Bioinformatics Advances: DepLink: an R Shiny app to systematically link genetic and pharmacologic dependencies of cancer (Zheng, Houghton, & Chen Labs)

June 27, 2023

Tapsya Nayak, Li-Ju Wang, Michael Ning, Gabriela Rubannelsonkumar, Eric Jin, Siyuan Zheng, Peter J Houghton, Yufei Huang, Yu-Chiao Chiu, Yidong Chen Abstract Motivation Large-scale genetic and pharmacologic dependency maps are generated to reveal genetic vulnerabilities and drug sensitivities of cancer. However, user-friendly software is needed to link such maps systematically. Results Here, we present DepLink, a web server to identify genetic and pharmacologic perturbations [...]

Neuro-Oncology: Lysine-specific histone demethylase 1A (KDM1A/LSD1) inhibition attenuates DNA double strand break repair and augments efficacy of temozolomide in glioblastoma (Chen, Lai, Zheng Labs)

March 23, 2023

Salvador Alejo, Bridgitte E Palacios, Prabhakar Pitta Venkata, Yi He, Wenjing Li, Jessica D Johnson, Chen Yihong, Sridharan Jayamohan, Uday P Pratap, Kyra Clarke, Yi Zou, Yingli Lv, Korri Weldon, Suryavathi Viswanadhapalli, Zhao Lai, Zhenqing Ye, Yidong Chen, Andrea R Gilbert, Takayoshi Suzuki, Rajeshwar R Tekmal, Weixing Zhao, Siyuan Zheng, Ratna K Vadlamudi, Andrew J Brenner, Gangadhara R Sareddy Abstract Background Efficient DNA repair in response to standard chemo and radiation therapies often contributes to GBM therapy resistance. [...]

Star Protocols: Protocol to benchmark gene expression signature scoring techniques for single-cell RNA sequencing data in cancer (Zheng Lab)

January 4, 2023

Nighat Noureen123 Xiaojing Wang12 Siyuan Zheng124 • Protocol for benchmarking signature scoring techniques in scRNAseq data analysis • Comparing single-cell and bulk-based approaches in sensitivity and specificity • Using down sampling to simulate the impact of dropouts on signature scoring techniques Summary Scoring gene signatures are common for bulk and single-cell RNA sequencing (scRNAseq) data. [...]

Genomics, Proteomics & Bioinformatics: Genome of White-blotched River Stingray Provides Novel Clues for Niche Adaptation and Skeleton Formation (Zheng Lab)

December 8, 2022

Jingqi Zhoua Ake Liub Funan He Yunbin Zhang Libing Shenef JunYugh XiangZhangi Abstract The white-blotched river stingray (Potamotrygon leopoldi) is a cartilaginous fish native to the Xingu River, a tributary of the Amazon River system. As a rare freshwater-dwelling cartilaginous fish in the Potamotrygonidae family that no member has the genome sequencing information, P. leopoldi [...]

Nature Communications: Genomic disparities between cancers in adolescent and young adults and in older adults (Wang, Langevin, Houghton, & Zheng)

December 6, 2022

Xiaojing Wang, Anne-Marie Langevin, Peter J. Houghton & Siyuan Zheng Cancers cause significant mortality and morbidity in adolescents and young adults (AYAs), but their biological underpinnings are incompletely understood. Here, we analyze clinical and genomic disparities between AYAs and older adults (OAs) in more than 100,000 cancer patients. We find significant differences in clinical presentation between [...]

Cancers: Inhibition of LIFR Blocks Adiposity-Driven Endometrioid Endometrial Cancer Growth (Chen, Lai, Zheng)

November 15, 2022

by  Logan Blankenship Uday P. Pratap Xue Yang Zexuan Liu Kristin A. Altwegg Bindu Santhamma Kumaraguruparan Ramasamy Swapna Konda Yidong Chen Zhao Lai Siyuan Zheng Gangadhara R. Sareddy Philip T. Valente Edward R. Kost Hareesh B. Nair Rajeshwar R. Tekmal Ratna K. Vadlamudi and Suryavathi Viswanadhapalli Simple Summary In this study, we utilized global RNA-seq [...]

Cancer Research: M6A RNA Methylation Regulates Histone Ubiquitination to Support Cancer Growth and Progression (Gupta, Zheng, Houghton, Chen, and Rao Labs)

March 21, 2022

Pooja Yadav; Panneerdoss Subbarayalu; Daisy Medina, Saif Nirzhor;  Santosh Timilsina; Subapriya Rajamanickam; Vijay K. Eedunuri; Yogesh Gupta Siyuan Zheng Nourhan Abdelfattah Yufei Huang Ratna Vadlamudi Robert Hromas; Paul Meltzer Peter Houghton; Yidong Chen Manjeet K. Rao Abstract Osteosarcoma is the most common malignancy of the bone, yet the survival for osteosarcoma patients is virtually unchanged [...]

eLife: Signature-scoring methods developed for bulk samples are not adequate for cancer single-cell RNA sequencing data (Zheng, Chen, & Wang Labs)

March 7, 2022

Nighat Noureen,  Zhenqing Ye,  Yidong Chen,  Xiaojing Wang,  Siyuan Zheng  Abstract Quantifying the activity of gene expression signatures is common in analyses of single-cell RNA sequencing data. Methods originally developed for bulk samples are often used for this purpose without accounting for contextual differences between bulk and single-cell data. More broadly, these methods have not [...]

MSN: Using Next Generation Sequencing, the Greehey CCRI bioinformatics team is helping determine COVID19 strains (Chen, Lai, Zheng, Wang Labs)

December 17, 2021

"Since the coronavirus pandemic began almost two years ago there have been over a dozen strains of the virus. Here at UT Health San Antonio, they have a lab which differentiates between each of the strains in an effort to save lives. UT Health San Antonio uses a technology called next-generation sequencing to differentiate the [...]

CANCER RESEARCH: SNAI2-Mediated Repression of BIM Protects Rhabdomyosarcoma from Ionizing Radiation (Houghton, Ignatius, Vaseva, and Zheng labs)

November 24, 2021

Long Wang, Nicole R. Hensch, Kathryn Bondra, Prethish Sreenivas, Xiang R. Zhao, Jiangfei Chen, Rodrigo Moreno Campos, Kunal Baxi, Angelina V. Vaseva, Benjamin D. Sunkel, Berkley E. Gryder, Silvia Pomella, Benjamin Z. Stanton, Siyuan Zheng, Eleanor Y. Chen, Rossella Rota, Javed Khan, Peter J. Houghton and Myron S. Ignatius Abstract Ionizing radiation (IR) and chemotherapy [...]