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 […]

BMC Systems Biology: scdNet: a computational tool for single-cell differential network analysis

December 21, 2018

Yu-Chiao Chiu, Tzu-Hung Hsiao, Li-Ju Wang, Yidong Chen & Yu-Hsuan Joni Shao Abstract Background Single-cell RNA sequencing (scRNA-Seq) is an emerging technology that has revolutionized the research of tumor heterogeneity. However, the highly sparse data matrices generated by the technology have posed an obstacle to the analysis of differential gene regulatory networks. Results Addressing the challenges, this study presents, as […]

PLoS One: microRNA-2110 functions as an onco-suppressor in neuroblastoma by directly targeting Tsukushi

December 14, 2018

Zhenze Zhao, Veronica Partridge, Michaela Sousares, Spencer D. Shelton, Cory L. Holland, Alexander Pertsemlidis, Liqin Du  Abstract microRNA-2110 (miR-2110) was previously identified as inducing neurite outgrowth in neuroblastoma cell lines BE(2)-C, suggesting its differentiation-inducing and oncosuppressive function in neuroblastoma. In this study, we demonstrated that synthetic miR-2110 mimic had a generic effect on reducing cell […]

Frontiers in Genetics: Estrogen-Dependent Upregulation of Adcyap1r1 Expression in Nucleus Accumbens Is Associated With Genetic Predisposition of Sex-Specific QTL for Alcohol Consumption on Rat Chromosome 4

December 4, 2018

John Paul Spence 1, Jill L Reiter 1, Bin Qiu 2, Hao Gu 2, Dawn K Garcia 3, Lingling Zhang 2, Tamara Graves 1, Kent E Williams 1, Paula J Bice 4, Yi Zou 3, Zhao Lai 4, Weidong Yong 2, Tiebing Liang 1 Abstract Humans show sex differences related to alcohol use disorders (AUD). Animal model research has the potential to provide important insight into how sex differences affect alcohol consumption, particularly because female animals frequently drink more than […]

Clinical Cancer Research: Abemaciclib Is Active in Preclinical Models of Ewing Sarcoma via Multipronged Regulation of Cell Cycle, DNA Methylation, and Interferon Pathway Signaling

December 1, 2018

Michele Dowless, Caitlin D. Lowery, Terry Shackleford, Matthew Renschler, Jennifer Stephens, Robert Flack, Wayne Blosser, Simone Gupta, Julie Stewart, Yue Webster, Jack Dempsey, Alle B. VanWye, Philip Ebert, Philip Iversen, Jonathan B. Olsen, Xueqian Gong, Sean Buchanan, Peter Houghton, and Louis Stancato Abstract Purpose: Ewing sarcoma (ES) is a rare and highly malignant cancer that occurs in the bone and surrounding tissue of children and adolescents. The EWS/ETS fusion transcription factor that drives ES pathobiology was previously demonstrated to modulate cyclin D1 expression. In this study, we evaluated abemaciclib, a small-molecule CDK4, and CDK6 (CDK4 […]

Genome Biology: The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data

December 1, 2018

Gerben Menschaert, Xiaojing Wang, Andrew R Jones, Fawaz Ghali, David Fenyö, Volodimir Olexiouk, Bing Zhang, Eric W Deutsch, Tobias Ternent, Juan Antonio Vizcaíno On behalf of The Human Proteome Organization (HUPO) Proteomics Standards Initiative, we introduce here two novel standard data formats, proBAM and proBed, that have been developed to address the current challenges of […]