Current Students

Showing {startItem} to {endItem} of {itemsNumber} matching students

= Website   = Email
Will Sullivan

Degree: PhD
Matriculation Year: 2023

Advisor(s):

  • Jina Ko
  • Ben Stanger

Rotations:

  • Yi Xing
  • Ben Stanger
  • Jina Ko
Wendy Su (she/her/hers)

Degree: PhD
Matriculation Year: 2023

Advisor(s):

  • Joseph Romano

Rotations:

  • Shefali Setia Verma
  • Joseph Romano
  • Lewis Chodosh
Tram Anh Nguyen (she/her/hers)

Degree: PhD
Matriculation Year: 2023

Advisor(s):

  • Joseph Romano

Rotations:

  • Kai Wang
  • Joseph Romano
  • Kevin Johnson
Makayla Reed

Degree: PhD
Matriculation Year: 2023

Rotations:

  • Ingo Helbig
  • Michael Gandal
  • Li Shen
Travyse Edwards

Degree: PhD
Matriculation Year: 2023

Advisor(s):

  • Qi Long
  • Li Shen

Rotations:

  • Li Shen
  • Qi Long
  • Joseph Romano
Jake Spruance (he/him/his)

Degree: PhD
Matriculation Year: 2023

Advisor(s):

  • Yi Xing

Rotations:

  • Pablo G. Camara
  • Yi Xing
  • Golnaz Vahedi
Lexi Li (she/her/hers)

Degree: PhD
Matriculation Year: 2023

Rotations:

  • Dokyoon Kim
  • Taki Shinohara
  • Mingyao Li
Zhuoran Xu

Degree: PhD
Matriculation Year: 2023

Advisor(s):

  • Kai Wang

Rotations:

  • Kai Wang
  • Ingo Helbig
  • Wanding Zhou
Liran Mao

Degree: PhD
Matriculation Year: 2023

Rotations:

  • Mingyao Li
  • Yanxiang Deng
  • Katalin Susztak
Julia Malnak

Degree: PhD
Matriculation Year: 2023

Advisor(s):

  • Noam Auslander
  • Frederic Bushman

Rotations:

  • Frederic Bushman
  • Noam Auslander
  • Avi Srivastava
Lina Takemaru

Degree: PhD
Matriculation Year: 2023

Advisor(s):

  • Dokyoon Kim
  • Derek Oldridge

Rotations:

  • Li Shen
  • Dokyoon Kim
  • Derek Oldridge
William Gao (he/him/his)

Degree: MD/PhD
Matriculation Year: 2023

Project Title: Mechanistic investigation of transcriptional bursting in vivo

Advisor(s):

  • Hao Wu

Rotations:

  • Hao Wu
  • Zoltan Arany
Yuhao Tan

Degree: PhD
Matriculation Year: 2023

Project Title: Deep Learning Approach to Analyzing Gene Expression and Antigen Presentation in Cancer

Advisor(s):

  • Bo Li

Rotations:

  • Bo Li
Ijeoma Meremikwu (she/her/hers)

Degree: PhD
Matriculation Year: 2023

Advisor(s):

  • Derek Oldridge

Rotations:

  • Andy Minn
  • Derek Oldridge
  • Golnaz Vahedi
Thomas Westbrook (he/him/his)

Degree: PhD
Matriculation Year: 2023

Advisor(s):

  • Dokyoon Kim

Rotations:

  • Iain Mathieson
  • Kai Tan
  • Dokyoon Kim
Barbara Xiong

Degree: MD/PhD
Matriculation Year: 2023

Project Title: Spatiotemporal evolution and ecological dynamics of acute myeloid leukemia upon chemotherapy

Advisor(s):

  • Kai Tan

Rotations:

  • Kai Tan
  • Mingyao Li
  • Pablo G. Camara
Rachit Kumar

Degree: MD/PhD
Matriculation Year: 2022

Project Title: Network representations of clinical and multiomics data to investigate mechanisms and predict outcomes of Alzheimer's disease

Advisor(s):

