MD Anderson Cancer Center UTHealth
Graduate School of Biomedical Sciences

Current Students

All First-authored papers notated with *

Jiun-Sheng Chen

*Targeted Gene Sequencing in Children with Crohn’s Disease and Their Parents: Implications for Missing Heritability
Jiun-Sheng Chen, Fulan Hu, Subra Kugathasan, Lynn B. Jorde, David Nix, Ann Rutherford, Lee Denson, W. Scott Watkins, Sampath Prahalad, Chad Huff, Stephen L. Guthery
G3 (Bethesda) 2018 Sep; 8(9): 2881–2888. Published online 2018 Aug 30. doi: 10.1534/g3.118.200404
PMCID: PMC6118318

Integrated case-control and somatic-germline interaction analyses of melanoma susceptibility genes
Yao Yu, Hao Hu, Jiun-Sheng Chen, Fulan Hu, Jerry Fowler, Paul Scheet, Hua Zhao, Chad D. Huff
Biochim Biophys Acta Mol Basis Dis. Author manuscript; available in PMC 2019 Jun 1.
Published in final edited form as: Biochim Biophys Acta Mol Basis Dis. 2018 Jun; 1864(6 Pt B): 2247–2254. Published online 2018 Jan 6. doi: 10.1016/j.bbadis.2018.01.007
PMCID: PMC6501568

TGF-β/β2-spectrin/CTCF-regulated tumor suppression in human stem cell disorder Beckwith-Wiedemann syndrome
Jian Chen, Zhi-Xing Yao, Jiun-Sheng Chen, Young Jin Gi, Nina M. Muñoz, Suchin Kundra, H. Franklin Herlong, Yun Seong Jeong, Alexei Goltsov, Kazufumi Ohshiro, Nipun A. Mistry, Jianping Zhang, Xiaoping Su, Sanaa Choufani, Abhisek Mitra, Shulin Li, Bibhuti Mishra, Jon White, Asif Rashid, Alan Yaoqi Wang, Milind Javle, Marta Davila, Peter Michaely, Rosanna Weksberg, Wayne L. Hofstetter, Milton J. Finegold, Jerry W. Shay, Keigo Machida, Hidekazu Tsukamoto, Lopa Mishra
J Clin Invest. 2016 Feb 1; 126(2): 527–542. Published online 2016 Jan 19. doi: 10.1172/JCI80937
PMCID: PMC4731168

Evidence of intracellular stages in Trypanosoma (Megatrypanumtheileri in non-phagocytic mammalian cells
Yen-Feng Lee, Ching-Chang Cheng, Jiun-Sheng Chen, Nai-Nu Lin, Yi-Wen Hung, Jiunn-Min Wang, Wu-Chun Tu, Kwong-Chung Tung, Yung-Tsung Chiu
Veterinary Parasitology. Volume 191, Issues 3–4, 31 January 2013, Pages 228-239. doi: 10.1016/j.vetpar.2012.08.027

Targeting TGF-β signaling in cancer
Lior H Katz, Ying Li, Jiun-Sheng Chen, Nina M Muñoz, Avijit Majumdar, Jian Chen, Lopa Mishra
Expert Opin Ther Targets. Author manuscript; available in PMC 2013 Aug 16.
Published in final edited form as: Expert Opin Ther Targets. 2013 Jul; 17(7): 743–760. Published online 2013 May 7. doi: 10.1517/14728222.2013.782287
PMCID: PMC3745214

Effect of oxidized regenerated cellulose on the healing of pharyngeal wound: An experimental animal study
Shih-An Liu, Ching-Chang Cheng, Jiun-Sheng Chen, Yi-Wen Hung, Fun-Jou Chen, Yung-Tsung Chiu
Journal of the Chinese Medical Association
Volume 75, Issue 4, 2012, Pages 176-182, ISSN 1726-4901, doi: 10.1016/j.jcma.2012.03.007

Medina Colic

CRISPR/CAS9-based DNA damage response screens reveal gene-drug interactions DNA Repair
Dan Su, Xu Feng, Medina Colic, Yunfei Wang, Chunchao Zhang, Chao Wang, Mengfan Tang, Traver Hart, Junjie Chen,
Volume 87, 2020, 102803, ISSN 1568-7864, doi: 10.1016/j.dnarep.2020.102803

*Identifying chemogenetic interactions from CRISPR screens with drugZ.
Colic M, Wang G, Zimmermann M, Mascall K, McLaughlin M, Bertolet L, Lenoir WF, Moffat J, Angers S, Durocher D, Hart T.
Genome Med. 2019 Aug 22;11(1):52. doi: 10.1186/s13073-019-0665-3.
PMID: 31439014 

