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Current Students

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Will Sullivan

Will Sullivan

Degree: PhD
Matriculation Year: 2023

Rotations:

  • Yi Xing
  • Ben Stanger

Wendy Su (she/her/hers)

Wendy Su (she/her/hers)

Degree: PhD
Matriculation Year: 2023

Rotations:

  • Shefali Setia Verma
  • Joseph Romano
  • Lewis Chodosh

Tram Anh Nguyen (she/her/hers)

Tram Anh Nguyen (she/her/hers)

Degree: PhD
Matriculation Year: 2023

Rotations:

  • Kai Wang
  • Joseph Romano
  • Kevin Johnson

Makayla Reed

Makayla Reed

Degree: PhD
Matriculation Year: 2023

Rotations:

  • Ingo Helbig
  • Michael Gandal
  • Li Shen

Travyse Edwards

Travyse Edwards

Degree: PhD
Matriculation Year: 2023

Rotations:

  • Li Shen
  • Qi Long
  • Joseph Romano

Jake Spruance (he/him/his)

Jake Spruance (he/him/his)

Degree: PhD
Matriculation Year: 2023

Rotations:

  • Pablo G. Camara
  • Yi Xing
  • Golnaz Vahedi

Lexi Li (she/her/hers)

Lexi Li (she/her/hers)

Degree: PhD
Matriculation Year: 2023

Rotations:

  • Dokyoon Kim
  • Taki Shinohara
  • Mingyao Li

Zhuoran Xu

Zhuoran Xu

Degree: PhD
Matriculation Year: 2023

Rotations:

  • Kai Wang
  • Ingo Helbig
  • Wanding Zhou

Liran Mao

Liran Mao

Degree: PhD
Matriculation Year: 2023

Rotations:

  • Mingyao Li
  • Yanxiang Deng
  • Katalin Susztak

Julia Malnak

Julia Malnak

Degree: PhD
Matriculation Year: 2023

Rotations:

  • Frederic Bushman
  • Noam Auslander
  • Avi Srivastava

Lina Takemaru

Lina Takemaru

Degree: PhD
Matriculation Year: 2023

Rotations:

  • Li Shen
  • Dokyoon Kim
  • Derek Oldridge

William Gao (he/him/his)

William Gao (he/him/his)

Degree: MD/PhD
Matriculation Year: 2023

Advisor(s):

  • Hao Wu

Rotations:

  • Hao Wu
  • Zoltan Arany

Yuhao Tan

Yuhao Tan

Degree: PhD
Matriculation Year: 2023

Advisor(s):

  • Bo Li

Rotations:

  • Bo Li

Ijeoma Meremikwu (she/her/hers)

Ijeoma Meremikwu (she/her/hers)

Degree: PhD
Matriculation Year: 2023

Rotations:

  • Andy Minn
  • Derek Oldridge
  • Golnaz Vahedi

Thomas Westbrook (he/him/his)

Thomas Westbrook (he/him/his)

Degree: PhD
Matriculation Year: 2023

Rotations:

  • Iain Mathieson
  • Kai Tan
  • Dokyoon Kim

Barbara Xiong

Barbara Xiong

Degree: MD/PhD
Matriculation Year: 2023

Advisor(s):

  • Kai Tan

Rotations:

  • Kai Tan
  • Mingyao Li
  • Pablo G. Camara

Rachit Kumar

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)

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)

Rasika Venkatesh (she/her/hers)

Degree: PhD
Matriculation Year: 2022

Advisor(s):

  • Marylyn Ritchie

Rotations:

  • Marylyn Ritchie
  • Yoseph Barash
  • Dokyoon Kim

Connor Parker

Connor Parker

Degree: PhD
Matriculation Year: 2022

Advisor(s):

  • Rui Feng

Rotations:

  • Rui Feng
  • Yi Xing
  • Struan Grant

Fabian Ramos-Almodovar (he/him/his)

Fabian Ramos-Almodovar (he/him/his)

Degree: PhD
Matriculation Year: 2022

Advisor(s):

  • Iain Mathieson

Rotations:

  • Iain Mathieson
  • Ziyue Gao
  • Benjamin Voight

Georgia Mies

Georgia Mies

Degree: PhD
Matriculation Year: 2022

Advisor(s):

  • Iain Mathieson

Rotations:

  • Sarah Tishkoff
  • Iain Mathieson
  • Ziyue Gao

Chloé Paris (she/her/hers)

Chloé Paris (she/her/hers)

