From reads to insight: a hitchhiker's guide to ATAC-seq data analysis

F Yan, DR Powell, DJ Curtis, NC Wong - Genome biology, 2020 - Springer
Abstract Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) is widely
used in studying chromatin biology, but a comprehensive review of the analysis tools has …

Multiscale simulations of biological membranes: the challenge to understand biological phenomena in a living substance

G Enkavi, M Javanainen, W Kulig, T Róg… - Chemical …, 2019 - ACS Publications
Biological membranes are tricky to investigate. They are complex in terms of molecular
composition and structure, functional over a wide range of time scales, and characterized by …

SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies

M Goel, H Sun, WB Jiao, K Schneeberger - Genome biology, 2019 - Springer
Genomic differences range from single nucleotide differences to complex structural
variations. Current methods typically annotate sequence differences ranging from SNPs to …

[HTML][HTML] Mechanism of alternative splicing and its regulation

Y Wang, J Liu, BO Huang, YM Xu, J Li… - Biomedical …, 2015 - spandidos-publications.com
Alternative splicing of precursor mRNA is an essential mechanism to increase the
complexity of gene expression, and it plays an important role in cellular differentiation and …

The roles of post-translational modifications in the context of protein interaction networks

G Duan, D Walther - PLoS computational biology, 2015 - journals.plos.org
Among other effects, post-translational modifications (PTMs) have been shown to exert their
function via the modulation of protein-protein interactions. For twelve different main PTM …

Whole‐genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations

AP Fuentes‐Pardo, DE Ruzzante - Molecular ecology, 2017 - Wiley Online Library
Whole‐genome resequencing (WGR) is a powerful method for addressing fundamental
evolutionary biology questions that have not been fully resolved using traditional methods …

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

Project management: Fulton Lucinda A. 1 Mardis … - Nature, 2004 - nature.com
We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the
chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to …

Reducing the racial achievement gap: A social-psychological intervention

GL Cohen, J Garcia, N Apfel, A Master - science, 2006 - science.org
Two randomized field experiments tested a social-psychological intervention designed to
improve minority student performance and increase our understanding of how psychological …

Long noncoding RNAs in development and cancer: potential biomarkers and therapeutic targets

R Fatima, VS Akhade, D Pal, SMR Rao - Molecular and cellular therapies, 2015 - Springer
Long noncoding RNAs are emerging as key players in various fundamental biological
processes. We highlight the varied molecular mechanisms by which lncRNAs modulate …

The human genome project: big science transforms biology and medicine

L Hood, L Rowen - Genome medicine, 2013 - Springer
Abstract The Human Genome Project has transformed biology through its integrated big
science approach to deciphering a reference human genome sequence along with the …