*Chemogenetic interactions in human cancer cells
Colic M, Hart T
Computational and Structural Biotechnology Journal. Volume 17, 2019, Pages 1318-1325, ISSN 2001-0370

Darlan Conterno Minussi

*esiCancer: Evolutionary In Silico Cancer Simulator
Darlan Conterno Minussi,
 Bernardo Henz, Mariana dos Santos Oliveira, Eduardo C. Filippi-Chiela, Manuel M. Oliveira and Guido Lenz
Cancer Res March 1 2019 (79) (5) 1010-1013; DOI: 10.1158/0008-5472.CAN-17-3924

 Analysis of NTPDase2 in the cell membrane using fluorescence recovery after photobleaching (FRAP)
Kipper, Franciele Cristina,Tamajusuku, Alessandra Sayuri Kikuchi, Minussi, Darlan Conterno, Vargas, José Eduardo, Battastini, Ana Maria Oliveira, Kaczmarek, Elzbieta, Robson, Simon Christopher, Lenz, Guido, A Wink, Márcia Rosângela
Cytometry Part A
24 January 2108, P 232-238, V 93, N 2, @ 1552-4922, doi: 10.1002/cyto.a.23317

A20 Regulates Atherogenic Interferon (IFN)-γ Signaling in Vascular Cells by Modulating Basal IFNβ Levels
Herwig P. Moll, Andy Lee, Darlan C. Minussi, Cleide G. da Silva, Eva Csizmadia, Manoj Bhasin, Christiane Ferran
J Biol Chem. 2014 Nov 7; 289(45): 30912–30924. Published online 2014 Sep 12. doi: 10.1074/jbc.M114.591966
PMCID: PMC4223299

Nazanin Esmaeili Anvar

*Association between Interleukin 16 Gene Polymorphisms (rs1131445, rs4072111) and Late Onset of Alzheimer’s Disease in Iranian Patients
Nazanin Esmaeili Anvar
, Niloofar Bazazzadegan, Mina Ohadi, Kourosh Kamali, Hamidreza Khorram Khorshid
Salmand: Iranian Journal of Ageing 2016, 11(1): 64-71. Doi: 10.21859/sija-110164

Siyuan He

Methylation silencing of TGF-β receptor type II is involved in malignant transformation of esophageal squamous cell carcinoma
Yarui Ma, Siyuan He, Aiai Gao, Ying Zhang, Qing Zhu, Pei Wang, Beibei Yang, Huihui Yin, Yifei Li, Jinge Song, Pinli Yue, Mo Li, Dandan Zhang, Yun Liu, Xiaobing Wang, Mingzhou Guo, Yuchen Jiao
Clin Epigenetics. 2020; 12: 25. Published online 2020 Feb 11. doi: 10.1186/s13148-020-0819-6
PMCID: PMC7014638

*Data mining of esophageal squamous cell carcinoma from The Cancer Genome Atlas database
He SY, Wang XB, Jiao YC.
Zhonghua Zhong Liu Za Zhi. 2018 Jul 23;40(7):517-522. Chinese. doi: 10.3760/cma.j.issn.0253-3766.2018.07.007
PMID: 30060360

Swaminathan Kumar

Gene set analysis of post-lactational mammary gland involution gene signatures in inflammatory and triple-negative breast cancer
Arvind Bambhroliya, Renae D. Van Wyhe, Swaminathan Kumar, Bisrat G. Debeb, Jay P. Reddy, Steve Van Laere, Randa El-Zein, Arvind Rao, Wendy A. Woodward
PLoS One. 2018; 13(4): e0192689. Published online 2018 Apr 4. doi: 10.1371/journal.pone.0192689
PMCID: PMC5884491

Tapsi Kumar

SCMarker: Ab initio marker selection for single cell transcriptome profiling
Fang Wang, Shaoheng Liang, Tapsi Kumar, Nicholas Navin, Ken Chen
PLoS Comput Biol. 2019 Oct; 15(10): e1007445. Published online 2019 Oct 28. doi: 10.1371/journal.pcbi.1007445
PMCID: PMC6837541

Jake Leighton

Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types.
Ge Z, Leighton JS, Wang Y, Peng X, Chen Z, Chen H, Sun Y, Yao F, Li J, Zhang H, Liu J, Shriver CD, Hu H; Cancer Genome Atlas Research Network, Piwnica-Worms H, Ma L, Liang H.
Cell Rep. 2018 Apr 3;23(1):213-226.e3. doi: 10.1016/j.celrep.2018.03.047.
PMID: 29617661

