Michael Love
Genetics, bioinformatics, comp bio, statistics, data science, open source, open science!
- Reposted by Michael Love@mikelove.bsky.social : There was PyDESeq2, and now there is rust_deseq2! crates.io/crates/rust_...
- Reposted by Michael LoveI started offering career advice to two junior colleagues today in separate meetings, and both times I caught myself thinking that, if I'm honest, I don't have very good advice on navigating the current funding and job climate. I think it's important to say that no one does.
- Reposted by Michael LoveWe're donating PyDESeq2 to @scverse.bsky.social for long-term maintenance & development. Python reimplementation of DESeq2, ecosystem member since 2023, now in the hands of one of the best open source communities in omics. Good science requires good open source. github.com/scverse/PyDE...
- Reposted by Michael LoveAlphaGenome is out in @nature.com today along with model weights! 🧬 📄 Paper: www.nature.com/articles/s41... 💻 Weights: github.com/google-deepm... Getting here wasn’t a straight path. We discussed the story behind the model, paper & API in the following roundtable: youtu.be/V8lhUqKqzUc
- Reposted by Michael LoveOur @varianteffect.bsky.social annual reports summarize, celebrate and showcase our collective work. Read the latest 🔖 zenodo.org/records/1833... View them all 📖 www.varianteffect.org/annual-repor... #AnnualReport #GlobalAlliance #FunctionalGenomics #Consortium
- Reposted by Michael Love[Not loaded yet]
- Check out this work from Abdalla Alkhawaja et al in Karen Mohlke's group @klmohlke.bsky.social Profiling RNA and ATAC of 68k+ nuclei from 39 individuals to better understand mechanism and context for GWAS loci
- Excited to share our latest work in @ajhgnews.bsky.social 🧬📄 We mapped the regulatory landscape of human liver at single-nucleus resolution using snMultiome, connecting genetic variants to the cell-type mechanisms underlying cardiometabolic disease. www.sciencedirect.com/science/arti...
- Reposted by Michael LoveExcited to share our latest work in @ajhgnews.bsky.social 🧬📄 We mapped the regulatory landscape of human liver at single-nucleus resolution using snMultiome, connecting genetic variants to the cell-type mechanisms underlying cardiometabolic disease. www.sciencedirect.com/science/arti...
- Reposted by Michael LoveIt is a PROBLEM that the new MANDATORY ScienCV platform does not (as far as I can tell) enable one to indicate co-first or co-senior authorship in your bibliography. This is a massive disincentive to collaborative science and it needs to be fixed.
- Reposted by Michael Love
- Reposted by Michael LoveOur paper on the Expanded Registry of candidate cis-Regulatory Elements (cCREs) is out 🎉 www.nature.com/articles/s41... To celebrate, here’s a "meme-torial" walkthrough of the science. Let’s get started 🧵 1/11
- Reposted by Michael LoveWe used a similar design in this paper: www.sciencedirect.com/science/arti... Found that in cis-MR with multiple colocalising instruments (i.e. multiple indepdent signals colocalise between eQTL and pQTL traits) sign concordance was around 95%:
- Reposted by Michael LoveClever use of proteomic data to stress-test TWAS and QTL colocalization methods, revealing a high false sign rate. This hypothesis about high-LD and cross-tissue confounding is particularly interesting:
- How well does TWAS estimate a gene’s direction of effect on a trait? We think of this as an important stress-test for the accuracy of TWAS. In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time! doi.org/10.64898/202... 1/n
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View full threadReposted by Michael LoveIf you like larger sample sizes, then do check out our reprocessed and fine mapped cis-eQTLs and cis-sQTLs (leafCutter and MAJIQ!) from the INTERVAL cohort (whole blood, n up to 4,729)! zenodo.org/records/1795... These will be on the eQTL Catalogue FTP soon as well. cc @yosephbarash.bsky.social
- Reposted by Michael LoveIt would be interesting to revisit these specific analyses with eQTL sample sizes in 1000s like in @mikelove.bsky.social 's recent work. IMO it's very plausible that while typical cis-eQTL sample sizes find lots of eQTLs, the relevant ones with enough power for colocalization need a bigger N.
- Reposted by Michael LoveWe used a similar design in this paper together with @mikelove.bsky.social: doi.org/10.1016/j.xh... Found that in cis-MR with multiple colocalising instruments (i.e. multiple indepdent signals that colocalise between matched eQTL and pQTL genes) sign concordance was around 95%:
- Reposted by Michael LoveReproducibility is key to science. In computational biology, we routinely manipulate high-dimensional data (spatial, single-cell, bulk) through filtering, normalisation and transformation. Capturing those steps clearly improves reproducibility and transparency. tidyomics.github.io/tidyomicsBlo...
- Reposted by Michael LoveHappy to share our new preprint from @sashagusevposts.bsky.social and @nmancuso.bsky.social labs! We introduce Mr. PEG, a framework integrating perturbational screens, eQTL, and GWAS data to identify mediating genes for complex traits. (1/n) www.medrxiv.org/content/10.6...
- Reposted by Michael LoveGWAS has been an incredible discovery tool for human genetics: it regularly identifies *causal* links from 1000s of SNPs to any given trait. But mechanistic interpretation is usually difficult. Our latest work on causal models for this is out yesterday: www.nature.com/articles/s41... A short🧵:
- Reposted by Michael LoveHappy to share our new method F-MoDA to find motifs in genomic attribution maps just published in MLCB 2025 proceedings! F-MoDA has improved specificity, sensitivity, accuracy, conciseness, and runtime compared to TF-MoDISco. Led by Ofir Yaish: proceedings.mlr.press/v311/yaish25...
- Reposted by Michael LoveWhile we've been somewhat successful in spurring adoption of alevin-fry/simpleaf for scRNAseq processing, an impediment Dongze brought to our attention (now working directly w/ many experimentalists) was the need for a nice QC report for it's output; hence QCatch www.biorxiv.org/content/10.1... 1/x
- Reposted by Michael LoveIt's bittersweet to describe the success of #NIHPREP Scholars. You are awesome #scientists. Don't let anyone tell you otherwise. www.biorxiv.org/content/10.6...
- Reposted by Michael LoveCausalGRN: deciphering causal gene regulatory networks from single-cell CRISPR screens biorxiv.org/content/10.64898/20…
- Reposted by Michael LoveDo transcriptional activators work on any promoter? Our data says no. 🙅♂️ Despite driving ~2/3 of mammalian genes, CpG island (CGI) promoters have remained a puzzle. We identified >50 activators that are exclusively compatible with this promoter class. 🧬
- Reposted by Michael Love…and we don’t have this matrix at good completeness & precision, despite many efforts (including our own 👇). Hopefully we will in not too distant future, but given the difficulty of this task, I’m not holding my breath regarding virtual cells. pubmed.ncbi.nlm.nih.gov/41173850/
- Reposted by Michael LoveLooking into industry bioinformatics / comp bio / data science careers. If you have any leads, message me! CV is in bio. Currently a postdoc data scientist at @mdanderson.bsky.social, have published work in both wet + dry lab multi-omics of non-model organisms & humans. 🧪🧬🖥️
- Reposted by Michael LoveRepeat after me: GENE 👏 EXPRESSION 👏 PROFILING 👏 DOES 👏 NOT 👏 A 👏 VIRTUAL 👏 CELL 👏 MAKE 👏
- Reposted by Michael LoveOur preprint "Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo" is on bioRxiv: www.biorxiv.org/content/10.6... . Amazing collaboration by @shenzhichen1999.bsky.social, Vincent Loubiere (@impvienna.bsky.social,@viennabiocenter.bsky.social),... (1/2)
- Reposted by Michael LoveI've been thinking about the "virtual cell" concept and wanted to write up a few thoughts. Specifically on how I think the prior experience in GWAS informs the most likely way these models will be useful. andrewcarroll.github.io/2025/12/23/t...
- Reposted by Michael LoveLittle over a month left to submit an abstract to #EuroBioC2026 (eurobioc2026.bioconductor.org/pages/submis...), which will be held in Turku, Finland. Here are a couple of Finnish Christmas traditions that you might not know:
- Reposted by Michael LoveOur new preprint is out: www.biorxiv.org/content/10.6... We show that GRN benchmarks commonly used can overestimate performance due to negative-sampling choices, sometimes allowing simple degree-based baselines to rival more complex GNNs. A reminder of why bias-aware evaluation matters!
- Reposted by Michael LoveBiologists who teach: in what order do you teach the four forces of evolution? Genetic drift first or selection first? And I'm still struggling to smoothly fit in HWE so that its utility is emphasized (students focus so much on how likely it is that assumptions are violated). #iteachbio 🧪 #Evolution
- Reposted by Michael Love
Thanks to the AWS Open Data program, this dataset along some derived data is also openly accessible via @AWSCloud at openhgl.s3.us-east-1.amazonaws.com/index.html- 579 high-quality human genomes from @humanpangenome.bsky.social, Arab Pangenome and individual papers (CHM13, CN1, KSA001, I002C, YAO and KOREF1). Sequences available in the AGC format (3.7GB) and FM-index in the ropebwt3 format (20.3GB). For details, see github.com/lh3/human-asm
- Reposted by Michael LoveI have seen many people say that no academic needs to use LLMs for writing, because of course we are all already excellent at writing. I fear that risks exacerbating imposter syndrome in early career researchers. I therefore want to raise my hand and say while I enjoy writing, I find it hard.
- Reposted by Michael LoveAnnouncing the Ascona Workshop "Statistical and AI methods for multi-modal multi-scale modeling of biological systems" on 28 June - 3 July 2026 in Ascona, CH www.huber.embl.de/group/events... Reserve the dates!
