Jeff Hammerbacher

Analysis-ready VCF at Biobank scale using Zarr

The paper introduces VCF Zarr, a format for efficiently storing and processing large-scale genetic variation data, demonstrating improved performance and scalability over traditional VCF formats.

Clinical Advancement Forecasting

This paper develops a statistical learning framework to predict clinical trial success for target-disease pairs using longitudinal evidence, outperforming existing scores and identifying high-potential targets.

Cytokit: A single-cell analysis toolkit for high dimensional fluorescent microscopy imaging

Cytokit processes and analyzes large-scale fluorescent microscopy data to quantify cell properties, validated through experiments and public datasets.

Vaxrank: A Computational Tool For Designing Personalized Cancer Vaccines

Vaxrank selects neoantigen vaccine peptides from tumor mutations, RNA data, and HLA type to design personalized cancer vaccines.

Coral: Clear and customizable visualization of human kinome data

Coral provides an interactive web tool for visualizing human kinome data with customizable features and high-resolution outputs.

Computational pipeline for the PGV-001 neoantigen vaccine trial

The paper describes a computational pipeline for a personalized neoantigen vaccine trial, including tools for variant calling, peptide selection, and sequence reconstruction.

Prohlatype: A Probabilistic Framework for HLA Typing

Prohlatype improves HLA typing from sequencing data using a probabilistic framework with Profile Hidden Markov Models, reducing computational burden.

Infino: a Bayesian hierarchical model improves estimates of immune infiltration into tumor microenvironment

Infino improves immune infiltration estimates in tumor microenvironments by using a Bayesian hierarchical model to deconvolve bulk RNA-seq data and enhance accuracy.

Bioinformatics Workflow Management With The Wobidisco Ecosystem

The paper introduces a set of open-source workflow management tools for bioinformatics, emphasizing reliability and flexibility.

Informatics for Cancer Immunotherapy

This paper reviews informatics techniques used in cancer immunotherapy, focusing on data analysis of tumors, immune microenvironment, and therapy development.

Contribution of systemic and somatic factors to clinical response and resistance in urothelial cancer: an exploratory multi-omic analysis

This study explores factors influencing response and resistance to atezolizumab in urothelial cancer using multi-omic data, finding associations between TCR clonality and clinical outcomes.

Cycledash: a web application for the interactive analysis and exploration of variants

Cycledash provides a web tool for validating and analyzing somatic variants by integrating existing tools and workflows.

Predicting Peptide-MHC Binding Affinities With Imputed Training Data

The paper develops an allele-specific MHC peptide binding predictor using imputed training data, achieving performance comparable to existing methods.