Mervin Fansler
@mfansler.bsky.social
Postdoc in Cvejic Group, BRIC, Københavns Universitet. PhD from Mayr Lab at Sloan Kettering Institute. Reproducible research enthusiast. Conda Forge R Team. Creator of scUTRquant.
Pinned
Mervin Fansler
@mfansler.bsky.social
· Nov 12
mfansler - Overview
R Team @conda-forge. Postdoc in Cvejic Lab, BRIC, UCPH. PhD from @Mayrlab MSKCC. scUTRquant creator. Reproducible research enthusiast. - mfansler
github.com
📣 Heads up for new followers (welcome! 🫶). I work in #RNAbiology (3' UTRs) and now #hematopoiesis #grns. I’m always eager to help make #bioinfo workflows more reproducible, so if you ever need #conda #condaforge #bioconda help please reach out! 🚀
github.com/mfansler
github.com/mfansler
Reposted by Mervin Fansler
www.biorxiv.org/content/10.1...
Delighted to share the story of two germline RBPs - one with little (DND1) and one with no (NANOS3) intrinsic sequence-specificity - that together build a continuous RNA binding surface recognizing a 7-mer (AUGAAUU) in target mRNA 3’UTRs, leading to deadenylation.
Delighted to share the story of two germline RBPs - one with little (DND1) and one with no (NANOS3) intrinsic sequence-specificity - that together build a continuous RNA binding surface recognizing a 7-mer (AUGAAUU) in target mRNA 3’UTRs, leading to deadenylation.
The DND1-NANOS3 complex shapes the primordial germ cell transcriptome via a heptanucleotide sequence in mRNA 3'UTRs
The RNA-binding proteins DND1 and NANOS3 are essential for primordial germ cell survival. Their co-immunoprecipitation and overlapping loss-of-function phenotypes suggest joint function, yet how they ...
www.biorxiv.org
September 27, 2025 at 3:39 PM
www.biorxiv.org/content/10.1...
Delighted to share the story of two germline RBPs - one with little (DND1) and one with no (NANOS3) intrinsic sequence-specificity - that together build a continuous RNA binding surface recognizing a 7-mer (AUGAAUU) in target mRNA 3’UTRs, leading to deadenylation.
Delighted to share the story of two germline RBPs - one with little (DND1) and one with no (NANOS3) intrinsic sequence-specificity - that together build a continuous RNA binding surface recognizing a 7-mer (AUGAAUU) in target mRNA 3’UTRs, leading to deadenylation.
Reposted by Mervin Fansler
A useful analogy.
One can say that much of the progress in computer programming is aligned with ever increasing levels abstraction.
LLM-based coding tools are "just" a next level.
The choice of objective, and the measure of success, still remains something external to the tool.
One can say that much of the progress in computer programming is aligned with ever increasing levels abstraction.
LLM-based coding tools are "just" a next level.
The choice of objective, and the measure of success, still remains something external to the tool.
September 29, 2025 at 9:35 AM
A useful analogy.
One can say that much of the progress in computer programming is aligned with ever increasing levels abstraction.
LLM-based coding tools are "just" a next level.
The choice of objective, and the measure of success, still remains something external to the tool.
One can say that much of the progress in computer programming is aligned with ever increasing levels abstraction.
LLM-based coding tools are "just" a next level.
The choice of objective, and the measure of success, still remains something external to the tool.
Reposted by Mervin Fansler
Do you like theoretical biology, mathematical&conceptual modelling and want to apply yourself to cutting-edge research at all levels of biology, from molecules to ecosystems?
Come to EMBL! Scope includes physics-based models, emergence, statistics, ML/AI
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Come to EMBL! Scope includes physics-based models, emergence, statistics, ML/AI
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
September 29, 2025 at 7:03 AM
Do you like theoretical biology, mathematical&conceptual modelling and want to apply yourself to cutting-edge research at all levels of biology, from molecules to ecosystems?
Come to EMBL! Scope includes physics-based models, emergence, statistics, ML/AI
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Come to EMBL! Scope includes physics-based models, emergence, statistics, ML/AI
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Why so many #rstats packages unnecessarily link `$(FLIBS)`? I'd guess 90% packages that do this never need it. Maybe a tutorial everyone follows, i.e., copy-pasta of an example `Makevars`?
Also see linking LAPACK, when only BLAS needed, but a bit more understandable.
Also see linking LAPACK, when only BLAS needed, but a bit more understandable.
September 29, 2025 at 9:39 AM
Why so many #rstats packages unnecessarily link `$(FLIBS)`? I'd guess 90% packages that do this never need it. Maybe a tutorial everyone follows, i.e., copy-pasta of an example `Makevars`?
