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Cade Mirchandani

@cademirch.bsky.social
72 followers 130 following 23 posts

mostly genomics github.com/cademirch vollgerlab.github.io

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Reposted by Cade Mirchandani
Changyi Xiao @changyi-xiao.bsky.social · 19/08/2026
Glad to share our new paper published in Genetics!!🧬 Using experimental evolution data and forward genetic simulations, we explored how haplotype structure shapes the genomic response. doi.org/10.1093/gene...
doi.org
Haplotype structure: an overlooked key factor shaping the genomic selection response
Abstract. Genetic redundancy, a hallmark of polygenic adaptation, implies that new trait optima can be reached by frequency changes of a subset of contribu
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Brian Helsel @bchelsel.bsky.social · 17/09/2026
I just finished my first paper written entirely in Quarto, and it has changed how I think about the manuscript-writing process. If you’re not an #RStats or #Quarto user, the biggest benefit is that you can automate repetitive workflows. Here are 5 things that made my writing process more efficient.
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Vijay Ramani @vram142.bsky.social · 14/09/2026
Everything you wanted to know about single-molecule epigenomics but were too afraid to ask! Wonderful to co-write (h/t ENORMOUS lift by @arnaudkr.bsky.social) this primer on our nascent field. Also, a 💯 example of wonderful colleagues building something *together*, not in competition =)
nature.com
A practical guide to studying genome function using single-molecule genomics
Nature Reviews Molecular Cell Biology - Single-molecule genomics methods are used to study the activity of regulatory factors on individual DNA molecules genome-wide, thereby enabling...
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Noam Teyssier @noamteyssier.bsky.social · 12/09/2026
I often find pure research to be a lot more like art than science. I understand completely that feeling they describe of wanting to solve a problem to understand it in the same way I like to learn songs just to be able to feel them under my fingers. Journey before destination - right?
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Blosc Development Team @blosc.org · 11/09/2026
📢 Python-Blosc2 4.13.0 is out! One lazy API for unite all remote data: browse B2Z/Zarr/HDF5 hierarchies over S3/GCS/HTTP, slice only what you need, cache in RAM or on disk, and export portable snapshots. b2view demo below👇 github.com/Blosc/python... Compress Better, Compute Bigger 🚀
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Samuel Lampa @smllmp.bsky.social · 11/09/2026
Super stoked that SciCommander (track provenance for any file produced by your ad-hoc shell usage into HTML reports & more) is now on @conda-forge.org! 🥳 Install with: conda install conda-forge::scicommander pixi add scicommander anaconda.org/channels/con... Poster for info 👇
Poster with title: SciCommander - Track provenance of interactive shell usage. Showing a longer text explaining it, some screenshots of using scicommander in shell mode and an example HTML report, together with some artistic line drawings.
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Aaron Quinlan (he/him) @aaronquinlan.bsky.social · 28/08/2026
I am delighted to announce that The Department of Human Genetics at the University of Utah is continuing a multi-year recruiting initiative for multiple tenure-track faculty positions at the rank of Assistant Professor. Please share and consider applying! utah.peopleadmin.com/postings/208...
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E. Anne Chambers @chamberea.bsky.social · 14/08/2026
We're hiring! The Chambers Lab is recruiting grad students interested in landsacpe & conservation genomics or species delimitation of reptiles & amphibians. Find more info here (or reach out with questions!): chamberslab.org/opportunitie...
chamberslab.org
opportunities – Chambers Lab
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Chuliang Song @clsong.com · 16/06/2026
Spent the last two years developing a new Intro to Physics course for undergrad biology majors. It features tons of examples from biology (especially Ecology & Evolution!) and requires only middle school-level math. Lecture note here shorturl.at/0PiVp Any comments or feedback are highly welcome!
drive.google.com
physics_for_biologists.pdf
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Andrew Gallant @burntsushi.net · 26/05/2026
I've added an AI policy to ripgrep that was shamelessly copied from uv's policy. I plan to add this to the rest of my projects, but if anyone wants to offer feedback on wording, now would be a good time! github.com/BurntSushi/r...
github.com
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Seth Stadick @ducktapeprogrammer.bsky.social · 25/05/2026
lucumr.pocoo.org/2026/4/11/th... from Armin seems pretty related.
lucumr.pocoo.org
The Center Has a Bias
Why a measured position on AI tends to lean towards actually trying it.