  • Marylyn Ritchie

Rotations:

  • Jason Moore
  • Marylyn Ritchie
Annan Timon (he/him/his)

Degree: PhD
Matriculation Year: 2022

Advisor(s):

  • Pablo G. Camara

Rotations:

  • Pablo G. Camara
  • Ziyue Gao
  • Yoseph Barash
Rasika Venkatesh (she/her/hers)

Degree: PhD
Matriculation Year: 2022

Project Title: Using Electronic Health Records and Multi-Omics Approaches to Improve Understanding of Pharmacogenomics

Advisor(s):

  • Marylyn Ritchie

Rotations:

  • Marylyn Ritchie
  • Yoseph Barash
  • Dokyoon Kim
Connor Parker

Degree: PhD
Matriculation Year: 2022

Advisor(s):

  • Rui Feng

Rotations:

  • Rui Feng
  • Yi Xing
  • Struan Grant
Fabian Ramos-Almodovar (he/him/his)

Degree: PhD
Matriculation Year: 2022

Project Title: Identifying genetic and environmental drivers of inter and intra-specific mutation rate spectra evolution

Advisor(s):

  • Iain Mathieson

Rotations:

  • Iain Mathieson
  • Ziyue Gao
  • Benjamin Voight
Georgia Mies

Degree: PhD
Matriculation Year: 2022

Project Title: Modeling local ancestry to detect selection in admixed human populations

Advisor(s):

  • Iain Mathieson

Rotations:

  • Sarah Tishkoff
  • Iain Mathieson
  • Ziyue Gao
Chloé Paris (she/her/hers)

Degree: PhD
Matriculation Year: 2022

Project Title: Characterizing the Role of Maternal Environmental Exposures on Preeclampsia Using Biomedical Knowledge Graphs

Advisor(s):

  • Joseph Romano

Rotations:

  • Mary Regina Boland
  • Daniel Herman
  • Joseph Romano
Robert Hu (he/him/his)

Degree: PhD
Matriculation Year: 2022

Project Title: Characterizing cell morphology and subcellular protein localization using optimal transport

Advisor(s):

  • Pablo G. Camara

Rotations:

  • Pablo G. Camara
  • Nancy Zhang
  • Derek Oldridge
Yidi Huang (he/him/his)

Degree: PhD
Matriculation Year: 2022

Project Title: Generative summarization of autoimmune clinical histories

Advisor(s):

  • Dokyoon Kim

Rotations:

  • Qi Long
  • Kevin Johnson
  • Dokyoon Kim
Anastasia Lucas (she/her/hers)

Degree: PhD
Matriculation Year: 2022

Project Title: Improving the functional characterization of gut microbial proteins to enable human disease research

Advisor(s):

  • Noam Auslander

Rotations:

  • Danielle Mowery
  • Noam Auslander
  • Dokyoon Kim
Alexis Garófalo

Degree: PhD
Matriculation Year: 2022

Project Title: Identification and characterization of hereditary genetic risk factors in hepatocellular carcinoma

Advisor(s):

  • Anurag Verma

Rotations:

  • Dokyoon Kim
  • Danielle Mowery
  • Anurag Verma
Lindsay Guare

Degree: PhD
Matriculation Year: 2022

Project Title: Leveraging Deep Clinical Insights and Genomic Integration for Precise Phenotyping and Prognostic Prediction for Endometriosis

Advisor(s):

  • Shefali Setia Verma

Rotations:

  • Suneeta Senapati
  • Anurag Verma
  • Daniel Herman
  • Shefali Setia Verma
Emilia Chen

Degree: PhD
Matriculation Year: 2022

Project Title: Characterizing the development of epigenetically encoded inflammatory memory in single cells

Advisor(s):

  • Andy Minn
  • Nancy Zhang

Rotations:

  • Andy Minn
  • Derek Oldridge
  • Nancy Zhang
Jonathan Sussman

Degree: MD/PhD
Matriculation Year: 2022

Project Title: Dissecting the Spatial Immune Landscape of Epigenetically Driven Gliomas

Advisor(s):

  • Kai Tan

Rotations:

  • Robert Babak Faryabi
  • Kai Tan
Jenna Ballard (she/her/hers)

Degree: PhD
Matriculation Year: 2022

Project Title: Integrating incomplete multimodal longitudinal imaging and -omics data in Alzheimer’s Disease research

Advisor(s):

  • Qi Long
  • Li Shen

Rotations:

  • Li Shen
  • Dokyoon Kim
  • Qi Long
David Zhang

Degree: MD/PhD
Matriculation Year: 2022

Project Title: Investigating quantitative trait associations with ancestry-specific variants and haplotypes in diverse patient biobanks

Advisor(s):

  • Marylyn Ritchie
  • Daniel Rader

Rotations:

  • Marylyn Ritchie
  • Daniel Rader
Emerson Hunter (she/her/hers)

Degree: VMD/PhD
Matriculation Year: 2022

Project Title: ESPRESSO-TEA: A long-read RNA sequencing workflow to study locus-specific expression of transposable elements

Advisor(s):

  • Yi Xing

Rotations:

  • Yi Xing
  • Lan Lin
Jiazhen Rong

Degree: PhD
Matriculation Year: 2021

Project Title: Multi-modal lineage tracing in single cell and spatial omics data

Advisor(s):

  • Nancy Zhang

Rotations:

  • Nancy Zhang
  • Kai Tan
  • Pablo G. Camara
Andrew Patterson

Degree: PhD
Matriculation Year: 2021

Project Title: Investigating the interactions between cancer genomics and host immune responses

Advisor(s):

  • Noam Auslander
  • Bin Tian

Rotations:

  • Wanding Zhou
  • Noam Auslander
  • Daniel Herman
Chris Jones (he/him/his)

Degree: PhD
Matriculation Year: 2021

Project Title: Impact of Natural Selection on Disease Phenotypes

Advisor(s):

  • Marylyn Ritchie
  • Sarah Tishkoff

Rotations:

  • Sarah Tishkoff
  • Frederic Bushman
  • Marylyn Ritchie
Matthew Lee

Degree: PhD
Matriculation Year: 2021

Project Title: Characterizing the development and functions of tertiary lymphoid structures in human disease

Advisor(s):

  • Dokyoon Kim
  • John Wherry

Rotations:

  • Li Shen
  • Dokyoon Kim
  • Marylyn Ritchie
Anni Moore

Degree: PhD
Matriculation Year: 2021

Project Title: Determining clinical connections between Alzheimer’s Disease and its comorbidities using genetics and electronic health records

Advisor(s):

  • Marylyn Ritchie

Rotations:

  • Kai Tan
  • Dokyoon Kim
  • Marylyn Ritchie
  • Benjamin Voight
Matt Mouck (he/him/his)

Degree: PhD
Matriculation Year: 2021

Project Title: Long-read RNA Sequencing and Its Applications to Cancer Immunotherapy

Advisor(s):

  • Yi Xing

Rotations:

  • John Maris
  • Yi Xing
  • Li Shen
Jackie Peng (she/her/hers)

Degree: PhD
Matriculation Year: 2021

Project Title: Characterizing cellular interactions in the acute myeloid leukemia bone marrow microenvironment to overcome therapy resistance

Advisor(s):

  • Dana Silverbush

Rotations:

  • Kai Tan
  • Cesar de la Fuente
  • Kai Wang
Manu Shivakumar

Degree: PhD
Matriculation Year: 2021

Project Title: Enhancing the risk stratification in Alzheimer’s disease (AD) by augmenting the polygenic risk score (PRS) with rare variants and transcriptome-wide association study (TWAS) data

Advisor(s):

  • Dokyoon Kim

Rotations:

  • Marylyn Ritchie
  • Li Shen
  • Dokyoon Kim
Alice Wang (she/her/hers)

Degree: PhD
Matriculation Year: 2021

Project Title: Molecular Determinants of CAR T-cell Therapy Exhaustion and Long-term Persistence

Advisor(s):

