hammad-farooq.bsky.social - Profile | ThreadSky | a Reddit-style client for Bluesky

Gene-Gene Interactions Between A LMNA Variant and Common Polymorphisms Drive Early-Onset Atrial Fibrillation https://www.medrxiv.org/content/10.1101/2025.05.05.25326834v1

submitted 31 days ago • 0 comments

🚨 New preprint is out! Excited to share our work on how a rare LMNA mutation alters chromatin accessibility at atrial fibrillation–associated loci. We used iPSC-derived cardiomyocytes and CRISPR to study gene regulation in a human disease model. 📄 medrxiv.org/content/10.1101/2025.05.05.25326834v2

submitted 28 days ago • 1 comment

@maxdudek.bsky.social applied a deep learning algorithm to ATAC-seq from 170 livers to measure TF binding at non-coding variants. We show "footprint QTLs" (#fpQTLs) can fine-map causal variants. @ajhgnews.bsky.social @penngenetics.bsky.social @chopresearch.bsky.social www.cell.com/ajhg/abstrac...

submitted 50 days ago • 3 comments

Effects of Lamina-Chromatin Attachment on Super Long-Range Chromatin Interactions https://www.biorxiv.org/content/10.1101/2025.02.13.638183v1

submitted 108 days ago • 0 comments

📢Attending @biophysicalsoc.bsky.social in LA?📢 Excited about uncovering functional links between non-coding regulatory variants and target genes? 🧬 Join me for: 🎤 Flash Talk (#1682) – Feb 18 | 12:30 PM 📊 Poster (#2754-Pos / B218) – Feb 19| 10:30 AM See you there! #BPS25 #Genetics #Epigenetic

submitted 110 days ago • 0 comments

Excited to present the results of my 20% project in collaboration with @broadinstitute.org and @danafarber.bsky.social . In our new paper we demonstrate a long-range model capable of detecting regulatory elements at distances beyond a million base pairs.

submitted 127 days ago • 1 comment

One month to go until the CSHL Biology of Genomes abstract deadline! My all-time fav meeting, and one of the few covering genomics broadly. We have a ✨🤩 lineup of speakers, but it's the abstract talks & posters that really make the meeting - send us your best work! meetings.cshl.edu/meetings.asp...

submitted 143 days ago • 1 comment

How to do differential expression with scRNAseq data? State of the art is "pseudo-bulk" analysis with RNA-seq methods like edgeR or DESeq2, where "cell type" is encoded as discrete categories. Biologically, discrete categories are not always the most appropriate concept.(1/3) doi.org/10.1038/s415...

submitted 154 days ago • 7 comments

1/2 We’re hiring a Postdoc to join us at the University of Copenhagen. Are you fascinated by 3D chromatin function and super-resolution microscopy? Then this might be the job for you. Start date 1st of April 2025, starting salary 4700 Euro/month. Apply here: candidate.hr-manager.net/ApplicationI...

submitted 159 days ago • 1 comment

Boundaries between TADs often extend over considerable distance. But how variable is this width of boundaries? And does it matter? Find out in our new pre-print with the group of David Holcman. www.biorxiv.org/content/10.1...

submitted 162 days ago • 2 comments

Our ChromBPNet preprint out! www.biorxiv.org/content/10.1... Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/

submitted 162 days ago • 8 comments

Check EpiGePT, a breakthrough #Transformer model for human #epigenomics. By using #3Dgenome data & #transcriptionfactor activities, it outshines current models in predicting context-specific signals. A game-changer for unseen cellular contexts! PMID:39696471, Genome Biol 2024 doi.org/10.1186/s130...

submitted 163 days ago • 0 comments

By definition, enhancers can activate from a distance. But with increased distance between enhancer and promoter, the activation drops. To study this systematically, we build a synthetic locus: www.cell.com/molecular-ce... 1/12

submitted 186 days ago • 14 comments

Ever wondered how 3D chromatin rewires during differentiation? We wanted to understand this process better & distinguish if different processes or elements drive this rewiring. To do so, we used mESC=>NPC differentiation and focused on a single locus. biorxiv.org/content/10.110… 1/17

submitted 187 days ago • 3 comments

🔺🔺🔺RED TRIANGLE ALERT 🔺🔺🔺 Ever wonder how #TADs compare across the tree of life?Look no further & read our Review!!! Find out what genes & 3D chromatin can & can't do in Bacteria! Archeae! Yeast! Plants! Animals! SMCs & RNA-Pol are the only thing they have in common www.nature.com/articles/s41...

submitted 190 days ago • 3 comments

Wow, this is a life changing Unix tip. Add the following to your ~/.ssh/config, and now SSH connections are persistent for 3 hours, meaning no 2FA each login (or scp/rsync). Thanks @apoorvalal.com! Host * ControlMaster auto ControlPath ~/.ssh/%r@%h:%p ControlPersist 3h

submitted 191 days ago • 9 comments

bsky.app/profile/did:... A 3D genome feed if anyone is interested

submitted 200 days ago • 0 comments

Excited to share that we are hiring a Bridge to Faculty Postdoc in Microbiology and Immunology at the University of Illinois Chicago. Please reach out if you have any questions about the program. And please share broadly. uic.csod.com/ux/ats/caree...

