Deep learning for computational biology

C Angermueller, T Pärnamaa, L Parts… - Molecular systems …, 2016 - embopress.org
Technological advances in genomics and imaging have led to an explosion of molecular
and cellular profiling data from large numbers of samples. This rapid increase in biological …

The role of regulatory variation in complex traits and disease

FW Albert, L Kruglyak - Nature Reviews Genetics, 2015 - nature.com
We are in a phase of unprecedented progress in identifying genetic loci that cause variation
in traits ranging from growth and fitness in simple organisms to disease in humans …

Proteogenomics: concepts, applications and computational strategies

AI Nesvizhskii - Nature methods, 2014 - nature.com
Proteogenomics is an area of research at the interface of proteomics and genomics. In this
approach, customized protein sequence databases generated using genomic and …

Genetic variability in the regulation of gene expression in ten regions of the human brain

A Ramasamy, D Trabzuni, S Guelfi, V Varghese… - Nature …, 2014 - nature.com
Germ-line genetic control of gene expression occurs via expression quantitative trait loci
(eQTLs). We present a large, exon-specific eQTL data set covering ten human brain regions …

Defining the consequences of genetic variation on a proteome-wide scale

JM Chick, SC Munger, P Simecek, EL Huttlin, K Choi… - Nature, 2016 - nature.com
Genetic variation modulates protein expression through both transcriptional and post-
transcriptional mechanisms. To characterize the consequences of natural genetic diversity …

The role of alternative splicing in adaptation and evolution

JP Verta, A Jacobs - Trends in Ecology & Evolution, 2022 - cell.com
Regulation of gene expression plays a central role in adaptive divergence and evolution.
Although the role of gene regulation in microevolutionary processes is gaining wide …

The evolution of gene expression in cis and trans

SA Signor, SV Nuzhdin - Trends in Genetics, 2018 - cell.com
There is abundant variation in gene expression between individuals, populations, and
species. The evolution of gene regulation and expression within and between species is …

[HTML][HTML] Functional genetic variants revealed by massively parallel precise genome editing

E Sharon, SAA Chen, NM Khosla, JD Smith… - Cell, 2018 - cell.com
A major challenge in genetics is to identify genetic variants driving natural phenotypic
variation. However, current methods of genetic mapping have limited resolution. To address …

Impact of regulatory variation from RNA to protein

A Battle, Z Khan, SH Wang, A Mitrano, MJ Ford… - Science, 2015 - science.org
The phenotypic consequences of expression quantitative trait loci (eQTLs) are presumably
due to their effects on protein expression levels. Yet the impact of genetic variation, including …

Genetics of trans-regulatory variation in gene expression

FW Albert, JS Bloom, J Siegel, L Day, L Kruglyak - Elife, 2018 - elifesciences.org
Heritable variation in gene expression forms a crucial bridge between genomic variation
and the biology of many traits. However, most expression quantitative trait loci (eQTLs) …