Sean Bresnahan
@seantbres.bsky.social
Postdoc at MD Anderson: Omics of reproduction, development, cancer, and conflict | PhD, Penn State: functional genomics in social insects
Opinions are my own.
https://seantbresnahan.com
https://bhattacharya-lab.com
Opinions are my own.
https://seantbresnahan.com
https://bhattacharya-lab.com
Autumn in Oklahoma 🍂
November 9, 2025 at 5:16 PM
Autumn in Oklahoma 🍂
The joys of cleaning your garage: finding an Illumina P3 flow cell from your first sequencing run in grad school.
October 31, 2025 at 6:55 PM
The joys of cleaning your garage: finding an Illumina P3 flow cell from your first sequencing run in grad school.
Minor release v0.1.1: Reframes ODint and components as exploratory; defaults to bootstrap-based OD per Baldoni et al. Fixes v0.1.0 bug in extract_feature_vector() causing user-defined OD vectors to be missed.
August 14, 2025 at 2:15 PM
Minor release v0.1.1: Reframes ODint and components as exploratory; defaults to bootstrap-based OD per Baldoni et al. Fixes v0.1.0 bug in extract_feature_vector() causing user-defined OD vectors to be missed.
Strange: these CSH1 isoforms have intron retention events, regulatory mechanism of tissue-specific gene expression RE: cell stress, including aging-induced transposable element expression. This finding warrants further investigation: is this real, or canonical correlation in read assignments?
July 2, 2025 at 1:08 PM
Strange: these CSH1 isoforms have intron retention events, regulatory mechanism of tissue-specific gene expression RE: cell stress, including aging-induced transposable element expression. This finding warrants further investigation: is this real, or canonical correlation in read assignments?
The main result: assembly reveals the placenta mediates ~35% of GDM's effect on birth weight, with population-specific CSH1 isoforms contributing. This supports the DOHaD hypothesis that the intrauterine environment shapes developmental trajectories with lasting health implications.
July 2, 2025 at 1:08 PM
The main result: assembly reveals the placenta mediates ~35% of GDM's effect on birth weight, with population-specific CSH1 isoforms contributing. This supports the DOHaD hypothesis that the intrauterine environment shapes developmental trajectories with lasting health implications.
Why? We traced read assignments to show how adding novel transcripts + removing irrelevant ones redistributes reads among gene isoforms. We think this further reduces noise from spurious annotations & improves quantification accuracy, hopefully revealing the true signal.
July 2, 2025 at 1:08 PM
Why? We traced read assignments to show how adding novel transcripts + removing irrelevant ones redistributes reads among gene isoforms. We think this further reduces noise from spurious annotations & improves quantification accuracy, hopefully revealing the true signal.
A key insight enabled by assembly is the improved resolution for detecting transcriptomic changes in pregnancy complications like gestational diabetes. Comparing short-read quantification on our placenta isoforms vs GENCODE showed major differences in differential expression results.
July 2, 2025 at 1:08 PM
A key insight enabled by assembly is the improved resolution for detecting transcriptomic changes in pregnancy complications like gestational diabetes. Comparing short-read quantification on our placenta isoforms vs GENCODE showed major differences in differential expression results.
Important because developing tissues like placenta need tissue-specific references! We found extensive splicing diversity in key pregnancy-related genes (CSH1, GH2) and MS/MS validated novel protein-coding genes. These are missed by adult tissue and aggregate species-level references like GENCODE.
July 2, 2025 at 1:08 PM
Important because developing tissues like placenta need tissue-specific references! We found extensive splicing diversity in key pregnancy-related genes (CSH1, GH2) and MS/MS validated novel protein-coding genes. These are missed by adult tissue and aggregate species-level references like GENCODE.
Transcript (tx) quant with short-read data is notoriously challenging due to mapping ambiguity. Using Salmon & methods from @plbaldoni.bsky.social & @robp.bsky.social, we show how mapping to a tissue-specific reference reduces uncertainty & yields higher tx abundance by removing low-confidence txs.
![(F) Illumina short-read RNA-seq of villous placental tissue—from two independent birth cohort studies with approximately 20% of samples from GDM-affected pregnancies—were quantified against the GENCODE v45 transcript annotations and the high-confidence placenta-specific transcript annotations. Using Salmon113, for each cohort and annotation, the expression E of transcript Tj in sample Si was estimated for Bk bootstrap replicates, where j = 1,…,n transcripts in the given annotation, i = 1,…,n short-read samples, and k = 1,…,50 replicates. Bootstrap replicates were used to estimate overdispersion arising from read-to-transcript mapping ambiguity, which was divided from the counts prior to downstream analyses25, and to quantify inferential relative variance (InfRV), a measure of uncertainty in the read-to-transcript mapping54. (G) The total transcript expression (measured as transcripts per million [TPM]) per sample in each cohort when quantified against the GENCODE v45 annotations or the high-confidence placenta-specific annotations. (H) The mean and variance in the GUSTO short-read samples comparing transcripts that were shared between annotations (i.e., FSM transcripts in placenta), transcripts that were novel in placenta, GENCODE v45 transcripts that were initially recovered in the long-readss but removed in the filtering procedure, and GENCODE v45 transcripts that were not assembled from the long-readss. (I) Transcript-level InfRV in the GUSTO short-read samples when quantified against the GENCODE v45 annotations compared to the placenta-specific annotations, stratified by transcript structural category.](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:j7xbjo5jkgrh23c5jp3knoeo/bafkreidzql3dlo35yth5resbjvto3jua2yrypmedmwr6cmbcmzap2sg5xi@jpeg)
July 2, 2025 at 1:08 PM
Transcript (tx) quant with short-read data is notoriously challenging due to mapping ambiguity. Using Salmon & methods from @plbaldoni.bsky.social & @robp.bsky.social, we show how mapping to a tissue-specific reference reduces uncertainty & yields higher tx abundance by removing low-confidence txs.
