The Center for Computational Biology develops new and innovative methods of examining data in the biological sciences whose scale and complexity have historically resisted analysis.
Featured News

New research led by Flatiron Institute researchers reveals the source of the mysterious swirling flows in some of nature’s largest cells.
CCB’s mission is to develop modeling tools and theory for understanding biological processes and to create computational frameworks that will enable the analysis of the large, complex data sets being generated by new experimental technologies.
Research Areas





Collaborative Work

Underlying all biological processes are molecules and their interactions with each other. However, our ability to understand how these molecules function over biologically relevant scales remains very limited.
- CCB
- CCM

The Center for Computational Biologyx (CCBx) is an effort by the Center for Computational Biology (CCB) to (a) create and validate quantitative techniques and (b) develop and test theories of biological systems that are predictive of these systems’ behaviors and responses to genetic, chemical and physical perturbations.
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Upcoming Events
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10 Mon -
Meeting 10:30 a.m. - 12:00 p.m.
Developmental Dynamics Group Meeting
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Meeting 10:30 a.m. - 12:00 p.m.
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11 Tue -
Meeting 10:00 a.m. - 12:00 p.m.
Biophysical Modeling Group Meeting
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Meeting 2:00 - 3:00 p.m.
Structural & Molecular Biophysics Group Meeting
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Meeting 10:00 a.m. - 12:00 p.m.
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12 Wed -
Meeting 11:00 a.m. - 12:00 p.m.
Computer Visionaries Interest Group Meeting
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Meeting 12:00 - 1:00 p.m.
Biomolecular Design Group Meeting
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Meeting 3:00 - 4:00 p.m.
CCB Coffee Hour
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Meeting 11:00 a.m. - 12:00 p.m.
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13 Thu -
Colloquium 11:00 a.m. - 12:00 p.m.
CCB Colloquium: Kresten Lindorff-Larsen, Ph.D.
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Colloquium 11:00 a.m. - 12:00 p.m.
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18 Tue -
Meeting 10:00 a.m. - 12:00 p.m.
Biophysical Modeling Group Meeting
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Meeting 2:00 - 3:00 p.m.
Structural & Molecular Biophysics Group Meeting
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Meeting 10:00 a.m. - 12:00 p.m.
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19 Wed -
Meeting 11:00 a.m. - 12:00 p.m.
Computer Visionaries Interest Group Meeting
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Meeting 11:00 a.m. - 12:00 p.m.
Publication Highlights
Learning locally dominant force balances in active particle systems
We use a combination of unsupervised clustering and sparsity-promoting inference algorithms to learn locally dominant force balances that explain macroscopic…
Proceedings of the Royal Society AA minimal dynamical system and analog circuit for non-associative learning
Learning in living organisms is typically associated with networks of neurons. The use of large numbers of adjustable units has…
Proc. 63rd IEEE Conference on Decision and ControlA two-step dance commits collagen to folding
Director
Software

aLENS
This is the simulation tool for tracking assemblies of microtubules driven by motor proteins.

STKFMM
This is a numerical computation package for various single- and double-layer kernels for Laplace and Stokes operators in boundary integral methods, implemented on top of the highly-optimized kernel independent fast-multipole method package PVFMM.

humanbase
Data-driven predictions of gene expression, function, regulation, and interactions in human.

DeepSEA
Deep learning-based algorithmic framework for predicting chromatin effects

FNTM
Functional Networks of Tissues in Mouse

GIANT
Genome-wide Scale functional interaction networks for 144 human tissues and cell types

IMP 2.0
Integrative Multi-species Prediction

KNNimpute
K-Nearest Neighbors Imputation

Nano-Dissection
This server performs in silico nano-dissection, an approach we developed to identify genes with novel cell-lineage specific expression.

SEEK
Search-Based Exploration of Expression Compendium [Human]

SkellySim
SkellySim is a simulation package for simulating cellular components such as flexible filaments, motor proteins, and arbitrary rigid bodies.

Sleipnir
Sleipnir Library for Computational Functional Genomics

URSA(HD)
A data-driven perspective to your gene expression profile for human tissues and diseases.