Conor Kelly
@conorkelly.bsky.social
PhD candidate at UW Genome Sciences in the Beliveau lab | chromatin biology, gene regulation, & tool development | he/him 🏳️🌈
Reposted by Conor Kelly
Fantastic project led by @bo-wen.bsky.social. Excited to see the future uses of AI and transfer learning in proteomics. #massspec #proteomics
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Carafe enables high quality in silico spectral library generation for data-independent acquisition proteomics - Nature Communications
Accurate spectral libraries are essential for analyzing data-independent acquisition (DIA) proteomics data. Here, the authors present Carafe, which trains on DIA data to build experiment-specific spec...
www.nature.com
November 6, 2025 at 3:49 PM
Fantastic project led by @bo-wen.bsky.social. Excited to see the future uses of AI and transfer learning in proteomics. #massspec #proteomics
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Conor Kelly
Announcing such a major change to NSF GRFP this late in the cycle is incredibly cruel. 2nd yr students (mine included) have been working so hard on their proposals despite ongoing uncertainty. They are driven and passionate about being outstanding scientists and helping those coming up behind them.
September 26, 2025 at 5:46 PM
Announcing such a major change to NSF GRFP this late in the cycle is incredibly cruel. 2nd yr students (mine included) have been working so hard on their proposals despite ongoing uncertainty. They are driven and passionate about being outstanding scientists and helping those coming up behind them.
Reposted by Conor Kelly
Are you bravely deciding to do a postdoc in the US? And also interested in some combination of genomics, immunology, and transposons? If so, consider applying to my lab at the BioFrontiers Institute in Boulder, Colorado!
jobs.colorado.edu/jobs/JobDeta...
🧪🧬 #TESky #interferosky
jobs.colorado.edu/jobs/JobDeta...
🧪🧬 #TESky #interferosky
July 17, 2025 at 7:36 PM
Are you bravely deciding to do a postdoc in the US? And also interested in some combination of genomics, immunology, and transposons? If so, consider applying to my lab at the BioFrontiers Institute in Boulder, Colorado!
jobs.colorado.edu/jobs/JobDeta...
🧪🧬 #TESky #interferosky
jobs.colorado.edu/jobs/JobDeta...
🧪🧬 #TESky #interferosky
Reposted by Conor Kelly
Hello! Ever wonder what's "talking to" your favorite transcript, but were too scared to ask? In our review in @cp-cellreports.bsky.social, @mardakheh.bsky.social and I highlight new RNA-focused tools for discovering RNA interactions across organizational scales. Checkit!
tinyurl.com/ydn6e3ac
tinyurl.com/ydn6e3ac
June 30, 2025 at 9:15 PM
Hello! Ever wonder what's "talking to" your favorite transcript, but were too scared to ask? In our review in @cp-cellreports.bsky.social, @mardakheh.bsky.social and I highlight new RNA-focused tools for discovering RNA interactions across organizational scales. Checkit!
tinyurl.com/ydn6e3ac
tinyurl.com/ydn6e3ac
Reposted by Conor Kelly
Today, NSF added another 500 GRFP awardees, bringing this year’s total to 1500
www.research.gov/grfp/Awardee...
www.research.gov/grfp/Awardee...
June 13, 2025 at 3:43 PM
Today, NSF added another 500 GRFP awardees, bringing this year’s total to 1500
www.research.gov/grfp/Awardee...
www.research.gov/grfp/Awardee...
Reposted by Conor Kelly
💥🥳 At long last, our latest paper is out!
Gag proteins of endogenous retroviruses are required for zebrafish development
www.pnas.org/doi/10.1073/...
Led heroically by Sylvia Chang & @jonowells.bsky.social
A study which has changed the way I think of #transposons! No less! 🧵 1/n
Gag proteins of endogenous retroviruses are required for zebrafish development
www.pnas.org/doi/10.1073/...
Led heroically by Sylvia Chang & @jonowells.bsky.social
A study which has changed the way I think of #transposons! No less! 🧵 1/n
Gag proteins encoded by endogenous retroviruses are required for zebrafish development | PNAS
Transposable elements (TEs) make up the bulk of eukaryotic genomes and examples abound
of TE-derived sequences repurposed for organismal function. ...
www.pnas.org
April 30, 2025 at 10:45 AM
💥🥳 At long last, our latest paper is out!
