Current Students

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= Website   = Email
Joseph Aicher

Degree: MD/PhD
Matriculation Year: 2015

Project Title: Enhancing molecular diagnosis in suspected Mendelian disorders using clinically focused splicing prediction algorithms

Advisor(s):

  • Elizabeth Bhoj
  • Yoseph Barash

Rotations:

  • John Maris
  • Jennifer Cremins
  • Yoseph Barash
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

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
Christopher Adams

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

Degree: PhD
Matriculation Year: 2019

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. 

 


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Amy Campbell

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
Gregory Chen

Degree: MD/PhD
Matriculation Year: 2016

Project Title: Understanding the cellular and molecular basis of CAR Tcell therapy resistance.

Advisor(s):

  • Kai Tan

Rotations:

  • John Maris
  • Kai Tan
Kaylyn Clark

Degree: PhD
Matriculation Year: 2018

Advisor(s):

  • Li-San Wang

Rotations:

  • Marylyn Ritchie
  • Li-San Wang
  • Gerard Schellenberg
Jake Crawford

Degree: PhD
Matriculation Year: 2018

Project Title: Addressing heterogeneity in gene expression data using context-specific biological networks.

Advisor(s):

  • Casey Greene

Rotations:

  • Casey Greene
  • Danielle Bassett
  • Pablo G. Camara
Benjamin Emert

Degree: MD/PhD
Matriculation Year: 2014

Advisor(s):

  • Arjun Raj

Rotations:

  • Christopher Brown
  • Arjun Raj
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

Rotations:

  • Christopher Brown
  • Zhaolan (Joe) Zhou
  • Yoseph Barash
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

Rotations:

  • Jason Moore
  • Kai Wang
  • Casey Greene
Yun Hao

Degree: PhD
Matriculation Year: 2018

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

Advisor(s):

  • Jason Moore

Rotations:

  • Jason Moore
  • David Speicher
  • Casey Greene
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

Rotations:

  • Marylyn Ritchie
  • Casey Greene
  • Christopher Brown
Ariel Hippen Anderson

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

Degree: PhD
Matriculation Year: 2017

Project Title: Characterizing the epigenetic role of KMT2C in breast cancer metastasis and therapy resistance

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
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

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
Samantha Klasfeld

Degree: PhD
Matriculation Year: 2015

Project Title: Improving Resolution of Protein Binding Sites by filtering conserved ultra-high signals in Arabidopsis

Advisor(s):

  • Doris Wagner

Rotations:

  • Brian Gregory
  • Casey Greene
  • Lewis Chodosh
  • Doris Wagner
Jessica Lam

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
Alexandra Lee

Degree: PhD
Matriculation Year: 2017

Project Title: Modeling Pseudomonas aeruginosa infection in Cystic fibrosis patients

Advisor(s):

  • Casey Greene

Rotations:

  • Benjamin Voight
  • Casey Greene
  • Sharon Diskin
David Lee

Degree: MD/PhD
Matriculation Year: 2015

Advisor(s):

  • Yoseph Barash
  • Louis Ghanem

Rotations:

  • Andy Minn
  • Casey Greene
  • Yoseph Barash
Lobin 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

Rotations:

  • Mingyao Li
  • Klaus Kaestner
  • Junhyong Kim
Jacob Leiby

Degree: PhD
Matriculation Year: 2019

Advisor(s):

  • Dokyoon Kim

Rotations:

  • Elizabeth Grice
  • Daniel Beiting
  • Mingyao Li
  • Dokyoon Kim
Binglan Li

Degree: PhD
Matriculation Year: 2018

Project Title: Prioritizing Complex Disease-related Genes from Genome-wide Association Studies via Regulation-informed Gene-based Analyses

Advisor(s):

  • Marylyn Ritchie

Rotations:

  • Marylyn Ritchie
Zhen Miao

Degree: PhD
Matriculation Year: 2019

Advisor(s):

  • Junhyong Kim

Rotations:

  • Katalin Susztak
  • Pablo G. Camara
  • Junhyong Kim
Apexa Modi

Degree: PhD
Matriculation Year: 2015

Advisor(s):

