ROS generated from biotic stress: Effects on plants and alleviation by endophytic microbes

PK Sahu, K Jayalakshmi, J Tilgam, A Gupta… - Frontiers in Plant …, 2022 - frontiersin.org
Aerobic living is thought to generate reactive oxygen species (ROS), which are an inevitable
chemical component. They are produced exclusively in cellular compartments in aerobic …

Using machine learning approaches for multi-omics data analysis: A review

PS Reel, S Reel, E Pearson, E Trucco… - Biotechnology advances, 2021 - Elsevier
With the development of modern high-throughput omic measurement platforms, it has
become essential for biomedical studies to undertake an integrative (combined) approach to …

CheckV assesses the quality and completeness of metagenome-assembled viral genomes

S Nayfach, AP Camargo, F Schulz… - Nature …, 2021 - nature.com
Millions of new viral sequences have been identified from metagenomes, but the quality and
completeness of these sequences vary considerably. Here we present CheckV, an …

A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range

Q Lian, B Huettel, B Walkemeier, B Mayjonade… - Nature …, 2024 - nature.com
Although originally primarily a system for functional biology, Arabidopsis thaliana has, owing
to its broad geographical distribution and adaptation to diverse environments, developed …

The Pfam protein families database: towards a more sustainable future

RD Finn, P Coggill, RY Eberhardt, SR Eddy… - Nucleic acids …, 2016 - academic.oup.com
In the last two years the Pfam database (http://pfam. xfam. org) has undergone a substantial
reorganisation to reduce the effort involved in making a release, thereby permitting more …

Comparative genomics of the major parasitic worms

Nature genetics, 2019 - nature.com
Parasitic nematodes (roundworms) and platyhelminths (flatworms) cause debilitating
chronic infections of humans and animals, decimate crop production and are a major …

A census of human RNA-binding proteins

S Gerstberger, M Hafner, T Tuschl - Nature Reviews Genetics, 2014 - nature.com
Post-transcriptional gene regulation (PTGR) concerns processes involved in the maturation,
transport, stability and translation of coding and non-coding RNAs. RNA-binding proteins …

Determination and inference of eukaryotic transcription factor sequence specificity

MT Weirauch, A Yang, M Albu, AG Cote… - Cell, 2014 - cell.com
Transcription factor (TF) DNA sequence preferences direct their regulatory activity, but are
currently known for only∼ 1% of eukaryotic TFs. Broadly sampling DNA-binding domain …

A reference genome for common bean and genome-wide analysis of dual domestications

J Schmutz, PE McClean, S Mamidi, GA Wu… - Nature …, 2014 - nature.com
Common bean (Phaseolus vulgaris L.) is the most important grain legume for human
consumption and has a role in sustainable agriculture owing to its ability to fix atmospheric …

Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal

J Gao, BA Aksoy, U Dogrusoz, G Dresdner, B Gross… - Science …, 2013 - science.org
The cBioPortal for Cancer Genomics (http://cbioportal. org) provides a Web resource for
exploring, visualizing, and analyzing multidimensional cancer genomics data. The portal …