Eric Talevich (@etalevich) header
Eric Talevich (@etalevich) profile picture

Eric Talevich

@etalevich
 San Francisco, CA
etal.bio/
Joined March 2010
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Photo by Eric Talevich (@etalevich)
Reach out if you'd like to discuss how we can work together! Experience and services in: - Bioinformatics algorithm development, pipelines, data architecture - Cancer biology, infectious & autoimmune diseases, population genetics, multi-omics - Technical strategy & solutions
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CNVkit v0.9.10 is out! github.com/etal/cnvkit/relea… New plotting features, better GISTIC support, and many bug fixes and infrastructure improvements. Much thanks to contributors over the past ~2 years.
Release Version 0.9.10 · etal/cnvkit

Release Version 0.9.10 · etal/cnvkit

This long-awaited release includes major plotting enhancements in the heatmap, scatter, and diagram commands, as well as a new export gistic command, thanks to joint work by @tetedange13 and @tskir...

github.com
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If you could read the DNA of half a million people, would you do it and why? Would it work? What would you learn? To answer this and several related questions, let me walk you through the work my @RegeneronDNA colleagues just published in Nature. 1/24 nature.com/articles/s41586-0…
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CNVkit 0.9.9 is out the door: github.com/etal/cnvkit/relea… Thanks to @tskir1 and others for supporting users and numerous bug fixes!
Release Version 0.9.9 · etal/cnvkit

Release Version 0.9.9 · etal/cnvkit

This release contains a new script and, more importantly, a volley of bug fixes by @tskir, a new CNVkit collaborator. New script genome_instability_index.py For each given sample (.cnr or .cns, id...

github.com
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Eric Talevich retweeted
Jeremy Leipzig (@jermdemo) profile picture
Jeremy Leipzig
@jermdemo25 May 2021
If you're interested in trying @nf_core in the context of reproducible peer review I am looking for a participant for a short survey and a test of robustness on disputed m6a paper. $250 recompense. Please DM me for details.
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R has a number of packages that are just datasets, not code. Has this been tried with conda or other package managers in order to make datasets versioned and traceable?
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You can now link reviews from the preprint on biorxiv. Another step towards a journal-free open science utopia with preprint and post publication peer review. :D connect.biorxiv.org/eval/?pl…
Image from ChristofferFlensburg (@CFlensburg)
John Inglis (@JohnRInglis) profile pictureJohn Inglis@JohnRInglis19 May 2021
Smartly spotted by @PracheeAC -a new @biorxivpreprint feature from our tech wizards Ted and Michael. Links to a list of peer reviewed preprints can be found on each subject category specific page. Featuring reviews from @eLife, @ReviewCommons, and @EMBOPress
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R has a number of packages that are just datasets, not code. Is there a similar channel/repo in #conda / #anaconda? Guidelines, experiences?
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I'm hiring for the Data Core at @KariusInc! jobs.lever.co/kariusdx/7b209… We mine biological datasets to power a cfDNA test for infectious diseases. We discover new things every day. HQ is in the Bay Area; remote is also fine.
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Open source software experience and scientific community engagement would be great. We're looking to work with the global community to bring new discoveries into the open. Again, we've seen things in the blood microbiome that no one else has.
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The Karius test works for clinical diagnosis of infectious diseases: kariusdx.com/products/karius… What's next? We'll go beyond n-of-1, improve the assay itself and its clinical validity, use the assay to make discoveries, and much more.
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TODAY @ 3PM ET: Join @mlipsitch and other experts for The Science of Herd Immunity. They will explain the science of and misconceptions around herd immunity and discuss new research frontiers in immunology, infectious disease dynamics, and human behavior. stanford.io/3cYX2IZ
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I'm now at @KariusInc ! We have a lifesaving noninvasive test for infectious diseases, and from another perspective, a metagenomic cfDNA assay that works as a powerful new molecular microscope for understanding human physiology.
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We did it again! Now you can deploy your Nextflow pipelines to DNAnexus cloud platform! 🎉🎉
Evan Floden (@EvanFloden) profile pictureEvan Floden
@EvanFloden31 Mar 2021
We are very excited to offer Nextflow users a new execution platform for their pipelines! This partnership gives users the scale of Nextflow in the secure @dnanexus cloud environment. Read more: seqera.io/blog/dnanexus-rele…
Image from Evan Floden (@EvanFloden)
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I like libraries that try to do something defensible with almost any input. Sometimes you get a happy accident.
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Eric Talevich retweeted
The Pfam database (@PfamDB) profile picture
The Pfam database@PfamDB24 Mar 2021
We are delighted to announce the first fruits of our collaboration with Google Research on #DeepLearning for protein classification. Introducing Pfam-N: xfam.wordpress.com/2021/03/2…
Google Research Team bring Deep Learning to Pfam

Google Research Team bring Deep Learning to Pfam

We are delighted to announce the first fruits of a collaboration between the Pfam team and a Google Research team led by Dr Lucy Colwell, with Maxwell Bileschi and David Belanger. In 2019, Colwell’…

xfam.wordpress.com
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Eric Talevich retweeted
Sri Kosuri (@srikosuri) profile picture
Sri Kosuri
@srikosuri17 Mar 2021
We are hiring population geneticists/bioinformaticians to interpret genetic variation in biobanks through the lens of large experimental datasets like deep scanning mutagenesis in order to pick good drug targets. This will be a unique and fun job! octant.bio/job-description-c…
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Eric Talevich retweeted
Mike Lin (@DNAmlin) profile picture
Mike Lin@DNAmlin22 Jan 2021
NEW: 📣 gfabase 🚀 Indexed storage of assembly graphs and pangenome reference graphs; like 'tabix for GFA' but importantly, graph-aware. github.com/mlin/gfabase THREAD >>>
Image from Mike Lin (@DNAmlin)
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Delineating copy number and clonal substructure in human tumors from single-cell transcriptomes go.nature.com/2XY3J5r
Image from Nature Biotechnology (@NatureBiotech)
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One small preprint for the authors, a giant leap for bioinformatics. I'm pretty eager to start using this standard:
bioRxiv Bioinfo (@biorxiv_bioinfo) profile picturebioRxiv Bioinfo@biorxiv_bioinfo18 Jan 2021
The GA4GH Variation Representation Specification (VRS): a Computational Framework for the Precise Representation and Federated ... biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
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