Structural variation in the sequencing era

SS Ho, AE Urban, RE Mills - Nature Reviews Genetics, 2020 - nature.com
Identifying structural variation (SV) is essential for genome interpretation but has been
historically difficult due to limitations inherent to available genome technologies. Detection …

Toward better understanding of artifacts in variant calling from high-coverage samples

H Li - Bioinformatics, 2014 - academic.oup.com
Motivation: Whole-genome high-coverage sequencing has been widely used for personal
and cancer genomics as well as in various research areas. However, in the lack of an …

[HTML][HTML] Longitudinal multi-omics of host–microbe dynamics in prediabetes

W Zhou, MR Sailani, K Contrepois, Y Zhou, S Ahadi… - Nature, 2019 - nature.com
Type 2 diabetes mellitus (T2D) is a growing health problem, but little is known about its early
disease stages, its effects on biological processes or the transition to clinical T2D. To …

Population genomics of the critically endangered kākāpō

N Dussex, T Van Der Valk, HE Morales, CW Wheat… - Cell Genomics, 2021 - cell.com
The kākāpō is a flightless parrot endemic to New Zealand. Once common in the archipelago,
only 201 individuals remain today, most of them descending from an isolated island …

A longitudinal big data approach for precision health

SM Schüssler-Fiorenza Rose, K Contrepois… - Nature medicine, 2019 - nature.com
Precision health relies on the ability to assess disease risk at an individual level, detect early
preclinical conditions and initiate preventive strategies. Recent technological advances in …

The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease

HMP Integrative - Cell host & microbe, 2014 - pubmed.ncbi.nlm.nih.gov
Much has been learned about the diversity and distribution of human-associated microbial
communities, but we still know little about the biology of the microbiome, how it interacts with …

[HTML][HTML] Personal omics profiling reveals dynamic molecular and medical phenotypes

R Chen, GI Mias, J Li-Pook-Than, L Jiang, HYK Lam… - Cell, 2012 - cell.com
Personalized medicine is expected to benefit from combining genomic information with
regular monitoring of physiological states by multiple high-throughput methods. Here, we …

A survey of tools for variant analysis of next-generation genome sequencing data

S Pabinger, A Dander, M Fischer… - Briefings in …, 2014 - academic.oup.com
Recent advances in genome sequencing technologies provide unprecedented opportunities
to characterize individual genomic landscapes and identify mutations relevant for diagnosis …

Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing

J O'Rawe, T Jiang, G Sun, Y Wu, W Wang, J Hu… - Genome medicine, 2013 - Springer
Background To facilitate the clinical implementation of genomic medicine by next-generation
sequencing, it will be critically important to obtain accurate and consistent variant calls on …

Integrative personal omics profiles during periods of weight gain and loss

BD Piening, W Zhou, K Contrepois, H Röst, GJG Urban… - Cell systems, 2018 - cell.com
Advances in omics technologies now allow an unprecedented level of phenotyping for
human diseases, including obesity, in which individual responses to excess weight are …