Walter Frank Lenoir

network of human functional gene interactions from knockout fitness screens in cancer cells
Eiru Kim, Merve Dede, Walter F Lenoir, Gang Wang, Sanjana Srinivasan, Medina Colic, Traver Hart
Life Sci Alliance. 2019 Apr; 2(2): e201800278. Published online 2019 Apr 12. doi: 10.26508/lsa.201800278
PMCID: PMC6464042

*PICKLES: the database of pooled in-vitro CRISPR knockout library essentiality screens.
Lenoir WF, Lim TL, Hart T.
Nucleic Acids Res. 2018 Jan 4;46(D1):D776-D780. doi: 10.1093/nar/gkx993.
PMID: 29077937

Yiyun Lin

Advancing Cancer Research and Medicine with Single-Cell Genomics
Lim B, Lin Y, Navin N.
Cancer Cell. 2020 Apr 13;37(4):456-470. doi: 10.1016/j.ccell.2020.03.008.
PMID: 32289270

Reprogramming of lipid metabolism in cancer-associated fibroblasts potentiates migration of colorectal cancer cells
Gong J, Lin Y, Zhang H, Liu C, Cheng Z, Yang X, Zhang J, Xiao Y, Sang N, Qian X, Wang L, Cen X, Du X, Zhao Y.
Cell Death Dis. 2020 Apr 23;11(4):267. doi: 10.1038/s41419-020-2434-z. PMID: 32327627; PMCID: PMC7181758 

*Cocaine modifies brain lipidome in mice
Yiyun Lin, Hui Gu, Linhong Jiang, Wei Xu, Chunqi Liu, Yan Li, Xinying Qian, Dandan Li, Zhuoling Li, Jing Hu, Huaqin Zhang, Wei Guo, Yinglan Zhao, Xiaobo Cen,
Molecular and Cellular Neuroscience, Volume 85, 2017, Pages 29-44, ISSN 1044-7431,
Doi: 10.1016/j.mcn.2017.08.004

Remodeling of brain lipidome in methamphetamine-sensitized mice
Linhong Jiang, Hui Gu, Yiyun Lin, Wei Xu, Ruiming Zhu, Jueying Kong, Li Luo, Hailei Long, Bing Liu, Bo Chen, Yinglan Zhao, Xiaobo Cen,
Toxicology Letters, Volume 279, 2017, Pages 67-76, ISSN 0378-4274,
Doi: 10.1016/j.toxlet.2017.07.214.

Akash Mitra

*Spatially resolved analyses link genomic and immune diversity and reveal unfavorable neutrophil activation in melanoma
Akash Mitra, Miles C. Andrews, Whijae Roh, Marianna Petaccia De Macedo, Courtney W. Hudgens, Fernando Carapeto, Shailbala Singh, Alexandre Reuben, Feng Wang, Xizeng Mao, Xingzhi Song, Khalida Wani, Samantha Tippen, Kwok-Shing Ng, Aislyn Schalck, Donald A. Sakellariou-Thompson, Eveline Chen, Sangeetha M. Reddy, Christine N. Spencer, Diana Wiesnoski, Latasha D. Little, Curtis Gumbs, Zachary A. Cooper, Elizabeth M. Burton, Patrick Hwu, Michael A. Davies, Jianhua Zhang, Chantale Bernatchez, Nicholas Navin, Padmanee Sharma, James P. Allison, Jennifer A. Wargo, Cassian Yee, Michael T. Tetzlaff, Wen-Jen Hwu, Alexander J. Lazar, P. Andrew Futreal
Nat Commun. 2020; 11: 1839. Published online 2020 Apr 15. doi: 10.1038/s41467-020-15538-9
PMCID: PMC7160105

Aislyn Schalck

Multiclonal Invasion in Breast Tumors Identified by Topographic Single Cell Sequencing.
Casasent AK, Schalck A, Gao R, Sei E, Long A, Pangburn W, Casasent T, Meric-Bernstam F, Edgerton ME, Navin NE.
Cell. 2018 Jan 11;172(1-2):205-217.e12. doi: 10.1016/j.cell.2017.12.007. Epub 2018 Jan 4.
PMID: 29307488

Sahil Seth

*Pre-existing Functional Heterogeneity of Tumorigenic Compartment as the Origin of Chemoresistance in Pancreatic Tumors
Sahil Seth, Chieh-Yuan Li, I-Lin Ho,  Denise Corti, Sara Loponte, Luigi Sapio, Edoardo Del Poggetto, Er-Yen Yen, Frederick Scott Robinson, Michael Peoples, Tatiana Karpinets, Angela Kay Deem, Tapsi Kumar, Xingzhi Song, Shan Jiang, Ya’an Kang, Jason Fleming, Michael Kim, Jianhua Zhang, Anirban Maitra, Timothy Paul Heffernan, Virginia Giuliani, Giannicola Genovese, Andrew Futreal, Giulio Francesco Draetta, Alessandro Carugo, and Andrea Viale
Cell Reports. 2019 Feb; Vol 26, Issue 6, P1518-1532.E9, DOI: 10.1016/j.celrep.2019.01.048