- Reposted by Michael LoveHAPPY HOLIDAYS TO ALL OF YOU!🎄✨
- A nice summary of the year from the R Consortium. Expanded FDA file format support is huge r-consortium.org/posts/expand...
- R Consortium: 2025 in Review—growth, community, and a ton of momentum! Highlights: R/Medicine 2025, useR!, R+AI; Submissions WG + expanded FDA eCTD support for R packages; 13 infra projects funded; YouTube +1,472; LinkedIn +1,769. r-consortium.org/posts/2025-i... #rstats
- Reposted by Michael LoveI asked participants for tips attending scientific conferences #BES2025 youtu.be/ow_ickvkvbA?...
- Reposted by Michael LoveSo question for single-cell peeps. It seems that ParseBio is even more locked-down than 10x! Is it the case that if I'm not a "registered" ParseBio customer, I can't even access their splitpipe software? Is there any archived version of splitpipe available?
- Reposted by Michael LoveCSAMA 2026 - Biological Data Science Summer School Bressanone-Brixen, South Tyrol / Italy 24-29 May 2026 csama2026.bioconductor.eu Statistical & computational methods for single cell and spatial omics, with lectures and hands-on exercises in R/Bioconductor.
- Reposted by Michael Love"The only kind of thinking that matters in science is structured thinking. The only way to give structure and substance to your thoughts is to write them down. Writing. Is. Thinking." Thinking about this in the context of AI tools....
- Reposted by Michael Love📣 Opportunity for Pre-conference Workshops - EuroBioC2026 EuroBioC2026 will host on-site pre-conference workshops on 1–2 June 2026 in Turku, Finland, ahead of the main conference. If you’re interested in hosting a workshop, submit your interest here by 30 Jan 2026: docs.google.com/forms/d/16MR...
- Reposted by Michael LoveMy lab is recruiting postdocs in AI/ML for genetics & genomics through the Malone Postdoctoral Fellows program. Apply by Jan 30! Lots of other great labs across the Malone Center as well.
- Reposted by Michael LoveAnd it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j.... If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!
- Have you recently completed (or finishing soon) a PhD in CS or a related discipline? Do you want to do research advancing the theory & practice of algorithmic genomics & build tools that people love to use? I'll be looking to hire a postdoc! Official ad coming soon: docs.google.com/document/d/1...
- Reposted by Michael LoveHow excited am I allowed to be about Josh Starmer of #StatQuest joining us on the #DSHangout this week?! BECAUSE I AM EXCITED! Josh makes me feel seen bc we both love explaining stats stuff in friendly ways, helping folks, & not taking ourselves too seriously #databs #rstats #python #datascience
- Deadline today for submitting abstracts to STATGEN 2026 in Atlanta, May 18-20 bsky.app/profile/step...
- Consider submitting an abstract for an invited talk or poster at STATGEN 2026 by December 15th! Amazing keynote speakers and statistical leaders in #genetics and #genomics! 👏 Hope to see you there! statgen26.emory.edu 🧪 🧬 🖥️ 🧠 #statssky #imaging #SingleCell #spatial #omics #DigitalPathology
- Reposted by Michael LoveThe last #tidyomics meeting of the year is in 2 days. Everyone welcome! - 16 Dec, 3:30 pm (EST; New York) - 16 Dec, 9:30 pm (CET; Berlin) - 17 Dec, 7:30 am (AEDT; Melbourne) We will chat about plans for next year. Zoom link: shorturl.at/Epbbc @mikelove.bsky.social @bioconductor.bsky.social
- Reposted by Michael Love🇸🇰 Slovakia has become the newest member to join #ELIXIR, following the signature of the ELIXIR Consortium Agreement by the Ministry of Education, Research and Youth. 🙌 This brings the number of ELIXIR members to 23. Read the news 👉 loom.ly/h4CyhJo
- Reposted by Michael LoveAre you interested in adding alt text to your publications? It helps share your data visualisations with vision impaired readers. Try out github.com/numbats/auto... to get a reasonable first draft or maybe complete text. @r-forwards.hachyderm.io.ap.brid.gy @rladies.org @rconsortium.bsky.social
- Reposted by Michael Love“Brilliance wrapped in modesty, decency, and good humor.” So true. 😭 May his memory be a blessing.
- Reposted by Michael LoveWe learned today that Paul Rathouz of UT-Austin (previously Chicago and UW-Madison) died on Dec. 10. Few people I've known have enwrapped their brilliance with such modesty, decency, and good humor. A mensch's mensch. RIP.
- Reposted by Michael Love[This post could not be retrieved]
- Reposted by Michael LoveThe new Enabling Discovery through GEnomics (EDGE) Program page is posted. Please contact us at BIOEDGE@nsf.gov if you have questions. www.nsf.gov/funding/oppo...