Gag proteins of endogenous retroviruses are required for zebrafish development
www.pnas.org/doi/10.1073/...
Led heroically by Sylvia Chang & @jonowells.bsky.social
A study which has changed the way I think of #transposons! No less! 🧵 1/n
Gag proteins of endogenous retroviruses are required for zebrafish development
www.pnas.org/doi/10.1073/...
Led heroically by Sylvia Chang & @jonowells.bsky.social
A study which has changed the way I think of #transposons! No less! 🧵 1/n
Reposted by Conor Kelly
🚨 Preprint alert 🚨
Excited to share our work on "Ab-trapping," an antibody artifact causing misleading peripheral ("rim") staining in imaging & genomics (IF, CUT&Tag, CUT&RUN). Antibodies fail to penetrate structures, accumulating at the periphery. A 🧵👇
doi.org/10.1101/2025...
Excited to share our work on "Ab-trapping," an antibody artifact causing misleading peripheral ("rim") staining in imaging & genomics (IF, CUT&Tag, CUT&RUN). Antibodies fail to penetrate structures, accumulating at the periphery. A 🧵👇
doi.org/10.1101/2025...
Ab-trapping - a peripheral staining artifact in antibody-based microscopy and genomics
Antibodies (Ab) are essential for detecting specific epitopes in microscopy and genomics, but can produce artifacts leading to erroneous interpretations. Here, we characterize a novel artifact, Ab-tra...
doi.org
April 14, 2025 at 8:08 PM
🚨 Preprint alert 🚨
Excited to share our work on "Ab-trapping," an antibody artifact causing misleading peripheral ("rim") staining in imaging & genomics (IF, CUT&Tag, CUT&RUN). Antibodies fail to penetrate structures, accumulating at the periphery. A 🧵👇
doi.org/10.1101/2025...
Excited to share our work on "Ab-trapping," an antibody artifact causing misleading peripheral ("rim") staining in imaging & genomics (IF, CUT&Tag, CUT&RUN). Antibodies fail to penetrate structures, accumulating at the periphery. A 🧵👇
doi.org/10.1101/2025...
Reposted by Conor Kelly
Congratulations to Abby McGee and Val Browning on being awarded NSF Fellowships, and to Matt Chaw, Marazzano Colon, Bria Metzger, Rachel Powell, and Catherine Sniezek on receiving honorable mention!
April 8, 2025 at 11:11 PM
Congratulations to Abby McGee and Val Browning on being awarded NSF Fellowships, and to Matt Chaw, Marazzano Colon, Bria Metzger, Rachel Powell, and Catherine Sniezek on receiving honorable mention!
Reposted by Conor Kelly
🧪 NSF GRFP update!
New graduate NSF fellowships will likely be announced this week for the GRFP (see bottom of 🧵 for why).
First off, I'm *very* glad to hear of those going forward, given the otherwise bleak year so far for graduate training.
Some observations... 1/12
New graduate NSF fellowships will likely be announced this week for the GRFP (see bottom of 🧵 for why).
First off, I'm *very* glad to hear of those going forward, given the otherwise bleak year so far for graduate training.
Some observations... 1/12
March 31, 2025 at 12:32 AM
🧪 NSF GRFP update!
New graduate NSF fellowships will likely be announced this week for the GRFP (see bottom of 🧵 for why).
First off, I'm *very* glad to hear of those going forward, given the otherwise bleak year so far for graduate training.
Some observations... 1/12
New graduate NSF fellowships will likely be announced this week for the GRFP (see bottom of 🧵 for why).
First off, I'm *very* glad to hear of those going forward, given the otherwise bleak year so far for graduate training.
Some observations... 1/12
Reposted by Conor Kelly
We're so thrilled to finally share with you the published version of our CUT&Tag optimization and benchmarking paper "CUT&Tag recovers up to half of ENCODE ChIP-seq histone acetylation peaks" - out in @naturecomms.bsky.social today: www.nature.com/articles/s41...