Degree: PhD
Matriculation Year: 2022

Advisor(s):

  • Joseph Romano

Rotations:

  • Mary Regina Boland
  • Daniel Herman
  • Joseph Romano

Robert Hu (he/him/his)

Robert Hu (he/him/his)

Degree: PhD
Matriculation Year: 2022

Advisor(s):

  • Pablo G. Camara

Rotations:

  • Pablo G. Camara
  • Nancy Zhang
  • Derek Oldridge

Yidi Huang (he/him/his)

Yidi Huang (he/him/his)

Degree: PhD
Matriculation Year: 2022

Advisor(s):

  • Dokyoon Kim

Rotations:

  • Qi Long
  • Kevin Johnson
  • Dokyoon Kim

Anastasia Lucas (she/her/hers)

Anastasia Lucas (she/her/hers)

Degree: PhD
Matriculation Year: 2022

Advisor(s):

  • Noam Auslander

Rotations:

  • Danielle Mowery
  • Noam Auslander
  • Dokyoon Kim

Alexis Garófalo

Alexis Garófalo

Degree: PhD
Matriculation Year: 2022

Advisor(s):

  • Anurag Verma

Rotations:

  • Dokyoon Kim
  • Danielle Mowery
  • Anurag Verma

Lindsay Guare

Lindsay Guare

Degree: PhD
Matriculation Year: 2022

Advisor(s):

  • Shefali Setia Verma

Rotations:

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

Emilia Chen

Emilia Chen

Degree: PhD
Matriculation Year: 2022

Advisor(s):

  • Andy Minn
  • Nancy Zhang

Rotations:

  • Andy Minn
  • Derek Oldridge
  • Nancy Zhang

Jonathan Sussman

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)

Jenna Ballard (she/her/hers)

Degree: PhD
Matriculation Year: 2022

Advisor(s):

  • Qi Long
  • Li Shen

Rotations:

  • Li Shen
  • Dokyoon Kim
  • Qi Long

David Zhang

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)

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

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

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)

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

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

Rotations:

  • Li Shen
  • Dokyoon Kim
  • Marylyn Ritchie

Anni Moore

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)

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)

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):

  • Kai Tan

Rotations:

  • Kai Tan
  • Cesar de la Fuente
  • Kai Wang

Manu Shivakumar

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)

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

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

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

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

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

Lev Litichevskiy (he/him/his)

Lev Litichevskiy (he/him/his)

Degree: MD/PhD
Matriculation Year: 2020

Project Title: Interactions between aging, dietary restriction, and the gut microbiome

Advisor(s):

  • Mingyao Li
  • Christoph Thaiss

Rotations:

  • Yoseph Barash
  • Christoph Thaiss
  • Mingyao Li

Van Truong (she/her/hers)

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

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)

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

Rotations:

  • Frederic Bushman
  • Cesar de la Fuente
  • Michael Levy

Mary Ann Weidekamp

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)

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

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)

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

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. 

 


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. 

 

Kaylyn Clark

Kaylyn Clark

Degree: PhD
Matriculation Year: 2018

Project Title: The Role of the Innate Immune System in Alzheimer's Disease: A Human Genetics Approach

Advisor(s):

  • Li-San Wang

Rotations:

  • Marylyn Ritchie
  • Li-San Wang
  • Gerard Schellenberg

Matthew Gazzara

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)

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

Daniel Hui

Degree: PhD
Matriculation Year: 2019

Advisor(s):

  • Marylyn Ritchie
  • Sarah Tishkoff

Rotations:

  • Benjamin Voight
  • Marylyn Ritchie
  • Sarah Tishkoff

Jihoon Kim

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)

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

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

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

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

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

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

David Wang

David Wang

Degree: PhD
Matriculation Year: 2018

Project Title: Understanding The Heterogeneity of Alternative Splicing in Acute Myeloid Leukemia using Bayesian Machine Learning Models

Advisor(s):

  • Yoseph Barash

Rotations:

  • Yoseph Barash
  • Mingyao Li
  • Junhyong Kim

Robert Wang

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

Brenda Xiao

Brenda Xiao

Degree: PhD
Matriculation Year: 2019

Project Title: Integrating Various Risk Factors with Polygenic Risk Scores for Preeclampsia

Advisor(s):

  • Dokyoon Kim
  • Marylyn Ritchie

Rotations:

  • Dokyoon Kim
  • Sharon Diskin
  • Marylyn Ritchie

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