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Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding

Liangxi Wang
Tiegh Taylor
Kumaragurubaran Rathnakumar
Nadiya Khyzha
Minggao Liang
Azad Alizada Laura F. Campitelli Sara E. Pour Zain M. Patel Lina Antounians Ian C. Tobias Huayun Hou Timothy R. Hughes
... [+8 authors] ...,
Sushmita Roy
Jennifer A. Mitchell
Jason E. Fish
Michael D. Wilson

First Published June 6, 2025

A flexible repertoire of transcription factor binding sites and a diversity threshold determines enhancer activity in embryonic stem cells

Gurdeep Singh
Shanelle Mullany
Sakthi D. Moorthy
Richard Zhang
Tahmid Mehdi
Ruxiao Tian
Andrew G. Duncan
Alan M. Moses
Jennifer A. Mitchell

First Published March 12, 2021

Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes

Sakthi D. Moorthy
Scott Davidson
Virlana M. Shchuka
Gurdeep Singh
Nakisa Malek-Gilani
Lida Langroudi
... [+1 authors] ...,
Alexandre Martchenko
Vincent So
Neil N. Macpherson
Jennifer A. Mitchell

First Published November 28, 2016

The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements

Stefan Schoenfelder
Mayra Furlan-Magaril
Borbala Mifsud
Filipe Tavares-Cadete
Robert Sugar
Biola-Maria Javierre Takashi Nagano Yulia Katsman Moorthy Sakthidevi Steven W. Wingett Emilia Dimitrova Andrew Dimond Lucas B. Edelman Sarah Elderkin Kristina Tabbada Elodie Darbo Simon Andrews Bram Herman Andy Higgs Emily LeProust
... [+15 authors] ...,
Cameron S. Osborne
Jennifer A. Mitchell
Nicholas M. Luscombe
Peter Fraser

First Published March 9, 2015

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

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