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Kelly Sovacool @kelly.sova.cool · 21/05/2026
Deeply worried about deskilling in bioinformatics and software development. In parallel, also worried about low quality code being churned out rapidly by folks using these tools without doing proper quality control on the outputs 😬
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John Lovell @jotlovell.bsky.social · 19/05/2026
We are often asked whether pangenomes are worth the hassle. The files can be large and methods to explore them are much more challenging than linear references. Earlier this week, we preprinted a clear example of how and why pan-genome graphs are so important for trait discovery.
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David Aerne @meodai.bsky.social · 16/05/2026
still WIP but: better design-book examples incoming: meodai.github.io/design-book/
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Robert Aboukhalil @robert.bio · 14/05/2026
I've seen lots of AI rewrites in bioinformatics lately, and I’m concerned because LLMs can be confidently wrong. What do the best tool builders do to make sure their rewrites are correct? How can we tell if a rewrite is flawed? I interviewed 5 scientists to find out: youtu.be/0o2XnEBDxrI
youtu.be
I interviewed 5 bioinformatics experts about AI rewrites
YouTube video by OMGenomics
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amos @fasterthanli.me · 09/05/2026
coming soon in a github.com/bearcove/figue near you
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dorian @doriantaylor.com · 04/05/2026
me: maybe i will finally write some of that code <gets immediately tarpitted for six hours trying to fix something in dev setup, is now 11:30>
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Pascal @killercup.de · 30/04/2026
I spent some time writing about a #rust library I've been working on: seqair, an alternative to (a subset of) htslib. This is a big one! So much potential API surface to cover and I better have a good reason for it! deterministic.space/seqair.html
deterministic.space
Seqair, my Rust-native take on htslib
This post introduces seqair , a new Rust library for bioinformatics formats I’ve been working on. We’ll look in detail at one of my main design choices here, a columnar store for iterating BAM data, …
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Ethan Linck @elinck.bsky.social · 29/04/2026
This semester I developed and taught a course on applied population genomics. Lab activities proceed from the basics of the command line and Git to variant calling with workflow managers and a suite of downstream analyses (e.g., ADMIXTURE). All materials can be found here: elinck.org/genomics_eco...
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BF Francis Ouellette @bffo.bsky.social · 25/04/2026
From @davidmoreau.bsky.social & Kristina Wiebels in @plos.org #Computational #Biology | Nine quick tips for #software #containerization | I like all Tips, but particularly Tip 9: Plan for sharing & longevity | #Bioinformatics #Education #PLOSCBQT | 🧬 🖥️ 🧪 🔓 ⬇️ journals.plos.org/ploscompbiol...
journals.plos.org
Nine quick tips for software containerization
Software containerization has become a cornerstone of modern computational biology, enabling researchers to package code, dependencies, and execution environments in portable and reusable units. Conta...
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BF Francis Ouellette @bffo.bsky.social · 04/04/2026
From @robert.bio @helenechiapello.bsky.social @mthomaschollier.bsky.social & col. in @plos.org #Computational #Biology | Training biologists in #Unix command-line skills: From curriculum to interactive online tutorials|#Education #OpenEducationalResources | 🖥️ 🧪 ⬇️ journals.plos.org/ploscompbiol...
journals.plos.org
Training biologists in Unix command-line skills: From curriculum to interactive online tutorials
As the generation of data in the life and health sciences expands rapidly, there is a growing need for professionals and students in these fields to master core bioinformatics skills, particularly tho...
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Brant Faircloth @brantfaircloth.bsky.social · 04/04/2026
In about an hour using Claude Code (see disclaimer in repo) I put together code to do something that is a pain in the ass to do manually - find a good genome in NCBI then see what decent population level WGS data exist for that genome assembly in NCBI SRA: github.com/brantfairclo.... I'm impressed.
github.com
GitHub - brantfaircloth/pop-genome-checker
Contribute to brantfaircloth/pop-genome-checker development by creating an account on GitHub.
