Current Students & Alumni

Current Students

Beulah Agyemang-Barimah (Mezey) My research is currently centered around human genetics. I use programming languages (mainly R) to write algorithms and code simulations of phylogenetic trees. The point of this research is to estimate the probability of observing the data present and track specific alleles backward in time.

Brent Basso (Danko/Lis)

Justin Cha (Pugh/Lai)

Sam Champer (Messer) I am working to create high fidelity gene-drive models and am interested in exploring the dynamics of large-scale populations modeled in realistic spaces. I am also interested in augmenting realistic population models with machine-learning meta-models to allow for in-depth assessments of computationally complex models.

Meera Chaotai (Messer/Wei)

Vrushali Fangal (Yu)  

Taylor Ferebee (Buckler) Interested in both using principles of data fusion, statistical learning theory, and network science to develop cross-tissue, cross-genera, and cross-species methods for modelling transcriptional regulation in the Andropogoneae tribe of grasses, and in exploring biologically-informed priors for utilization in interpretable machine learning models.

Lucas Gallart (Hein)

Alejandro Garces (Rotating)

Abigail Grassick (Hein)

Shagun Gupta (Yu) Interested in using statistical and computational methods that leverage data generated from mass spectrometers to gain insight into protein-protein interaction networks.  

Adam He (Danko) My current research focuses on identifying how ba­sic transcriptional processes such as initiation, pausing, and stability are encoded in the genetic sequences of transcriptional regulatory elements (TREs). At present, I am working on developing interpretable models that predict how TRE sequence impacts proximal transcription initiation.

Chase Holdener (Rotating)

Keith Jamison (Kuceyeski) My research focuses on the relationship between different brain connectivity estimation techniques, and developing tools to extract robust scientifically or clinically meaningful representations.

Shaowen Jiang (De Vlaminck)

Alison Ke (Rotating)

Isabel Kim (Messer) 

Olivia Lang (Pugh/Lai)  I build tools for analyzing large genomics datasets and study the relationship between DNA organization and gene expression. More specifically, I investigate the mechanisms of transcription initiation around transcription start sites to develop models for global patterns of gene regulation.

Ian Lee (Brito) My research focuses on developing pipelines to decipher host-microbiome interactions via protein-protein interactions, by using protein language models and molecular docking. The gut microbiome plays a vital role in host health, yet the understanding of interactions via proteins is limited. In addition, I work on single-cell RNA sequencing data to explore cell responses in macrophages.

Zhaozhi Li (Kim)

Yilin Liu (Yu)

Amlan Nayak (Hein)

Ziqing Pan (Wei)

Yu Sun (Yu)

Nating Wang (Rotating)

Yiwen Wang (Rotating)

Meihan Wei (Rotating)

Ziyang Xia (Rotating)

Tianyu Xia (Rotating)

Weilin Xu (Gu) Interested in studying the genetics of mitochondrial DNA in the context of human diseases with the development of high-throughput sequencing approaches as well as the application of computational and statistical methods.

Hao Xue (Basu)

Li Yao (Yu) Using statistical and machine learning techniques to study mechanisms of transcription regulation from biological datasets, such as run-on sequencing.

Junke Zhang (Yu) Interested in using computational and statistical methods to study protein functions and protein-protein interactions in human diseases. Currently working on questions about gene fusions in cancer.   

Manqi Zhou (Wang)

Yutong Zhu (Yu)



