CSB 2019 Retreat


Sunday, Oct 13, 2019 to Monday, Oct 14, 2019


8:30 am to 1:30 pm


140 Ocean Avenue, Kennebunkport, ME 04046

Event Description: 

The Computational and Systems Biology Ph.D. Program will hold our annual retreat at the Colony Hotel in picturesque Kennebunkport, ME. Sunday October 13th - Monday October 14th 2019. Our retreat will feature a poster session, lobster buffet, and talks from: CSB students,MIT Faculty and invited external Faculty.

Our Career Panel is Monday from 11:00am - 12:00pm and will feature: Dr. Anders Hansen (MIT) Dr. Seychelle Vos (MIT), Dr. Bryan Bryson (MIT), Dr. Thomas Keating (ImmunoGen, Inc), Dr. Xiao Wang (MIT), Dr. Pulin Li (MIT/WI) and Dr. Lauren Foster (MIT).

We are pleased to announce our line up of speakers:

Guest Speakers : 

Dr. Anders Sejr Hansen

Assistant Professor of Biological Engineering, MIT (Starting February 2020)

Hansen Lab

Seminar Title: Dynamic of 3D Genome Organization in Live Cells at Single-Molecule Resolution

Seminar Date/Time:  Sunday October 13, 2019 /  11:30 AM – 12:00 PM


Anders obtained his undergraduate and Master’s degree in Chemistry at Oxford University in 2010. He received his PhD in Chemistry and Chemical Biology from Harvard University in 2015, where he worked with Erin O’Shea and applied systems biology approaches to understand how cells can encode and transmit information in the dynamics of transcription factor activation. For his post-doc at UC Berkeley with Robert Tjian and Xavier Darzacq, Anders developed new imaging approaches for dissecting the dynamics of 3D genome organization with single-molecule resolution in living cells. Anders will join MIT as an Assistant Professor of Biological Engineering in early 2020.

Dr. Seychelle Vos

Assistant Professor of Biology, MIT

Vos Lab

Seminar Title: Structural and functional characterization of transcription elongation complexes

Seminar Date/Time: Sunday October 13, 2019 / 12:00 - 12:30 PM


Seychelle Vos uses structural biology (cryo-electron microscopy and X-ray crystallography) and biochemistry to understand how gene expression and genome organization are physically coupled. 

Vos completed a bachelors in Genetics at the University of Georgia in 2008, followed by a PhD in Molecular and Cell Biology from the University of California, Berkeley in the laboratory of James M. Berger in 2013. Her doctoral research investigated molecular mechanisms regulating machines involved in DNA organization. She completed her post doctoral work in Patrick Cramer’s group at the Max Planck Institute for Biophysical Chemistry in Germany where she determined how the machine responsible for gene expression is regulated near gene promoters. Vos joined the faculty at MIT as an assistant professor in the Department of Biology in the fall of 2019.

 Dr. Bryan Byson

Assistant Professor of Biological Engineering

Bryson Lab

Seminar Title: Integrated analysis of human macrophage diversity

Seminar Date/Time: Sunday October 13, 2019 /  1:30 - 2:00 PM


Bryan Bryson obtained an undergraduate degree in mechanical engineering and a PhD in biological engineering at MIT. He then went on to pursue postdoctoral training with Sarah Fortune at the Harvard TH Chan School of Public Health where he became interested in understanding how to leverage modern approaches in biological engineering to contribute to our understanding of tuberculosis pathogenesis. His lab at MIT combines approaches in immunology, synthetic biology, microbiology, and systems biology to understand intracellular pathogen control and macrophage diversity.


Dr. Pulin Li

Assistant Professor of Biology, MIT; Member, Whitehead Institute

Li Lab

Seminar Title: Understanding Biological Patterning from the Bottom Up

Seminar Date/Time: Sunday October 13, 2019 /  2:00 - 2:30 PM


Pulin Li has joined the Department of Biology as an Assistant Professor and a member of the Whitehead Institute in the summer of 2019. She completed a PhD in Chemical Biology from Harvard University. She focused on discovering novel signaling pathways that regulate hematopoietic stem cells during embryo development and adult transplantation.  She then completed post doctoral work in the Division of Biology and Biological Engineering at California Institute of Technology, studying how cell-cell communication circuits coordinate multicellular behaviors to pattern tissues. To study this central question in developmental biology, she developed a bottom-up approach by genetically engineering communication circuits in individual cells and then reconstituting multicellular behaviors in a petri dish. This cell-based reconstitution approach, together with quantitative measurements and mathematical modeling, provides a new methodology for studying developmental and evolutionary questions. It could also offer a quantitative framework and molecular tools for tissue engineering.