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rOpenSci @handle.invalid · 02/04/2026
[blog] A Better R Programming Experience Thanks to Tree-sitter Did you know how Tree-sitter's support for R help you get ✨ reformatting through Air and linting through Jarl; ✨ auto-completion or help on hover in the Positron IDE; ✨ better search for R on GitHub; ✨ and more! By @maelle […]
hachyderm.io
Original post on hachyderm.io
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 31/03/2026
Panmap: Scalable phylogeny-guided alignment, genotyping, and placement on pangenomes www.biorxiv.org/content/10.64898/20…
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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 30/03/2026
The #SnakemakeHackathon2026 has ended, we are still preparing our preprint release. But, our host has prepared a note on their homepage: go.tum.de/946236 🥳 #Snakemake #ReproducibleComputing
mdsi.tum.de
Snakemake Hackathon 2026 – faster and further improved reproducible data analysis
Snakemake Hackathon 2026 delivers even faster and further improved support for reproducible data analysis. The 2026 Snakemake Hackathon brought together about 40 experts in Munich to deliver major improvements, new features, and performance enhancements for reproducible data analysis. Their community driven work strengthens Snakemake’s scalability, usability, and support for modern scientific workflows.
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Aaron Quinlan (he/him) @aaronquinlan.bsky.social · 24/03/2026
We've launched a department Trainee Emergency Fund, to help support EVERYONE BELONGING IN SCIENCE by meeting urgent financial needs of students and postdocs. Click to learn more about our goal with this fund and to donate! www.givecampus.com/schools/Univ...
lnkd.in
LinkedIn
This link will take you to a page that’s not on LinkedIn
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Michael Hall @mbhall88.bsky.social · 24/03/2026
🐍 For all ye #snakemake users out there who want consistent, opinionated formatting of their workflows: we have just released v1.0.0 of snakefmt 🥳 The major update is that it now sorts rule directives (e.g., input, output, resources, params, shell etc.). See github.com/snakemake/sn... for more
github.com
GitHub - snakemake/snakefmt: The uncompromising Snakemake code formatter
The uncompromising Snakemake code formatter. Contribute to snakemake/snakefmt development by creating an account on GitHub.
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Johannes Köster @johanneskoester.bsky.social · 16/03/2026
Another terminal based tool to interactively monitor all running #Snakemake workflows is #snkmt: github.com/cademirch/sn....
github.com
GitHub - cademirch/snkmt: A TUI for monitoring Snakemake workflows in real-time.
A TUI for monitoring Snakemake workflows in real-time. - cademirch/snkmt
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Wytamma @wytamma.bsky.social · 14/03/2026
At the #SnakemakeHackathon2026 in Munich last week I complied Snakemake to #Wasm and made a client-side webapp for creating and sharing workflows -> snakemake.github.io/snakemake-wa.... It has support for python, R, and a 32bit linux environment all running in your browser ❤️ 🐍
snakemake.github.io
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Chris Smith @chriscrsmith.bsky.social · 14/03/2026
I'm hiring a postdoc in population and evolutionary genetics at Indiana University Bloomington! Computational lab. Message me if interested, and can apply here: indiana.peopleadmin.com/postings/32547
indiana.peopleadmin.com
Postdoctoral Fellow, Biology
The department of Biology is a large, unified department with strong undergraduate degrees, nationally-ranked graduate programs, and world-class research spanning the breadth of biological questions a...
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Robert "The Bobby Yaga" McNees @mcnees.bsky.social · 26/02/2026
There's a "is anyone even reading this" sort of honesty you get in the software update release notes from a project that's been around for a long time.
The screenshot of the release notes reads:

A new version of TeX Live Utility is available!
TeX Live Utility 1.55 is now available-you have 1.54. Would you like to download it now?
Release Notes:
Changes Since 1.54
• Fix bug 137, homepage link in Help Book.
