Hammer Lab

We're a lab working to understand and improve the immune response to cancer at @muschollings

[Hammer Lab @hammer_lab]

Our lab member Eric Czech will present this work at #biodata18 on Saturday. The source code is available at https://t.co/9cEHh1GSLy. If you're interested in GPU-accelerated open source software for the analysis of multiplex tissue imaging data, we'd appreciate your feedback!

[bioRxiv @biorxivpreprint]

Cytokit: A single-cell analysis toolkit for high dimensional fluorescent microscopy imaging https://t.co/0OEIlEwhHq #bioRxiv

[B. Arman Aksoy @armish]

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: https://t.co/CUaGiSVE3g
- Code/data: https://t.co/xYqMYyKuZ6
- Protocols: https://t.co/6rm6W4q4mw

cc: @PINPINPINN @Chrystal_Paulos

[Hammer Lab @hammer_lab]

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! https://t.co/obbr1y5X1f

[alex rubinsteyn @iskander]

It's still a work in progress, but I just made a website for the new @openvax lab at Mount Sinai: https://t.co/S462kKP6xq.

Focus: machine learning applied to immunology, neoantigens, personalized cancer vaccines.

[Hammer Lab @hammer_lab]

New preprint! Prohlatype: A Probabilistic Framework for HLA Typing by @leonidrozenberg https://t.co/Ao5QKuTWYh

[Tim O'Donnell @timodonnell]

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! https://t.co/TqsdL4Lcri @hammer_lab

[Hammer Lab @hammer_lab]

Introducing spark-bam, a foundational library that enables the distributed processing of aligned reads with @ApacheSpark, by @RunsAsCoded: https://t.co/umWa8pI4yk

[Hammer Lab @hammer_lab]

New preprint from @smondet on how our lab uses @OCamlLang to manage complex bioinformatics workflows on cloud, Hadoop, and HPC environments https://t.co/k1vI1xShdn

[bioRxiv Bioinfo @biorxiv_bioinfo]

Bioinformatics Workflow Management With The Wobidisco Ecosystem https://t.co/v2vx4G1L9Q #biorxiv_bioinfo

[Hammer Lab @hammer_lab]

We've posted a preprint that describes the open source software powering the neoantigen vaccine trial described at https://t.co/myjNDkitSH https://t.co/qtk8oZl6L1

[alex rubinsteyn @iskander]

New preprint: "Computational pipeline for the PGV-001 neoantigen vaccine trial". https://t.co/Emz92vmNTH

[Hammer Lab @hammer_lab]

@timodonnell File issues and contribute code at https://t.co/pRny18TKF9

[Hammer Lab @hammer_lab]

@timodonnell Download the library from PyPI at https://t.co/zzL10mp9kn

[Hammer Lab @hammer_lab]

@timodonnell Read the preprint, "MHCflurry: open-source class I MHC binding affinity prediction”, at https://t.co/CPHwjKCQF3

[Hammer Lab @hammer_lab]

Benchmarking MHCflurry, take 2 by @timodonnell: https://t.co/GHfALlz1Wm

[Hammer Lab @hammer_lab]

Introducing SurvivalStan, with an epic introduction to Bayesian survival analysis with @mcmc_stan, by @jackiburos: https://t.co/9uQa5lNJni

[Hammer Lab @hammer_lab]

A broad but shallow review of informatics in cancer immunotherapy: https://t.co/SZNCkUAUts

[Hammer Lab @hammer_lab]

@RunsAsCoded @ApacheSpark @googlecloud You can too with Pageant, our Apache-licensed Parallel Genomic Analysis Toolkit: https://t.co/b1ATNGNTQn

[Hammer Lab @hammer_lab]

Watch: @RunsAsCoded shows how our lab uses @ApacheSpark on @googlecloud to process thousands of BAMs in a few hours https://t.co/lQNsYN8qSl

[Hammer Lab @hammer_lab]

For the Apache 2.0-licensed Vaxrank code, check out https://t.co/HyMxpyYJGO

[Hammer Lab @hammer_lab]

We use Vaxrank in our clinical trial that’s actively recruiting patients; for more on the trial see https://t.co/aYnqAT1kJP

[Hammer Lab @hammer_lab]

New preprint! Vaxrank: A Computational Tool For Designing Personalized Cancer Vaccines https://t.co/BnTkLlf2Of

[Hammer Lab @hammer_lab]

We’re quite proud of this paper! One reviewer: “It sets the bar for ... biomarker analyses in patients treated with checkpoint inhibitors” https://t.co/tdvi0k3C6C

[PLOS Medicine @PLOSMedicine]

Tumor and immune features associated w/ clinical response to checkpioint blockade therapy in urothelial #Cancer
https://t.co/RwEIM7voPw