Michael Love
@mikelove.bsky.social
Genetics, bioinformatics, comp bio, statistics, data science, open source, open science!
Reposted by Michael Love
Reproducibility 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...
tidyomics.github.io/tidyomicsBlo...
Omicslog – tidyomicsBlog
Providing logging capabilities for SummarizedExperiment objects.
tidyomics.github.io
January 6, 2026 at 3:13 AM
Reproducibility 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...
tidyomics.github.io/tidyomicsBlo...
Reposted by Michael Love
Happy 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...
Integrating perturbational screens, eQTL, and GWAS data identifies mediating genes for complex traits
Most current GWAS-eQTL approaches prioritize genes whose mediating effects on complex traits act through cis-regulation, while trans-acting genes remain largely underexplored. Recent perturbational sc...
www.medrxiv.org
January 5, 2026 at 10:27 PM
Happy 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 Love
GWAS 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🧵:
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:
Causal modelling of gene effects from regulators to programs to traits - Nature
Approaches combining genetic association and Perturb-seq data that link genetic variants to functional programs to traits are described.
www.nature.com
December 11, 2025 at 5:54 PM
GWAS 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🧵:
Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:
Reposted by Michael Love
Happy 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...
January 5, 2026 at 9:02 AM
Happy 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 Love
While 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
QCatch: A framework for quality control assessment and analysis of single-cell sequencing data
Motivation: Single-cell sequencing data analysis requires robust quality control (QC) to mitigate technical artifacts and ensure reliable downstream results. While tools like alevin-fry and simpleaf (...
www.biorxiv.org
January 3, 2026 at 6:18 PM
While 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 Love
It'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...
PREP-aring is worth it: Success of the Case Western Reserve University Post-baccalaureate Research Education Program and its Scholars
The Post-baccalaureate Research Education Program (PREP), established by the National Institute of General Medical Sciences (NIGMS) at the National Institutes of Health in 2000, was a research-intense...
www.biorxiv.org
January 3, 2026 at 2:02 PM
It'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 Love
CausalGRN: deciphering causal gene regulatory networks from single-cell CRISPR screens https://www.biorxiv.org/content/10.64898/2025.12.30.692369v1
December 31, 2025 at 10:46 AM
CausalGRN: deciphering causal gene regulatory networks from single-cell CRISPR screens https://www.biorxiv.org/content/10.64898/2025.12.30.692369v1
Reposted by Michael Love
Do 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. 🧬
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. 🧬
December 29, 2025 at 7:30 PM
Do 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. 🧬
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/
Large-scale causal discovery using interventional data sheds light on gene network structure in k562 cells - PubMed
Inference of directed biological networks is an important but notoriously challenging problem. The recent proliferation of large-scale CRISPR perturbation data provides a new opportunity to tackle this problem by leveraging the transcriptional response to the presence of a gene-targeting guide. Here …
pubmed.ncbi.nlm.nih.gov
December 27, 2025 at 4:58 PM
…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 Love
Looking 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. 🧪🧬🖥️
December 27, 2025 at 6:30 PM
Looking 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 Love
Repeat after me: GENE 👏 EXPRESSION 👏 PROFILING 👏 DOES 👏 NOT 👏 A 👏 VIRTUAL 👏 CELL 👏 MAKE 👏
December 26, 2025 at 12:11 PM
Repeat after me: GENE 👏 EXPRESSION 👏 PROFILING 👏 DOES 👏 NOT 👏 A 👏 VIRTUAL 👏 CELL 👏 MAKE 👏
Reposted by Michael Love
Our 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)
Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo
Enhancers control tissue-specific gene expression across metazoans. Although deep learning has enabled enhancer prediction and design in mammalian cell lines and invertebrate systems, it remains uncle...
www.biorxiv.org
December 24, 2025 at 3:06 PM
Our 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 Love
I'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...
andrewcarroll.github.io/2025/12/23/t...
The Virtual Cell Will Be More Like Gwas Than Alphafold
There has been significant discussion recently on the concept of the “virtual cell.” I want to summarize the key concepts regarding what the field wants from a virtual cell and the challenges we face....
andrewcarroll.github.io
December 24, 2025 at 1:52 AM
I'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...
andrewcarroll.github.io/2025/12/23/t...
Reposted by Michael Love
Little 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:
Here are a couple of Finnish Christmas traditions that you might not know:
December 23, 2025 at 7:55 PM
Little 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:
Here are a couple of Finnish Christmas traditions that you might not know:
Reposted by Michael Love
Our 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!
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!
Hidden sampling biases inflate performance in gene regulatory network inference
Accurate reconstruction of gene regulatory networks (GRNs) from single-cell transcriptomic data remains a major methodological challenge. Recent machine learning approaches, particularly graph neural ...
www.biorxiv.org
December 23, 2025 at 7:55 PM
Our 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!
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 Love
Biologists 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
#iteachbio 🧪 #Evolution
December 22, 2025 at 2:00 PM
Biologists 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
#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
December 22, 2025 at 5:01 PM
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
Reposted by Michael Love
I 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.
December 22, 2025 at 9:19 AM
I 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 Love
Announcing 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!
www.huber.embl.de/group/events...
Reserve the dates!
December 22, 2025 at 11:10 AM
Announcing 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!
www.huber.embl.de/group/events...
Reserve the dates!
Reposted by Michael Love
HAPPY HOLIDAYS TO ALL OF YOU!🎄✨
December 19, 2025 at 6:08 PM
HAPPY 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...
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
r-consortium.org/posts/2025-i...
#rstats
December 19, 2025 at 3:01 AM
A nice summary of the year from the R Consortium.
Expanded FDA file format support is huge r-consortium.org/posts/expand...
Expanded FDA file format support is huge r-consortium.org/posts/expand...
Reposted by Michael Love
I asked participants for tips attending scientific conferences #BES2025 youtu.be/ow_ickvkvbA?...
Tips for attending scientific conferences
YouTube video by Bill Sutherland's Conservation Concepts
youtu.be
December 18, 2025 at 7:15 AM
I asked participants for tips attending scientific conferences #BES2025 youtu.be/ow_ickvkvbA?...
Reposted by Michael Love
So 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?
December 17, 2025 at 6:46 PM
So 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 Love
CSAMA 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.
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.
December 17, 2025 at 2:34 PM
CSAMA 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.
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....
Thinking about this in the context of AI tools....
An open letter to graduate students and other procrastinators: it’s time to write - Nature Biotechnology
Nature Biotechnology - An open letter to graduate students and other procrastinators: it’s time to write
www.nature.com
March 25, 2025 at 2:46 PM
"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....
Thinking about this in the context of AI tools....