submitted 193 days ago • 1 comment

That's a great idea!

submitted 193 days ago • 0 comments

We have a new position for a bioinformatician / computational biologist exploring genomic and epigenomic features of #cfDNA to uncover new cancer biology. careers.petermac.org/job/MELBOURN...

submitted 197 days ago • 0 comments

Very interesting paper from @mitchguttman.bsky.social previously in @biorxivpreprint.bsky.social out in Nature Genetics. "ChIP-DIP generates context-specific protein localization maps at consortium scale" www.nature.com/articles/s41...

submitted 193 days ago • 0 comments

📣 Two ERC-funded positions are available in the lab! If you are interested in exploring the mechanisms underlying mutation, we’d love to hear from you. PhD: shorturl.at/Oc04N Postdoc: shorturl.at/1ShHB RPs and shares would be greatly appreciated! 🧪🧬🖥️ #ScienceJobs #PostdocJobs

submitted 193 days ago • 0 comments

In this review @gracebower.bsky.social & I discuss recent evidence showing that, unlike canonical enhancers, long-range enhancers located hundreds of kb from their targets rely on additional mechanisms to ensure robust gene activation during mammal development. www.sciencedirect.com/science/arti...

submitted 196 days ago • 1 comment

If you're interested in a discussion of statistical methodology for comparison of BioML tools, use the #BioMLeval hashtag. This paper linked by Anshul is a great starting point for discussion. It's oriented towards LLMs, but some ideas may be transferable. What benchmarks do you use for BioML?

submitted 196 days ago • 2 comments

Who should you nominate as reviewers for your manuscript? After a long chat with a post-grad it appears that there's a lot of misguided advice out there. Thread 👇

submitted 196 days ago • 18 comments

Clair3-RNA: A deep learning-based small variant caller for long-read RNA sequencing data. #LongReadRNAseq #VariantCalling #DeepLearning #Sequencing #Bioinformatics 🧬 🖥️ www.biorxiv.org/content/10.1...

submitted 198 days ago • 0 comments

Nice to see all you chromatin & epigenetics aficionados here! As we build our network back up please repost details for our upcoming webinar this Friday! We are delighted to welcome Emma Farley for her webinar 'Dependency Grammar of Developmental Enhancers' on November 22nd. Registration below 👇

submitted 199 days ago • 2 comments

Hey, a question for the genetics community. Does genetic fine-mapping work well? How often does it miss? We usually find that most fine-mapped variants do not fall within coding or regulatory regions. Is it a limitation of epigenomics or a limitation of fine-mapping? Please share your thoughts!

submitted 199 days ago • 9 comments

Hello 🦋 #protein / #microbio / #BioML community! We are excited to release Gaia🌎, a context-aware protein search tool, extending protein search and discovery capabilities beyond sequence and structure, to include genomic context. Search your favorite protein sequences with on gaia.tatta.bio

submitted 199 days ago • 10 comments

My app for finding 🦋 accounts you may want to follow has had a make-over: it now displays names and bios, and allows adding an "app password" for direct follow buttons in the listing bsky-follow-finder.theo.io

submitted 206 days ago • 102 comments

Interested in #singlecell and #spatial #metabolomics? Then book your calendar for December 10th! – Our online, free event will summarize major achievements of the field in 2024. #metabolism #omics #MALDI #EPFL With Giovanni D'Angelo and our #PhD students we prepared for you a fantastic lineup. 🧵 1/5

submitted 199 days ago • 2 comments

My goal is to understand the regulatory role of every nucleotide in the genome, and how this changes across every cell in the human body. If you are interested in doing a Ph.D. with me at UMass Chan Medical (Genomics and Comp Bio Department), see the links below. Deadline is Dec 1st.

submitted 200 days ago • 6 comments

Mechanistic interpretability on a protein language model www.biorxiv.org/content/10.1...

submitted 200 days ago • 1 comment

The fantastic Machine Learning in CompBio #MLCB2024 papers are up at proceedings.mlr.press/v261/! Reminder that all the talks are available on our yt channel www.youtube.com/@mlcbconf. Please RP!

submitted 200 days ago • 0 comments

We strongly suggest that academic publishers and other platforms that host research rapidly implement a Share to Bluesky button for their articles. Here's how: docs.bsky.app/docs/advance... #AcademicSky #HigherEd #Altmetrics

submitted 200 days ago • 173 comments

Thrilled to announce Boltz-1, the first open-source and commercially available model to achieve AlphaFold3-level accuracy on biomolecular structure prediction! An exciting collaboration with Jeremy, Saro, and an amazing team at MIT and Genesis Therapeutics. A thread!

submitted 201 days ago • 18 comments

Leonid Mirny and I wrote this for all interested in chromosomes: "The chromosome folding problem and how cells solve it" www.cell.com/action/showP...

submitted 204 days ago • 0 comments

Follow leading researchers, practitioners, and thought leaders exploring the intersection of #AI, machine learning, data science, and scientific research. 🦋 ➕We are just getting started, please send me others who should be added go.bsky.app/JeFdryY #ML

submitted 203 days ago • 42 comments

Just found a custom feed where you can follow posts that people you follow liked! Wish there was an option to merge some of these custom lists some day

submitted 202 days ago • 1 comment