Hammad Farooq

We're looking for an instructor for the algorithms course in our Bioinformatics MS program. The course assets have already been made (by me) and used in several previous offerings, but we need an instructor! If you're in the DMV area, check it out: www.linkedin.com/posts/robert...

#ASHG25

#ASHG25

Thanks for this. I've scheduled a slot with you. Looking forward to it.

As I wrap up my PhD, I’m exploring postdoctoral and industry research opportunities at the intersection of regulatory genomics and machine learning.
If you’ll be at #ASHG2025, I’d love to connect and chat!
#Genetics #Bioinformatics

Excited to present my poster, “A 3D Genome Framework for Causal Variant Fine-Mapping and Tissue-Specific Gene Regulation,” at @geneticssociety.bsky.social #ASHG2025 in Boston!

📌 Epigenetics Poster (Poster #8041F)
📅 Fri, Oct 17 | 2:30–4:30 PM EDT

#Genomics #Genetics #Epigenetics #3DGenome

Asking BlueSky for help: For a review, I am trying to accurately credit the first paper that measured pairwise 3D distances between 2 pieces of DNA on the same chromosome (or cosmid). Is Trask 1989 the first?
I know of earlier single-locus papers (1982).
www.sciencedirect.com/science/arti...

Kinetic organization of the genome revealed by ultraresolution multiscale live imaging Genome function requires regulated genome motion. However, tools to directly observe this motion in vivo have been limited in coverage and resolution. Here we introduce an approach to tile mammalian c...

Congrats to my friends in the Boettiger lab for this really beautiful live imaging work. A big leap forward in understanding the dynamic side of genome organization. www.science.org/doi/10.1126/...

bioRxiv - An unbiased survey of distal element-gene regulatory interactions with direct-capture targeted Perturb-seq

New preprint from our lab!

What can we learn about the properties of gene regulatory elements by CRISPR’ing a random set of accessible sites in human cells?

Find out here: www.biorxiv.org/content/10.1...

👇

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Activity of most genes is controlled by multiple enhancers, but is there activation coordinated? We leveraged Nanopore to identify a specific set of elements that are simultaneously accessible on the same DNA molecules and are coordinated in their activation. www.biorxiv.org/content/10.1...

I'd love to be added! I work on computational methods for 3D regulatory genomics.

A 3D genome compendium of breast cancer progression Genomics; Chromosome organization; Molecular Genetics; Cancer

We all know that cancers -even from the same subtype- are highly heterogeneous right? In a new study we asked whether this was also the case for the three-dimensional organization of the genome in breast cancer. The answer: it’s complicated. www.cell.com/iscience/ful...

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

Our study shows how combining chromatin profiling, CRISPR-based functional assays, and large-scale biobank data can advance our understanding of genetic risk in atrial fibrillation.
#AFib #LMNA #iPSC #Genomics #Preprint #RegulatoryGenomics #3DGenomics #AtrialFibrillation #Cardiogenomics

We applied a polygenic risk score (PRS) for AF to carriers of rare LMNA variants in UK Biobank and All of Us. Those with a high PRS had 2x higher risk of early-onset AF. This shows the value of combining rare and common variants in risk prediction. #Genomics #PRS

Gene-Gene Interactions Between A LMNA Variant and Common Polymorphisms Drive Early-Onset Atrial Fibrillation Atrial fibrillation (AF) is a common arrhythmia with a complex genetic basis, yet the molecular mechanisms linking rare and common variants remain unclear. Using induced pluripotent stem cell-derived ...

🚨 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

Congrats! Awesome news!

Characterization of non-coding variants associated with transcription-factor binding through ATAC-seq-defined footprint QTLs in liver Dudek et al. use chromatin accessibility data in liver from 170 human donors to measure transcription factor binding at genetic variants. They observed 809 variants associated with binding. Given bind...

@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...

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

📢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

A multi-modal transformer for cell type-agnostic regulatory predictions Javed and Weingarten et al. created a multi-modal transformer that learns generalizable representations of genomic sequence and chromatin accessibility by utilizing a novel masked-accessibility pre-tr...

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.

Topics: Population Genomics Evolutionary & Non-human Genomics Cancer Genomics Computational & Statistical Genomics Complex Traits & Genomic Medicine Functional Genomics Emerging Methods & Technologies Keynote Speakers: Steve McCarroll, Broad Institute of MIT and Harvard Trisha Wittkopp, University of Michigan Discussion Leaders: Nadav Ahituv, University of California, San Francisco Gemma Carvill, Northwestern University Nancy Chen, University of Rochester Gilad Evrony, New York University Simon Gravel, McGill University, Canada Stephanie Hicks, Johns Hopkins University Nada Jabado, McGill University, Canada Andrew Kern, University of Oregon Nicholas Mancuso, University of Southern California Sara Mostafavi, University of Washington Nicholas Navin, MD Anderson Cancer Center Soumya Raychaudhuri, Broad Institute of MIT and Harvard Gloria Sheynkman, University of Virginia School of Medicine Peter Sudmant, University of California, Berkeley

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...

Analysis of multi-condition single-cell data with latent embedding multivariate regression - Nature Genetics Latent embedding multivariate regression models multi-condition single-cell RNA-seq using a continuous latent space, enabling data integration, per-cell gene expression prediction and clustering-free ...

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...

a green background with red circles and a green circle in the middle ALT: a green background with red circles and a green circle in the middle

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...

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...

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/

EpiGePT: a pretrained transformer-based language model for context-specific human epigenomics - Genome Biology The inherent similarities between natural language and biological sequences have inspired the use of large language models in genomics, but current models struggle to incorporate chromatin interaction...

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...

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

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

Evolution and function of chromatin domains across the tree of life - Nature Structural & Molecular Biology Szalay et al. discuss cross-kingdom similarities and differences in 3D chromatin folding in relation to gene regulation, including in bacteria, archaea, mammals and plants. This comparison reveals cer...

🔺🔺🔺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...