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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

Rotations:

  • Pablo G. Camara
  • Ziyue Gao
  • Yoseph Barash

Rasika Venkatesh (she/her/hers)

Rasika Venkatesh (she/her/hers)

Degree: PhD
Matriculation Year: 2022

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

Rotations:

  • Iain Mathieson
  • Ziyue Gao
  • Benjamin Voight

Georgia Mies

Georgia Mies

Degree: PhD
Matriculation Year: 2022

Rotations:

  • Sarah Tishkoff
  • Iain Mathieson
  • Ziyue Gao

Chloé Paris (she/her/hers)

Chloé Paris (she/her/hers)

Degree: PhD
Matriculation Year: 2022

Rotations:

  • Mary Regina Boland
  • Daniel Herman
  • Joseph Romano

Robert Hu (he/him/his)

Robert Hu (he/him/his)

Degree: PhD
Matriculation Year: 2022

Rotations:

  • Pablo G. Camara
  • Nancy Zhang
  • Derek Oldridge

Yidi Huang (he/him/his)

Yidi Huang (he/him/his)

Degree: PhD
Matriculation Year: 2022

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

Rotations:

  • Dokyoon Kim
  • Danielle Mowery
  • Anurag Verma

Lindsay Guare

Lindsay Guare

Degree: PhD
Matriculation Year: 2022

Rotations:

  • Suneeta Senapati
  • Anurag Verma
  • Daniel Herman

Emilia Chen

Emilia Chen

Degree: PhD
Matriculation Year: 2022

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

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 neurodegenerative diseases using genetics and EHR data from large-scale biobanks

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

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

Jason Xu

Jason Xu

Degree: MD/PhD
Matriculation Year: 2020

Project Title: Analysis of Developmental Arrest and Treatment Resistance in High-risk T-ALL

Advisor(s):

  • Kai Tan

Rotations:

  • Andrew Tsourkas
  • Michael Silverman
  • Kai Tan

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 Hazuga

Mary Ann Hazuga

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

Christopher Adams (he/him/his)

Christopher Adams (he/him/his)

Degree: PhD
Matriculation Year: 2017

Project Title: A population-specific framework for mutation rate modeling

Advisor(s):

  • Benjamin Voight

Rotations:

  • Sarah Tishkoff
  • Benjamin Voight
  • Frederic Bushman

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. 

 

Benjamin Auerbach

Benjamin Auerbach

Degree: PhD
Matriculation Year: 2017

Project Title: Circadian Phase Inference in Single-Cell RNA-Seq

Advisor(s):

  • Mingyao Li
  • Garret FitzGerald

Rotations:

  • Jason Moore
  • Ian Barnett
  • Golnaz Vahedi

William Bone

William Bone

Degree: PhD
Matriculation Year: 2017

Project Title: Leveraging Genome-wide Pleiotropy to Improve Multi-trait Association Methods for Electronic Health Record Data

Advisor(s):

  • Benjamin Voight
  • Marylyn Ritchie

Rotations:

  • Christopher Brown
  • Marylyn Ritchie
  • Benjamin Voight

Amy Campbell (she/her/hers)

Amy Campbell (she/her/hers)

Degree: PhD
Matriculation Year: 2017

Project Title: The genetics of Staphylococcus aureus virulence: consequences for diabetic wound healing.

Advisor(s):

  • Elizabeth Grice

Rotations:

  • Elizabeth Grice
  • Frederic Bushman

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

Jake Crawford (he/him/his)

Jake Crawford (he/him/his)

Degree: PhD
Matriculation Year: 2018

Project Title: Linking cancer drivers through integrative analysis of genomic and transcriptomic alterations

Advisor(s):

  • Casey Greene
  • Marylyn Ritchie

Rotations:

  • Casey Greene
  • Danielle Bassett
  • Pablo G. Camara

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

John Gregg

John Gregg

Degree: PhD
Matriculation Year: 2018

Project Title: Modeling Gene-Environment Interactions with Multi-task Machine Learning Methods to Explain GWAS0 Missing Heritability

Advisor(s):

  • Jason Moore
  • Blanca Himes

Rotations:

  • Jason Moore
  • Kai Wang
  • Casey Greene

Yun Hao

Yun Hao

Degree: PhD
Matriculation Year: 2018

Project Title: Incorporating biological knowledge into machine learning models to predict organ toxicity

Advisor(s):

  • Jason Moore
  • Li Shen

Rotations:

  • Jason Moore
  • David Speicher
  • Casey Greene

Benjamin Heil

Benjamin Heil

Degree: PhD
Matriculation Year: 2018

Project Title: Increasing the Power of Gene Expression Models by Incorporating Publicly Available Data

Advisor(s):

  • Casey Greene
  • Jason Moore

Rotations:

  • Marylyn Ritchie
  • Casey Greene
  • Christopher Brown

Ariel Hippen (she/her/hers)

Ariel Hippen (she/her/hers)

Degree: PhD
Matriculation Year: 2018

Project Title: Investigating high-grade serous ovarian cancer heterogeneity through scRNA-seq

Advisor(s):

  • Casey Greene
  • John Wherry

Rotations:

  • Casey Greene
  • Struan Grant
  • Christopher Brown

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

Derek Kelly

Derek Kelly

Degree: PhD
Matriculation Year: 2014

Project Title: The genomic and gene expression context of adaptive variation in indigenous African populations.

Advisor(s):

  • Sarah Tishkoff

Rotations:

  • Junhyong Kim
  • Nancy Zhang
  • 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

Jingya Qiu (she/her/hers)

Jingya Qiu (she/her/hers)

Degree: PhD
Matriculation Year: 2016

Advisor(s):

  • Andy Minn

Rotations:

  • Christopher Brown
  • Katherine Nathanson
  • Andy Minn

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

Vivek Sriram (he/him/his)

Vivek Sriram (he/him/his)

Degree: PhD
Matriculation Year: 2019

Project Title: Exploring Genetic Drivers of Disease Complications through Network-based Integration of EHR-linked Biobank Data

Advisor(s):

  • Dokyoon Kim

Rotations:

  • Ryan Urbanowicz
  • Marylyn Ritchie
  • Dokyoon Kim

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

Yang Xu

Yang Xu

Degree: PhD
Matriculation Year: 2018

Project Title: Combining transcriptomics and proteomics data to discover novel protein isoforms and variants

Advisor(s):

  • Yi Xing

Rotations:

  • Yi Xing

Kevin Yang

Kevin Yang

Degree: MD/PhD
Matriculation Year: 2017

Project Title: Developing High-Throughput Bulk and Single-Cell RNA-Sequencing Methods for Targeted Splicing Detection and Quantification

Advisor(s):

  • Yoseph Barash
  • Peter Choi

Rotations:

  • Yoseph Barash
  • Peter Choi

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