Current Students
All First-authored papers notated with *
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
*Breast tumours maintain a reservoir of subclonal diversity during expansion.
Minussi DC, Nicholson MD, Ye H, Davis A, Wang K, Baker T, Tarabichi M, Sei E, Du H, Rabbani M, Peng C, Hu M, Bai S, Lin YW, Schalck A, Multani A, Ma J, McDonald TO, Casasent A, Barrera A, Chen H, Lim B, Arun B, Meric-Bernstam F, Van Loo P, Michor F, Navin NE.
Nature. 2021 Apr;592(7853):302-308. doi: 10.1038/s41586-021-03357-x. Epub 2021 Mar 24.
PMID: 33762732
*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 2018, 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
*Association between polymorphisms in Interleukin-16 gene and risk of late-onset Alzheimer's disease
Anvar NE, Saliminejad K, Ohadi M, Kamali K, Daneshmand P, Khorshid HR.
J Neurol Sci. 2015 Nov 15;358(1-2):324-7. doi: 10.1016/j.jns.2015.09.344. Epub 2015 Sep 11.
PMID: 26386715
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
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
Immuno-genomic landscape of osteosarcoma
Chia-Chin Wu, Hannah C. Beird, J. Andrew Livingston, Shailesh Advani, Akash Mitra, Shaolong Cao, Alexandre Reuben, Davis Ingram, Wei-Lien Wang, Zhenlin Ju, Cheuk Hong Leung, Heather Lin, Youyun Zheng, Jason Roszik, Wenyi Wang, Shreyaskumar Patel, Robert S. Benjamin, Neeta Somaiah, Anthony P. Conley, Gordon B. Mills, Patrick Hwu, Richard Gorlick, Alexander Lazar, Najat C. Daw, Valerae Lewis, P. Andrew Futreal
Nat Commun. 2020; 11: 1008. Published online 2020 Feb 21. doi: 10.1038/s41467-020-14646-w
PMCID: PMC7035358
Alexandria Plumer
Effects of acid challenges on type 2 angiotensin II receptor-sensitive ammonia production by the proximal tubule
Nagami GT, Plumer AK, Beyda RM, Schachter O.
Am J Physiol Renal Physiol. 2014 Jul 1;307(1):F53-7. doi: 10.1152/ajprenal.00466.2013. Epub 2014 May 14.
PMID: 24829505
Keith Sanders
Biomarkers of radiation-induced vascular injury
Venkatesulu BP, Sanders KL, Hsieh CE, Kim BK, Krishnan S.
Cancer Rep (Hoboken). 2019 Apr;2(2):e1152. doi: 10.1002/cnr2.1152. Epub 2018 Dec 3.
PMID: 32721134
Recent advances in radiation therapy of pancreatic cancer
Venkatesulu BP, Hsieh CE, Sanders KL and Krishnan S.
F1000Research 2018, 7(F1000 Faculty Rev):1931 doi.org/10.12688/f1000research.16272.1
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
Ziqiao Wang
*IMIX: a multivariate mixture model approach to association analysis through multi-omics data integration
Ziqiao Wang and Peng Wei (2020)
Bioinformatics, 2020, DOI: 10.1093/bioinformatics/btaa1001
Yun Yan
Widespread Transcriptional Scanning in the Testis Modulates Gene Evolution Rates
Xia B, Yan Y, Baron M, Wagner F, Barkley D, Chiodin M, Kim SY, Keefe DL, Alukal JP, Boeke JD, Yanai I.
Cell. 2020 Jan 23;180(2):248-262.e21. doi: 10.1016/j.cell.2019.12.015.
PMID: 31978344; PMCID: PMC7891839
Jinaho Zhou
DR-SIP: protocols for higher order structure modeling with distance restraints- and cyclic symmetry-imposed packing
Chan J, Zou J, Ortiz CL, Chang Chien CH, Pan RL, Yang LW.
Bioinformatics. 2020 Jan 15;36(2):449-461. doi: 10.1093/bioinformatics/btz579.
PMID: 31347658
S100B as an antagonist to block the interaction between S100A1 and the RAGE V domain
Khan MI, Su Y-K, Zou J, Yang L-W, Chou R-H, Yu C
(2018) PLoS ONE 13(2): e0190545. doi.org/10.1371/journal.pone.0190545