BMC Genomics: CeL-ID: cell line identification using RNA-seq data

February 4, 2019

Tabrez A. Mohammad, Yun S. Tsai, Safwa Ameer, Hung-I Harry Chen, Yu-Chiao Chiu & Yidong Chen Abstract Background Cell lines form the cornerstone of cell-based experimentation studies into understanding the underlying mechanisms of normal and disease biology including cancer. However, it is commonly acknowledged that contamination of cell lines is a prevalent problem affecting biomedical science and available methods for cell […]


Journal of Oral Pathology & Medicine: The novel capsazepine analog, CIDD‐99, significantly inhibits oral squamous cell carcinoma in vivo through a TRPV1‐independent induction of ER stress, mitochondrial dysfunction, and apoptosis

February 3, 2019

Jorge J. De La Chapa, Prajjal K. Singha, Kristen K. Self, McKay L. Sallaway, Stanton F. McHardy, Matthew J. Hart, Howard Stan McGuff, Matthew C. Valdez Francisco Ruiz II, Srikanth R. Polusani, Cara B. Gonzales Abstract Background Oral squamous cell carcinoma (OSCC) is a deadly disease with a mere 40% five‐year survival rate for patients with advanced disease. Previously, we discovered that capsazepine […]


Oncology Learning Network: Podcast – Daunorubicin Decreases Long-Term Cardiomyopathy Risk in Cancer Survivors

January 31, 2019

In an interview with Oncology Learning Network, Gregory J. Aune, MD, Assistant Professor of Pediatrics at UT Health San Antonio and Greehey Children’s Cancer Research Institute, discussed his team’s findings from a multicenter study evaluating the long-term risk for anthracycline-related cardiomyopathy in survivors of childhood cancer (JAMA Oncol. 2019 Jan 31. Epub ahead of print).


Drug Discovery & Development: Do All Chemotherapies Have Equal Long-Term Heart Risk?

January 31, 2019

Gregory Aune, MD, PhD, of UT Health San Antonio, served on a team that found different chemotherapy drugs used to treat children with cancer appear to have different risks long term for cardiomyopathy (abnormal heart muscle with impaired function). The study was in more than 28,000 childhood cancer survivors. Credit: UT Health San Antonio In […]


BMC Medical Genomics: Predicting drug response of tumors from integrated genomic profiles by deep neural networks

January 31, 2019

Yu-Chiao Chiu, Hung-I Harry Chen, Tinghe Zhang, Songyao Zhang, Aparna Gorthi, Li-Ju Wang, Yufei Huang & Yidong Chen Abstract Background The study of high-throughput genomic profiles from a pharmacogenomics viewpoint has provided unprecedented insights into the oncogenic features modulating drug response. A recent study screened for the response of a thousand human cancer cell lines to a wide collection of anti-cancer drugs and […]


JAMA Oncology: Derivation of Anthracycline and Anthraquinone Equivalence Ratios to Doxorubicin for Late-Onset Cardiotoxicity

January 31, 2019

Elizabeth A. M. Feijen, PhD1,2; Wendy M. Leisenring, ScD3,4; Kayla L. Stratton, MS3,4; Kirsten K. Ness, PT, PhD5; Helena J. H. van der Pal, MD, PhD2; Elvira C. van Dalen, MD, PhD1,2; Gregory T. Armstrong, MD, MSCE5; Gregory J. Aune, MD, PhD6; Daniel M. Green, MD5; Melissa M. Hudson, MD7; Jacqueline Loonen, MD, PhD8; Kevin C. Oeffinger, MD9; Leslie L. Robison, PhD5; Yutaka Yasui, PhD5; Leontien C. M. Kremer, MD, PhD1,2; Eric J. Chow, MD, MPH3,4,10 Abstract Importance  Anthracyclines are part of many effective pediatric cancer treatment protocols. Most pediatric oncology treatment groups assume that the hematologic toxicity of anthracycline agents is equivalent […]


MDPI: CENP-A Ubiquitylation Contributes to Maintaining the Chromosomal Location of the Centromere

January 15, 2019

Yohei Niikura 1,2,* Risa Kitagawa 1 and Katsumi Kitagawa 1,* Abstract The centromere plays an essential role in accurate chromosome segregation, and the chromosomal location of the centromere is determined by the presence of a histone H3 variant, centromere protein A (CENP-A), in centromeric nucleosomes. However, the precise mechanisms of deposition, maintenance, and inheritance of CENP-A at […]


PLOS Computational Biology: Global analysis of N6-methyladenosine functions and its disease association using deep learning and network-based methods

January 2, 2019

Song-Yao Zhang, Shao-Wu Zhang, Xiao-Nan Fan, Jia Meng, Yidong Chen, Shou-Jiang Gao, Yufei Huang Abstract N6-methyladenosine (m6A) is the most abundant methylation, existing in >25% of human mRNAs. Exciting recent discoveries indicate the close involvement of m6A in regulating many different aspects of mRNA metabolism and diseases like cancer. However, our current knowledge about how m6A levels are controlled and […]


BMC Systems Biology: GSAE: an autoencoder with embedded gene-set nodes for genomics functional characterization

December 21, 2018

Hung-I Harry Chen, Yu-Chiao Chiu, Tinghe Zhang, Songyao Zhang, Yufei Huang & Yidong Chen Abstract Background Bioinformatics tools have been developed to interpret gene expression data at the gene set level, and these gene set-based analyses improve the biologists’ capability to discover the functional relevance of their experiment design. While elucidating gene set individually, inter-gene sets association is rarely taken into […]