Dr. Xiao Wang

Assistant Professor of Chemistry, MIT; Core Member of the Broad Institute of MIT and Harvard

Wang Lab

Seminar Title: Spatially resolved cell typing in the brain

Seminar Date/Time: Sunday October 13, 2019 /   5:00 - 5:30 PM


Xiao Wang is a core institute member of the Broad Institute of MIT and Harvard and an assistant professor in the Department of Chemistry at MIT. At Broad, she creates and applies new chemical, biophysical and genomic tools to better understand brain function and dysfunction at the molecular level. Xiao received her B.S. in chemistry and molecular engineering from Peking University in 2010. She received her Ph.D. in chemistry from the University of Chicago in 2015 where she elucidated the cellular functions of RNA modifications with Prof. Chuan He. She then conducted postdoctoral research with Prof. Karl Deisseroth, where she was a fellow of Life Science Research Foundation and developed in situ RNA sequencing methods to map the spatial organization of cell types in the mouse brain.

Dr. Hagen Tilgner

Assistant Professor of Neuroscience at the Brain and Mind Research Institute (BMRI), Weill Cornell Medicine

Tilgner Lab

Seminar Title: Getting the entire message: Full-length isoforms in cell lines and thousands of single cells of complex tissue

Seminar Date/Time: Sunday October 13, 2019 /   5:30 - 6:00 PM


Dr. Tilgner is an Assistant Professor of Neuroscience at the Brain and Mind Research Institute (BMRI) of Weill Cornell Medicine as of 2016. He obtained his M.Sc. degrees from Germany (Karlsruhe Institute of Technology) and from France (Ecole Nationale d’Informatique et des Mathematiques Appliquees de Grenoble – ENSIMAG and Universite Joseph Fourier) in Computer Science and Bioinformatics. After an internship at the Sanger Institute (Cambridge, UK), he carried out his PhD research under the supervision of Professor Roderic Guigo at the Center for Genomic Research (CRG) in Barcelona, Spain, focusing on the mechanism and dynamics of RNA splicing.  In 2011, he moved to the Genetics Department of Stanford University to the laboratory of Professor Michael Snyder, where he focused on developing various techniques for full-length RNA isoform profiling. His main interest is understanding how different isoforms (“what genes are saying”) expand on simple gene expression measurements (“how much genes are talking”) in specifying cellular function in single cells of the nervous system and disease. 

Dr. Kevin Esvelt

Assistant Professor of Media Arts and Sciences, MIT;  NEC Career Development Professor of Computer and Communications

Esvelt Lab

Seminar Title: Understanding evolution and preventing catastrophe

Seminar Date/Time: Monday October 14, 2019 /  9:15 - 9:45 AM


Kevin M. Esvelt is an assistant professor of the MIT Media Lab, where he leads the Sculpting Evolution Group in exploring evolutionary and ecological engineering.

He received his Ph.D. from Harvard University for inventing a synthetic microbial ecosystem to rapidly evolve useful biomolecules, and subsequently helped pioneer the development of CRISPR, a powerful new method of genome engineering.

In 2013, Esvelt was the first to identify the potential for CRISPR “gene drive” systems to alter wild populations of organisms. Recognizing the implications of an advance that could enable individual scientists to alter the shared environment, he and his colleagues chose to break with scientific tradition by revealing their findings and calling for open discussion and safeguards before they demonstrated the technology in the laboratory.

At MIT, the Sculpting Evolution Group develops safer “daisy drives” that only spread locally, as well as ways of restoring populations to their original genetics. Together with the communities of Nantucket and Martha's Vineyard, they are advancing the “Mice Against Ticks” project aiming to prevent tick-borne disease. Other research interests include unraveling the workings of molecular evolution and reducing animal suffering. An outspoken advocate of freely sharing research plans to accelerate discovery and improve safety, Kevin seeks to use gene drive as a catalyst to reform the scientific ecosystem.

His work is frequently published in top scientific journals, including Nature and Science, and covered in The New York TimesThe New YorkerThe Atlantic, PBS NOVA, and NPR.

Dr. Lauren C. Foster

Associate Director of the Technology Licensing Office, MIT; Director of IP and Strategic Alliances at Koch Institute Medicine, Cell Biology, Biotechnology, Diagnostics

Seminar Date/TIme: Monday October 14, 2019 /  9:45 - 10:45 AM


Lauren C. Foster is the Associate Director of M.I.T.'s Technology Licensing Office (TLO), focusing principally on licensing and commercialization of technologies in the biomedical, biotechnology and medical device fields. She also serves as Director of Intellectual Property and Strategic Alliances at the Koch Institute for Integrative Cancer Research at M.I.T. where she is involved in the strategic management of the Koch Institute’s industrial partnerships and intellectual property portfolio.  Prior to joining M.I.T., Lauren was Senior Director, IP and Technology Acquisition at Antigenics, Inc., a public biotechnology company, where she played an integral role in envisioning and implementing the company’s business, intellectual property and technology strategies.  Lauren was also a Technical Specialist at the law firm Lahive & Cockfield LLP where she focused on strategic development of intellectual property rights for biotechnology and pharmaceutical companies and universities.  Ms. Foster holds a D.Sc. from Harvard University and a B.S. from Haverford College, and is a registered Patent Agent.


