2018 CSB Retreat


Saturday, Oct 13, 2018 to Sunday, Oct 14, 2018


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 Saturday October 13th - Sunday October 14th. Our retreat will feature a poster session, lobster buffet, and talks from:  CSB students, CSB Alumna, MIT and Harvard Faculty, as well as industry leaders.

We are pleased to announce our line up of speakers:

Tamara Broderick, PhD, ITT Career Development Assistant Professor of Electrical Engineering and Computer Science, MIT

Angela DePace, PhD, Associate Professor of Systems Biology, Harvard Medical School

Vadim Gladyshev, PhD, Professor, Medicine, Harvard Medical School; Director of Redox Medicine, Brigham and Women's Hospital

Ankur Jain, PhD,  Assistant Professor of Biology, MIT; Member, Whitehead Institute

Rajeev Sivasankaran, PhD, Novartis

Sabrina Spencer,PhD, Assistant Professor of Chemistry and Biochemistry, University of Colorado-Boulder *CSB Alumna

Guest Speakers : 

Dr. Sabrina Spencer

Assistant Professor of Chemistry and Biochemistry, University of Colorado-Boulder 

Spencer Lab

Dr. Spencer is an Assistant Professor in the Department of Biochemistry at the University of Colorado-Boulder, as well as a member of the BioFrontiers Institute and the University of Colorado Comprehensive Cancer Center.  She received her bachelor's degrees from the George Washington University, and her PhD from MIT in Computational and Systems Biology working with Peter Sorger on the origins of cell-to-cell variability in apoptosis.  She then became a Damon Runyon Postdoctoral Fellow in Tobias Meyer's lab at Stanford University where she studied the proliferation-quiescence decision at the single-cell level using a novel live-cell sensor for Cyclin-Dependent Kinase 2 activity. Dr. Spencer started her own lab at the University of Colorado-Boulder in August 2014, where she and her lab are using single-cell time-lapse microscopy and cell tracking to study how variations in cell signaling lead to heterogeneity in cell-fate decisions.  Dr. Spencer is also a recipient of a K22 Career Transition Award from the National Cancer Institute, a Boettcher Foundation Early Career Investigator Award, a Kimmel Scholar Award, a Searle Scholar Award, a Beckman Young Investigator Award, a Pew-Stewart Scholar Award, and an NIH Director's New Innovator Award.  

Seminar Title: "Single-cell analysis of heterogeneity in proliferation-quiescence decisions"

Seminar Date/Time:  Saturday October 13, 2018 1:30 pm – 2:00 pm

Dr. Rajeev Sivasankaran 

Head- Rare Diseases, Neuroscience Division, NIBR

Novartis Neurobiology

Rajeev Sivasankaran PhD, leads the Rare Diseases group in the Neuroscience Division at Novartis Institutes of Biomedical Research (NIBR). His group is responsible for initiating and establishing drug discovery programs focused on genetically defined targets in orphan neurodegenerative diseases. He has led multiple target validation efforts, screening campaigns and drug discovery programs during his 14 years at NIBR. His experience extends from early discovery to first in human clinical trials. Dr Sivasankaran completed his doctoral work in molecular biology from the University of Zurich and his post-doctoral work at Children’s Hospital / Harvard Medical School.

Seminar Title: "Making sure the Splice is right – drug discovery for Spinal Muscular Atrophy"

Seminar Date/Time: Saturday October 13, 2018 2:00 pm – 2:30 pm


Dr. Angela DePace

Associate Professor of Systems Biology, Harvard Medical School

DePace Lab

Angela DePace joined the Department of Systems Biology at Harvard Medical School in 2008, where her laboratory investigates the mechanism and evolution of gene expression in animals — fundamental biology with implications forpersonalized medicine.  Her research couples mathematical theory to quantitative experiments in Drosophila embryos to test basic assumptions about how transcription is controlled, and to predict the output of regulatory sequences in the genome.

She teaches scientific communication and co-authored the book “Visual Strategies: A Practical Guide to Graphics for Scientists and Engineers”. She is widely recognized for her commitment to mentoring and career development for graduate students, and has shared her methods through invited seminars, a populararticle, and an online course offered by iBiology.  She received an NSF CAREER award in acknowledgement of herinnovative research and teaching.  She is also the founding faculty director of the Scientific Citizenship Initiative (SCI), which aims to train scientists for effective civic engagement, and facilitate a cultural shift in academia to enable and value engagement of scientists at all career stages.

