Research Paper
SA Express-News: Childhood cancer survivor active in Obama’s ‘precision medicine’ effort
February 9, 2015
S.A. scientist also a cancer survivor As a childhood cancer survivor, San Antonio pediatric oncologist Greg Aune understood the excitement felt by cancer patients and their families when President Barack Obama announced his “precision medicine” initiative nearly two weeks ago. The groundbreaking initiative — for which Obama has requested an initial $215 million in his […]
International Journal of Molecular Sciences (MDPI): Potential Relationship between Inadequate Response to DNA Damage and Development of Myelodysplastic Syndrome
January 5, 2015
Ting Zhou 1,2,Peishuai Chen 1,3,Jian Gu 3,Alexander J. R. Bishop 1,2,4,5,Linda M. Scott 6,Paul Hasty 4,5,7 and Vivienne I. Rebel 1,2,4,5,* Abstract Hematopoietic stem cells (HSCs) are responsible for the continuous regeneration of all types of blood cells, including themselves. To ensure the functional and genomic integrity of blood tissue, a network of regulatory pathways tightly controls the proliferative status of HSCs. […]
Journal of Biological Chemistry: Hormone-induced and DNA Demethylation-induced Relief of a Tissue-specific and Developmentally Regulated Block in Transcriptional Elongation*
December 19, 2014
Abstract Genome-wide studies have revealed that genes commonly have a high density of RNA polymerase II just downstream of the transcription start site. This has raised the possibility that genes are commonly regulated by transcriptional elongation, but this remains largely untested in vivo, particularly in vertebrates. Here, we show that the proximal promoter from the Rhox5 homeobox […]
American Journal of Physiology – Heart & Circulatory Physiology: The tell-tale heart: molecular and cellular responses to childhood anthracycline exposure
November 15, 2014
Merry L. Lindsey, Richard A. Lange, Helen Parsons, Thomas Andrews, and Gregory J. Aune Abstract Since the modern era of cancer chemotherapy that began in the mid-1940s, survival rates for children afflicted with cancer have steadily improved from 10% to current rates that approach 80% (60). Unfortunately, many long-term survivors of pediatric cancer develop chemotherapy-related health effects; 25% are […]
American Journal of Physiology: The tell-tale heart: molecular and cellular responses to childhood anthracycline exposure
November 14, 2014
Abstract Since the modern era of cancer chemotherapy that began in the mid-1940s, survival rates for children afflicted with cancer have steadily improved from 10% to current rates that approach 80% (60). Unfortunately, many long-term survivors of pediatric cancer develop chemotherapy-related health effects; 25% are afflicted with a severe or life-threatening medical condition, with cardiovascular […]
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 […]