Recent Student Publications

  • Chen, Y., Paramo, M. I., Zhang, Y., Yao, L., Shah, S. R., Jin, Y., Zhang, J., Pan, X., & Yu, H. (2023). Finding Needles in the Haystack: Strategies for Uncovering Noncoding Regulatory Variants. Annual Review of Genetics, 57(1).
  • Leung, A. K.-Y., Yao, L., & Yu, H. (2022). Functional genomic assays to annotate enhancer–promoter interactions genome wide. Human Molecular Genetics, 31(R1), R97–R104.
  • Yao, L., Liang, J., Ozer, A., Leung, A. K.-Y., Lis, J. T., & Yu, H. (2022). A comparison of experimental assays and analytical methods for genome-wide identification of active enhancers. Nature Biotechnology, 40(7), Article 7.
  • Meyer, M. J., Beltrán, J. F., Liang, S., Fragoza, R., Rumack, A., Liang, J., ... & Yu, H. (2018). Interactome INSIDER: a structural interactome browser for genomic studies. Nature methods15(2), 107.
  • Wierbowski, S. D., Fragoza, R., Liang, S., & Yu, H. (2018). Extracting Complementary Insights from Molecular Phenotypes for Prioritization of Disease-Associated Mutations. Current Opinion in Systems Biology.
  • Duneau D., Sun H., Revah J., San Miguel K., Kunerth H.D., Caldas I.V., Messer P.W., Scott J.G., and Buchon, N. (2018). Signatures of Insecticide Selection in the Genome of Drosophila melanogaster. G3: Genes, Genomes, Genetics, Early online September 6, 2018.
  • Wei K.H.-C., Lower S.E., Caldas I.V., Sless T.J., Barbash D.A., and Clark, A.G. (2018). Variable Rates of Simple Satellite Gains across the Drosophila Phylogeny. Molecular Biology and Evolution, 35(4) pp. 925-941.
  • Jackson Champer, Jingxian Liu, Suh Yeon Oh, Riona Reeves, Anisha Luthra, Nathan Oakes, Andrew G. Clark, and Philipp W. Messer (2018). Reducing resistance allele formation in CRISPR gene drive. Proceedings of the National Academy of Sciences (PNAS).
  • Tinyi Chu, Edward J. Rice, Gregory T. Booth, H. Hans Salamanca, hong Wang, Leighton J. Core, Sharon L. Longo, Robert J. Corona, Lawrence S. Chin, John T. Lis, Hojoong Kwak, Charles G. Danko, Chromatin run-on and sequencing maps the transcriptional regulatory landscape of glioblastoma multiforme, Nature Genetics (2018).
  • Jacob M. Tome, Nathaniel D. Tippens, John T. Lis, Single-Molecule nascent RNA sequencing identifies regulatory domain architecture at promoters and enhancers, Nature Genetics (2018).
  • Saikia, M., Burnham, P., Keshavjee, S. H., Wang, M. F. Z., Heyang, M., Moral-Lopez, P., Hinchman, M. M., Danko, C. G., Parker, J. S. L. and De Vlaminck, I. (2018). Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells. Nature Methods. doi: 10.1038/s41592-018-0259-9, Nature (2018)
  • Borthakur, Ayon, Cleland, Thomas A., A Spike Time-Dependent Online Learning Algorithm Derived From Biological Olfaction, Frontiers in Neuroscience, 2019
  • Borthakur, Ayon, Cleland, Thomas A., Signal Conditioning for Learning in the Wild, DL Association for Computing Machinery, 2019


