Computational Biology Summer Program Alumni

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2020 Alumni

Vanesa Getseva

Vanesa Getseva
American College of Greece, Ramapo College

Mentor: Iman Hajirasouliha
Institution: Weill Cornell Medicine
Project: Weakly-supervised tumour purity prediction from H&E stained slides


Tonatiuh Gonzalez

Tonatiuh Gonzalez
Harvey Mudd College

Mentor: Ekta Khurana
Institution: Weill Cornell Medicine
Project: ATAC Seq Cancer Genomics


Ciaran Hassan

Ciaran Hassan
Yale University

Mentor: Christopher Mason
Institution: Weill Cornell Medicine
Project: Cancer genomics & Epigenomics


Mikako Inaba

Mikako Inaba
Princeton University

Mentor: Dan Landau
Institution: NY Genome
Project: Modelling RNA Editing in MPN Patients Treated with Interferon-a


Ketan Jog

Ketan Jog
Columbia University

Mentor: Marcin Imielinski
Institution: Weill Cornell Medicine
Project: Algorithms SCNA Markers


Ishaani Khatri

Ishaani Khatri
Brown University

Mentor: Michael Berger
Institution: Memorial Sloan Kettering Cancer Center
Project: Machine Learning-Based Tumor Type Prediction from MSK-IMPACT Data


Lior Kofman

Lior Kofman
Tufts University

Mentor: Olivier Elemento
Institution: Weill Cornell Medicine
Project: Applying Machine Learning to Determine Cancer Susceptibility Scores


Qianzi Li

Qianzi Li
Carleton College

Mentor: Sohrab Shah
Institution: Memorial Sloan Kettering Cancer Center
Project: Assessing Single Cell Cancer Phylogeny Trees Using Sankoff Parsimony


Michael Luo

Michael Luo
The College of New Jersey

Mentor: Benjamin Greenbaum
Institution: Memorial Sloan Kettering Cancer Center
Project: Quantify Fitness Levels in Evolving Immune Response Networks Using ϕ-evo


Joshua Morin-Baxter

Joshua Morin-Baxter
Augustana College

Mentor: Samuel Jaffrey
Institution: Memorial Sloan Kettering Cancer Center
Project: The m6A Pathway and Cancer


Kathleen Navas

Kathleen Navas
University of California Berkeley

Mentor: Quaid Morris
Institution: Memorial Sloan Kettering Cancer Center
Project: Improving outcome predictions in head and neck cancers by classifying new-onset auto-immunity using peripheral blood values


Felix Steinruecke

Felix Steinruecke
Duke University

Mentor: Nikolaus Schutlz
Institution: Memorial Sloan Kettering Cancer Center
Project: Investigating Mutations in the Context of Whole-Genome Doubling


Yingxuan (Jason) Tan

Yingxuan (Jason) Tan
Rice University

Mentor: Christina Leslie
Institution: Memorial Sloan Kettering Cancer Center
Project: Learning Immune Cell Differentiation with Deep Learning

2019 Alumni
Computational Biology Summer Program Alumni 2019

(From Left to Right) Top row: Noah Lee, Darshan Kalola, Darnell Granberry, Benjamin Lee, Rafe Batchelor, Viraj Rapolu; Bottom row: Druv Patel, James Xu, Lindsey Hall, Manaswitha Edupalli, Ronit Langer, Uriel Restrepo

Rafe Batchelor

Rafe Batchelor
Bucknell University

Mentor: Ekta Khurana
Institution: Weill Cornell Medicine
Project: Using Nucleosome Positioning Derived from Cell-free DNA for Cancer Detection


Manaswitha Edupalli

Manaswitha Edupalli
Carnegie Mellon University

Mentor: Eduard Reznik
Institution: Memorial Sloan Kettering Cancer Center
Project: Metabolic Determinants of Immune Cell Infiltration in the Tumor Microenvironment