CUT&Tag recovers up to half of ENCODE ChIP-seq histone acetylation peaks - Nature Communications
Cleavage Under Targets & Tagmentation is a rapidly expanding technique, but thorough evaluation and benchmarking against established ChIP-seq datasets are required. This study shows that CUT&T...
www.nature.com
March 27, 2025 at 11:16 AM
We're so thrilled to finally share with you the published version of our CUT&Tag optimization and benchmarking paper "CUT&Tag recovers up to half of ENCODE ChIP-seq histone acetylation peaks" - out in @naturecomms.bsky.social today: www.nature.com/articles/s41...
Reposted by Conor Kelly
Here is the peer-reviewed version of our study showing how some TAD borders are essential for gene regulation and development.
Loss of a single CTCF motif is sufficient to cause embryonic lethality.
www.sciencedirect.com/science/arti...
Loss of a single CTCF motif is sufficient to cause embryonic lethality.
www.sciencedirect.com/science/arti...
Deletion of a single CTCF motif at the boundary of a chromatin domain with three FGF genes disrupts gene expression and embryonic development
Chromatin domains delimited by CTCF can restrict the range of enhancer action. However, disruption of some domain boundaries results in mild gene dysr…
www.sciencedirect.com
February 26, 2025 at 9:22 PM
Here is the peer-reviewed version of our study showing how some TAD borders are essential for gene regulation and development.
Loss of a single CTCF motif is sufficient to cause embryonic lethality.
www.sciencedirect.com/science/arti...
Loss of a single CTCF motif is sufficient to cause embryonic lethality.
www.sciencedirect.com/science/arti...
Reposted by Conor Kelly
😡 F'ing ridiculous. After updating its FAQ yesterday, NSF refused to directly answer a simple question:
"Will the NSF Graduate Research Fellowship Program (GRFP) continue to award fellowships in 2025?"
GRFPs are a lifeline that support 2,000+ graduate students/year.
www.nsf.gov/executive-or...
"Will the NSF Graduate Research Fellowship Program (GRFP) continue to award fellowships in 2025?"
GRFPs are a lifeline that support 2,000+ graduate students/year.
www.nsf.gov/executive-or...
February 22, 2025 at 7:33 PM
😡 F'ing ridiculous. After updating its FAQ yesterday, NSF refused to directly answer a simple question:
"Will the NSF Graduate Research Fellowship Program (GRFP) continue to award fellowships in 2025?"
GRFPs are a lifeline that support 2,000+ graduate students/year.
www.nsf.gov/executive-or...
"Will the NSF Graduate Research Fellowship Program (GRFP) continue to award fellowships in 2025?"
GRFPs are a lifeline that support 2,000+ graduate students/year.
www.nsf.gov/executive-or...
Reposted by Conor Kelly
Our new review on how the #chromatin domain is formed in the cell is now available @Curr Opin Struct Biol.📄✨
We critically discuss the domain formation mechanism from a physical perspective, including #phase-separation and #condensation.
📥 Free-download link:
authors.elsevier.com/a/1keGn,LqAr...
We critically discuss the domain formation mechanism from a physical perspective, including #phase-separation and #condensation.
📥 Free-download link:
authors.elsevier.com/a/1keGn,LqAr...
February 20, 2025 at 11:15 AM
Our new review on how the #chromatin domain is formed in the cell is now available @Curr Opin Struct Biol.📄✨
We critically discuss the domain formation mechanism from a physical perspective, including #phase-separation and #condensation.
📥 Free-download link:
authors.elsevier.com/a/1keGn,LqAr...
We critically discuss the domain formation mechanism from a physical perspective, including #phase-separation and #condensation.
📥 Free-download link:
authors.elsevier.com/a/1keGn,LqAr...
Reposted by Conor Kelly
@science.org RNA polymerase II at histone genes predicts outcome in human cancer 🧬💊 @fredhutch.bsky.social @hhmi.bsky.social www.science.org/doi/10.1126/...
February 16, 2025 at 11:25 PM
@science.org RNA polymerase II at histone genes predicts outcome in human cancer 🧬💊 @fredhutch.bsky.social @hhmi.bsky.social www.science.org/doi/10.1126/...
Reposted by Conor Kelly
Hello Bluesky from UW Genome Sciences! We're happy to join other members of our department over here bsky.app/starter-pack... .
bsky.app
January 22, 2025 at 4:49 PM
Hello Bluesky from UW Genome Sciences! We're happy to join other members of our department over here bsky.app/starter-pack... .
