Hammad Farooq
@hammad-farooq.bsky.social
Bioinformatics PhD Candidate at University of Illinois Chicago | 3D genome folding | Human genetics
https://hammadfarooq.github.io
https://hammadfarooq.github.io
Pinned
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
📌 Epigenetics Poster (Poster #8041F)
📅 Fri, Oct 17 | 2:30–4:30 PM EDT
#Genomics #Genetics #Epigenetics #3DGenome
Reposted by 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...
October 17, 2025 at 2:56 PM
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...
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
If you’ll be at #ASHG2025, I’d love to connect and chat!
#Genetics #Bioinformatics
October 14, 2025 at 10:41 AM
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
📌 Epigenetics Poster (Poster #8041F)
📅 Fri, Oct 17 | 2:30–4:30 PM EDT
#Genomics #Genetics #Epigenetics #3DGenome
October 14, 2025 at 10:41 AM
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
📌 Epigenetics Poster (Poster #8041F)
📅 Fri, Oct 17 | 2:30–4:30 PM EDT
#Genomics #Genetics #Epigenetics #3DGenome
October 8, 2025 at 12:38 AM
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
📌 Epigenetics Poster (Poster #8041F)
📅 Fri, Oct 17 | 2:30–4:30 PM EDT
#Genomics #Genetics #Epigenetics #3DGenome
Reposted by Hammad Farooq
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...
I know of earlier single-locus papers (1982).
www.sciencedirect.com/science/arti...
September 21, 2025 at 6:54 PM
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...
I know of earlier single-locus papers (1982).
www.sciencedirect.com/science/arti...
Reposted by Hammad Farooq
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/...
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...
www.science.org
September 19, 2025 at 6:20 AM
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/...
Reposted by Hammad Farooq
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...
👇
1/
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...
👇
1/
September 19, 2025 at 3:03 AM
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...
👇
1/
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...
👇
1/
Reposted by Hammad Farooq
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...
August 18, 2025 at 12:23 PM
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...
Reposted by Hammad Farooq
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...
A 3D genome compendium of breast cancer progression
Genomics; Chromosome organization; Molecular Genetics; Cancer
www.cell.com
August 18, 2025 at 2:41 PM
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...
Reposted by Hammad Farooq
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
May 6, 2025 at 1:56 AM
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
🚨 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
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
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 ...
medrxiv.org
May 9, 2025 at 3:04 AM
🚨 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
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
Reposted by Hammad Farooq
@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...
www.cell.com/ajhg/abstrac...
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...
www.cell.com
April 17, 2025 at 3:05 PM
@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...
www.cell.com/ajhg/abstrac...
Reposted by Hammad Farooq
Effects of Lamina-Chromatin Attachment on Super Long-Range Chromatin Interactions https://www.biorxiv.org/content/10.1101/2025.02.13.638183v1
February 18, 2025 at 4:33 AM
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
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
February 16, 2025 at 4:58 PM
📢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
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
Reposted by Hammad Farooq
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.
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...
www.cell.com
January 30, 2025 at 4:51 PM
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.
Reposted by Hammad Farooq
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...
January 14, 2025 at 1:57 PM
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...
Reposted by Hammad Farooq
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...
doi.org/10.1038/s415...
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 ...
doi.org
January 3, 2025 at 7:18 PM
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...
doi.org/10.1038/s415...
Reposted by Hammad Farooq
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...
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
media.tenor.com
December 29, 2024 at 8:46 PM
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...
Reposted by Hammad Farooq
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...
December 26, 2024 at 12:10 PM
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...
Reposted by Hammad Farooq
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/
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/
December 25, 2024 at 11:48 PM
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/
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/
Reposted by Hammad Farooq
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...
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...
doi.org
December 25, 2024 at 5:27 AM
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...
Reposted by Hammad Farooq
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
Redirecting
doi.org
December 2, 2024 at 4:44 PM
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
Reposted by Hammad Farooq
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
https://biorxiv.org/content/10.110…
December 1, 2024 at 2:55 PM
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
Reposted by Hammad Farooq
🔺🔺🔺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...
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...
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...
www.nature.com
November 28, 2024 at 12:48 PM
🔺🔺🔺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...
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...