Structural variant calling: the long and the short of it

M Mahmoud, N Gobet, DI Cruz-Dávalos, N Mounier… - Genome biology, 2019 - Springer
Recent research into structural variants (SVs) has established their importance to medicine
and molecular biology, elucidating their role in various diseases, regulation of gene …

Building pan-genome infrastructures for crop plants and their use in association genetics

M Jayakodi, M Schreiber, N Stein, M Mascher - DNA Research, 2021 - academic.oup.com
Pan-genomic studies aim at representing the entire sequence diversity within a species to
provide useful resources for evolutionary studies, functional genomics and breeding of …

Comparative analysis of 16S rRNA gene and metagenome sequencing in pediatric gut microbiomes

D Peterson, KS Bonham, S Rowland… - Frontiers in …, 2021 - frontiersin.org
The colonization of the human gut microbiome begins at birth, and over time, these microbial
communities become increasingly complex. Most of what we currently know about the …

VISTA: computational tools for comparative genomics

KA Frazer, L Pachter, A Poliakov, EM Rubin… - Nucleic acids …, 2004 - academic.oup.com
Abstract Comparison of DNA sequences from different species is a fundamental method for
identifying functional elements in genomes. Here, we describe the VISTA family of tools …

Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes

WJ Kent, R Baertsch, A Hinrichs… - Proceedings of the …, 2003 - National Acad Sciences
This study examines genomic duplications, deletions, and rearrangements that have
happened at scales ranging from a single base to complete chromosomes by comparing the …

The diploid genome sequence of an individual human

S Levy, G Sutton, PC Ng, L Feuk, AL Halpern… - PLoS …, 2007 - journals.plos.org
Presented here is a genome sequence of an individual human. It was produced from∼ 32
million random DNA fragments, sequenced by Sanger dideoxy technology and assembled …

A Switch Between Topological Domains Underlies HoxD Genes Collinearity in Mouse Limbs

G Andrey, T Montavon, B Mascrez, F Gonzalez… - Science, 2013 - science.org
Introduction During vertebrate limb development, gene members of the HoxD cluster are
transcribed in two subsequent waves, following a collinear strategy. Early on, genes located …

Evolution of metal hyperaccumulation required cis-regulatory changes and triplication of HMA4

M Hanikenne, IN Talke, MJ Haydon, C Lanz, A Nolte… - Nature, 2008 - nature.com
Little is known about the types of mutations underlying the evolution of species-specific
traits. The metal hyperaccumulator Arabidopsis halleri has the rare ability to colonize heavy …

Genome-wide analysis of Foxp3 target genes in developing and mature regulatory T cells

Y Zheng, SZ Josefowicz, A Kas, TT Chu, MA Gavin… - Nature, 2007 - nature.com
Transcription factor Foxp3 (forkhead box P3), restricted in its expression to a specialized
regulatory CD4+ T-cell subset (TR) with a dedicated suppressor function, controls TR …

Computational identification of DrosophilamicroRNA genes

EC Lai, P Tomancak, RW Williams, GM Rubin - Genome biology, 2003 - Springer
Background MicroRNAs (miRNAs) are a large family of 21-22 nucleotide non-coding RNAs
with presumed post-transcriptional regulatory activity. Most miRNAs were identified by direct …