Reposted by Conor Kelly
Very excited to share our paper on Gene and Transposable Element expression in mammalian preimplantation development, online today! www.cell.com/cell/fulltex...
A short thread to highlight some of our findings 🧵
A short thread to highlight some of our findings 🧵
January 20, 2025 at 8:29 PM
Very excited to share our paper on Gene and Transposable Element expression in mammalian preimplantation development, online today! www.cell.com/cell/fulltex...
A short thread to highlight some of our findings 🧵
A short thread to highlight some of our findings 🧵
Reposted by Conor Kelly
Excited to share James Jusuf's preprint:
By integrating Micro-C with SuperRes Live-Imaging we can calibrate genomics&imaging to perform absolute quantification of looping (e.g. this loop is present 3%)
We quantify mESC 36k loops: are generally rare (2.3%)
www.biorxiv.org/content/10.1...
By integrating Micro-C with SuperRes Live-Imaging we can calibrate genomics&imaging to perform absolute quantification of looping (e.g. this loop is present 3%)
We quantify mESC 36k loops:
www.biorxiv.org/content/10.1...
January 16, 2025 at 1:35 PM
Excited to share James Jusuf's preprint:
By integrating Micro-C with SuperRes Live-Imaging we can calibrate genomics&imaging to perform absolute quantification of looping (e.g. this loop is present 3%)
We quantify mESC 36k loops: are generally rare (2.3%)
www.biorxiv.org/content/10.1...
By integrating Micro-C with SuperRes Live-Imaging we can calibrate genomics&imaging to perform absolute quantification of looping (e.g. this loop is present 3%)
We quantify mESC 36k loops:
www.biorxiv.org/content/10.1...
Reposted by Conor Kelly
How proximal is proximity labeling❓ Using DNA nanorulers we found that TurboID/BioID are largely contact labeling, while APEX2 also bears a major contact labeling pathway in parallel with diffusive labeling.
www.biorxiv.org/content/10.1...
Special thanks to @aliceyting.bsky.social for discussions
www.biorxiv.org/content/10.1...
Special thanks to @aliceyting.bsky.social for discussions
December 19, 2024 at 2:22 AM
How proximal is proximity labeling❓ Using DNA nanorulers we found that TurboID/BioID are largely contact labeling, while APEX2 also bears a major contact labeling pathway in parallel with diffusive labeling.
www.biorxiv.org/content/10.1...
Special thanks to @aliceyting.bsky.social for discussions
www.biorxiv.org/content/10.1...
Special thanks to @aliceyting.bsky.social for discussions
Reposted by Conor Kelly
This work just out in Science Advances by Tom Sexton’s lab (to which Mariano Barbieri from our lab contributed modeling data) is a thorough demonstration of how extrusion- and transcription-centric interactions are predominantly antagonistic. Must read!
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Transcription processes compete with loop extrusion to homogenize promoter and enhancer dynamics
Gene promoters and enhancers share the same constrained mobilities during transcription, opposing cohesin-mediated loop extrusion.
www.science.org
December 14, 2024 at 9:23 AM
This work just out in Science Advances by Tom Sexton’s lab (to which Mariano Barbieri from our lab contributed modeling data) is a thorough demonstration of how extrusion- and transcription-centric interactions are predominantly antagonistic. Must read!
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Conor Kelly
I’m excited to share our latest study led by @giuliapasquesi.bsky.social out today in @cellpress.bsky.social , uncovering a new way transposons have been repurposed for human interferon signaling! Read on for a thread on cryptic splice variants, decoy receptors, and viruses (1/N) 👇🧵 #TESky 🧪
Regulation of human interferon signaling by transposon exonization
Transposable element exonization can yield functional protein isoforms as seen for primate-specific IFNAR2.