  • Madhav Mantri, PhD Computational Biology, August 2023
    Advisor: Iwijn De Vlaminck
  • Siddarth Avadhanam, PhD Computational Biology, May 2023
    Advisors: Amy Williams & April Wei
  • Parker Singleton, PhD Computational Biology, May 2023
    Advisor: Amy Kuceyeski
  • Ian Caldas, PhD Computational Biology, August 2022
    Advisor: Andrew Clark
  • Michael Wang, PhD Computational Biology, August 2022
    Advisor: Iwijn De Vlaminck
  • Daniel Seidman, PhD Computational Biology, August 2022
    Advisor: Amy Williams
  • Shayne Wierbowski, PhD Computational Biology, May 2022
    Advisor: Haiyuan Yu
  • Runxi Shen, PhD Computational Biology, May 2022
    Advisor: Philipp Messer
  • Siqi (Charles) Liang, PhD Computational Biology, Spring 2021
    Advisor: Haiyuan Yu
  • Paul Munn, PhD Computational Biology, Fall 2020
    Advisor: Charles Danko
  • Manisha Munasinghe, PhD Computational Biology, Fall 2020
    Advisor: Andrew Clark
  • Konnor La, PhD Computational Biology & Medicine, Fall 2020
    Advisor: Andrew Clark
  • Afrah Shafquat, PhD Computational Biology, Fall 2020
    Advisor: Jason Mezey|Weill Cornell Medical College
  • Juan Beltran, PhD Computational Biology, Fall 2020
    Advisor: Ilana Brito|Postdoc Brito Lab
  • Melissa Hubisz, PhD Computational Biology, Fall 2019
    Advisor: Adam Siepel/Amy Williams|Program Analyst, Cornell University
  • Tinyi Chu, PhD Computational Biology, Fall 2019
    Advisor: Charles Danko
  • Yiping Wang, PhD Computational Biology, Fall 2019
    Advisor: Zhenglong Gu|Postdoc, Columbia University
  • Lenore Pipes, PhD Computational Biology & Medicine, August 2017,
    Advisor: Adam Siepel/Chris Mason|Postdoctoral Scholar, University of California-Berkeley
  • Nicholas Cheney, PhD Computational Biology, August 2017,
    Advisor: Steven Strogatz/Hod Lipson|Research Assistant Professor, University of Vermont
  • Kelson Zawack, PhD Computational Biology & Medicine, May 2017,
    Advisors: James Booth/Yrjo Grohn|Postdoctoral Fellow, Yale University
  • Monica Ramstetter, PhD Computational Biology, May 2017,
    Advisor: Jason Mezey|Sr. Scientist, Pfizer
  • Feng Gao, PhD Computational Biology, January 2017,
    Advisor: Alon Keinan|Data Scientist
  • Lei Huang, PhD Computational Biology, January 2017,
    Advisor: Chris Myers|Bioinformatics Scientist, Human Longevity, Inc.
  • Michael Meyer, PhD Computational Biology & Medicine, January 2017,
    Advisor: Haiyuan Yu|Senior Scientist, 4Catalyzer
  • Jishnu Das, PhD Computational Biology, August 2016,
    Advisor: Haiyuan Yu|Postdoctoral Associate, MIT/Ragon Institute of MGH
  • Katherine Wilkins, PhD Computational Biology, August 2016,
    Advisor: Adam Bogdanove|Sr. Computational Biologist, Agilent Technologies, Santa Clara
  • Jaaved Mohammed, PhD Computational Biology & Medicine, May 2016,
    Advisors: Adam Siepel/Eric Lai|Postdoctoral Research Fellow, Stanford University
  • Eyal Nitzany, PhD Computational Biology & Medicine, August 2015,
    Advisor: Shimon Edelman|Postdoctoral Researcher, University of Chicago
  • Brandon Barker, PhD Computational Biology & Medicine, August 2014,
    Advisor: Zhenglong Gu|Computational Scientist, Cornell Center for Advanced Computing
  • Diana Chang, PhD Computational Biology & Medicine, August 2014,
    Advisor: Alon Keinan,|Scientist, Genentech, San Francisco
  • Haley Hunter-Zinck, PhD Computational Biology & Medicine, August 2014,
    Advisor: Andy Clark|Health Science Specialist, VA Boston Healthcare System
  • Andre Martins, PhD Computational Biology, August 2014,
    Advisor: Adam Siepel|Sr. Software Development Engineer, Hitachi Vantara
  • Theodore Cornforth, PhD Computational Biology & Medicine, January 2014,
    Advisor: Hod Lipson
  • Chuan Gao, PhD Computational Biology, May 2012,
    Advisor: Jason Mezey|Senior Scientist, Parexel International Corp.
  • Benjamin Logsdon, PhD Computational Biology, January 2011,
    Advisor: Jason Mezey|Director, University of Washington, Brain & Memory Wellness Center
  • Michael Schmidt, PhD Computational Biology, January 2011,
    Advisor: Hod Lipson, Chief Scientist, DataRobot
  • Jeremiah Degenhardt, PhD Computational Biology, May 2010,
    Advisor: Carlos Bustamante|Sr. Director, Translational Oncology & Bioinformatics/Maverick Therapeutics
  • Lin Li, PhD Computational Biology, May 2010,
    Advisor: Carlos Bustamante|Director of Biostatistics & Scientific Operations, Biostat Solutions, Inc
  • Mark Albert, PhD Computational Biology, January 2010,
    Advisor: David Field|Assistant Professor of Computer Science, Loyola University