Also see linking LAPACK, when only BLAS needed, but a bit more understandable.
Also see linking LAPACK, when only BLAS needed, but a bit more understandable.
Reposted by Mervin Fansler
New #miRNA paper from Lai lab!! 🧬🔥
some think this field, despite recent Nobel to Ambros and Ruvkun, doesn't have much surprises left. but, do we EVEN KNOW WHAT a miRNA precursor LOOKS LIKE? we found some conserved miRNA hairpins up to 10x longer than suspected. this is mir-12, just bonkers! 1/n
some think this field, despite recent Nobel to Ambros and Ruvkun, doesn't have much surprises left. but, do we EVEN KNOW WHAT a miRNA precursor LOOKS LIKE? we found some conserved miRNA hairpins up to 10x longer than suspected. this is mir-12, just bonkers! 1/n
September 12, 2025 at 2:02 AM
New #miRNA paper from Lai lab!! 🧬🔥
some think this field, despite recent Nobel to Ambros and Ruvkun, doesn't have much surprises left. but, do we EVEN KNOW WHAT a miRNA precursor LOOKS LIKE? we found some conserved miRNA hairpins up to 10x longer than suspected. this is mir-12, just bonkers! 1/n
some think this field, despite recent Nobel to Ambros and Ruvkun, doesn't have much surprises left. but, do we EVEN KNOW WHAT a miRNA precursor LOOKS LIKE? we found some conserved miRNA hairpins up to 10x longer than suspected. this is mir-12, just bonkers! 1/n
Empirical quantiles in the violin plots! That's a nice improvement for scientific publishing. 🎉
I am beyond excited to announce that ggplot2 4.0.0 has just landed on CRAN.
It's not every day we have a new major #ggplot2 release but it is a fitting 18 year birthday present for the package.
Get an overview of the release in this blog post and be on the lookout for more in-depth posts #rstats
It's not every day we have a new major #ggplot2 release but it is a fitting 18 year birthday present for the package.
Get an overview of the release in this blog post and be on the lookout for more in-depth posts #rstats
ggplot2 4.0.0
A new major version of ggplot2 has been released on CRAN. Find out what is new here.
www.tidyverse.org
September 11, 2025 at 7:34 PM
Empirical quantiles in the violin plots! That's a nice improvement for scientific publishing. 🎉
Reposted by Mervin Fansler
So excited that this is finally out. This was among the longest and most uncertain (no)pun intended during my PhD, with different challenges, starting my from evaluation metrics to finding the right datasets, to tweak the method and interpreting the results.
github.com/NPSDC/mehenDi
github.com/NPSDC/mehenDi
August 22, 2025 at 1:21 PM
So excited that this is finally out. This was among the longest and most uncertain (no)pun intended during my PhD, with different challenges, starting my from evaluation metrics to finding the right datasets, to tweak the method and interpreting the results.
github.com/NPSDC/mehenDi
github.com/NPSDC/mehenDi
Still much to be characterized about mRNAs beyond just templating proteins.
"Rethinking RNA-binding proteins: Riboregulation challenges prevailing views" www.cell.com/cell/fulltex...
"Rethinking RNA-binding proteins: Riboregulation challenges prevailing views" www.cell.com/cell/fulltex...
Rethinking RNA-binding proteins: Riboregulation challenges prevailing views
The advent of system-wide proteomic approaches has largely expanded the number of
RNA-binding proteins (RBPs). This review discusses how recent discoveries are transforming
our understanding of biolog...
www.cell.com
September 8, 2025 at 11:45 AM
Still much to be characterized about mRNAs beyond just templating proteins.
"Rethinking RNA-binding proteins: Riboregulation challenges prevailing views" www.cell.com/cell/fulltex...
"Rethinking RNA-binding proteins: Riboregulation challenges prevailing views" www.cell.com/cell/fulltex...
Reposted by Mervin Fansler
Noor (@noorpratap.bsky.social) has been working on this for quite some time! It took a bit of work to figure out, but now you can map your scATAC-seq reads directly to the genome and sort and dedup them with alevin-fry-atac. You get a BED file with counts ready for downstream analysis! 1/
Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic pseudoalignment https://www.biorxiv.org/content/10.1101/2024.11.27.625771v1
Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic pseudoalignment https://www.biorxiv.org/content/10.1101/2024.11.27.625771v1
Ultrafast mapping of short reads to transcriptomic and metagenomic references via lightweight mappin
www.biorxiv.org
December 2, 2024 at 11:25 PM
Noor (@noorpratap.bsky.social) has been working on this for quite some time! It took a bit of work to figure out, but now you can map your scATAC-seq reads directly to the genome and sort and dedup them with alevin-fry-atac. You get a BED file with counts ready for downstream analysis! 1/
Reposted by Mervin Fansler
Not checking nuclear markers like MALAT1 or intronic reads in your scRNA-seq data?🚨
We show their power to flag low-quality cells—even in top public datasets. It’s time to prioritize better QC for cleaner, more reliable genomics research!