• First release in a long time, since I don't use TeX anymore and resent the very idea of paying Apple annually for the privilege of giving away free and open-source software. Also, I'm really lazy. Please accept my apologies for all the annoying issues you've encountered in this mission-critical software.
• Updated mirror list, which was three years out of date.
• Added missing legacy mirrors, which was even more out of date.
• Added an alert on startup when user tries Homebrew's lobotomized MacTex, because those lunatics left timgr but removed its database.
Thanks for nothing, guys. Bug 142 and 144.
• Use a custom user-agent to work around the Anubis bot trap on texlive.info. Can't wait to see what else breaks because of this, thanks to the profusion of degenerate Artificial Insemination fetishists scraping websites to feed their models.
• Lists of countries in Repository/Continent are now sorted. No idea how you people let me get away with that one for the last fifteen years.
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Daniel Abraham @abraham.bsky.social · 26/02/2026
Came across the phrase "cognitive DDOS" to describe our present culture. Understood instantly what it meant.
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Rob Patro @robp.bsky.social · 15/02/2026
I’ve written a post about my recent experiences (successes) with AI coding models; the experiences that caused me to re-evaluate my initial judgements, the surprise I had at what can be accomplished, & some fears I have about these tools. Discussion welcome! combine-lab.github.io/blog/2026/02...
combine-lab.github.io
COMBINE-lab - The skeptic’s guide to generative AI assisted coding
An easy-to-use, flexible website template for labs, with automatic citations, GitHub tag imports, pre-built components, and more.
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Graham Coop @gcbias.bsky.social · 10/02/2026
Excited for this. Teaching popgen is one of my favourite parts of my job and I've wondered about doing an online version of the class for sometime. Teaming up with @jrossibarra.bsky.social to do this is wonderful.
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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 05/02/2026
Playing with sandbox.bio. This was remarkably cathartic.
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David Asboth @davidasboth.com · 05/02/2026
A succinct and useful list of rules for teaching data science, including some of my favourites: "teach with real data" and "have students do projects". #databs #datasky
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Johannes Köster @johanneskoester.bsky.social · 29/01/2026
I've just released #rust-htslib 1.0. After a long time with a pretty stable API usage of rust-htslib in production, it feels like the right time to finally move to 1.0. Most important change is probably a switch to thread-safe pointers in BAM record handling. github.com/rust-bio/rus...
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Richard Lenski @relenski.bsky.social · 20/01/2026
Looking for something new to integrate into an #evolution or #microbiology course? Useful for lectures, labs, homework? Have a look at our STEPS program, which simulates bacterial evolution, including the #LTEE. Easy web-based interface & lab manual w/ exercises to help develop students' intuition.
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Ragnar {Groot Koerkamp} @curiouscoding.nl · 19/01/2026
vibe coding is the new doom scrolling?
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Sina Majidian @sinamajidian.bsky.social · 17/01/2026
Super-pangenome analyses across 35 accessions of 23 Avena species highlight their complex evolutionary history and extensive genomic diversity doi.org/10.1038/s415... Common oat=Avena sativa
Fig. 2 | Inferred phylogeny, origin and evolution of Avena species.
a, Phylogenetic relationships and timescale of 44 subgenomes in 25 species
(40 subgenomes in 23 species are from Avena) inferred on the basis of 2,456 single-copy orthologous groups using RAxML taking T. aestivum and L. perenne as outgroup species. Orange, purple, green, red and blue backgrounds represent A, B, C and D lineages and outgroups, respectively. Bootstrap support values
are indicated with black, red and green dots. The scale bar represents branch lengths, which correspond to the mean number of substitutions per site in the alignments. The gray bar indicates the confidence interval of differentiation time for each node. Trees for each single-copy gene are depicted by gray lines.21. Shi, T. et al. The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees. Mol. Plant 2024
88. Zhang, Y. et al. Telomere-to-telomere Citrullus super-pangenome provides direction for watermelon breeding. Nat. Genet. 56, 1750–1761 (2024).
89. Huang, Y. et al. Pangenome analysis provides insight into the evolution of the orange subfamily and a key gene for citric acid accumulation in citrus fruits. Nat. Genet. 55, 1964–1975 (2023).
