Defining the Environmental Adaptations of Genus Devosia: Insights into its Expansive Short Peptide Transport System and Positively Selected Genes

C Talwar, S Nagar, R Kumar, J Scaria, R Lal… - Scientific reports, 2020 - nature.com
Devosia are well known for their dominance in soil habitats contaminated with various toxins
and are best characterized for their bioremediation potential. In this study, we compared the …

[PDF][PDF] Collaboro: a collaborative (meta) modeling tool

JLC Izquierdo, J Cabot - PeerJ Computer Science, 2016 - peerj.com
Motivation Scientists increasingly rely on intelligent information systems to help them in their
daily tasks, in particular for managing research objects, like publications or datasets. The …

Molecular adaptation in the world's deepest‐living animal: Insights from transcriptome sequencing of the hadal amphipod Hirondellea gigas

Y Lan, J Sun, R Tian, DH Bartlett, R Li… - Molecular …, 2017 - Wiley Online Library
Abstract The Challenger Deep in the Mariana Trench is the deepest point in the oceans of
our planet. Understanding how animals adapt to this harsh environment characterized by …

FREEDA: An automated computational pipeline guides experimental testing of protein innovation

D Dudka, RB Akins, MA Lampson - Journal of Cell Biology, 2023 - rupress.org
Cell biologists typically focus on conserved regions of a protein, overlooking innovations that
can shape its function over evolutionary time. Computational analyses can reveal potential …

Human follicular mites: Ectoparasites becoming symbionts

G Smith, A Manzano-Marín… - Molecular Biology …, 2022 - academic.oup.com
Most humans carry mites in the hair follicles of their skin for their entire lives. Follicular mites
are the only metazoans that continuously live on humans. We propose that Demodex …

Monkeypox virus: phylogenomics, host–pathogen interactome and mutational cascade

R Kumar, S Nagar, S Haider, U Sood… - Microbial …, 2023 - microbiologyresearch.org
While the world is still recovering from the Covid-19 pandemic, monkeypox virus (MPXV)
awaits to cause another global outbreak as a challenge to all of mankind. However, the …

PosiGene: automated and easy-to-use pipeline for genome-wide detection of positively selected genes

A Sahm, M Bens, M Platzer… - Nucleic Acids …, 2017 - academic.oup.com
Many comparative genomics studies aim to find the genetic basis of species-specific
phenotypic traits. A prevailing strategy is to search genome-wide for genes that evolved …

The 4-Celled Tetrabaena socialis Nuclear Genome Reveals the Essential Components for Genetic Control of Cell Number at the Origin of Multicellularity in the …

J Featherston, Y Arakaki, ER Hanschen… - Molecular Biology …, 2018 - academic.oup.com
Multicellularity is the premier example of a major evolutionary transition in individuality and
was a foundational event in the evolution of macroscopic biodiversity. The volvocine …

The diversity and distribution of D1 proteins in cyanobacteria

KJ Sheridan, EJ Duncan, JJ Eaton-Rye… - Photosynthesis …, 2020 - Springer
The psbA gene family in cyanobacteria encodes different forms of the D1 protein that is part
of the Photosystem II reaction centre. We have identified a phylogenetically distinct D1 group …

plotnineSeqSuite: a Python package for visualizing sequence data using ggplot2 style

T Cao, Q Li, Y Huang, A Li - BMC genomics, 2023 - Springer
Background The visual sequence logo has been a hot area in the development of
bioinformatics tools. ggseqlogo written in R language has been the most popular API since it …