Read more: bmcgenomics.biomedcentral.com/articles/10....
1/8
High content of nuclei-free low-quality cells in reference single-cell atlases: a call for more stringent quality control using nuclear fraction - BMC Genomics
The advent of droplet-based single-cell RNA-sequencing (scRNA-seq) has dramatically increased data throughput, enabling the release of a diverse array of tissue cell atlases to the public. However, we...
bmcgenomics.biomedcentral.com
December 3, 2024 at 8:38 AM
Not checking nuclear markers like MALAT1 or intronic reads in your scRNA-seq data?🚨
We show their power to flag low-quality cells—even in top public datasets. It’s time to prioritize better QC for cleaner, more reliable genomics research!
Read more: bmcgenomics.biomedcentral.com/articles/10....
1/8
Reposted by Mervin Fansler
Are you looking for job opportunities where your #Nextflow skills are valued? Check the list we've compiled below. 👇 #Jobs #Opportunities
December 3, 2024 at 6:08 PM
Are you looking for job opportunities where your #Nextflow skills are valued? Check the list we've compiled below. 👇 #Jobs #Opportunities
Reposted by Mervin Fansler
Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements - Nature Genetics
ChIP-DIP (ChIP done in parallel) is a highly multiplex assay for protein–DNA binding, scalable to hundreds of proteins including modified histones, chromatin regulators and transcription factors, offe...
www.nature.com
November 27, 2024 at 4:13 AM
Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Mervin Fansler
I'm excited to share the preprint for the first chunk of my PhD work! We combined DMS structure probing with nascent RNA enrichment to report high-resolution, dynamic structures of transcripts just after synthesis - inside cells. @karlaneugebauer.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Rapid folding of nascent RNA regulates eukaryotic RNA biogenesis
An RNA′s catalytic, regulatory, or coding potential depends on RNA structure formation. Because base pairing occurs during transcription, early structural states can govern RNA processing events and d...
www.biorxiv.org
November 27, 2024 at 1:48 PM
I'm excited to share the preprint for the first chunk of my PhD work! We combined DMS structure probing with nascent RNA enrichment to report high-resolution, dynamic structures of transcripts just after synthesis - inside cells. @karlaneugebauer.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Mervin Fansler
We did this crazy project where we tried to see if proteins could interact with their mirror image ligand. Seems impossible when proteins need to form 3D structures to interact. But what about if the interaction remains disordered???
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Stereochemistry in the disorder–order continuum of protein interactions - Nature
Studies on protein–protein interactions using proteins containing d- or l-amino acids show that stereoselectivity of binding varies with the degree of disorder within the complex.
www.nature.com
November 27, 2024 at 8:31 PM
We did this crazy project where we tried to see if proteins could interact with their mirror image ligand. Seems impossible when proteins need to form 3D structures to interact. But what about if the interaction remains disordered???
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Mervin Fansler
Check it out! The RNA Society 2025 Meeting Site is now live! Registration will open in January RNASociety Note the fabulous artwork by former EmoryBCDB student Dr. Carly Lancaster- make your plans now to join us in San Diego May 27-June 1, 2025
November 19, 2024 at 2:55 AM
Check it out! The RNA Society 2025 Meeting Site is now live! Registration will open in January RNASociety Note the fabulous artwork by former EmoryBCDB student Dr. Carly Lancaster- make your plans now to join us in San Diego May 27-June 1, 2025
Reposted by Mervin Fansler
Single-molecule states link transcription factor binding to gene expression www.nature.com/articles/s41...
Single-molecule states link transcription factor binding to gene expression - Nature
A study uses single-molecule footprinting to measure protein occupancy at regulatory elements on individual molecules in human cells and describes how different properties of transcription factor bind...
www.nature.com
November 20, 2024 at 8:34 PM
Single-molecule states link transcription factor binding to gene expression www.nature.com/articles/s41...
Reposted by Mervin Fansler
A cell atlas foundation model for scalable search of similar human cells | Nature
Develops SCimilarity which they use to query 23.4M cell atlas to find similar cell profiles.
#Genomics #SingleCell
www.nature.com/articles/s41...
Develops SCimilarity which they use to query 23.4M cell atlas to find similar cell profiles.
#Genomics #SingleCell
www.nature.com/articles/s41...
November 20, 2024 at 11:33 PM
A cell atlas foundation model for scalable search of similar human cells | Nature
Develops SCimilarity which they use to query 23.4M cell atlas to find similar cell profiles.
#Genomics #SingleCell
www.nature.com/articles/s41...
Develops SCimilarity which they use to query 23.4M cell atlas to find similar cell profiles.
#Genomics #SingleCell
www.nature.com/articles/s41...
Reposted by Mervin Fansler
Well, with the new activity here, thought I'd post some threads with some of our recent work -- starting with our paper where we use Bayesian statistical modeling to show bacterial transcripts have subminute half-lives, far shorter than previously thought 🧫🦠🧬💻 #RNAsky www.pnas.org/doi/10.1073/...
Improved RNA stability estimation through Bayesian modeling reveals most Salmonella transcripts have subminute half-lives | PNAS
RNA decay is a crucial mechanism for regulating gene expression in response to environmental
stresses. In bacteria, RNA-binding proteins (RBPs) are...
www.pnas.org
November 16, 2024 at 6:41 PM
Well, with the new activity here, thought I'd post some threads with some of our recent work -- starting with our paper where we use Bayesian statistical modeling to show bacterial transcripts have subminute half-lives, far shorter than previously thought 🧫🦠🧬💻 #RNAsky www.pnas.org/doi/10.1073/...
Reposted by Mervin Fansler
The latest from our group, led by Megan Ostrowski and @martyyang.bsky.social, is now published in final form (www.cell.com/cell/fulltex...! Many thanks to our excellent peer reviewers for suggesting several experiments (including CAF-1 perturbation) to really improve the study =) #epigenetics
The single-molecule accessibility landscape of newly replicated mammalian chromatin
By developing a long-read sequencing method to simultaneously map replication status
and protein-DNA contacts in cells, Ostrowski, Yang, et al. show that newly replicated
chromatin is enriched for unw...
www.cell.com
November 15, 2024 at 3:35 PM
The latest from our group, led by Megan Ostrowski and @martyyang.bsky.social, is now published in final form (www.cell.com/cell/fulltex...! Many thanks to our excellent peer reviewers for suggesting several experiments (including CAF-1 perturbation) to really improve the study =) #epigenetics
Reposted by Mervin Fansler
Reposted by Mervin Fansler
Let's make a thread of RNA-related conferences in 2025 🧵 (add missing!)
November 13, 2024 at 6:03 AM
Let's make a thread of RNA-related conferences in 2025 🧵 (add missing!)
Reposted by Mervin Fansler
Excited to share our latest work! In it, we develop a new method for studying RNA localization via proximity labeling: OINC-seq! In contrast to other proximity-based methods, labels deposited on RNAs are read directly by sequencing without the need for biotinylation. biorxiv.org/cgi/content/...
November 13, 2024 at 4:46 PM
Excited to share our latest work! In it, we develop a new method for studying RNA localization via proximity labeling: OINC-seq! In contrast to other proximity-based methods, labels deposited on RNAs are read directly by sequencing without the need for biotinylation. biorxiv.org/cgi/content/...
📣 Heads up for new followers (welcome! 🫶). I work in #RNAbiology (3' UTRs) and now #hematopoiesis #grns. I’m always eager to help make #bioinfo workflows more reproducible, so if you ever need #conda #condaforge #bioconda help please reach out! 🚀
github.com/mfansler
github.com/mfansler
mfansler - Overview
R Team @conda-forge. Postdoc in Cvejic Lab, BRIC, UCPH. PhD from @Mayrlab MSKCC. scUTRquant creator. Reproducible research enthusiast. - mfansler
github.com
November 12, 2024 at 7:54 PM
📣 Heads up for new followers (welcome! 🫶). I work in #RNAbiology (3' UTRs) and now #hematopoiesis #grns. I’m always eager to help make #bioinfo workflows more reproducible, so if you ever need #conda #condaforge #bioconda help please reach out! 🚀
github.com/mfansler
github.com/mfansler
Reposted by Mervin Fansler
Our collaborative work with Narry Kim on the kinetics of mRNA poly(A) tail shortening. Led by Young-suk Lee, who established his own lab while the work was in progress, and Yevgen Levdansky in my lab. #RNASky #RNABiology www.nature.com/articles/s41...
Deadenylation kinetics of mixed poly(A) tails at single-nucleotide resolution - Nature Structural & Molecular Biology
Here, using mathematical modeling and an in vitro deadenylation system, the authors quantitatively demonstrate the effect of non-adenosines in the poly(A) tail and exemplify how tail sequence regulate...
www.nature.com
February 19, 2024 at 12:45 PM
Our collaborative work with Narry Kim on the kinetics of mRNA poly(A) tail shortening. Led by Young-suk Lee, who established his own lab while the work was in progress, and Yevgen Levdansky in my lab. #RNASky #RNABiology www.nature.com/articles/s41...