  • Kai Tan

Rotations:

  • Yi Xing
  • Kai Tan
  • Pablo G. Camara
Jakob Woerner

Degree: PhD
Matriculation Year: 2021

Project Title: Exploring the genetic architecture underlying disease connections with biologically meaningful networks

Advisor(s):

  • Dokyoon Kim

Rotations:

  • Marylyn Ritchie
  • Dokyoon Kim
  • Benjamin Voight
Jingxuan Bao

Degree: PhD
Matriculation Year: 2021

Project Title: Statistical strategies for Alzheimer’s disease research through analyzing genetics, multi-omics, and imaging data

Advisor(s):

  • Li Shen
  • Qi Long

Rotations:

  • Mingyao Li
  • Li Shen
  • Qi Long
Preeti Bhanap

Degree: PhD
Matriculation Year: 2021

Project Title: Unraveling Commensal and Pathogen Interactions in Skin Microbial Transplants

Advisor(s):

  • Elizabeth Grice

Rotations:

  • Frederic Bushman
  • Elizabeth Grice
  • Li Shen
Max Dudek

Degree: PhD
Matriculation Year: 2021

Project Title: Integrating QTL and 3D genomic data for variant-to-gene mapping in liver-related complex disease

Advisor(s):

  • Struan Grant
  • Laura Almasy

Rotations:

  • Dokyoon Kim
  • Junhyong Kim
  • Christopher Brown
Van Truong (she/her/hers)

Degree: PhD
Matriculation Year: 2020

Project Title: Incorporating Structured Immunological Knowledge into Graph Data Science Models to Improve Understanding of Autoimmunity

Advisor(s):

  • John Wherry
  • Marylyn Ritchie

Rotations:

  • Jason Moore
  • Junhyong Kim
  • John Wherry
Erica Suh

Degree: PhD
Matriculation Year: 2020

Project Title: Multi-omics data integration for Alzheimer’s disease risk and progression prediction

Advisor(s):

  • Dokyoon Kim

Rotations:

  • Casey Greene
  • Dokyoon Kim
  • Jason Moore
Carter Merenstein (he/him/his)

Degree: PhD
Matriculation Year: 2020

Project Title: The Respiratory Microbiome in COVID-19: Associations with Severity, Risk Factors, and Host Pathways

Advisor(s):

  • Frederic Bushman
  • Ron Collman

Rotations:

  • Frederic Bushman
  • Cesar de la Fuente
  • Michael Levy
Mary Ann Weidekamp

Degree: PhD
Matriculation Year: 2020

Project Title: Elucidating Causal Genes for Type 2 Diabetes Risk in the Pancreas

Advisor(s):

  • Struan Grant
  • Benjamin Voight

Rotations:

  • Blanca Himes
  • Benjamin Voight
  • Struan Grant
Karl Keat (he/him/his)

Degree: PhD
Matriculation Year: 2020

Project Title: Augmenting Pharmacogenetics with Multi-Omics Data and Techniques

Advisor(s):

  • Dokyoon Kim
  • Marylyn Ritchie

Rotations:

  • Audrey Odom John
  • Dokyoon Kim
  • Marylyn Ritchie
Yuntian Fu

Degree: PhD
Matriculation Year: 2020

Project Title: Single cell long read sequencing and perturbation analysis reveals splicing heterogeneity and logic

Advisor(s):

  • Nancy Zhang

Rotations:

  • Mingyao Li
  • Pablo G. Camara
  • Nancy Zhang
Mitchell Conery (he/him/his)

Degree: PhD
Matriculation Year: 2020

Project Title: Uncovering Bone Mineral Density Genetic Etiology by Genomic Colocalization and CRISPRi Screening

Advisor(s):

  • Struan Grant
  • Benjamin Voight

Rotations:

  • Li-San Wang
  • Benjamin Voight
  • Struan Grant
Jenea Adams

Degree: PhD
Matriculation Year: 2019

Project Title: Developing an age-specific transcriptomic model of pediatric AML through robust large-scale multi-omic data analysis

Advisor(s):

  • Yi Xing

Rotations:

  • Li-San Wang
  • Yi Xing
  • Ophir Shalem

Jenea is the founder of The Black Women in Computational Biology Network. The Network is a global community for Black women advancing biology through a computational lens. The Network is comprised of exciting women across all degree and professional levels from an array of backgrounds in biology, computer science, mathematics, bioengineering, biochemistry, biophysics, medicine, public health data science and much more connecting, collaborting, exchaning resources, and communicating science to our communities. 

