Current lab members

  • Chris Bailey-Kellogg
  • Amelia Antrim
  • Yoonjoo Choi
  • Karen Dowell
  • Lu He
  • Li Jiang
  • Liane Makatura
  • Deeptak Verma

Highlighted projects

  • deimmunization
  • antibody effector functions
  • MHC:peptide:TCR
  • graphical models
  • recombination
  • oligomer

Current/upcoming classes

Spring 2014: Probabilistic Graphical Models (CS 89/189)
CS 89/189

Recent papers

  • Polyfunctional Fc-Effector Profiles Mediated by IgG Subclass Selection Distinguish RV144 and VAX003 Vaccines
  • Stoichiometries and affinities of interacting proteins from concentration series of solution scattering data:  Decomposition by least squares and quadratic optimization
  • Integrated assessment of predicted MHC binding and cross-conservation with self reveals patterns of viral camouflage
  • Learning sequence determinants of protein:protein interaction specificity with sparse graphical models
  • Divergent antibody subclass and specificity profiles but not protective HLA-B alleles are associated with variable antibody effector function among HIV-1 controllers
  • Improved Multiple Sequence Alignments using Coupled Pattern Mining

[more...]

News

Jul 14An additional postdoctoral position is available in machine learning / computational immunology
Jul 143dsig / ISMB presentations by the lab: Deep ("Structure-based design of combinatorial mutagenesis libraries"), Karen ("Integrated Predictive Models of Antibody Features and Effector Cell Functions Provide Insights into Immune Response to Natural HIV Infection"), and Yoonjoo ("Structure-based antibody humanization").
Jun 14Welcome to Ryan Amos and Jai Woo Lee, who will be doing summer research projects in the lab
Jun 14Congratulations to Amelia, who was awarded departmental honors at graduation. Her honors thesis is titled "Discontinuous B-cell epitope prediction from peptide binding data"
May 14Congratulations to Regina (Karl Griwsold's lab), Andrew, et al., whose paper "Computationally Driven Deletion of Broadly Distributed T cell Epitopes in a Biotherapeutic Candidate" was accepted to Cellular and Molecular Life Sciences
May 14Our CHOPPI paper ("CHOPPI: a web tool for the analysis of immunogenicity risk from host cell proteins in CHO-based protein production") has been accepted to Biotechnology & Bioengineering
May 14Chris is giving a best poster presentation at PEGS, for "Structure-based design of combinatorial mutagenesis libraries" (Deep's work, collaborative with Gevorg Grigoryan)

[more...]

Contact

cbk -at- cs -dot- dartmouth -dot- edu
6211 Sudikoff Lab, Hanover, NH 03755, USA
Sudikoff Lab (corner of Maynard & College), room 250
603-646-3385