MD Anderson Cancer Center UTHealth
Graduate School of Biomedical Sciences

Current Students

All First-authored papers notated with *

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

Medina Colic

*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

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

*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

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

Alumni

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