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Computational Aspects of Biological Information 2013
Computational Aspects of Biological Information 2013

Computational Aspects of Biological Information (CABI) 2013 is a one day workshop on challenges in computational biology. CABI 2013 will be held at Microsoft Research New England on December 16, 2013 and will bring together experts in the Boston/Cambridge area to discuss computational solutions to problems in systems biology, genomics, and related areas. The workshop is open to everyone and registration is free of charge. Continental breakfast and lunch will be served.

Workshop program

Where applicable, links to video replays of select workshops are provided.

9:00 - 9:50  Registration and breakfast 
9:50 - 10:00  Opening remarks 
10:00 - 10:30  Computational Genomic Medicine
Jill P. Mesirov (Broad Institute) 
10:30 - 11:00  Synthetic Biology and Biocomputation: Life Redesigned
Jim Collins (Boston University, Howard Hughes Medical Institute, Wyss Institute, Harvard University)
11:00 - 11:15  Coffee break 
11:15 - 11:45  Evolutionary Forces in Humans and Pathogens
Pardis Sabeti (Harvard University, Broad Institute)
Watch the video replay >> 
11:45 - 12:15  Transcription Factors and DNA Regulatory Elements
Martha Bulyk (Brigham & Women's Hospital, Harvard Medical School)  
12:15 - 1:00  Lunch 
1:00 - 1:30  Poster session 
1:30 - 2:00  Instrumenting the Healthcare Enterprise
Isaac (Zak) Kohane (Harvard Medical School)
Watch the video replay >>  
2:00 - 2:30  Analysis of Cell-Cell Communication Networks in Inflammatory Pathologies
Doug Lauffenburger (Massachusetts Institute of Technology)
Watch the video replay >> 
2:30 - 3:00  Computational Discovery of Directional Pioneer Factors
David Gifford (Massachusetts Institute of Technology)
Watch the video replay >> 
3:00 - 3:45  Coffee break / Posters
3:45 - 4:15  Message Passing: Modeling the Flow of Information in Cellular Networks
John Quackenbush (Dana-Farber Cancer Institute, Harvard School of Public Health)
Watch the video replay >> 
4:15 - 4:45  Computational Analysis of Mutational Heterogeneity in Cancer
Ben Raphael (Brown University) 
4:45 - 5:15  Interpreting Cancer Copy-Number Alterations
Rameen Beroukhim (Harvard Medical School, Broad Institute, Dana-Farber Cancer Institute)
Watch the video replay >> 
5:15 - 5:20     Closing remarks 












Poster session

The following posters will be presented at CABI 2013:

  • A tunable coarse-grained model for ligand-receptor interaction. Teresa Ruiz-Herrero, Javier Estrada, Raúl Guantes, David G. Míguez.
  • Going the distance for protein function prediction. Mengfei Cao, Hao Zhang, Jisoo Park, Noah Daniels, Mark Crovella, Lenore Cowen, Benjamin Hescott.
  • Got a way to extract those one thousand words from your images? Tiao Xie, Hunter Elliott, Joy Yichao Xu.
  • Position-specific effects of codon choice in an essential gene. Eric Kelsic, Hattie Chung, Harris Wang, Roy Kishony.
  • PathSeq: Computational tool to identify or discover microbes by deep sequencing of human tissue. Chandra Sekhar Pedamallu, Akinyemi I Ojesina, Joonil Jung, Aleksandar D Kostic, Ami Bhatt, Samuel Freeman, Fujiko Duke, Peter Carr, Gad Getz, Matthew Meyerson.
  • Genecentric: A package to uncover graph-theoretic structure in high-throughput epistasis data. Andrew Gallant, Mark D.M. Leiserson, Maxim Kachalov, Lenore J. Cowen, Benjamin J. Hescott.
  • Different RTK ligands induce heterogeneous FOXO3a translocation dynamics. Somponnat Sampattavanich*, Bernhard Kramer*, John G. Albeck, Peter K. Sorger.
  • Analysis of Chromatin State Plasticity Identifies Cell-type Specific Regulators of H3K27me3 Patterns. Luca Pinello, Jian Xu, Stuart H. Orkin*, Guo-Cheng Yuan*.
  • Analysis of Complex Variants From High‐Throughput DNA Sequencing Data. Layla Oesper, Gryte Satas, Max Song, Simone Dantas, Benjamin J. Raphael.
  • Inferring Dynamic Signatures of Microbes in Complex Host Ecosystems. Georg K. Gerber, Andrew Onderdonk, Lynn Bry.
  • RNA folding pathways and kinetics using 2D energy grids. Evan Senter, Ivan Dotu, Peter Clote.
  • GenomeSpace: An Environment for Frictionless Bioinformatics. Barbara Hill Meyers, Michael Reich, Ted Liefeld, Marco Ocana, Dongkeun Jang, Jon Bistline, James Robinson, Peter Carr, Nathalie Pochet, Diego Borges-Rivera, Thorin Tabor, Helga Thorvaldsdóttir, Aviv Regev, Jill P Mesirov.
  • A Randomized Approach to Fast Read Processing. Roy Lederman.
  • Knowledge based bioinformatics methods for understanding the genetic architecture of Complex Diseases. Alper Uzun, Andrew Dewan, Bethany Mcgonnigal, James Padbury.
  • Predicting xenobiotic transformations through human cytochrome P450. Mona Yousofshahi, Sara Manteiga, Charmian Wu, Kyongbum Lee, Soha Hassoun.
  • TILSH: A Method to Detect Interchromosomal Translocations and Interchromosomal Insertions using Sliding Window Fingerprints and Locality Sensitive Hashing. Roshanak Farhoodi, Nurit Haspel, Rohith Kotla, Jennifer Rosen, Dan Simovici, Rosanne Vetro, David Weisman.
  • Dendrix++: A Probabilistic Method for Identifying Mutated Driver Pathways in Cancer. Mark DM Leiserson, Hsin-Ta Wu, Vivian Hsiao, Fabio Vandin, Benjamin J. Raphael.
  • Improving the accuracy and performance of robust pipelines for genetic variation calling from NGS data. GSA-GATK Team @ Broad Institute.
  • Using a Population Genome Graph Reference for Sequence Alignment & Genotyping Structural Variants. Deniz Kural, Gabor Marth.
  • RNAiFold: A constraint programming algorithm for RNA inverse folding and molecular design. Juan Antonio Garcia Martin, Ivan Dotu, Peter Clote.
  • Massively Parallel Model of Cardiovascular Hemodynamics. Amanda Randles, Erik Draeger, Efthimios Kaxiras, Franziska Michor.
  • Patient stratification in secondary progressive multiple sclerosis (SPMS) using a mixture of experts model. Raghavendra Hosur, Suzanne Szak, Jadwiga Bienkowska.

* Equal contribution


Organizing committee

Christian Borgs (Microsoft Research New England)
Jennifer Chayes (Microsoft Research New England)
Ernest Fraenkel (Massachusetts Institute of Technology)
Anthony Gitter (Microsoft Research New England)
Franziska Michor (Dana-Farber Cancer Institute, Harvard School of Public Health)



Date & time

Monday, December 16, 2013
Registration and breakfast begin at 9 AM



Microsoft Research New England
Horace Mann Conference Room
First Floor Conference Center
One Memorial Drive, Cambridge, MA


Arrival guidance

Upon arrival, be prepared to show a picture ID and sign the Building Visitor Log when approaching the Lobby Floor Security Desk. Alert them to the name of the event you are attending and ask them to direct you to the appropriate floor. The talks will be held the First Floor Conference Center, Horace Mann Conference Room.

Send questions to: