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
Center for Computational Biology
The Machinery That Helps Divide Your Cells Self-Organizes Like an Active Liquid Crystal
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Flatiron Institute scientists and experimental collaborators tested a theory that treats chromosome-separating cellular structures called spindles as active liquid crystals. They found that the theory largely succeeds in predicting how spindles self-organize to carry out their signature function.
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
Structural and Molecular Biophysics
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.
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CCBx
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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29 Wed -
Meeting 12:00 - 1:00 p.m.
Computer Vision & Machine Learning Meeting
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Meeting 1:30 - 3:30 p.m.
Genomics Group Meeting
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Meeting 12:00 - 1:00 p.m.
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04 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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05 Tue -
Meeting 10:00 - 11:00 a.m.
Biophysical Modeling Group Meeting
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Meeting 12:00 - 2:00 p.m.
Genomics Group Meeting
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Meeting 2:00 - 3:00 p.m.
COMPASS Meeting
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Meeting 10:00 - 11:00 a.m.
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06 Wed -
Meeting 12:00 - 1:00 p.m.
Computer Vision & Machine Learning Meeting
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Meeting 2:00 - 3:00 p.m.
Biomolecular Design Group Meeting
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Meeting 12:00 - 1:00 p.m.
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11 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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12 Tue -
Meeting 10:00 - 11:00 a.m.
Biophysical Modeling Group Meeting
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Meeting 10:00 - 11:00 a.m.
Publication Highlights
A stabilized finite element formulation for simulating ordered arrays of immersed flexible fibers with applications in cellular mechanics
We present a new computational tool for the simulation of aligned assemblies of thin, bendable, but inextensible fibers immersed in…
Computer Methods in Applied Mechanics and EngineeringMachine learning-based prediction of peptide aggregation during chemical synthesis
Solid-phase peptide synthesis enables the study of countless peptides, but aggregation during synthesis hinders production of many sequences of interest.…
Nature ChemistryExploring How Workflow Variations in Denaturation-Based Assays Impact Global Protein–Protein Interaction Predictions
Tavis J. Reed, Laura M. Haubold, O. Troyanskaya, et al.
Protein denaturation-based assays, such as thermal proximity coaggregation (TPCA) and ion-based proteome-integrated solubility alteration (I-PISA), are powerful tools for characterizing…
Molecular & Cell ProteomicsDirector
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.
Masala
The public repository for the Core library of the Masala software suite. Masala is a set of free and open-source tools for biomolecular modelling, with a plugin-based infrastructure that makes it easy to extend other software.