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Immune epitope database analysis resource
TLDR
The immune epitope database analysis resource (IEDB-AR: http://tools.iedb.org) is a collection of tools for prediction and analysis of molecular targets of T- and B-cell immune responses (i.e. epitopes). Expand
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Immune epitope database analysis resource (IEDB-AR)
TLDR
We present a new release of the immune epitope database analysis resource (IEDB-AR, http://tools.immuneepitope.org), a repository of web-based tools for the prediction and analysis of immune epitopes. Expand
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Pairwise Alignment of Protein Interaction Networks
TLDR
We propose a mathematical model that extends the concepts of match, mismatch, and gap in sequence alignment and evaluates similarity between graph structures through a scoring function that accounts for evolutionary events. Expand
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Peptide binding predictions for HLA DR, DP and DQ molecules
TLDR
We provide a large scale and homogenous dataset of experimental binding affinities for HLA class II molecules, along with a comprehensive evaluation of prediction performances for a number of algorithms. Expand
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Derivation of an amino acid similarity matrix for peptide:MHC binding and its application as a Bayesian prior
TLDR
A novel amino acid similarity matrix (PMBEC) is directly derived from the binding affinity data of combinatorial peptide mixtures. Expand
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Robustly Hedging Variable Annuities with Guarantees under Jump and Volatility Risks
Recent variable annuities offer participation in the equity market and attractive protection against downside movements. Accurately quantifying this additional equity market risk and robustly hedgingExpand
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Automated benchmarking of peptide-MHC class I binding predictions
TLDR
We present a framework for the automated benchmarking of peptide-MHC class I binding prediction tools. Expand
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Detecting Conserved Interaction Patterns in Biological Networks
TLDR
This paper presents an innovative graph simplification technique based on ortholog contraction, which is ideally suited to biological networks, for detecting frequently occurring patterns and modules in biological networks. Expand
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A closed form approximation of the sum rate upperbound of random beamforming
TLDR
In this letter, a closed form expression of the sum rate upperbound is derived for random beamforming. Expand
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Dataset size and composition impact the reliability of performance benchmarks for peptide-MHC binding predictions
TLDR
We identify and quantify the specific factors contributing to this effect for MHC-I binding predictions and derive quantitative rules of how large and diverse datasets need to be to provide generalizable performance estimates. Expand
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