[HTML][HTML] PRIMUS: rapid reconstruction of pedigrees from genome-wide estimates of identity by descent

J Staples, D Qiao, MH Cho, EK Silverman… - The American Journal of …, 2014‏ - cell.com
Understanding and correctly utilizing relatedness among samples is essential for genetic
analysis; however, managing sample records and pedigrees can often be error prone and …

Phylogenomics from low‐coverage whole‐genome sequencing

F Zhang, Y Ding, CD Zhu, X Zhou… - Methods in Ecology …, 2019‏ - Wiley Online Library
Phylogenetic studies are increasingly reliant on next‐generation sequencing.
Transcriptomic and hybrid enrichment sequencing techniques remain the most prevalent …

Optimal sequencing depth design for whole genome re-sequencing in pigs

Y Jiang, Y Jiang, S Wang, Q Zhang, X Ding - Bmc Bioinformatics, 2019‏ - Springer
Background As whole-genome sequencing is becoming a routine technique, it is important
to identify a cost-effective depth of sequencing for such studies. However, the relationship …

An evaluation of sequencing coverage and genoty** strategies to assess neutral and adaptive diversity

B Benjelloun, F Boyer, I Streeter… - Molecular ecology …, 2019‏ - Wiley Online Library
Whole genome sequences (WGS) greatly increase our ability to precisely infer population
genetic parameters, demographic processes, and selection signatures. However, WGS may …

Genetic factors associated with suicidal behaviors and alcohol use disorders in an American Indian population

Q Peng, DA Gilder, RA Bernert, KJ Karriker-Jaffe… - Molecular …, 2024‏ - nature.com
American Indians (AI) demonstrate the highest rates of both suicidal behaviors (SB) and
alcohol use disorders (AUD) among all ethnic groups in the US. Rates of suicide and AUD …

Deep whole-genome sequencing of 90 Han Chinese genomes

T Lan, H Lin, W Zhu, TCAM Laurent, M Yang, X Liu… - …, 2017‏ - academic.oup.com
Next-generation sequencing provides a high-resolution insight into human genetic
information. However, the focus of previous studies has primarily been on low-coverage …

Genetic loci for alcohol-related life events and substance-induced affective symptoms: indexing the “dark side” of addiction

Q Peng, C Bizon, IR Gizer, KC Wilhelmsen… - Translational …, 2019‏ - nature.com
A limited number of genetic variants have been identified in traditional GWAS as risk or
protective factors for alcohol use disorders (AUD) and related phenotypes. We herein report …

Testing rare-variant association without calling genotypes allows for systematic differences in sequencing between cases and controls

YJ Hu, P Liao, HR Johnston, AS Allen, GA Satten - PLoS genetics, 2016‏ - journals.plos.org
Next-generation sequencing of DNA provides an unprecedented opportunity to discover
rare genetic variants associated with complex diseases and traits. However, the common …

A bioinformatic platform to integrate target capture and whole genome sequences of various read depths for phylogenomics

P G. Ribeiro, MF Torres Jiménez… - Molecular …, 2021‏ - Wiley Online Library
The increasing availability of short‐read whole genome sequencing (WGS) provides
unprecedented opportunities to study ecological and evolutionary processes. Although loci …

Whole genome sequence study of cannabis dependence in two independent cohorts

IR Gizer, C Bizon, DA Gilder, CL Ehlers… - Addiction …, 2018‏ - Wiley Online Library
Recent advances in genome wide sequencing techniques and analytical methods allow for
more comprehensive examinations of the genome than microarray‐based genome‐wide …