With @arjunbhattac.bsky.social & @jonhuang.bsky.social, a collab with @mikelove.bsky.social + others across Singapore, Canada & USA (not on bsky), we found that fetal-facing placentae at term express ~37k isoforms across ~12k genes, 2x that of other tissues in GTEx. Placenta != an "expression void!"
July 2, 2025 at 1:08 PM
With @arjunbhattac.bsky.social & @jonhuang.bsky.social, a collab with @mikelove.bsky.social + others across Singapore, Canada & USA (not on bsky), we found that fetal-facing placentae at term express ~37k isoforms across ~12k genes, 2x that of other tissues in GTEx. Placenta != an "expression void!"
Using a commercial beekeeping technique to induce the development of queens (grafting), whole genome sequencing, mRNA-seq, and ChIP-seq of H3K27me3, H3K27ac, and H3K4me3…
June 18, 2025 at 3:30 PM
Using a commercial beekeeping technique to induce the development of queens (grafting), whole genome sequencing, mRNA-seq, and ChIP-seq of H3K27me3, H3K27ac, and H3K4me3…
Birds-eye view (or gene’s-eye view @arvidagren.bsky.social): honey bee caste differentiation (an extreme example of developmental plasticity, where differences in larval diet result in either sterile workers or reproductive queens) is associated with parent-of-origin intragenomic conflict.
June 18, 2025 at 3:30 PM
Birds-eye view (or gene’s-eye view @arvidagren.bsky.social): honey bee caste differentiation (an extreme example of developmental plasticity, where differences in larval diet result in either sterile workers or reproductive queens) is associated with parent-of-origin intragenomic conflict.
Progress on mine, lol. Been hearing this from others about BMC journals lately. What’s up with that?
May 21, 2025 at 3:50 AM
Progress on mine, lol. Been hearing this from others about BMC journals lately. What’s up with that?
Love is All. Yesterday, one year of marriage with my dearest friend @veronicarichards.bsky.social 🖤
May 4, 2025 at 4:10 PM
Love is All. Yesterday, one year of marriage with my dearest friend @veronicarichards.bsky.social 🖤
“To meet this moment, to survive as a field, and to serve our patients and society, the only way forward is to stand together and speak out continuously and forcefully. We must speak for those who cannot: muzzled colleagues…, vulnerable patient populations, and future generations.”
March 24, 2025 at 3:34 PM
“To meet this moment, to survive as a field, and to serve our patients and society, the only way forward is to stand together and speak out continuously and forcefully. We must speak for those who cannot: muzzled colleagues…, vulnerable patient populations, and future generations.”
Couldn’t focus this afternoon *for some reason* so we burnt off some energy getting the biggest possible stick. A common persimmon - Diospyros virginiana - we unfortunately had to remove to prevent Lola from an obstructed bowel (would not stop eating the fruit, which are ~1% flesh and ~99% seeds!)
January 28, 2025 at 10:59 PM
Couldn’t focus this afternoon *for some reason* so we burnt off some energy getting the biggest possible stick. A common persimmon - Diospyros virginiana - we unfortunately had to remove to prevent Lola from an obstructed bowel (would not stop eating the fruit, which are ~1% flesh and ~99% seeds!)
I lied, she made them
December 26, 2024 at 1:22 AM
I lied, she made them
🎄spending the day with @veronicarichards.bsky.social, making espresso martinis for my family and slipping Lola strips of ham
December 25, 2024 at 8:39 PM
🎄spending the day with @veronicarichards.bsky.social, making espresso martinis for my family and slipping Lola strips of ham
Pathetic! (I love them)
November 30, 2024 at 2:32 PM
Pathetic! (I love them)
Using reciprocal crosses, whole genome sequencing, mRNA-seq, & ChIP-seq, we see that queen and worker-destined honey bee larvae show predictable differences in parent-of-origin gene expression, in addition to parental differences in H3K27me3, H3K27ac & H3K4me3 at these genes.
November 29, 2024 at 1:43 PM
Using reciprocal crosses, whole genome sequencing, mRNA-seq, & ChIP-seq, we see that queen and worker-destined honey bee larvae show predictable differences in parent-of-origin gene expression, in addition to parental differences in H3K27me3, H3K27ac & H3K4me3 at these genes.
Using reciprocal crosses, whole genome sequencing, mRNA-seq, & ChIP-seq, we see that queen and worker-destined honey bee larvae show predictable differences in parent-of-origin gene expression, in addition to parental differences in H3K27me3, H3K27ac & H3K4me3 at these genes.
November 29, 2024 at 1:17 PM
Using reciprocal crosses, whole genome sequencing, mRNA-seq, & ChIP-seq, we see that queen and worker-destined honey bee larvae show predictable differences in parent-of-origin gene expression, in addition to parental differences in H3K27me3, H3K27ac & H3K4me3 at these genes.
I like to post about science, my animal friends, my wife @veronicarichards.bsky.social, and hobbies like DIY projects & rock climbing.
November 28, 2024 at 2:38 PM
I like to post about science, my animal friends, my wife @veronicarichards.bsky.social, and hobbies like DIY projects & rock climbing.
Career milestone reddit.com/r/science/s/... 🧬 #evosky
October 16, 2023 at 10:34 AM
Career milestone reddit.com/r/science/s/... 🧬 #evosky