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GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes

Tomáš Brůna
Alexandre Lomsadze
Mark Borodovsky

First Published June 12, 2024

BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA

Lars Gabriel
Tomáš Brůna
Katharina J. Hoff
Matthis Ebel
Alexandre Lomsadze
Mark Borodovsky
Mario Stanke

First Published June 12, 2024

Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes

Alexandre Lomsadze
Karl Gemayel
Shiyuyun Tang
Mark Borodovsky

First Published May 17, 2018

Complex selection on 5′ splice sites in intron-rich organisms

Manuel Irimia
Scott William Roy
Daniel E. Neafsey
Josep F. Abril
Jordi Garcia-Fernandez
Eugene V. Koonin

First Published September 10, 2009

Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training

Vardges Ter-Hovhannisyan
Alexandre Lomsadze
Yury O. Chernoff
Mark Borodovsky

First Published August 29, 2008

Evolution of protein domain promiscuity in eukaryotes

Malay Kumar Basu
Liran Carmel
Igor B. Rogozin
Eugene V. Koonin

First Published January 29, 2008

Three distinct modes of intron dynamics in the evolution of eukaryotes

Liran Carmel
Yuri I. Wolf
Igor B. Rogozin
Eugene V. Koonin

First Published May 10, 2007

Evolutionarily conserved genes preferentially accumulate introns

Liran Carmel
Igor B. Rogozin
Yuri I. Wolf
Eugene V. Koonin

First Published May 10, 2007

Origins and impact of constraints in evolution of gene families

Boris E. Shakhnovich
Eugene V. Koonin

First Published October 19, 2006

Coelomata and Not Ecdysozoa: Evidence From Genome-Wide Phylogenetic Analysis

Yuri I. Wolf
Igor B. Rogozin
Eugene V. Koonin

First Published January 5, 2004

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