Alumni

Alexander Davis

Single-cell DNA sequencing reveals a late-dissemination model in metastatic colorectal cancer.
Leung ML, Davis A, Gao R, Casasent A, Wang Y, Sei E, Vilar E, Maru D, Kopetz S, Navin NE.
Genome Res. 2017 Aug;27(8):1287-1299. doi: 10.1101/gr.209973.116. Epub 2017 May 25.
PMID: 28546418 

*Tumor evolution: Linear, branching, neutral or punctuated?
Davis A, Gao R, Navin N.
Biochim Biophys Acta. 2017 Apr;1867(2):151-161. doi: 10.1016/j.bbcan.2017.01.003. Epub 2017 Jan 19. Review.
PMID:28110020

Punctuated copy number evolution and clonal stasis in triple-negative breast cancer.
Gao R, Davis A, McDonald TO, Sei E, Shi X, Wang Y, Tsai PC, Casasent A, Waters J, Zhang H, Meric-Bernstam F, Michor F, Navin NE.
Nat Genet. 2016 Oct;48(10):1119-30. doi: 10.1038/ng.3641. Epub 2016 Aug 15.
PMID:27526321

*Computing tumor trees from single cells.
Davis A, Navin NE.
Genome Biol. 2016 May 26;17(1):113. doi: 10.1186/s13059-016-0987-z.
PMID: 27230879

Yihua Liu

*Identification of thresholds for dichotomizing DNA methylation data.
Liu Y, Ji Y, Qiu P.
EURASIP J Bioinform Syst Biol. 2013 Jun 6;2013(1):8. doi: 10.1186/1687-4153-2013-8.
PMID: 23742247

Smruthy Sivakumar

TBX2 subfamily suppression in lung cancer pathogenesis: a high-potential marker for early detection.
Khalil AA, Sivakumar S, Lucas FAS, McDowell T, Lang W, Tabata K, Fujimoto J, Yatabe Y, Spira A, Scheet P, Nemer G, Kadara H.
Oncotarget. 2017 Aug 4;8(40):68230-68241. doi: 10.18632/oncotarget.19938. eCollection 2017 Sep 15.
PMID: 28978111

*Genomic Landscape of Atypical Adenomatous Hyperplasia Reveals Divergent Modes to Lung Adenocarcinoma.
Sivakumar S, Lucas FAS, McDowell TL, Lang W, Xu L, Fujimoto J, Zhang J, Futreal PA, Fukuoka J, Yatabe Y, Dubinett SM, Spira AE, Fowler J, Hawk ET, Wistuba II, Scheet P, Kadara H.
Cancer Res. 2017 Nov 15;77(22):6119-6130. doi: 10.1158/0008-5472.CAN-17-1605. Epub 2017 Sep 26.
PMID: 28951454

Rapid and powerful detection of subtle allelic imbalance from exome sequencing data with hapLOHseq.
San Lucas FA, Sivakumar S, Vattathil S, Fowler J, Vilar E, Scheet P.
Bioinformatics. 2016 Oct 1;32(19):3015-7. doi: 10.1093/bioinformatics/btw340. Epub 2016 Jun 10.
PMID: 27288500

Youyi Zhang

Radiomic analysis in prediction of Human Papilloma Virus status.
Yu K, Zhang Y, Yu Y, Huang C, Liu R, Li T, Yang L, Morris JS, Baladandayuthapani V, Zhu H.
Clin Transl Radiat Oncol. 2017 Nov 6;7:49-54. doi: 10.1016/j.ctro.2017.10.001. eCollection 2017 Dec.
PMID: 29594229


Heng Zhou

*Accuracy, Safety, and Reliability of Novel Phase I Trial Designs.
Zhou H, Yuan Y, Nie L.
Clin Cancer Res. 2018 Apr 16. pii: clincanres.0168.2018. doi: 10.1158/1078-0432.CCR-18-0168. [Epub ahead of print]
PMID: 29661774

*BOP2: Bayesian optimal design for phase II clinical trials with simple and complex endpoints.
Zhou H, Lee JJ, Yuan Y.
Stat Med. 2017 Sep 20;36(21):3302-3314. doi: 10.1002/sim.7338. Epub 2017 Jun 7.
PMID: 28589563