@shefflab
Joined May 2017
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  • Following27
  • Followers43
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I'm hosting a virtual open house today at 2-3pm Eastern Time -- Drop in if you're interested in hearing about getting a PhD in Computational Biology at UVA. compbio.med.virginia.edu/mee…

Meet COBI - Virtual Open House | UVA Computational Biology PhD

Join our virtual open house sessions to meet faculty, students, and administrators from the UVA Computational Biology PhD program.

compbio.med.virginia.edu
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Interested in learning about doing a PhD in computational biology? Join us for open office hours tomorrow at 11am Eastern. compbio.med.virginia.edu/mee…

Meet COBI - Virtual Open House | UVA Computational Biology PhD

Join our virtual open house sessions to meet faculty, students, and administrators from the UVA Computational Biology PhD program.

compbio.med.virginia.edu
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Taming the reference genome jungle: the refget sequence collection standard biorxiv.org/content/10.1101/… #biorxiv_genomic

Taming the reference genome jungle: the refget sequence collection standard

Reference genomes are foundational to genomics but suffer from widespread ambiguity and incompatibility due to inconsistent naming, undocumented differences, and lack of formal mechanisms for...

biorxiv.org
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We launched a new website for our PhD program in computational biology at UVA. Visit: compbio.med.virginia.edu/

UVA Computational Biology

UVA's PhD Program in Computational Biology combines AI, data science, and biology to prepare the next generation of scientists. 100% funded positions with world-class faculty.

compbio.med.virginia.edu
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Need to combine BED files into a consensus set? Our paper with methods to do this just came out in NAR! --Methods for constructing and evaluating consensus genomic interval sets academic.oup.com/nar/article…

Methods for constructing and evaluating consensus genomic interval sets

Abstract. The amount of genomic region data continues to increase. Integrating across diverse genomic region sets requires consensus regions, which enable

academic.oup.com
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BEDMS: A metadata standardizer for genomic regionattributes biorxiv.org/cgi/content/shor… #biorxiv_genomic
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From biomedical cloud platforms to microservices: next steps in FAIR data and analysis: doi.org/10.1038/s41597-022-0… -- Read our new perspective on biomedical cloud computing at Scientific Data.

From biomedical cloud platforms to microservices: next steps in FAIR data and analysis

Scientific Data - The biomedical research community is investing heavily in biomedical cloud platforms. Cloud computing holds great promise for addressing challenges with big data and ensuring...

nature.com
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Our paper on standardizing sample metadata is out in GigaScience: academic.oup.com/gigascience…
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ATAC-seq pipeline PEPATAC paper now published in NARGAB: doi.org/10.1093/nargab/lqab1…

PEPATAC: an optimized pipeline for ATAC-seq data analysis with serial alignments

Abstract. As chromatin accessibility data from ATAC-seq experiments continues to expand, there is continuing need for standardized analysis pipelines. Here

academic.oup.com
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New bioinformatics paper: Embeddings of genomic region sets capture rich biological associations in lower dimensions doi.org/10.1093/bioinformati…

Embeddings of genomic region sets capture rich biological associations in lower dimensions

AbstractMotivation. Genomic region sets summarize functional genomics data and define locations of interest in the genome such as regulatory regions or tra

academic.oup.com
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Identity and compatibility of reference genome resources paper is out in NARGAB: academic.oup.com/nargab/arti…

Identity and compatibility of reference genome resources

Abstract. Genome analysis relies on reference data like sequences, feature annotations, and aligner indexes. These data can be found in many versions from

academic.oup.com
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New paper in Genome Biology! genomebiology.biomedcentral.…

PEPPRO: quality control and processing of nascent RNA profiling data

Genome Biology - Nascent RNA profiling is growing in popularity; however, there is no standard analysis pipeline to uniformly process the data and assess quality. Here, we introduce PEPPRO, a...

link.springer.com
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Refget: standardised access to reference sequences biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
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Identity and compatibility of reference genome resources biorxiv.org/cgi/content/shor… #biorxiv_genomic
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Anyone else interested in switching from HPC environment modules to linux containers to manage shared group software? Here's how I did it: databio.org/posts/modules_to…
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Ref genie is some pretty slick work from @shefflab. If you don’t know, now you know.
S. Carson Callahan@scarsoncallahan
18 Nov 2020
Replying to @tangming2005
My lazy approach has been to use refgenie when possible: academic.oup.com/gigascience… It's pretty easy to pull things and if someone asks which versions of files you used, you just link the repo.

Refgenie: a reference genome resource manager

AbstractBackground. Reference genome assemblies are essential for high-throughput sequencing analysis projects. Typically, genome assemblies are stored on

academic.oup.com
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Bedshift: perturbation of genomic interval sets biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
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Great example of multiple awesome #communities working well #together. Honored to have been able to contribute. #usegalaxy #refgenie #cvmfs #referencedata #opendata
Michał Stolarczyk@m_stolarczyk
12 Oct 2020
Refgenie assets can be the source of reference datasets in Galaxy @galaxyproject Happy to share the preprint on the integration of refgenie into the Galaxy platform: biorxiv.org/content/10.1101/…

Expanding the Galaxy’s reference data

Summary Properly and effectively managing reference datasets is an important task for many bioinformatics analyses. Refgenie is a reference asset management system that allows to easily organize,...

biorxiv.org
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PEPATAC: An optimized ATAC-seq pipeline with serial alignments biorxiv.org/cgi/content/shor… #biorxiv_genomic
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Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects biorxiv.org/content/10.1101/… Code: github.com/pepkit docs: pep.databio.org/en/latest/. Really useful stuff out of @shefflab
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