The role of conformational dynamics and allostery in modulating protein evolution

P Campitelli, T Modi, S Kumar… - Annual review of …, 2020 - annualreviews.org
Advances in sequencing techniques and statistical methods have made it possible not only
to predict sequences of ancestral proteins but also to identify thousands of mutations in the …

Earth BioGenome Project: Sequencing life for the future of life

HA Lewin, GE Robinson, WJ Kress… - Proceedings of the …, 2018 - National Acad Sciences
Increasing our understanding of Earth's biodiversity and responsibly stewarding its
resources are among the most crucial scientific and social challenges of the new …

Phylogenomics and the genetic architecture of the placental mammal radiation

WJ Murphy, NM Foley, KR Bredemeyer… - Annual Review of …, 2021 - annualreviews.org
The genomes of placental mammals are being sequenced at an unprecedented rate.
Alignments of hundreds, and one day thousands, of genomes spanning the rich living and …

Whole-genome sequencing of the snub-nosed monkey provides insights into folivory and evolutionary history

X Zhou, B Wang, Q Pan, J Zhang, S Kumar, X Sun… - Nature …, 2014 - nature.com
Colobines are a unique group of Old World monkeys that principally eat leaves and seeds
rather than fruits and insects. We report the sequencing at 146× coverage, de novo …

Next generation exome sequencing of paediatric inflammatory bowel disease patients identifies rare and novel variants in candidate genes

K Christodoulou, AE Wiskin, J Gibson, W Tapper… - Gut, 2013 - gut.bmj.com
Background Multiple genes have been implicated by association studies in altering
inflammatory bowel disease (IBD) predisposition. Paediatric patients often manifest more …

Evolutionary informatics: unifying knowledge about the diversity of life

CS Parr, R Guralnick, N Cellinese… - Trends in ecology & …, 2012 - cell.com
The accelerating growth of data and knowledge in evolutionary biology is indisputable.
Despite this rapid progress, information remains scattered, poorly documented and in …

DFNB16 is a frequent cause of congenital hearing impairment: implementation of STRC mutation analysis in routine diagnostics

B Vona, MAH Hofrichter, C Neuner, J Schröder… - Clinical …, 2015 - Wiley Online Library
Increasing attention has been directed toward assessing mutational fallout of stereocilin
(STRC), the gene underlying DFNB16. A major challenge is due to a closely linked …

Structural dynamics flexibility informs function and evolution at a proteome scale

ZN Gerek, S Kumar, SB Ozkan - Biophysical Journal, 2013 - cell.com
Protein structures are dynamic entities with a myriad of atomic fluctuations, side chain
rotations, and collective domain movements. While the importance of these dynamics to …

Dynamic coupling of residues within proteins as a mechanistic foundation of many enigmatic pathogenic missense variants

NJ Ose, BM Butler, A Kumar, IC Kazan… - PLoS computational …, 2022 - journals.plos.org
Many pathogenic missense mutations are found in protein positions that are neither well-
conserved nor fall in any known functional domains. Consequently, we lack any mechanistic …

A gene gravity model for the evolution of cancer genomes: a study of 3,000 cancer genomes across 9 cancer types

F Cheng, C Liu, CC Lin, J Zhao, P Jia… - PLoS computational …, 2015 - journals.plos.org
Cancer development and progression result from somatic evolution by an accumulation of
genomic alterations. The effects of those alterations on the fitness of somatic cells lead to …