  • Sharon Diskin

Rotations:

  • Lewis Chodosh
  • Sharon Diskin
  • Kai Tan
David Nicholson

Degree: PhD
Matriculation Year: 2015

Advisor(s):

  • Casey Greene

Rotations:

  • Jason Moore
  • Casey Greene
  • Struan Grant
Joseph Park

Degree: MD/PhD
Matriculation Year: 2015

Project Title: Investigating the clinical ontologies of loss-of-function and gain-of-function human gene variants

Advisor(s):

  • Daniel Rader
  • Marylyn Ritchie

Rotations:

  • Mitchell Lazar
  • Daniel Rader
Matt Paul

Degree: PhD
Matriculation Year: 2014

Advisor(s):

  • Lewis Chodosh

Rotations:

  • Brian Gregory
  • Lewis Chodosh
  • Yoseph Barash
Jingya Qiu

Degree: PhD
Matriculation Year: 2016

Advisor(s):

  • Jason Moore
  • Andy Minn

Rotations:

  • Christopher Brown
  • Katherine Nathanson
  • Andy Minn
Vincent Reuter

Degree: PhD
Matriculation Year: 2019

Advisor(s):

  • Junhyong Kim

Rotations:

  • Junhyong Kim
  • Joshua Plotkin
  • Pablo G. Camara
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
Eric Sanford

Degree: MD/PhD
Matriculation Year: 2015

Advisor(s):

  • Arjun Raj

Rotations:

  • John Maris
  • Arjun Raj
Mengge Shan

Degree: PhD
Matriculation Year: 2013

Project Title: Characterizing the dynamics of RNA-protein interactions in two eukaryotic systems

Advisor(s):

  • Brian Gregory

Rotations:

  • Brian Gregory
  • Lewis Chodosh
  • Marcella Devoto
  • Nancy Spinner
Vivek Sriram

Degree: PhD
Matriculation Year: 2019

Advisor(s):

  • Dokyoon Kim

Rotations:

  • Ryan Urbanowicz
  • Marylyn Ritchie
  • Dokyoon Kim
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

Degree: PhD
Matriculation Year: 2019

Advisor(s):

  • Yi Xing

Rotations:

  • Yi Xing
  • Yoseph Barash
Amber Weiner

Degree: PhD
Matriculation Year: 2014

Project Title: An integrative approach to identify neuroblastoma immunotherapeutic targets

Advisor(s):

  • Benjamin Garcia
  • John Maris
  • Sharon Diskin

Rotations:

  • Sharon Diskin
  • John Maris
  • Benjamin Garcia
Chi-Yun Wu

Degree: PhD
Matriculation Year: 2017

Project Title: Multi-Omics Single-cell Analysis in Cancers

Advisor(s):

  • Nancy Zhang

Rotations:

  • Li-San Wang
  • Nancy Zhang
  • Lewis Chodosh
Brenda Xiao

Degree: PhD
Matriculation Year: 2019

Advisor(s):

  • Dokyoon Kim
  • Marylyn Ritchie

Rotations:

  • Dokyoon Kim
  • Sharon Diskin
  • Marylyn Ritchie
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

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
Di Zhang

Degree: MD/PhD
Matriculation Year: 2013

Advisor(s):

  • Gerd Blobel

Rotations:

  • Christopher Brown
  • Gerd Blobel
  • Arjun Raj
Xinyuan Zhang

Degree: PhD
Matriculation Year: 2018

Advisor(s):

  • Marylyn Ritchie

Rotations:

  • Marylyn Ritchie
Linda Zhou

Degree: MD/PhD
Matriculation Year: 2014

Advisor(s):

  • Jennifer Cremins

Rotations:

  • Benjamin Voight
  • Casey Greene
  • Jennifer Cremins
Qin Zhu

Degree: PhD
Matriculation Year: 2016

Project Title: Modeling dynamic regulatory networks during development and differentiation using single cell data.

Advisor(s):

  • Kai Tan
  • Junhyong Kim

Rotations:

  • Yoseph Barash
  • Kai Tan
  • Junhyong Kim

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