BMG Medical Genomics: Convolutional neural network models for cancer type prediction based on gene expression

April 3, 2020

Milad Mostavi, Yu-Chiao Chiu, Yufei Huang & Yidong Chen Abstract Background Precise prediction of cancer types is vital for cancer diagnosis and therapy. Through a predictive model, important cancer marker genes can be inferred. Several studies have attempted to build machine learning models for this task however none has taken into consideration the effects of tissue of origin that can […]

bioRxiv : Assessing the Heterogeneity of Cardiac Non-myocytes and the Effect of Cell Culture with Integrative Single Cell Analysis

March 4, 2020

Abstract Cardiac non-myocytes comprise a diverse and crucial cell population in the heart that plays dynamic roles in cardiac wound healing and growth. Non-myocytes broadly fall into four cell types: endothelium, fibroblasts, leukocytes, and pericytes. Here we characterize the diversity of the non-myocytes in vivo and in vitro using mass cytometry. By leveraging single-cell RNA […]

Greehey CCRI Receives Its First NIH K99 Award (Chen Lab)

March 2, 2020

      Yu-Chiao Chiu, PhD, a postdoctoral researcher at the Greehey Children’s Cancer Research Institute (GCCRI), received the prestigious NIH Pathway to Independence Award (K99/R00) from the National Cancer Institute (NCI). The highly competitive NIH grant is awarded to about 30 outstanding cancer researchers nationwide each year for them to complete mentored training (K99 […]

Advances in Urology: Microbiome within Primary Tumor Tissue from Renal Cell Carcinoma May Be Associated with PD-L1 Expression of the Venous Tumor Thrombus

February 18, 2020

Michael A. Liss,1 Yidong Chen,2 Ronald Rodriguez,1 Deepak Pruthi,1 Teresa Johnson-Pais,3 Hanzhang Wang,1 Ahmed Mansour,1 James R. White,4 and Dharam Kaushik1 Abstract Objective. To perform a proof of concept microbiome evaluation and PD-L1 expression profiling in clear-cell renal cell carcinoma (cc-RCC) with associated tumor thrombus (TT). Methods. After IRB approval, six patients underwent radical nephrectomy (RN) with venous tumor thrombectomy (VTT). We collected fresh tissue […]

Endocrinology: Inhibitory Interplay of SULT2B1b Sulfotransferase with AKR1C3 Aldo-keto Reductase in Prostate Cancer

January 2, 2020

Sulgi Park, Chung-Seog Song, Chun-Lin Lin, Shoulei Jiang, Pawel A Osmulski, Chiou-Miin Wang, Brett T Marck, Alvin M Matsumoto, Colm Morrissey, Maria E Gaczynska, Yidong Chen, Elahe A Mostaghel, Bandana Chatterjee Abstract SULT2B1b (SULT2B) is a prostate-expressed hydroxysteroid sulfotransferase, which may regulate intracrine androgen homeostasis by mediating 3β-sulfation of dehydroepiandrosterone (DHEA), the precursor for 5α-dihydrotestosterone (DHT) biosynthesis. The aldo-keto reductase (AKR)1C3 regulates androgen receptor (AR) activity in […]

BMG Genomics: An ancestry informative marker panel design for individual ancestry estimation of Hispanic population using whole exome sequencing data

December 30, 2019

Li-Ju Wang, Catherine W. Zhang, Sophia C. Su, Hung-I H. Chen, Yu-Chiao Chiu, Zhao Lai, Hakim Bouamar, Amelie G. Ramirez, Francisco G. Cigarroa, Lu-Zhe Sun & Yidong Chen Abstract Background Europeans and American Indians were the major genetic ancestry of Hispanics in the U.S. These ancestral groups have markedly different incidence rates and outcomes in many types of cancers. Therefore, the genetic admixture may cause a […]

Molecular Carcinogenesis: PELP1 signaling contributes to medulloblastoma progression by regulating the NF‐κB pathway

December 24, 2019

Yiliao Luo Mengxing Li Uday P. Pratap Suryavathi Viswanadhapalli Junhao Liu Prabhakar P. Venkata Kristin A. Altwegg Bridgitte E. Palacios Xiaonan Li Yihong Chen Manjeet K. Rao Andrew J. Brenner Gangadhara R. Sareddy Ratna K. Vadlamud Abstract Medulloblastoma (MB) is the most common and deadliest brain tumor in children. Proline‐, glutamic acid‐, and leucine‐rich protein […]

Briefings in Bioinformatics: Deep learning of pharmacogenomics resources: moving towards precision oncology

December 8, 2019

Yu-Chiao Chiu, Hung-I Harry Chen, Aparna Gorthi, Milad Mostavi, Siyuan Zheng, Yufei Huang, Yidong Chen Abstract The recent accumulation of cancer genomic data provides an opportunity to understand how a tumor’s genomic characteristics can affect its responses to drugs. This field, called pharmacogenomics, is a key area in the development of precision oncology. Deep learning (DL) methodology has emerged as a […]

Cell Reports: Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design

November 5, 2019

Author links open overlay panelJo LynneRokita123  Komal S.Rathi23  Maria F.Cardenas4  Kristen A.Upton1  JoyJayaseelan4  Katherine L.Cross5  JacobPfeil6  Laura E.Egolf17  Gregory P.Way8  AlvinFarrel2  Nathan M.Kendsersky19  KhushbuPatel2  Krutika S.Gaonkar23  ApexaModi18  Esther R.Berko1  GonzaloLopez12  ZalmanVaksman2  ChelseaMayoh10  JonasNance11  KristynMcCoy11  MichelleHaber10  KathrynEvans10  HannahMcCalmont10  KaterinaBendak10  Julia W.Böhm10  Glenn M.Marshall1012  VanessaTyrrell13  KarthikKalletla23  Frank K.Braun14  LinQi1516  YunchenDu1516  HuiyuanZhang1516Holly B.Lindsay1516  SiboZhao1516JackShu1516  PatriciaBaxter1516  ChristopherMorton17  DiasKurmashev18  SiyuanZheng18 […]

Journal of Immunology: Immune Sensing of Aeroallergen-Associated Double-Stranded RNA Triggers an IFN Response and Modulates Type 2 Lung Inflammation

November 1, 2019

Li She, Hamad H. Alanazi, Liping Yan, Yi Zou, Yilun Sun, Peter H. Dube, Edward G. Brooks, Gema D. Barrera, Zhao Lai, Yidong Chen, Yong Liu, Xin Zhang and Xiao-Dong Li Abstract The innate immune sensing of allergens or allergen-associated components regulates the development of type 2 inflammatory responses. However, the underlying molecular basis by which allergens or allergen-associated components are detected by innate immune receptors remains elusive. […]