55 results for "Li-San Wang"

The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer

Fan Ge; Li-San Wang; Junhyong Kim

PLoS Biology, Vol. 3 No. 10 · 2005 · English · PLOS Scopus

With the availability of increasing amounts of genomic sequences, it is becoming clear that genomes experience horizontal transfer and incorporation of genetic information. However, to what extent such horizontal gene transfer (HGT) affects the core genealogical history of organisms remains…

Also available at: DOAJ

The role of structural variations in Alzheimer’s disease and other neurodegenerative diseases

Hui Wang; Li-San Wang; Gerard Schellenberg et al.

Frontiers in Aging Neuroscience, Vol. 14 · 2023 · English · DOAJ Scopus

Dozens of single nucleotide polymorphisms (SNPs) related to Alzheimer’s disease (AD) have been discovered by large scale genome-wide association studies (GWASs). However, only a small portion of the genetic component of AD can be explained by SNPs observed from GWAS. Structural variation (SV) can…

Age-Correlated Gene Expression in Normal and Neurodegenerative Human Brain Tissues

Kajia Cao; Alice S. Chen-Plotkin; Joshua B. Plotkin et al.

PLoS ONE, Vol. 5 No. 9 · 2010 · English · PLOS Scopus

Background: Human brain aging has received special attention in part because of the elevated risks of neurodegenerative disorders such as Alzheimer's disease in seniors. Recent technological advances enable us to investigate whether similar mechanisms underlie aging and neurodegeneration, by…

Also available at: DOAJ

Analysis of Nonlinear Gene Expression Progression Reveals Extensive Pathway and Age-Specific Transitions in Aging Human Brains

Kajia Cao; Paul Ryvkin; Yih-Chii Hwang et al.

PLoS ONE, Vol. 8 No. 10 · 2013 · English · PLOS Scopus

Several recent gene expression studies identified hundreds of genes that are correlated with age in brain and other tissues in human. However, these studies used linear models of age correlation, which are not well equipped to model abrupt changes associated with particular ages. We developed a…

Also available at: DOAJ

Genomic Landscape of a Three-Generation Pedigree Segregating Affective Disorder

Shuzhang Yang; Kai Wang; Brittany Gregory et al.

PLoS ONE, Vol. 4 No. 2 · 2009 · English · PLOS Scopus

Bipolar disorder (BPD) is a common psychiatric illness with a complex mode of inheritance. Besides traditional linkage and association studies, which require large sample sizes, analysis of common and rare chromosomal copy number variants (CNVs) in extended families may provide novel insights into…

Also available at: DOAJ

GrafAnc: Reliable and reproducible inference of continental and regional population structure

Yumi Jin; Hui Wang; Adam C. Naj et al.

HGG Advances, Vol. 7 No. 1 · 2026 · English · DOAJ Scopus

Summary: Accurate inference of genetic ancestry is a fundamental step in population genetics, disease association studies, and understanding human history. However, most existing tools, whether model-based or model-free, are limited by dataset-specific characteristics, which restrict…

Genome-Wide Double-Stranded RNA Sequencing Reveals the Functional Significance of Base-Paired RNAs in Arabidopsis

Qi Zheng; Paul Ryvkin; Fan Li et al.

PLoS Genetics, Vol. 6 No. 9 · 2010 · English · PLOS Scopus

The functional structure of all biologically active molecules is dependent on intra- and inter-molecular interactions. This is especially evident for RNA molecules whose functionality, maturation, and regulation require formation of correct secondary structure through encoded base-pairing…

Also available at: DOAJ

HiPR: High-throughput probabilistic RNA structure inference

Pavel P. Kuksa; Fan Li; Sampath Kannan et al.

Computational and Structural Biotechnology Journal, Vol. 18 · 2020 · English · DOAJ Scopus

Recent high-throughput structure-sensitive genome-wide sequencing-based assays have enabled large-scale studies of RNA structure, and robust transcriptome-wide computational prediction of individual RNA structures across RNA classes from these assays has potential to further improve the prediction…

Copy Number Variation Identification on 3,800 Alzheimer’s Disease Whole Genome Sequencing Data from the Alzheimer’s Disease Sequencing Project

Wan-Ping Lee; Albert A. Tucci; Mitchell Conery et al.

Frontiers in Genetics, Vol. 12 · 2021 · English · DOAJ Scopus

Alzheimer’s Disease (AD) is a progressive neurologic disease and the most common form of dementia. While the causes of AD are not completely understood, genetics plays a key role in the etiology of AD, and thus finding genetic factors holds the potential to uncover novel AD mechanisms. For this…

McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes

Dina Hafez; Aslihan Karabacak; Sabrina Krueger et al.

Genome Biology, Vol. 18 No. 1 · 2017 · English · DOAJ Scopus

Abstract Transcriptional enhancers regulate spatio-temporal gene expression. While genomic assays can identify putative enhancers en masse, assigning target genes is a complex challenge. We devised a machine learning approach, McEnhancer, which links target genes to putative enhancers via a…

Reconcile the debate over protective effects of BCG vaccine against COVID-19

Wei Fu; Pei-Chuan Ho; Chia-Lun Liu et al.

Scientific Reports, Vol. 11 No. 1 · 2021 · English · DOAJ Scopus

Abstract While awaiting the COVID-19 vaccines, researchers have been actively exploring the effectiveness of existing vaccines against the new virus, among which the BCG vaccine (Bacillus Calmette-Guérin) receives the most attention. While many reports suggest a potential role for BCG immunization…

An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease

Raffaella Nativio; Yemin Lan; Greg Donahue et al.

Nature Genetics · 2020 · English · OpenAlex Scopus

The prediction of Alzheimer’s disease through multi-trait genetic modeling

Kaylyn Clark; Wei Fu; Chia-Lun Liu et al.

Frontiers in Aging Neuroscience, Vol. 15 · 2023 · English · DOAJ Scopus

To better capture the polygenic architecture of Alzheimer’s disease (AD), we developed a joint genetic score, MetaGRS. We incorporated genetic variants for AD and 24 other traits from two independent cohorts, NACC (n = 3,174, training set) and UPitt (n = 2,053, validation set). One standard…

Using community-based geographical information system (GIS) to recruit older Asian Americans in an Alzheimer’s disease study

Tiffany W Chow; Hyun-Sik Yang; Haeok Lee et al.

BMJ Open, Vol. 13 No. 8 · 2023 · English · DOAJ Scopus

Objective This study aims to show the usefulness of incorporating a community-based geographical information system (GIS) in recruiting research participants for the Asian Cohort for Alzheimer’s Disease (ACAD) study for using the subgroup of Korean American (KA) older adults. The ACAD study is the…

Transcriptomic Changes Due to Cytoplasmic TDP-43 Expression Reveal Dysregulation of Histone Transcripts and Nuclear Chromatin

Alexandre Amlie-Wolf; Paul Ryvkin; Rui Tong et al.

PLOS ONE, Vol. 10 No. 10 · 2015 · English · PLOS Scopus

TAR DNA-binding protein 43 (TDP-43) is normally a nuclear RNA-binding protein that exhibits a range of functions including regulation of alternative splicing, RNA trafficking, and RNA stability. However, in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration with TDP-43…