Darnell Granberry

Darnell Granberry
Massachusetts Institute of Technology

Mentor: John Chodera
Institution: Memorial Sloan Kettering Cancer Center
Project: A Customizable Sandbox for Developing and Evaluating Active-learning Algorithms for Computational Drug Discovery


Lindsey Hall

Lindsey Hall
University of Rochester

Mentor: Dan Landau
Institution: Weill Cornell Medicine
Project: Discovery of Sequence Motifs associated with DNA methylation cell-to-cell variability in Glioblastoma


Darshan Kalola

Darshan Kalola
The College of New Jersey

Mentor: David Christini
Institution: Weill Cornell Medicine
Project: Optimizing the optimization protocol to build better cell-specific cardiac myocyte models


Ronit Langer

Ronit Langer
Massachusetts Institute of Technology

Mentor: Elli Papaemmanuil
Institution: Memorial Sloan Kettering Cancer Center
Project: Detecting FLT3-ITD in AML from Tumor Sequencing Data


Benjamin Lee

Benjamin Lee
Harvard University

Mentor: Barry Taylor
Institution: Memorial Sloan Kettering Cancer Center
Project: In silico Analysis of Cancer Hotspot Immunogenecity


Noah Lee

Noah Lee
Carnegie Mellon University

Mentor: Michael Berger
Institution: Memorial Sloan Kettering Cancer Center
Project: Analyzing MMR Genes with MINNI-FLWR


Druv Patel

Druv Patel
University of Texas Austin

Mentor: Sorabh Shah
Institution: Memorial Sloan Kettering Cancer Center
Project: Classification of mutational signatures from whole-slide histology images using deep learning


Viraj Rapolu

Viraj Rapolu
University of North Carolina Chapel Hill

Mentor: Christina Leslie
Institution: Memorial Sloan Kettering Cancer Center
Project: CITE-Space: a word embedding approach for unsupervised clustering of CITE-seq data


Uriel Restrepo

Uriel Restrepo
New York University

Mentor: Christopher Mason
Institution: Weill Cornell Medicine
Project: Nanopore Sequencing and Fast Similarity Search on DNA Long Reads


James Xu

James Xu
Columbia University

Mentor: Nikolaus Schultz
Institution: Memorial Sloan Kettering Cancer Center
Project: Routine Identification of Mutational Hotspots in Large Cancer Genomics Datasets


2018 Alumni
Computational Biology Summer Program Alumni 2018

(From Left to Right) Top row: Richard Mortenson, Elliot Youth, William Khomtchenko, Zining Chen, Siddharth Annaldasula, Brennan Lee, Waris Barakzai (not pictured); Bottom Row: Madison Darmofal, Max Zhou, Marjorie Liebling, Hurlink Vongsachang, Ana Berthel, Jocelyn Ao

Siddharth Annaldasula

Siddharth Annaldasula
Carnegie Mellon University

Mentor: Samie Jaffrey
Institution: Weill Cornell Medicine
Project: High-throughput computational screen for genetic perturbations that alter ribosomal RNA chemical modifications


Jocelyn Ao

Jocelyn Ao
Binghamton University

Mentor: Travis Hollman
Institution: Memorial Sloan Kettering Cancer Center
Project: The application of cancer immunotherapy


Waris Nabi Barakzai

Waris Nabi Barakzai
New York University

Mentor: Iman Hajirasouliha
Institution: Weill Cornell Medicine
Project: A New Method for Barcode Deconvolution of Linked Read Sequencing Data Sets


Ana Berthel

Ana Berthel
Mount Holyoke College

Mentor: Andrea Ventura
Institution: Memorial Sloan Kettering Cancer Center
Project: A Tale of Two RNAs: Generating CRISPR guide RNAs to Target microRNA Binding Sites


Zining Chen

Zining Chen
Cornell University

Mentor: Alex Kentsis
Institution: Memorial Sloan Kettering Cancer Center
Project: ProteomeGenerator 2.0: open and scalable framework for comprehensive proteogenomics


