Research Paper
IEEE Xplore: Analyzing Differential Regulatory Networks Modulated by Continuous-State Genomic Features in Glioblastoma Multiforme
December 5, 2016
Yu-Chiao Chiu; Tzu-Hung Hsiao; Li-Ju Wang; Yidong Chen; Eric Y. Chuang Abstract: Gene regulatory networks are a global representation of complex interactions between molecules that dictate cellular behavior. The study of a regulatory network modulated by single or multiple modulators’ expression levels, including microRNAs (miRNAs) and transcription factors (TFs), in different conditions can further reveal the modulators’ roles in […]
Genome Biology: Functional genomics analyses of RNA-binding proteins reveal the splicing regulator SNRPB as an oncogenic candidate in glioblastoma
December 1, 2016
Bruna R Correa, Patricia Rosa de Araujo, Mei Qiao, Suzanne C Burns, Chen Chen, Richard Schlegel, Seema Agarwal, Pedro AF Galante, Luiz OF Penalva Background Glioblastoma (GBM) is the most common and aggressive type of brain tumor. Currently, GBM has an extremely poor outcome and there is no effective treatment. In this context, genomic and […]
Molecular Cancer Therapeutics: Alkylating Agent–Induced NRF2 Blocks Endoplasmic Reticulum Stress–Mediated Apoptosis via Control of Glutathione Pools and Protein Thiol Homeostasis
December 1, 2016
Alfeu Zanotto-Filho, V. Pragathi Masamsetti, Eva Loranc, Sonal S. Tonapi, Aparna Gorthi, Xavier Bernard, Rosângela Mayer Gonçalves, José C.F. Moreira, Yidong Chen and Alexander J.R. Bishop Abstract Alkylating agents are a commonly used cytotoxic class of anticancer drugs. Understanding the mechanisms whereby cells respond to these drugs is key to identify means to improve therapy while reducing toxicity. By integrating genome-wide gene expression profiling, protein analysis, and functional cell validation, we herein demonstrated a direct […]
Aging: Aging is associated with an expansion of CD49fhi mammary stem cells that show a decline in function and increased transformation potential
November 15, 2016
Qiaoxiang Dong1,2 , Hui Gao1,2 , Yuanshuo Shi1,3 , Fuchuang Zhang1,3 , Xiang Gu1 , Anqi Wu3 , Danhan Wang3 , Yuanhong Chen3 , Abhik Bandyopadhyay1 , I-Tien Yeh4 , Benjamin J. Daniel5 , Yidong Chen6,8 , Yi Zou8 , Vivienne L. Rebel1,7,8 , Christi A. Walter1 , Jianxin Lu2 , Changjiang Huang3 , Lu-Zhe Sun1,7 Abstract Breast cancer incidence increases during aging, yet the mechanism of age-associated mammary tumorigenesis is unclear. Mammary stem cells are believed to play an important role in breast tumorigenesis, but how their function changes with age are unknown. We compared mammary epithelial cells isolated from young and old mammary glands of […]
Scientific Reports: Differential network analysis reveals the genome-wide landscape of estrogen receptor modulation in hormonal cancers
November 12, 2016
Tzu-Hung Hsiao, Yu-Chiao Chiu, Pei-Yin Hsu, Tzu-Pin Lu, Liang-Chuan Lai, Mong-Hsun Tsai, Tim H.-M. Huang, Eric Y. Chuang Yidong Chen Abstract Several mutual information (MI)-based algorithms have been developed to identify dynamic gene-gene and function-function interactions governed by key modulators (genes, proteins, etc.). Due to intensive computation, however, these methods rely heavily on prior knowledge […]
JoVE: Methyl-binding DNA capture Sequencing for Patient Tissues
October 31, 2016
Rohit R Jadhav 1, Yao V Wang 1, Ya-Ting Hsu 1, Joseph Liu 1, Dawn Garcia 2, Zhao Lai 2, Tim H M Huang 1, Victor X Jin 3 Abstract Methylation is one of the essential epigenetic modifications to the DNA, which is responsible for the precise regulation of genes required for stable development and differentiation of different tissue types. Dysregulation of this process is often the hallmark of various […]
Hyundai Hope on Wheels Awards $250,000 Research Grant to Ut Health Science Center San Antonio in Honor of National Childhood Cancer Awareness Month
September 12, 2016
San Antonio, TX – September 12 – Hyundai Hope On Wheels® (HHOW) and San Antonio-area Hyundai dealers will present UT Health Science Center San Antonio with a $250,000 Scholar Grant to be used to improve care and increase treatment options for kids with cancer. UT Health Science Center San Antonio was one of 24 recipients across the […]
UT Health SA Newsroom: Health Science Center, UTSA gain $4.6 million for cancer research
August 25, 2016
The Center for Innovative Drug Discovery (CIDD), a joint program of the UT Health Science Center San Antonio and The University of Texas at San Antonio (UTSA), is receiving a $4,598,728 grant from the Cancer Prevention & Research Institute of Texas (CPRIT). The grant, announced Aug. 17, will support CIDD research to design more-effective cancer drugs through […]
BMC Genomics: Detection of high variability in gene expression from single-cell RNA-seq profiling
August 22, 2016
Hung-I Harry Chen, Yufang Jin, Yufei Huang & Yidong Chen Abstract Background The advancement of the next-generation sequencing technology enables mapping gene expression at the single-cell level, capable of tracking cell heterogeneity and determination of cell subpopulations using single-cell RNA sequencing (scRNA-seq). Unlike the objectives of conventional RNA-seq where differential expression analysis is the integral component, the most important […]
BMC Genomics: CrossLink: a novel method for cross-condition classification of cancer subtypes
August 22, 2016
Chifeng Ma, Konduru S. Sastry, Mario Flore, Salah Gehani, Issam Al-Bozom, Yusheng Feng, Erchin Serpedin, Lotfi Chouchane, Yidong Chen & Yufei Huang Abstract Background We considered the prediction of cancer classes (e.g. subtypes) using patient gene expression profiles that contain both systematic and condition-specific biases when compared with the training reference dataset. The conventional normalization-based approaches cannot guarantee that the gene signatures in the reference […]