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Titus Brown @titus.idyll.org · 14/01/2026
Once more unto the breach: A fast introduction to snakemake, in 5 examples.
hackmd.io
A fast introduction to snakemake (in 5 examples) - HackMD
# A rapid introduction to snakemake (in 5 examples) See github repo: [ctb/2026-rapid-snakemake-intr
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Felix Wiegand @fxwiegand.bsky.social · 08/01/2026
🚀 Our new paper on Alignoth just published in Bioinformatics! Alignoth generates self-contained interactive HTML read alignment plots from BAM files – Rust-based, portable, and ideal for headless workflows. 📄 doi.org/10.1093/bioi... #bioinformatics #genomics #rust @johanneskoester.bsky.social
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Tristan A.F. Long @thelonglab.bsky.social · 10/01/2026
With population genetics on deck for #BI111 this week, preparations for HWE exercises for 1100+!students means lots of card-sorting!
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Ethan Linck @elinck.bsky.social · 22/12/2025
I've slowly been reformatting notes from my population and conservation genetics course at Montana State University into a web book—a rough draft is now live here: elinck.org/popgen_conge...
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Bioinformatics Advances @bioinfoadv.bsky.social · 18/12/2025
🧬 Just out in Bioinformatics Advances: “tskit arg visualizer: Interactive plotting of ancestral recombination graphs.”  Read the full paper here: doi.org/10.1093/bioadv/vbaf302 Authors include: @kitchensjn.bsky.social, @yanwong.bsky.social
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Dr. K. Lotterhos @drk-lo.bsky.social · 19/12/2025
New special issue in Molecular Ecology on Conservation Genomics #popGen #evolution 🧪🧬🖥️ onlinelibrary.wiley.com/toc/1365294x...
onlinelibrary.wiley.com
Special Issue: CONSERVATION GENOMICS ‐ MAKING A DIFFERENCE: Molecular Ecology: Vol 34, No 23
Molecular Ecology is an international journal for research using molecular genetic techniques to address questions in ecology, evolution, behavior and conservation.
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UC Santa Cruz Genomics Institute @ucscgenomics.bsky.social · 16/12/2025
Announcing bamdam: a new open source tool for studying ancient DNA 🧬 It shrinks massive metagenomic files by 10x and helps distinguish ancient sequences from contamination. Tested on the oldest DNA yet uncovered (2M years) link.springer.com/article/10.1... @bdesan.bsky.social @russcd.bsky.social
link.springer.com
Bamdam: a post-mapping authentication toolkit for ancient metagenomics - Genome Biology
Ancient metagenomic studies using capture or shotgun sequencing often perform pairwise alignment of individual reads against large reference databases followed by lowest common ancestor assignment for...
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Dmitri Petrov @petrovadmitri.bsky.social · 17/12/2025
What a beautiful paper! www.nature.com/articles/s41...
nature.com
Gene-specific selective sweeps are pervasive across human gut microbiomes - Nature
Development and application of the integrated linkage disequilibrium score (iLDS) reveals both selective pressures impacting the human gut microbiome and the mechanisms by which gut bacteria adapt to ...
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Molecular Biology and Evolution @molbioevol.bsky.social · 15/12/2025
@cademirch.bsky.social @erikenbody.bsky.social TB Sackton & @russcd.bsky.social introduce Callable Loci And More (clam), a tool that leverages callable loci to accurately estimate population genetic statistics (π, dxy, and FST). 🔗 doi.org/10.1093/molbev/msaf282 #evobio #molbio #compbio
doi.org
Efficient Estimation of Nucleotide Diversity and Divergence Using Callable Loci (and More)
Abstract. The increasing scale of population genomic datasets presents computational challenges in estimating summary statistics such as nucleotide diversi
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patak @patak.cat · 05/12/2025
The changed code is a small fraction of an open source contribution. Your commitment to understand the issue, how your proposed solution fits with the project, and be ready to own and push the review process forward is the biggest chunk of the work. Your effort is the contribution, not the code.
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