@nv1ctus

computational biologist / biological computer / asst prof @UMassChan / phd @MIT / https://xitter.cf/t.co/Sv8B6sBNdS

 Greater Boston Area
lifeinbytes.substack.com/
Joined October 2013
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Many of you may have received pessimism from me over the years about using Hi-C to predict distal regulatory effects, mired with paradoxical optimism that cohesin loop extrusion is key. Well, the story behind all that rambling is finally ready to be told.
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Ever wanted to watch chromosomes fold? lefsim simulates loop extrusion live in your browser. Add, remove and drag CTCF sites around, watch contact maps emerge, and more. lefsim.abdenlab.org
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Underneath is a blazing fast Rust engine with Python and JavaScript packages, for research-scale use. The story behind it: lifeinbytes.substack.com/p/w…
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Nezar Abdennur retweeted
Ming "Tommy" Tang@tangming2005Jul 20
pretty interesting tool: Oxbow makes genomic data ready for high-performance analytics. oxbow.readthedocs.io/en/late…
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Really enjoyed presenting our genomics talk "Declare, don't parse" at #SciPy2026 with Conrad Bzura! Slides here: abdenlab.org/scipy26
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tl; dr Problem #1: Genomics is coupled to file formats, not data Problem #2: Most genomic operations aren't even "genomic" Solution: Be composable!
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Also excited to kick off a new initiative with @jmschreiber91 the polars-bio team at Warsaw University of Technology: composeq.dev/ Interested in a new substrate for agent-ready genomics? Get in touch!

CompoSeq

Composable foundations for genomic data.

composeq.dev
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You can observe some of the features of the cohesin bridging model here (WIP): abdenlab.org/cohesin-bridgin…
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Huge congratulations to lead authors Timothy (Mirny lab) and Karissa (Nora lab), and to Max, Henrik, Geoff and everyone else involved!
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I mean, most of bioinformatics data is just tabular data with bad conventions, formats. @nv1ctus is pushing a pretty good software to make things better with bioframe and oxbow :)
Ming "Tommy" Tang@tangming2005Apr 30
🧵 You filtered your VCF. But the output broke your pipeline. Why? You didn’t keep the header. Let's fix that.
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I’m excited to be co-chairing the Biological & Medical Sciences track for the #SciPy2026 conference 🎉 in July, along with Aishwarya Chander and Jacqueline Valeri. scipy2026.scipy.org/ 🗓️Submit your proposal by Feb 25th 👉 pretalx.com/scipy-2026/cfp

SciPy 2026

scipy2026.scipy.org
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🌟 Sign up for office hours to learn more about preparing your proposal 👉 scipy2026.scipy.org/#officeh…

SciPy 2026

scipy2026.scipy.org
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💡 SciPy is a vibrant, interdisciplinary conference that brings together researchers, developers, and innovators who are shaping the future of computing, data science, and AI for scientific research (and a love for Python!). et a taste of past talks on YT: youtube.com/@SciPy-Conf/vide…

SciPy

youtube.com
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Nezar Abdennur retweeted
SciPyConf@SciPyConfJan 27
🤔 Thinking about submitting a proposal to SciPy 2026 and want feedback or guidance? We’ve got you covered ✨ 🚀 Join our Proposal Writing Office Hours 📅 First session is next week 👉 Register here: scipy2026.scipy.org/#officeh…
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