Theoretical Biology and Biophysics
Modeling biological systems and analysis and informatics of molecular and cellular biological data
Mathematical Biology/Immunology
Fundamental science and modeling enabling host-pathogen science 
Computational Structural Biology
Understanding biomolecule function by determining their 3-D macromolecular structure 
Bioinformatics and Epidemiology
Sequence analysis using advanced algorithms, software, computational hardware
Mathematical modeling and computational analysis of cellular and molecular biology
One of the few research groups in the world devoted to mathematical modeling and computational analysis of problems in cellular and molecular biology.
People
Staff
- Ben McMahon, Group Leader
- Carrie Manore, Deputy Group Leader
- Marisa K. Chavez, Adminstrator
- Werner Abfalterer
- Katie Belobrajdic
- Sayera Dhaubhadel
- Mira Dimitrijevic
- Paul Fenimore
- William Fischer
- Brian Foley
- Elizabeth-Sharon Fung
- Elena Edi Giorgi
- S. "Gnana" Gnanakaran
- Emma Goldberg
- Nick Hengartner
- William Hlavacek
- Ruian Ke
- Better Korber
- Thomas Leitner
- Cesar Bautista Lopez
- Jennifer Macke
- Carmen Molina-Paris
- Arshan Nasier
- Chris Neale
- Alan Perelson
- Ruy Ribeiro
- Ethan Romero-Severson
- Karissa Sanbonmatsu
- Sumantra Sarkar
- James Szinger
- Kshitij Wagh
- Hyejin Yoon
Postdocs
- Susmit Chaudhury
- Dylan Girodat
- Sarafa Iyaniwura
- Greg Linchangco
- Erik Lundgren
- Pedro Manrique
- Kien Nguyen
- Jigneshkumar Prajapati
- Lara Anne Patel
- Tin Phan
- Imelda Trejo
- Narmada Sambatura
- Kristen Wilding
Students
- Beauty Kolade
- Rebecca Hehl
- Liam Kai Herndon
- Michael Kupperman
- Emmett Leddin
- Aicha Mabene
- Bella Root
- Anna Maria Quintana
- Carolin Zitzmann
Guests/Affiliates
- Beverly Bender
- Bryon Goldstein
- James L. Hyman (Mac)
- John Pearson
- David Sharp
- Chang-Shung Tung
Capabilities
Mathematical biology
Fundamental science and modeling enabling host-pathogen science
- Mathematical biology of viral dynamics and evolution
- Multi-scale modeling of host-pathogen interactions, host immunity, and within-host infection
- RNA interference (RNAi) screens to identify key human genes that function in pathogenesis and host response
- Characterization of pathogen and host small RNAs as potential targets for therapeutic development
Structural biology
Understanding biomolecule function by determining their 3-D macromolecular structure
- Novel approaches to experimentally and computationally learn about secondary structures of large RNAs. These may be related to epigenetics.
- Develop models that exploit neutron crystallography to enable understanding of 3d structures of proteins — key to the mechanism of enzymes & ribozymes.
- Large-scale simulations using enhanced sampling methods on high-performance computing platforms produce new insight in the dynamics of enzymes and mechanism of biomolecular complexes
Bioinformatics and epidemiology
Sequence analysis using advanced algorithms, software and computational hardware
- World-class databases and tools for HIV, hepatitis C virus, hemorrhagic fever viruses, and Influenza sequences
- Leader in metagenome data analysis (assembly, kmer-based signature calculations, binning, classification, comparisons)
- Developing algorithms that leverages our understanding of evolution to develop vaccines and bring new insights into epidemics using sequence data
Research
- Dynamics and treatment of viral diseases such as
- HIV
- influenza
- hepatitis
- Immune system modeling
- Receptor-ligand interactions and cell signaling
- Computational aspects of the human genome initiative
- Pattern recognition in DNA sequences
- Characterization and prediction of macromolecular structure
- Protein function and dynamics
- Protein folding
