Illuminating an ecological blackbox: using high throughput sequencing to characterize the plant virome across scales

F Maclot, T Candresse, D Filloux… - Frontiers in …, 2020 - frontiersin.org
The ecology of plant viruses began to be explored at the end of the 19th century. Since then,
major advances have revealed mechanisms of virus-host-vector interactions in various …

A benchmark study of k-mer counting methods for high-throughput sequencing

SC Manekar, SR Sathe - GigaScience, 2018 - academic.oup.com
The rapid development of high-throughput sequencing technologies means that hundreds of
gigabytes of sequencing data can be produced in a single study. Many bioinformatics tools …

Gerbil: a fast and memory-efficient k-mer counter with GPU-support

M Erbert, S Rechner, M Müller-Hannemann - Algorithms for Molecular …, 2017 - Springer
Background A basic task in bioinformatics is the counting of k-mers in genome sequences.
Existing k-mer counting tools are most often optimized for small k< 32 and suffer from …

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 …

Kourami: graph-guided assembly for novel human leukocyte antigen allele discovery

H Lee, C Kingsford - Genome biology, 2018 - Springer
Accurate typing of human leukocyte antigen (HLA) is important because HLA genes play
important roles in immune responses and disease genesis. Previously available …

Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution

JG Roscito, K Sameith, G Parra, BE Langer… - Nature …, 2018 - nature.com
Detecting the genomic changes underlying phenotypic changes between species is a main
goal of evolutionary biology and genomics. Evolutionary theory predicts that changes in cis …

Convergent and lineage-specific genomic differences in limb regulatory elements in limbless reptile lineages

JG Roscito, K Sameith, BM Kirilenko, N Hecker… - Cell reports, 2022 - cell.com
Loss of limbs evolved many times in squamate reptiles. Here we investigated the genomic
basis of convergent limb loss in reptiles. We sequenced the genomes of a closely related …

[PDF][PDF] Computational errors and biases in short read next generation sequencing

I Abnizova, R te Boekhorst, Y Orlov - J Proteomics Bioinform, 2017 - academia.edu
Proteomics & Bioinformatics Page 1 Research Article Review Article Irina et al., J Proteomics
Bioinform 2017, 10:1 DOI: 10.4172/jpb.1000420 Journal of Proteomics & Bioinformatics Jou rn …

Dynamics of soil microbial communities involved in carbon cycling along three successional forests in southern China

M Hu, S Zhou, X Xiong, X Wang, Y Sun… - Frontiers in …, 2024 - frontiersin.org
Dynamics of plant communities during forest succession have been received great attention
in the past decades, yet information about soil microbial communities that are involved in …

The genome of a Far Eastern isolate of Diaporthe caulivora, a soybean fungal pathogen

A Muterko, T Surina, O Dobrovolskaya - Applied Microbiology and …, 2023 - Springer
Diaporthe caulivora is an economically important fungal pathogen and a causal agent of
soybean stem canker and seed decay. Here, the genome of a Russian Far Eastern isolate of …