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De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data

Arthur Dondi
Nico Borgsmüller
Pedro F. Ferreira
Brian J. Haas
Francis Jacob
Viola Heinzelmann-Schwarz
Niko Beerenwinkel

First Published March 19, 2025

Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution

Qian Qin
Victoria Popic
Kirsty Wienand
Houlin Yu
Emily White
Akanksha Khorgade Asa Shin Christophe Georgescu Catarina D. Campbell Arthur Dondi
... [+5 authors] ...,
Niko Beerenwinkel
Francisca Vazquez
Aziz M. Al'Khafaji
Brian J. Haas

First Published March 14, 2025

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

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

Gene Loss, Protein Sequence Divergence, Gene Dispensability, Expression Level, and Interactivity Are Correlated in Eukaryotic Evolution

Dmitri M. Krylov
Yuri I. Wolf
Igor B. Rogozin
Eugene V. Koonin

First Published October 2, 2003

The Role of Lineage-Specific Gene Family Expansion in the Evolution of Eukaryotes

Olivier Lespinet
Yuri I. Wolf
Eugene V. Koonin
L. Aravind

First Published July 1, 2002

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