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Inferring Orthologs: Open Questions and Perspectives

author

Fredj Tekaia

published in: Genomics insights

date of publication: 2016

language: English

Cites articles 133

Date

Title

Authors

2015

OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy

David Emms, Steven Kelly
2015-05

Inferring horizontal gene transfer

Christophe Dessimoz, Matt Ravenhall, Florent Lassalle
2015

Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes

Malcolm Perry, Alastair Crisp, Gos Micklem
2015-05-13

Domain similarity based orthology detection

Erich Bornberg-Bauer, Tristan Bitard-Feildel, Carsten Kemena
2015-04-14

A new method to scan genomes for introgression in a secondary contact model

Anthony J. Geneva, Daniel Garrigan
2015-01-30

Macrotene chromosomes provide insights to a new mechanism of high-order gene amplification in eukaryotes

Ingrid Lafontaine
2014-06

Phenotypic comparisons of consensus variants versus laboratory resurrections of Precambrian proteins

José A. Gavira, Jose Manuel Sanchez Ruiz
2014-12-15

Interspecific introgressive origin of genomic diversity in the house mouse

Luay Nakhleh
2014-11-04

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

Sofia K. Forslund, Peer Bork, Christian von Mering, Sean T Powell, Tobias Doerks, Kalliopi Trachana
2014-05-18

Improvement of domain-level ortholog clustering by optimizing domain-specific sum-of-pairs score

Hirokazu Chiba, Ikuo Uchiyama
2014-01-30

Global patterns of protein domain gain and loss in superkingdoms

Arshan Nasir, Gustavo Caetano-Anollés
2013-12-31

Reconstructed ancestral Myo-inositol-3-phosphate synthases indicate that ancestors of the Thermococcales and Thermotoga species were more thermophilic than their descendants

Nicholas C Butzin, Anna G Green, Johann Peter Gogarten
2013-02-25

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

Christophe Dessimoz, Adrian M Altenhoff
2013-04-04

Functional and evolutionary implications of gene orthology.

Toni Gabaldón, Eugene Koonin
2012-08-29

Evolutionary implications of horizontal gene transfer
2012-01-01

Evolution of protein domain architectures

Sofia K. Forslund, Erik Sonnhammer
2011-10

Orthology prediction methods: a quality assessment using curated protein families

Peer Bork, Tobias Doerks, Sean T Powell, Jean Muller
2011-01

IsoBase: a database of functionally related proteins across PPI networks

Michael Baym, Bonnie Berger
2011-12-15

Horizontal gene transfer in fungi

David A Fitzpatrick
2011-10-20

SuperPartitions: detection and classification of orthologs

Fredj Tekaia
2011-10-19

The dynamics and evolutionary potential of domain loss and emergence

Erich Bornberg-Bauer
2011-08-05

Domain architecture conservation in orthologs

Sofia K. Forslund, Erik Sonnhammer
2011-06-28

Ortholog identification in the presence of domain architecture rearrangement

Kimmen Sjölander
2011-06-19

Computational methods for Gene Orthology inference

Eugene Koonin, Yuri Wolf, Arcady Mushegian, David Møbjerg Kristensen
2011-04-13

Evaluating ortholog prediction algorithms in a yeast model clade

Antonis Rokas
2011-03-31

A comprehensive benchmark study of multiple sequence alignment methods: current challenges and future perspectives

Odile Lecompte
2011-03-10

Amplification of a Zygosaccharomyces bailii DNA segment in wine yeast genomes by extrachromosomal circular DNA formation

Frédéric Bigey, Jean-Luc Legras, Maite Novo
2011-03-07

Model organisms for genetics in the domain Archaea: methanogens, halophiles, Thermococcales and Sulfolobales

Sonja-Verena Albers
2011-01-10

OrthoInspector: comprehensive orthology analysis and visual exploration

Odile Lecompte
2011-01-01

Consistency properties of species tree inference by minimizing deep coalescences.

Noah Rosenberg
2011-02-01

Human genome 10th anniversary. Tracing the tree of life

Elizabeth Pennisi
2010-04-30

Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution

Eugene Koonin, Michael Y. Galperin, Yuri Wolf, Marina V Omelchenko

Article - wd:Q26766407

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