Dr. DePace received her bachelor’s degree in Molecular Biophysics and Biochemistry from Yale College, andher PhD in Biochemistry from the University of California, San Francisco. She was a Helen Hay Whitneypostdoctoral fellow at the University of California, Berkeley.

Seminar Title: "Precision and Plasticity in Animal Transcription"

Seminar Date/Time: Saturday October 13, 2018 5:00 pm – 5:30 pm

Dr. Vadim Gladyshev

Professor, Medicine, Harvard Medical School; Director of Redox Medicine, Brigham and Women's Hospital

Gladysev Lab

Dr. Vadim Gladyshev is Professor of Medicine at Brigham and Women’s Hospital, Harvard Medical School, Director of the Center for Redox Medicine, and Associate Member of the Broad Institute. He graduated and obtained his PhD from Moscow State University, followed by postdoctoral training at NIH and a first faculty position at University of Nebraska. Dr. Gladyshev has a long-term interest in the understanding of mechanisms of aging and regulation of lifespan, and also works in the areas of selenium and redox biology. He uses a variety of model organisms and applies high-throughput approaches to achieve systems level understanding of aging. His work on the naked mole rat and Brandt’s bat was the first when the genomes were sequenced with the primary goal of understanding longevity. Last year, Dr. Gladyshev developed a mouse epigenetic clock that reports the biological age of animals and the effects of longevity interventions. He also developed the concept of the deleteriome to describe the aging process. Dr. Gladyshev has published approximately 350 articles. He is a recipient of the NIH Director’s Pioneer Award to study mechanisms of lifespan control.

Seminar Title: “Mechanisms of aging and lifespan control”

Seminar Date/Time:Saturday October 13, 2018 5:30 pm – 6:00 pm


Dr. Ankur Jain

Assistant Professor of Biology, MIT; Member, Whitehead Institute

Ankur Jain

Ankur Jain explores the biology of RNA aggregation. Several genetic neuromuscular disorders such as myotonic dystrophy and amyotrophic lateral sclerosis are caused by expansions of nucleotide repeats in their cognate disease genes. Such repeats cause the transcribed RNA to form pathogenic clumps or aggregates. Jain uses a variety of biophysical approaches to understand how the RNA aggregates form, and how they can be disrupted to restore normal cell function. Jain will also study the role of RNA-DNA interactions in chromatin organization, investigating how the RNA transcribed from telomeres (the protective repetitive sequences that cap the ends of chromosomes) modulate telomere architecture and function. 

Jain completed a Bachelor of Technology in biotechnology and biochemical engineering at the Indian Institute of Technology Kharagpur, India in 2007, followed by a PhD in biophysics and computational biology at the University of Illinois at Urbana-Champaign under the direction of Taekjip Ha in 2013. Following a postdoctoral fellowship at the University of California San Francisco, he joins the MIT faculty in the Department of Biology as an assistant professor with an appointment as a member of the Whitehead Institute for Biomedical Research in the fall of 2018.

Seminar Title: "Cellular RNA aggregation"

Seminar Date/Time: Sunday October 14, 2018 9:30 am – 10:00 am 

Dr. Tamara Broderick

ITT Career Development Assistant Professor of Electrical Engineering and Computer Science, MIT

Broderick Lab

Tamara Broderick is the ITT Career Development Assistant Professor in the Department of Electrical Engineering and Computer Science at MIT. She is a member of the MIT Computer Science and Artificial Intelligence Laboratory (CSAIL), the MIT Statistics and Data Science Center, and the Institute for Data, Systems, and Society (IDSS). She completed her Ph.D. in Statistics at the University of California, Berkeley in 2014. Previously, she received an AB in Mathematics from Princeton University (2007), a Master of Advanced Study for completion of Part III of the Mathematical Tripos from the University of Cambridge (2008), an MPhil by research in Physics from the University of Cambridge (2009), and an MS in Computer Science from the University of California, Berkeley (2013). Her recent research has focused on developing and analyzing models for scalable Bayesian machine learning. She has been awarded an NSF CAREER Award (2018), a Sloan Research Fellowship (2018), an Army Research Office Young Investigator Program award (2017), Google Faculty Research Awards, the ISBA Lifetime Members Junior Researcher Award, the Savage Award (for an outstanding doctoral dissertation in Bayesian theory and methods), the Evelyn Fix Memorial Medal and Citation (for the Ph.D. student on the Berkeley campus showing the greatest promise in statistical research), the Berkeley Fellowship, an NSF Graduate Research Fellowship, a Marshall Scholarship, and the Phi Beta Kappa Prize (for the graduating Princeton senior with the highest academic average).