Student Speakers & Posters: 

Max Shen

Liu / Regev Lab

Seminar Title: Conditional sequence models for predicting and optimizing base editing outcome distributions

Seminar Date/Time: Sunday October 13, 2019 /   11:15 - 11:30 AM


Max W. Shen is a fifth-year Ph.D. candidate in the CSB program and co-advised by David Liu and Aviv Regev. He bridges data science and machine learning with genome editing and directed evolution. Beyond research, he has an interest in data visualization, and is proud of developing an interactive web app that ~500 scientists use monthly for designing experiments with CRISPR/Cas9

Carles Boix

Kellis Lab

Seminar Title: Integrative analysis of 10,000 epigenomic maps across 800 samples for regulatory genomics and disease dissection.

Seminar Date/Time: Sunday October 13, 2019 /   7:30 - 7:45 PM


 Carles is a 5th year PhD CSB student in Manolis Kellis' group, where he studies both the epigenomic diversity of tissues and primary cells and brain cellular variation in the context of neurodegenerative disease. Prior to coming to MIT, he studied Molecular Biology at Princeton, where he worked on non-parametric tests on genomic data with John Storey.

Jesse Tordoff

Weiss Lab

Seminar Title: Uncovering Design Principles of Self-Organizing Multicellular Patterns

Seminar Date/Time: Sunday October 13, 2019 /   7:45 - 8:00 PM


Jesse Tordoff is a 5th year PhD student in the CSB program. She graduated from Yale University in 2015 where she majored in computer science and biology. At MIT, her research is on controlling pattern formation using synthetic biology, with a specific focus on designing structures that self-organize. 

Alvin Shi

Kellis Lab

Seminar Title: Plasma-derived exosomal analysis and deconvolution enables prediction and tracking of melanoma checkpoint blockade response 

Seminar Date/Time: Sunday October 13, 2019 /   8:00 - 8:15 PM


Alvin is currently a 5th year PhD CSB student working with Manolis Kellis on various projects related to tracking and understanding cancer immunotherapy resistance. Prior to joining CSB, he was an undergraduate student at Duke University, where he double-majored in Chemistry and Biology and minored in computer science. While at Duke, he did work related to genetics of C. elegans gonadal development in the lab of Dr. David Sherwood. After graduating Duke, he worked at the NIH for two years as a post-baccalaureate IRTA fellow with Dr. Nan-ping Weng at the National Institute of Aging, where he worked on how the dynamics of T-cell receptor repertoire evolved during aging. He is currently supported by a NSF Graduate Research Fellowship




Poster Title

Max Gold


Ernest Fraenkel

Modeling Molecular Regulation in Medulloblastoma Subgroups using Proteomics and Chromatin Accessibility

Jennifer Hammelman


David Gifford

Multiplexed Integrated Accessibility Assay Identifies Sequence Features of Differential Chromatin Accessibility

Sarah Nyquist


Alex Shalek/Bonnie Berger

Longitudinal scRNA-seq reveals progenitor populations in breast milk

Miriam Shiffman


Aviv Regev/ Tamara Broderick

Reconstructing probabilistic trees of cellular differentiation from single-cell RNA-seq data

Adam Atanas


Steve Flavell

Determining the mechanisms of associative learning with whole-brain imaging

Cameron Flower


Forest White

Real-time, High-density Monitoring of pTyr Signaling Targets in Human Tumors using SureQuant Heavy Peptide Triggered Targeted Quantitation

Conner Kummerlowe


Alex Shalek

Towards a single-cell atlas of environmental enteropathy - a potential cause of child stunting

Brian Trippe


Tamara Broderick

LR-GLM: High-Dimensional Bayesian Inference Using Low-Rank Data Approximations

Ellen Zhong


Joey Davis/Bonnie Berger

Reconstructing continuous distributions of 3D protein structure from cryo-EM images

Susana Hawken


Rick Young

Differential Partitioning of Cancer Therapeutics in Nuclear Condensates

Mirae Parker


Gene-Wei Li

Minimal I-MAP MCMC: Accessible Software for Bayesian Inference of Bayesian Networks