We're a lab working to understand and improve the immune response to cancer at @muschollings
Charleston, SC
Joined June 2014
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Our lab member Eric Czech will present this work at #biodata18 on Saturday. The source code is available at github.com/hammerlab/cytokit. If you're interested in GPU-accelerated open source software for the analysis of multiplex tissue imaging data, we'd appreciate your feedback!
Cytokit: A single-cell analysis toolkit for high dimensional fluorescent microscopy imaging biorxiv.org/cgi/content/shor… #bioRxiv
Hammer Lab retweeted
This is what we have been working on at @hammer_lab for the last few months:
Human Primary T Cells: A Practical Guide
- Live document: docs.google.com/document/d/1…
- Code/data: github.com/hammerlab/t-cell-…
- Protocols: protocols.io/view/human-prim…
cc: @PINPINPINN @Chrystal_Paulos
A few of our former lab members have formed a new lab to continue their work on open source software for neoantigen vaccines. Go follow them at @OpenVax! xitter.cf/iskander/status/951198…
It's still a work in progress, but I just made a website for the new @openvax lab at Mount Sinai: openvax.org/.
Focus: machine learning applied to immunology, neoantigens, personalized cancer vaccines.
New preprint! Prohlatype: A Probabilistic Framework for HLA Typing by @leonidrozenberg biorxiv.org/content/early/20…
Hammer Lab retweeted
We just released MHCflurry 1.0, our MHC I ligand prediction package. 20% more alleles, over 10X faster, docs, and an accuracy boost. Happy predicting! bit.ly/2p9sT2M @hammer_lab
Introducing spark-bam, a foundational library that enables the distributed processing of aligned reads with @ApacheSpark, by @RunsAsCoded: hammerlab.org/2017/12/11/int…
New preprint from @smondet on how our lab uses @OCamlLang to manage complex bioinformatics workflows on cloud, Hadoop, and HPC environments xitter.cf/biorxiv_bioinfo/status…
Bioinformatics Workflow Management With The Wobidisco Ecosystem biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
We've posted a preprint that describes the open source software powering the neoantigen vaccine trial described at clinicaltrials.gov/ct2/show/… xitter.cf/iskander/status/895753…
New preprint: "Computational pipeline for the PGV-001 neoantigen vaccine trial". biorxiv.org/content/early/20…
Download the library from PyPI at pypi.python.org/pypi/mhcflur…
Read the preprint, "MHCflurry: open-source class I MHC binding affinity prediction”, at biorxiv.org/content/early/20…
Introducing SurvivalStan, with an epic introduction to Bayesian survival analysis with @mcmc_stan, by @jackiburos: hammerlab.org/2017/06/26/int…
A broad but shallow review of informatics in cancer immunotherapy: biorxiv.org/content/early/20…
You can too with Pageant, our Apache-licensed Parallel Genomic Analysis Toolkit: github.com/hammerlab/pageant
Watch: @RunsAsCoded shows how our lab uses @ApacheSpark on @googlecloud to process thousands of BAMs in a few hours youtu.be/d6kPsSawCRY
For the Apache 2.0-licensed Vaxrank code, check out github.com/hammerlab/vaxrank
We use Vaxrank in our clinical trial that’s actively recruiting patients; for more on the trial see explorer.opentrials.net/tria…
New preprint! Vaxrank: A Computational Tool For Designing Personalized Cancer Vaccines biorxiv.org/content/early/20…
We’re quite proud of this paper! One reviewer: “It sets the bar for ... biomarker analyses in patients treated with checkpoint inhibitors” xitter.cf/PLOSMedicine/status/87…
Tumor and immune features associated w/ clinical response to checkpioint blockade therapy in urothelial #Cancer
journals.plos.org/plosmedici…