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
Cutting-Edge Computational Study Provides ‘Gut Check’ to How We Thought Proteins Function
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In using AI-powered tools to map proteins in the human gut microbiome, researchers have challenged the traditional view of the relationship between protein sequence, structure and 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 Collaboration
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
Publication Highlights
Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data
X. Chen, O. Troyanskaya, et al.
Resolving chromatin remodeling-linked gene expression changes at cell type resolution is important for understanding disease states. We describe MAGICAL, a…
medRxivCultured Renal Proximal Tubular Epithelial Cells Resemble a Stressed/Damaged Kidney While Supporting BK Virus Infection
Ping An, Maria Teresa Sáenz Robles, R. Sealfon, et al
BK virus (BKV; human polyomavirus 1) infections are asymptomatic in most individuals, and the virus persists throughout life without harm.…
Journal of VirologyA methylation clock model of mild SARS-CoV-2 infection provides insight into immune dysregulation
W. Mao , R. Sealfon, et al.
DNA methylation comprises a cumulative record of lifetime exposures superimposed on genetically determined markers. Little is known about methylation dynamics…
Molecular Systems BiologyDirector
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.