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)

TRI-I COMPUTATIONAL BIOLOGY & MEDICINE CURRENT STUDENTS IN ITHACA