerJ, January 2019, PeerJ

    Dr Christophe Dessimoz

  19. 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

  20. Inferring Orthology and Paralogy

    Article • January 2019, Springer Science + Business Media

    Dr Christophe Dessimoz

  21. Enabling semantic queries across federated bioinformatics databases

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

    Dr Christophe Dessimoz

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

    Article • January 2019, Springer Science + Business Media

    Dr Christophe Dessimoz

  23. How Much Does GenoGuard Really "Guard"?

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

    Dr Christophe Dessimoz

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

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

    Dr Christophe Dessimoz

  25. 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

  26. Prioritising candidate genes causing QTL using hierarchical orthologous groups

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

    Dr Christophe Dessimoz

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

    Article • August 2018, Cold Spring Harbor Laboratory Press

    Dr Christophe Dessimoz

  28. GOATOOLS: A Python library for Gene Ontology analyses

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

    Dr Christophe Dessimoz

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

    Article • PLoS Computational Biology, May 2018, PLOS

    Dr Christophe Dessimoz

  30. RecPhyloXML - a format for reconciled gene trees

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

    Dr Christophe Dessimoz

  31. 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

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

    Article • Cell, October 2017, Elsevier

    Dr Christophe Dessimoz

  33. 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

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

    Article • August 2017, Cold Spring Harbor Laboratory Press

    Dr Christophe Dessimoz

  35. 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

  36. 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

  37. 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

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

    Article • New England Journal of Medicine, June 2017, New England Journal of Medicine (NEJM/MMS)

    Dr Christophe Dessimoz

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

    Article • Nature, April 2017, Nature

    Dr Christophe Dessimoz

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

    Article • Scientific Reports, March 2017, Nature

    Dr Christophe Dessimoz

  41. 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

  42. The Gene Ontology Handbook

    Article • January 2017, Springer Science + Business Media

    Dr Christophe Dessimoz

  43. OUP accepted manuscript

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

    Dr Christophe Dessimoz, Dr. Jose F Parodi

  44. A Gene Ontology Tutorial in Python

    Article • November 2016, Springer Science + Business Media

    Dr Christophe Dessimoz

  45. Gene Ontology: Pitfalls, Biases, and Remedies

    Article • November 2016, Springer Science + Business Media

    Dr Christophe Dessimoz

  46. Primer on the Gene Ontology

    Article • November 2016, Springer Science + Business Media

    Dr Christophe Dessimoz

  47. 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

  48. 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

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

    Article • Trends in Plant Science, July 2016, Elsevier

    Dr Christophe Dessimoz

  50. 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

  51. 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

  52. Standardized benchmarking in the quest for orthologs

    Article • Nature Methods, April 2016, Nature

    Dr Christophe Dessimoz

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

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

    Dr Christophe Dessimoz

  54. Clustering Genes of Common Evolutionary History

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

    Dr Christophe Dessimoz

  55. 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

  56. Inferring Horizontal Gene Transfer

    Article • PLoS Computational Biology, May 2015, PLOS

    Dr Christophe Dessimoz

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

    Article • Current Biology, May 2015, Elsevier

    Dr Christophe Dessimoz

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

    Article • PLoS ONE, February 2015, PLOS

    Dr Christophe Dessimoz

  59. 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

  60. 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

  61. 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

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

    Article • PeerJ, October 2014, PeerJ

    Dr Christophe Dessimoz

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

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

    Dr Christophe Dessimoz

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

    Article • June 2014, PeerJ

    Dr Christophe Dessimoz

  65. CAFA and the Open World of protein function predictions

    Article • Trends in Genetics, November 2013, Elsevier

    Dr Christophe Dessimoz

  66. 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

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

    Article • August 2013, Springer Science + Business Media

    Dr Christophe Dessimoz

  68. 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

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

    Article • Nature, January 2013, Nature

    Dr Christophe Dessimoz

  70. Inferring Hierarchical Orthologous Groups from Orthologous Gene Pairs

    Article • PLoS ONE, January 2013, PLOS

    Dr Christophe Dessimoz

  71. Approximate Bayesian Computation

    Article • PLoS Computational Biology, January 2013, PLOS

    Dr Christophe Dessimoz

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

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

    Dr Christophe Dessimoz

  73. Quality of Computationally Inferred Gene Ontology Annotations

    Article • PLoS Computational Biology, May 2012, PLOS

    Dr Christophe Dessimoz

  74. 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

  75. Toward community standards in the quest for orthologs

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

    Dr Christophe Dessimoz

  76. Inferring Orthology and Paralogy

    Article • January 2012, Springer Science + Business Media

    Dr Christophe Dessimoz

  77. ALF--A Simulation Framework for Genome Evolution

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

    Dr Christophe Dessimoz

  78. Editorial: Orthology and applications

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

    Dr Christophe Dessimoz

  79. 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

  80. 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

  81. 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

  82. 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

  83. 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

  84. Base-calling for next-generation sequencing platforms

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

    Dr Christophe Dessimoz

  85. OMA 2011: orthology inference among 1000 complete genomes

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

    Dr Christophe Dessimoz

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

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

    Dr Christophe Dessimoz

  87. The Microbe browser for comparative genomics

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

    Dr Christophe Dessimoz

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

    Article • PLoS Computational Biology, January 2009, PLOS

    Jonathan Eisen, Dr Christophe Dessimoz

  89. Algorithm of OMA for large-scale orthology inference

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

    Dr Christophe Dessimoz

  90. Joining forces in the quest for orthologs

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

    Dr Christophe Dessimoz

  91. 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

  92. Algorithm of OMA for large-scale orthology inference

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

    Dr Christophe Dessimoz

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

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

    Dr Christophe Dessimoz

  94. 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

  95. 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

  96. OMA Browser Exploring orthologous relations across 352 complete genomes

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

    Dr Christophe Dessimoz

  97. 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

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

    Dr Christophe Dessimoz

  99. 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

  100. 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

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

    Article • Springer Science + Business Media

    Dr Christophe Dessimoz

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

    Article • Springer Science + Business Media

    Dr Christophe Dessimoz