A reference genome for pea provides insight into legume genome evolution

J Kreplak, MA Madoui, P Cápal, P Novák, K Labadie… - Nature …, 2019 - nature.com
We report the first annotated chromosome-level reference genome assembly for pea, Gregor
Mendel's original genetic model. Phylogenetics and paleogenomics show genomic …

expVIP: a customizable RNA-seq data analysis and visualization platform

P Borrill, R Ramirez-Gonzalez, C Uauy - Plant physiology, 2016 - academic.oup.com
The majority of transcriptome sequencing (RNA-seq) expression studies in plants remain
underutilized and inaccessible due to the use of disparate transcriptome references and the …

Sequenceserver: a modern graphical user interface for custom BLAST databases

A Priyam, BJ Woodcroft, V Rai, I Moghul… - Molecular biology …, 2019 - academic.oup.com
Comparing newly obtained and previously known nucleotide and amino-acid sequences
underpins modern biological research. BLAST is a well-established tool for such …

The long intergenic noncoding RNA landscape of human lymphocytes highlights the regulation of T cell differentiation by linc-MAF-4

V Ranzani, G Rossetti, I Panzeri, A Arrigoni… - Nature …, 2015 - nature.com
Long noncoding RNAs are emerging as important regulators of cellular functions, but little is
known of their role in the human immune system. Here we investigated long intergenic …

PolyMarker: a fast polyploid primer design pipeline

RH Ramirez-Gonzalez, C Uauy, M Caccamo - Bioinformatics, 2015 - academic.oup.com
The design of genetic markers is of particular relevance in crop breeding programs. Despite
many economically important crops being polyploid organisms, the current primer design …

Discovery of a novel methanogen prevalent in thawing permafrost

R Mondav, BJ Woodcroft, EH Kim, CK McCalley… - Nature …, 2014 - nature.com
Thawing permafrost promotes microbial degradation of cryo-sequestered and new carbon
leading to the biogenic production of methane, creating a positive feedback to climate …

Tools and data services registry: a community effort to document bioinformatics resources

J Ison, K Rapacki, H Ménager, M Kalaš… - Nucleic acids …, 2016 - academic.oup.com
Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to
improvement in human health, agriculture and the environment. In support of these …

Ten simple rules for the open development of scientific software

A Prlić, JB Procter - PLoS Computational Biology, 2012 - journals.plos.org
Open-source software development has had significant impact, not only on society, but also
on scientific research. Papers describing software published as open source are amongst …

bio-samtools 2: a package for analysis and visualization of sequence and alignment data with SAMtools in Ruby

GJ Etherington, RH Ramirez-Gonzalez… - …, 2015 - academic.oup.com
Motivation: bio-samtools is a Ruby language interface to SAMtools, the highly popular library
that provides utilities for manipulating high-throughput sequence alignments in the …

An in-silico study of the mutation-associated effects on the spike protein of SARS-CoV-2, Omicron variant

TA Shishir, T Jannat, IB Naser - PLoS One, 2022 - journals.plos.org
The emergence of Omicron (B. 1.1. 529), a new Variant of Concern in the COVID-19
pandemic, while accompanied by the ongoing Delta variant infection, has once again fueled …