Scaling accurate genetic variant discovery to tens of thousands of samples

R Poplin, V Ruano-Rubio, MA DePristo, TJ Fennell… - BioRxiv, 2017 - biorxiv.org
Comprehensive disease gene discovery in both common and rare diseases will require the
efficient and accurate detection of all classes of genetic variation across tens to hundreds of …

Alignment-free inference of hierarchical and reticulate phylogenomic relationships

G Bernard, CX Chan, Y Chan, XY Chua… - Briefings in …, 2019 - academic.oup.com
We are amidst an ongoing flood of sequence data arising from the application of high-
throughput technologies, and a concomitant fundamental revision in our understanding of …

Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest …

SL Pearce, DF Clarke, PD East, S Elfekih, KHJ Gordon… - BMC biology, 2017 - Springer
Abstract Background Helicoverpa armigera and Helicoverpa zea are major caterpillar pests
of Old and New World agriculture, respectively. Both, particularly H. armigera, are extremely …

Denoising DNA deep sequencing data—high-throughput sequencing errors and their correction

D Laehnemann, A Borkhardt… - Briefings in …, 2016 - academic.oup.com
Characterizing the errors generated by common high-throughput sequencing platforms and
telling true genetic variation from technical artefacts are two interdependent steps, essential …

Rare biosphere exploration using high-throughput sequencing: research progress and perspectives

A Zhan, HJ MacIsaac - Conservation Genetics, 2015 - Springer
Identification of rare species and mapping their distributions is crucial for understanding
natural species distributions and causes and consequences of accelerating species …

Complex modular architecture around a simple toolkit of wing pattern genes

SM Van Belleghem, P Rastas, A Papanicolaou… - Nature ecology & …, 2017 - nature.com
Identifying the genomic changes that control morphological variation and understanding
how they generate diversity is a major goal of evolutionary biology. In Heliconius butterflies …

Environmental DNA metabarcoding studies are critically affected by substrate selection

A Koziol, M Stat, T Simpson, S Jarman… - Molecular Ecology …, 2019 - Wiley Online Library
Effective biomonitoring is critical for driving management outcomes that ensure long‐term
sustainability of the marine environment. In recent years, environmental DNA (eDNA) …

High‐throughput monitoring of wild bee diversity and abundance via mitogenomics

M Tang, CJ Hardman, Y Ji, G Meng… - Methods in Ecology …, 2015 - Wiley Online Library
Bee populations and other pollinators face multiple, synergistically acting threats, which
have led to population declines, loss of local species richness and pollination services, and …

Initial characterization of the large genome of the salamander Ambystoma mexicanum using shotgun and laser capture chromosome sequencing

MC Keinath, VA Timoshevskiy, NY Timoshevskaya… - Scientific reports, 2015 - nature.com
Vertebrates exhibit substantial diversity in genome size and some of the largest genomes
exist in species that uniquely inform diverse areas of basic and biomedical research. For …

Karect: accurate correction of substitution, insertion and deletion errors for next-generation sequencing data

A Allam, P Kalnis, V Solovyev - Bioinformatics, 2015 - academic.oup.com
Motivation: Next-generation sequencing generates large amounts of data affected by errors
in the form of substitutions, insertions or deletions of bases. Error correction based on the …