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 […]

BMC Genomics: MBDDiff: an R package designed specifically for processing MBDcap-seq datasets

August 18, 2016

Yuanhang Liu,  Desiree Wilson,  Robin J. Leach   Yidong Chen  Abstract Background Since its initial discovery in 1975, DNA methylation has been intensively studied and shown to be involved in various biological processes, such as development, aging, and tumor progression. Many experimental techniques have been developed to measure the level of DNA methylation. Methyl-CpG binding […]

Clinical Cancer Research: Inhibition of FoxM1-Mediated DNA Repair by Imipramine Blue Suppresses Breast Cancer Growth and Metastasis

July 1, 2016

Subapriya Rajamanickam, Subbarayalu Panneerdoss, Aparna Gorthi, Santosh Timilsina, Benjamin Onyeagucha, Dmytro Kovalsky, Dmitri Ivanov, Martha A. Hanes, Ratna K. Vadlamudi, Yidong Chen, Alexander J. Bishop, Jack L. Arbiser and Manjeet K. Rao Abstract Purpose: The approaches aimed at inhibiting the ability of cancer cells to repair DNA strand breaks have emerged as promising targets for treating cancers. Here, we assessed the potential of imipramine blue (IB), a novel analog of antidepressant imipramine, to suppress breast cancer growth and metastasis by inhibiting […]

Bioinformatics: A novel algorithm for calling mRNA m 6 A peaks by modeling biological variances in MeRIP-seq data

June 11, 2016

Abstract Motivation: N 6 -methyl-adenosine (m 6 A) is the most prevalent mRNA methylation but the precise prediction of its mRNA location is important for understanding its function. A recent sequencing technology, known as Methylated RNA Immunoprecipitation Sequencing technology (MeRIP-seq), has been developed for transcriptome-wide profiling of m 6 A. We previously developed a peak calling algorithm called exomePeak. However, […]

SA Business Journal: Cancer money to boost local pediatric research

June 3, 2016

The Cancer Prevention & Research Institute of Texas has awarded nearly $11 million to the University of Texas Health Science Center at San Antonio in its latest funding round. That award includes $5 million to help establish the Texas Pediatric Patient-Derived Xenograft Facility. Peter Houghton, director of the Greehey Children’s Cancer Research Institute at the […]

UT Health SA Newsroom: CPRIT awards $10.9 million to Greehey institute for cancer research

May 20, 2016

The Greehey Children’s Cancer Research Institute at the Health Science Center garnered $10.9 million from the Cancer Prevention & Research Institute of Texas (CPRIT)―a larger amount than any other academic institution in the state. The Health Science Center received 24 percent of the $45.3 million awarded to 13 academic institutions on May 18. The grant was the […]

UT Health SA Newsroom: CPRIT awards $10.9 million to Greehey institute for cancer research

May 20, 2016

The Greehey Children’s Cancer Research Institute at the Health Science Center garnered $10.9 million from the Cancer Prevention & Research Institute of Texas (CPRIT)―a larger amount than any other academic institution in the state. The Health Science Center received 24 percent of the $45.3 million awarded to 13 academic institutions on May 18. The grant was the […]

Dr. Yidong Chen awarded a $3.7M CPRIT Core facility award

May 1, 2016

In May 2016, Dr. Yidong Chen was awarded a $3.7M CPRIT Core facility award (RP160732) to upgrade and expand NGS capacity and further accelerate the adoption of high-throughput technology in translational cancer genetics and epigenetics research at UT Health San Antonio and the South Texas region. An Illumina NextSeq 500 was acquired by funding support […]

Clinical Cancer Research: Recurrent Mutations of Chromatin-Remodeling Genes and Kinase Receptors in Pheochromocytomas and Paragangliomas

May 1, 2016

Rodrigo A. Toledo, Yuejuan Qin, Zi-Ming Cheng, Qing Gao, Shintaro Iwata, Gustavo M. Silva, Manju L. Prasad, I. Tolgay Ocal, Sarika Rao, Neil Aronin, Marta Barontini, Jan Bruder, Robert L. Reddick, Yidong Chen, Ricardo C.T. Aguiar and Patricia L.M. Dahia Abstract Purpose: Pheochromocytomas and paragangliomas (PPGL) are genetically heterogeneous tumors of neural crest origin, but the molecular basis of most PPGLs is unknown. Experimental Design: We performed exome or transcriptome sequencing of 43 samples from 41 patients. A validation set of 136 PPGLs was used for amplicon-specific resequencing. In […]