Madison Darmofal

Madison Darmofal
Massachusetts Institute of Technology

Mentor: Ekta Khurana
Institution: Weill Cornell Medicine
Project: A machine learning approach for identifying chromatin loop regions from gene expression data


William Khomtchenko

William Khomtchenko
University of Tennessee

Mentor: Eric Lai
Institution: Memorial Sloan Kettering Cancer Center
Project: Genome-wide Analysis of the m6A Pathway in Drosophila melanogaster


Brennan Lee

Brennan Lee
Massachusetts Institute of Technology

Mentor: John Chodera
Institution: Memorial Sloan Kettering Cancer Center
Project: Dimension Reduction of Time Series Data for Metastable Protein Dynamics


Marjorie Liebling

Marjorie Liebling
Yeshiva University

Mentor: Thomas Fuchs
Institution: Memorial Sloan Kettering Cancer Center
Project: Deep Learning for Morphology-Based Subtyping of Brain Tumors


Robert Mortenson

Robert Mortenson
Duke University

Mentor: Marcin Imielinski
Institution: Weill Cornell Medicine
Project: Software gGnome to help visualize DNA segments


Hurlink Vongsachang

Hurlink Vongsachang
Harvard University

Mentor: Michael Berger
Institution: Memorial Sloan Kettering Cancer Center
Project: Assessing Collapsing Methods for High-Sensitivity Cell-Free DNA Sequencing


Elliot Youth

Elliot Youth
Brown University

Mentor: Elli Papaemmanuil
Institution: Memorial Sloan Kettering Cancer Center
Project: A Diagnostic Framework for Computational Detection of FLT3 Internal Tandem Duplications


Max Zhou

Max Zhou
Cornell University

Mentor: Amber Simpson
Institution: Memorial Sloan Kettering Cancer Center
Project: A Deep Learning Approach to Identify MSI Status from CT Images in Colon Cancer


2017 Alumni
Computational Biology Summer Program Alumni 2017

(From left to right) Top row: Vincent Liu, Alice Thum, Anna Jacobson, Elena Gavrila; Bottom row: Daniel Alarcon, Rajesh Bollapragada, Parisa Samareh, Kylie Getz

Daniel Alarcon

Daniel Alarcon
New York University

Mentor: Christina Leslie
Institution: Memorial Sloan Kettering Cancer Center
Project: Modeling the effect of methylation on in vitro transcription factor binding affinities


Rajesh Bollapragada

Rajesh Bollapragada
Cornell University

Mentor: Ekta Khurana
Institution: Weill Cornell Medicine
Project: Cornell Noncoding Driver Database


Elena Gavrila

Elena Gavrila
College of William and Mary

Mentor: Andrea Ventura
Institution: Memorial Sloan Kettering Cancer Center
Project: CRISPR and Gene Editing using GuideScan


Kylie Getz

Kylie Getz
The College of New Jersey

Mentor: Christopher Mason
Institution: Weill Cornell Medicine
Project: Comparison of Diagnosis and Relapse Methylation Patterns within Pediatric Acute Lymphocytic Leukemia Patients


Anna Jacobson

Anna Jacobson
Tufts University

Mentor: David Christini
Institution: Weill Cornell Medicine
Project: Computationally Optimizing Models of the Human Ventricular Myocyte


Vincent Liu

Vincent Liu
Columbia University

Mentor: Dana Pe’er
Institution: Memorial Sloan Kettering Cancer Center
Project: SCRAS: Single Cell RNA Analysis Suite


Parisa Samareh

Parisa Samareh
Virginia Polytechnic Institute and State University

Mentor: Michael Berger
Institution: Memorial Sloan Kettering Cancer Center
Project: Creating a Quality Control Module for the Multiple Steps Involved in Sequencing


Alice Thurn

Alice Thum
Barnard College

Mentor: Nikolaus Schultz
Institution: Memorial Sloan Kettering Cancer Center
Project: Genome Nexus: A web resource for the comprehensive annotation of cancer variants