www.cell.com
December 12, 2024 at 6:57 PM
I’m excited to share our latest study led by @giuliapasquesi.bsky.social out today in @cellpress.bsky.social , uncovering a new way transposons have been repurposed for human interferon signaling! Read on for a thread on cryptic splice variants, decoy receptors, and viruses (1/N) 👇🧵 #TESky 🧪
Reposted by Conor Kelly
Imagine a mouse in which all 10 billion cells keep a diary from fertilization. Imagine sentinel cells recording your experiences and sending out dispatches in the form of DNA. Here's a story I wrote about cell recorders 🧪 Gift link: nyti.ms/3Z3Mqza
‘DNA Typewriters’ Can Record a Cell’s History
Labs around the world are trying to turn cells into autobiographers, tracking their own development from embryos to adults.
nyti.ms
November 25, 2024 at 4:19 PM
Imagine a mouse in which all 10 billion cells keep a diary from fertilization. Imagine sentinel cells recording your experiences and sending out dispatches in the form of DNA. Here's a story I wrote about cell recorders 🧪 Gift link: nyti.ms/3Z3Mqza
Reposted by Conor Kelly
It's my great pleasure to present the next big preprint from SheqLab! An exciting application of our O-MAP platform that I hope will transform the study of nuclear architecture.
If you've ever wanted to dissect the subnuclear "neighborhood" around an individual locus, read on! (1/30)
If you've ever wanted to dissect the subnuclear "neighborhood" around an individual locus, read on! (1/30)
November 21, 2024 at 1:27 AM
It's my great pleasure to present the next big preprint from SheqLab! An exciting application of our O-MAP platform that I hope will transform the study of nuclear architecture.
If you've ever wanted to dissect the subnuclear "neighborhood" around an individual locus, read on! (1/30)
If you've ever wanted to dissect the subnuclear "neighborhood" around an individual locus, read on! (1/30)
Reposted by Conor Kelly
I made a starter pack of folks affiliated with UW Genome Sciences (past and present)
go.bsky.app/L8RAbiJ
It's fairly sparse for now, so please let me know if you'd like to be added!
go.bsky.app/L8RAbiJ
It's fairly sparse for now, so please let me know if you'd like to be added!
UW Genome Sciences
Join the conversation
go.bsky.app
November 8, 2024 at 10:24 PM
I made a starter pack of folks affiliated with UW Genome Sciences (past and present)
go.bsky.app/L8RAbiJ
It's fairly sparse for now, so please let me know if you'd like to be added!
go.bsky.app/L8RAbiJ
It's fairly sparse for now, so please let me know if you'd like to be added!
Reposted by Conor Kelly
"Dark TFs": new manuscript mapped 166 uncharacterized human transcription factors, finding half bind genomic "dark matter," often closed chromatin rich in transposable elements.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
November 19, 2024 at 11:41 PM
"Dark TFs": new manuscript mapped 166 uncharacterized human transcription factors, finding half bind genomic "dark matter," often closed chromatin rich in transposable elements.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Conor Kelly
The pSABER paper is now online!
pSABER is a new method for amplifying in situ hybridization signals
This work was driven by Sahar Attar and co-led by Ram Akliesh ([at] podocytes on the other app) with help from @shechnerlab.bsky.social @dschweppe.bsky.social
doi.org/10.1038/s415...
🧵 1/12
pSABER is a new method for amplifying in situ hybridization signals
This work was driven by Sahar Attar and co-led by Ram Akliesh ([at] podocytes on the other app) with help from @shechnerlab.bsky.social @dschweppe.bsky.social
doi.org/10.1038/s415...
🧵 1/12
Efficient and highly amplified imaging of nucleic acid targets in cellular and histopathological samples with pSABER - Nature Methods
pSABER combines the power of signal amplification by exchange reaction (SABER) with the deposition of fluorescent or colorimetric substrates by horseradish peroxidase to enable enhanced signals for in...
doi.org
November 15, 2024 at 10:27 PM
The pSABER paper is now online!
pSABER is a new method for amplifying in situ hybridization signals
This work was driven by Sahar Attar and co-led by Ram Akliesh ([at] podocytes on the other app) with help from @shechnerlab.bsky.social @dschweppe.bsky.social
doi.org/10.1038/s415...
🧵 1/12
pSABER is a new method for amplifying in situ hybridization signals
This work was driven by Sahar Attar and co-led by Ram Akliesh ([at] podocytes on the other app) with help from @shechnerlab.bsky.social @dschweppe.bsky.social
doi.org/10.1038/s415...
🧵 1/12