Seminar Title: “Automated Scalable Bayesian Inference via Data Summarization”

Seminar Date/Time: Sunday October 14, 2018  10:00 am – 10:30 am


Student Speakers & Posters: 

Cassandra Schaening Burgos                                           

Lab(s): Gene-Wei Li (MIT) and Wendy Gilbert (Yale)

5th year CSB PhD Student

Cassandra was born in San Juan, Puerto Rico, where she obtained a Bachelor's in Computer Science from the University of Puerto Rico. She is a graduate student in Gene-Wei Li's lab, jointly advised with Wendy Gilbert at Yale University. She is interested in the ways that RNA modifications can affect the life cycle of an mRNA, and is currently studying the distribution and function of pseudouridines in bacterial RNAs. Previously, she has also studied the basis for these modifications, identifying the sequence and structure features that allow enzymes that typically modify tRNAs and rRNAs to also modify mRNAs.

Seminar Title: "Spb1 targets mRNAS for regulated modification with 2' O-methyl ribose"

Seminar Date/Time: Saturday October 13, 2018 11:15 am - 11:30 am

     Natasha Patel-Murray 

6th year CSB PhD student

Lab: Ernest Fraenkel

Natasha received her B.S. in Mathematical Biology from the University of Michigan in 2013.  At MIT, she combines experimental and computational approaches in Ernest Fraenkel's lab.  She works on integrating multiple omics datasets with the goal of identifying potential therapeutic targets in Huntington's Disease.  

Seminar Title:"Mapping Therapeutic Pathways Using Omics Data Integration"

Seminar Date/Time: Saturday October 13, 2018  11:30 am – 11:45 am

        Tristan Bepler

5th year CSB PhD Student

Lab: Bonnie Berger

Tristan Bepler is a PhD student in Bonnie Berger's group at MIT. He received his bachelors of science from Duke University in 2014 where he double majored in computer science and biology. As an undergraduate, he worked in the Garcia-Blanco lab studying the role of mesenchymal to epithelial transition in tumor metastasis and then with Raluca Gordân studying the sequence specificity of ETS family transcription factor binding. At MIT, his work has focused on the development of machine learning methods for a range of problems in protein biology, synthetic biology, and cryo-electron microscopy. 

Seminar Title: "Learning protein sequence embeddings using information from structure"

Seminar Date/Time: Saturday October 13, 2018 11:45 am – 12:00 pm

             Grace Yeo

5th year CSB PhD student

Lab: David Gifford

Grace Yeo is currently a fifth-year student in the Gifford Lab. She previously did her undergraduate studies in Biomedical Engineering at Johns Hopkins University, where she first became interested in the intersection of biology and computer science. While at Hopkins, she worked in the Karchin Lab to develop bayesian models for relating genotype to phenotype. She subsequently spent a year at the Genome Institute of Singapore developing algorithms for calling low frequency insertions and deletions in heterogeneous populations. Her current research interests are in the analysis, integration and representation of single-cell RNA-sequencing data. 

Seminar Title:  “Elucidation of combinatorial signaling logic with multiplexed barcodelet single-cell RNA-seq”

Seminar Date/Time: Saturday October 13, 2018 12:00 pm – 12:15 pm







Boix, Carles


"Leveraging single-cell RNA-seq to infer cell type-specific somatic mutations and mosaicism in Alzheimer’s disease"


Gold, Max


"Shallow Sparsely-Connected Autoencoders for Gene Set Projection”


Hammelman, Jennifer


"Learning Representative Chromatin Accessibility Profiles at Transcription Factor Sites"


McCue, Kayla


"Models of Pre-mRNA Splicing Under Intron and Exon Definition"


Nyquist, Sarah


"Pseudotime reconstruction algorithms provide insight into mechanisms of human epithelial barrier dysfunction"


Shi, Alvin


"Transcriptomic and epigenomic correlates of resistance to checkpoint blockade immunotherapy"


Shiffman, Miriam


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


Tordoff, Jesse


"Programming self-organizing multicellular shapes"


Witten, Jacob


"Characterizing the physicochemical selectivity of the mucus barrier"


Wolf, Maxim


"Identifying and interpreting the function of coding regions with unusual levels of constraint"


Yang, Joy


"Methods for identifying mechanisms of phage-host interactions"