[HTML][HTML] An integrated map of structural variation in 2,504 human genomes

…, F Yu, C Zhang, J Zhang, X Zheng-Bradley, W Zhou… - Nature, 2015 - ncbi.nlm.nih.gov
Summary Structural variants (SVs) are implicated in numerous diseases and make up the
majority of varying nucleotides among human genomes. Here we describe an integrated set
of eight SV classes comprising both balanced and unbalanced variants, which we

Clinical actionability enhanced through deep targeted sequencing of solid tumors

…, Y Qi, Y Mao, T Chen, Z Chong, W Zhou… - Clinical …, 2015 - clinchem.aaccjnls.org
BACKGROUND: Further advances of targeted cancer therapy require comprehensive in-
depth profiling of somatic mutations that are present in subpopulations of tumor cells in a
clinical tumor sample. However, it is unclear to what extent such intratumor heterogeneity is

[HTML][HTML] Properties of metabolic graphs: biological organization or representation artifacts?

W Zhou, L Nakhleh - BMC bioinformatics, 2011 - bmcbioinformatics.biomedcentral …
Background Standard graphs, where each edge links two nodes, have been extensively
used to represent the connectivity of metabolic networks. It is based on this representation
that properties of metabolic networks, such as hierarchical and small-world structures, have

[HTML][HTML] Convergent evolution of modularity in metabolic networks through different community structures

W Zhou, L Nakhleh - BMC evolutionary biology, 2012 - bmcevolbiol.biomedcentral.com
Background It has been reported that the modularity of metabolic networks of bacteria is
closely related to the variability of their living habitats. However, given the dependency of the
modularity score on the community structure, it remains unknown whether organisms

The involvement of NADPH oxidase-mediated ROS in cytokine secretion from macrophages induced by Mycobacterium tuberculosis ESAT-6

W Liu, Y Peng, Y Yin, Z Zhou, W Zhou, Y Dai - Inflammation, 2014 - Springer
Abstract The 6-kDa early secretory antigenic target (ESAT-6) of Mycobacterium tuberculosis
is strongly correlated with subversion of innate immune responses against invading
mycobacteria. To understand the role of ESAT-6 in macrophage response against M.

[HTML][HTML] Modeling integrated cellular machinery using hybrid petri-boolean networks

N Berestovsky, W Zhou, D Nagrath… - PLoS computational …, 2013 - journals.plos.org
Abstract The behavior and phenotypic changes of cells are governed by a cellular circuitry
that represents a set of biochemical reactions. Based on biological functions, this circuitry is
divided into three types of networks, each encoding for a major biological process: signal

Bias from removing read duplication in ultra-deep sequencing experiments

W Zhou, T Chen, H Zhao, AK Eterovic… - …, 2014 - academic.oup.com
Abstract Motivation: Identifying subclonal mutations and their implications requires accurate
estimation of mutant allele fractions from possibly duplicated sequencing reads. Removing
duplicate reads assumes that polymerase chain reaction amplification from library

Vitamin C increases viral mimicry induced by 5-aza-2′-deoxycytidine

M Liu, H Ohtani, W Zhou, AD Ørskov… - Proceedings of the …, 2016 - National Acad Sciences
Abstract Vitamin C deficiency is found in patients with cancer and might complicate various
therapy paradigms. Here we show how this deficiency may influence the use of DNA
methyltransferase inhibitors (DNMTis) for treatment of hematological neoplasias. In vitro,

[HTML][HTML] TransVar: a trans-level variant annotator for precision genomics

W Zhou, T Chen, Z Chong, MA Rohrdanz… - Nature …, 2015 - ncbi.nlm.nih.gov
One DNA sequence can code for multiple different mRNAs, and therefore many different
proteins. Conversely, a variant identified at the protein or transcript level may have
nonunique genomic origins. For example, EGFR: p. L747S, which mediates acquired

[HTML][HTML] novoBreak: local assembly for breakpoint detection in cancer genomes

Z Chong, J Ruan, M Gao, W Zhou, T Chen… - Nature …, 2017 - pubmedcentralcanada.ca
Abstract We present novoBreak, a novel genome-wide local assembly algorithm that
discovers somatic and germline structural variation breakpoints in whole genome
sequencing data. In the ICGC-TCGA DREAM 8.5 Somatic Mutation Calling Challenge and