Population-based 3D genome structure analysis reveals driving forces in spatial genome organization
…, K Gong, Y Zhou, H Li, XJ Zhou… - Proceedings of the …, 2016 - National Acad Sciences
Conformation capture technologies (eg, Hi-C) chart physical interactions between chromatin
regions on a genome-wide scale. However, the structural variability of the genome between …
regions on a genome-wide scale. However, the structural variability of the genome between …
[PDF][PDF] Mining coherent dense subgraphs across massive biological networks for functional discovery
Motivation: The rapid accumulation of biological network data translates into an urgent need
for computational methods for graph pattern mining. One important problem is to identify …
for computational methods for graph pattern mining. One important problem is to identify …
Dense chromatin activates Polycomb repressive complex 2 to regulate H3 lysine 27 methylation
Polycomb repressive complex 2 (PRC2)–mediated histone H3 lysine 27 (H3K27) methylation
is vital for Polycomb gene silencing, a classic epigenetic phenomenon that maintains …
is vital for Polycomb gene silencing, a classic epigenetic phenomenon that maintains …
[HTML][HTML] CancerLocator: non-invasive cancer diagnosis and tissue-of-origin prediction using methylation profiles of cell-free DNA
We propose a probabilistic method, CancerLocator, which exploits the diagnostic potential
of cell-free DNA by determining not only the presence but also the location of tumors. …
of cell-free DNA by determining not only the presence but also the location of tumors. …
[HTML][HTML] Joint genome-wide profiling of miRNA and mRNA expression in Alzheimer's disease cortex reveals altered miRNA regulation
…, CC Liu, TE Morgan, CE Finch, XJ Zhou - PloS one, 2010 - journals.plos.org
Although microRNAs are being extensively studied for their involvement in cancer and
development, little is known about their roles in Alzheimer's disease (AD). In this study, we used …
development, little is known about their roles in Alzheimer's disease (AD). In this study, we used …
Discovery of multi-dimensional modules by integrative analysis of cancer genomic data
Recent technology has made it possible to simultaneously perform multi-platform genomic
profiling (eg DNA methylation (DM) and gene expression (GE)) of biological samples, …
profiling (eg DNA methylation (DM) and gene expression (GE)) of biological samples, …
TopDom: an efficient and deterministic method for identifying topological domains in genomes
Genome-wide proximity ligation assays allow the identification of chromatin contacts at
unprecedented resolution. Several studies reveal that mammalian chromosomes are composed …
unprecedented resolution. Several studies reveal that mammalian chromosomes are composed …
A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules
Motivation: It is well known that microRNAs (miRNAs) and genes work cooperatively to form
the key part of gene regulatory networks. However, the specific functional roles of most …
the key part of gene regulatory networks. However, the specific functional roles of most …
Identifying multi-layer gene regulatory modules from multi-dimensional genomic data
W Li, S Zhang, CC Liu, XJ Zhou - Bioinformatics, 2012 - academic.oup.com
Motivation: Eukaryotic gene expression (GE) is subjected to precisely coordinated multi-layer
controls, across the levels of epigenetic, transcriptional and post-transcriptional regulations…
controls, across the levels of epigenetic, transcriptional and post-transcriptional regulations…
CancerDetector: ultrasensitive and non-invasive cancer detection at the resolution of individual reads using cell-free DNA methylation sequencing data
The detection of tumor-derived cell-free DNA in plasma is one of the most promising directions
in cancer diagnosis. The major challenge in such an approach is how to identify the tiny …
in cancer diagnosis. The major challenge in such an approach is how to identify the tiny …