Research Paper
BMC Bioinformatics: Selected articles from the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2013): Bioinformatics
November 6, 2014
Zijing Mao, Chifeng Ma, Tim H-M Huang, Yidong Chen & Yufei Huang Abstract DNA methylation is a common epigenetic marker that regulates gene expression. A robust and cost-effective way for measuring whole-genome methylation is Methyl-CpG binding domain-based capture followed by sequencing (MBDCap-seq). In this study, we proposed BIMMER, a Hidden Markov Model (HMM) for differential Methylation Regions (DMRs) identification, where […]
Nucleic Acids Research: MeT-DB: a database of transcriptome methylation in mammalian cells
November 6, 2014
Hui Liu, Mario A Flores, Jia Meng, Lin Zhang, Xinyu Zhao, Manjeet K. Rao, Yidong Chen, Yufei Huang Abstract Methyltranscriptome is an exciting new area that studies the mechanisms and functions of methylation in transcripts. The MethylTranscriptome DataBase (MeT-DB, http://compgenomics.utsa.edu/methylation/) is the first comprehensive resource for N6-methyladenosine (m6A) in the mammalian transcriptome. It includes a database that records publicly available data sets from […]
Plant Physiology: De novo genome assembly of the economically important weed horseweed using integrated data from multiple sequencing platforms
November 1, 2014
Yanhui Peng 1, Zhao Lai 1, Thomas Lane 1, Madhugiri Nageswara-Rao 1, Miki Okada 1, Marie Jasieniuk 1, Henriette O’Geen 1, Ryan W Kim 1, R Douglas Sammons 1, Loren H Rieseberg 1, C Neal Stewart Jr 2 Erratum in Plant Physiol. 2014 Dec;166(4):2218 Abstract Horseweed (Conyza canadensis), a member of the Compositae (Asteraceae) family, was the first broadleaf weed to evolve resistance to glyphosate. Horseweed, one of the most problematic weeds in the world, is […]
Breast Cancer Research and Treatment: Use of risk-reducing surgeries in a prospective cohort of 1,499 BRCA1 and BRCA2 mutation carriers
October 14, 2014
Xinglei Chai 1, Tara M Friebel, Christian F Singer, D Gareth Evans, Henry T Lynch, Claudine Isaacs, Judy E Garber, Susan L Neuhausen, Ellen Matloff, Rosalind Eeles, Nadine Tung, Jeffrey N Weitzel, Fergus J Couch, Peter J Hulick, Patricia A Ganz, Mary B Daly, Olufunmilayo I Olopade, Gail Tomlinson, Joanne L Blum, Susan M Domchek, Jinbo Chen, Timothy R Rebbeck Abstract Inherited mutations in BRCA1 or BRCA2 (BRCA1/2) confer a very high risk of breast and ovarian […]
Methods: A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package
October 1, 2014
Author links open overlay panelJiaMenga, ZhiliangLua, HuiLiub, LinZhangb, ShaowuZhangc, YidongChende, Manjeet K.Raoef, YufeiHuanggd Abstract Despite the prevalent studies of DNA/Chromatin-related epigenetics, such as, histone modifications and DNA methylation, RNA epigenetics has not drawn deserved attention until a new affinity-based sequencing approach MeRIP-Seq was developed and applied to survey the global mRNA N6-methyladenosine (m6A) in mammalian cells. As a marriage of […]
Congressional Childhood Cancer Caucus: Caucus Applauds NCI for Naming Pediatric Oncologist to Council of Research Advocates
September 30, 2014
National Cancer Institute Names UTHSCSA Pediatric Hematologist-Oncologist to Council of Research Advocates The National Cancer Institute (NCI) recently nominated a new member to its NCI Council of Research Advocates, Greg Aune, a pediatric hematologist-oncologist from The University of Texas Health Science Center at San Santonio. The announcement was made last Friday by NCI director Harold Varmus in a closed-door briefing on pediatric cancer for childhood cancer […]
San Antonio Report: Greehey Institute Receives $3.7 Million Cancer Grant
September 26, 2014
A cancer diagnosis is difficult news for anyone, and it can be particularly frightening and heart-wrenching for a family with a cancer-stricken child living in a lower-income area without access to adequate health care. The National Cancer Institute has awarded a $3.7 million grant to the Greehey Children’s Cancer Research Institute at the UT Health Science Center to address […]
TPR: $3.7 Million Grant Will Help UTHSCSA Study Children’s Cancer
September 24, 2014
Children’s cancer research in San Antonio is getting a boost from the National Cancer Institute. A new infusion of $3.7 million is dedicated to helping an underserved population in South Texas. South Central Texas is designated is one of 12 sites in the United States with the largest populations of underserved minority children.
New England Journal of Medicine: AR-V7 and Resistance to Enzalutamide and Abiraterone in Prostate Cancer
September 11, 2014
Emmanuel S. Antonarakis, MD, Changxue Lu, PhD, Hao Wang, PhD, Brandon Luber, Sc.M., Mary Nakazawa, M.H.S., Jeffrey C. Roeser, B.S., Yan Chen, PhD, Tabrez A. Mohammad, PhD, Yidong Chen, PhD, Helen L. Fedor, B.S., Tamara L. Lotan, MD, Qizhi Zheng, MD, Angelo M. De Marzo, MD, PhD, John T. Isaacs, PhD, William B. Isaacs, PhD, Rosa Nadal, MD, Channing J. Paller, MD, Samuel R. Denmeade, MD, Michael A. Carducci, MD, Mario A. Eisenberger, MD, and […]
Mechanisms of Ageing and Development: Short-term rapamycin treatment in mice has few effects on the transcriptome of white adipose tissue compared to dietary restriction
September 1, 2014
Wilson C.Foka CarolinaLivibc AlexBokovcd ZhenYue YidongChendfg ArlanRichardsonah Viviana I.Pérezhi Abstract Rapamycin, a drug that has been shown to increase lifespan in mice, inhibits the target of rapamycin (TOR) pathway, a major pathway that regulates cell growth and energy status. It has been hypothesized that rapamycin and dietary restriction (DR) extends lifespan through similar mechanisms/pathways. Using […]