 


Matthew Gazzara

Degree: PhD
Matriculation Year: 2018

Project Title: Detection and quantification of alternative polyadenylation from RNA-seq to suggest novel regulators in health and disease

Advisor(s):

  • Yoseph Barash
  • Kristen Lynch

Rotations:

  • Christopher Brown
  • Zhaolan (Joe) Zhou
  • Yoseph Barash
Katherine Huang (she/her/hers)

Degree: PhD
Matriculation Year: 2017

Project Title: Pathway Analysis of Recurrent Breast Cancer

Advisor(s):

  • Lewis Chodosh

Rotations:

  • Lewis Chodosh
  • Sarah Tishkoff
  • Elizabeth Grice
Daniel Hui

Degree: PhD
Matriculation Year: 2019

Advisor(s):

  • Marylyn Ritchie
  • Sarah Tishkoff

Rotations:

  • Benjamin Voight
  • Marylyn Ritchie
  • Sarah Tishkoff
Jihoon Kim

Degree: PhD
Matriculation Year: 2017

Project Title: From RNA Distribution in Neuron Dendrites to Synaptic Plasticity

Advisor(s):

  • Junhyong Kim

Rotations:

  • Mitchell Lazar
  • Eric Joyce
  • Struan Grant
Jessica Lam (she/her/hers)

Degree: MD/PhD
Matriculation Year: 2017

Project Title: Role of YY1 in chromatin looping throughout the cell cycle

Advisor(s):

  • Gerd Blobel

Rotations:

  • Jennifer Cremins
  • Gerd Blobel
  • Hao Wu
L. Alex Lee

Degree: PhD
Matriculation Year: 2017

Project Title: Searching for Non-Coding Mechanisms of Disease in Neuroblastoma

Advisor(s):

  • John Maris
  • Sharon Diskin

Rotations:

  • Katherine Nathanson
  • Lewis Chodosh
  • Sharon Diskin
  • John Maris
Michelle Lee

Degree: PhD
Matriculation Year: 2019

Project Title: Multi-modal profiling of pancreatic islet cells in type 2 diabetes

Advisor(s):

  • Klaus Kaestner
  • Mingyao Li

Rotations:

  • Mingyao Li
  • Klaus Kaestner
  • Junhyong Kim
Jacob Leiby

Degree: PhD
Matriculation Year: 2019

Project Title: Leveraging histopathology whole-slide images and genomic data to improve prognostication of glioblastoma multiforme patients

Advisor(s):

  • Dokyoon Kim

Rotations:

  • Elizabeth Grice
  • Daniel Beiting
  • Mingyao Li
  • Dokyoon Kim
Zhen Miao

Degree: PhD
Matriculation Year: 2019

Project Title: Time series modeling of acute kidney injury using single cell multiomics data

Advisor(s):

  • Junhyong Kim

Rotations:

  • Katalin Susztak
  • Pablo G. Camara
  • Junhyong Kim
Parisa Samareh

Degree: PhD
Matriculation Year: 2018

Project Title: Defining Regulatory Mechanisms in CD8 T-cell Senescence with a Deep Interrogation of LINE-1

Advisor(s):

  • Shelley Berger

Rotations:

  • Robert Babak Faryabi
  • Shelley Berger
  • Kai Tan
Robert Wang

Degree: PhD
Matriculation Year: 2019

Project Title: Combining short- and long-read transcriptome sequencing to improve genetic diagnosis in Mendelian disease

Advisor(s):

  • Yi Xing

Rotations:

  • Yi Xing
  • Yoseph Barash

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