Gamze Gürsoy
@gamzeandgursoy.bsky.social
Herbert Irving Assistant Professor of Biomedical Informatics at Columbia University; Core Faculty Member at New York Genome Center (she/her)
g2lab.org
g2lab.org
Reposted by Gamze Gürsoy
Big congratulations to @luisasantus.bsky.social for winning one of the awards for good open data management in her research. 👏🎊
Luisa is currently visiting @gamzeandgursoy.bsky.social lab at @columbiauniversity.bsky.social during her PhD in Cedric Notredame's Lab at @crg.eu
#OAWeek2025
Luisa is currently visiting @gamzeandgursoy.bsky.social lab at @columbiauniversity.bsky.social during her PhD in Cedric Notredame's Lab at @crg.eu
#OAWeek2025
#OAWeek2025
Després, s’entregaran els premis a la bona gestió en obert de les seves dades de recerca als tres estudiants de doctorat premiats aquest 2025. Luisa Santus (@melisupf.bsky.social) i Recep Oguz Araz i Benno Weck-Hufnagel (@enginyeria-upf.bsky.social)
ℹ️ tuit.cat/PQn0M
Després, s’entregaran els premis a la bona gestió en obert de les seves dades de recerca als tres estudiants de doctorat premiats aquest 2025. Luisa Santus (@melisupf.bsky.social) i Recep Oguz Araz i Benno Weck-Hufnagel (@enginyeria-upf.bsky.social)
ℹ️ tuit.cat/PQn0M
October 20, 2025 at 8:13 AM
Big congratulations to @luisasantus.bsky.social for winning one of the awards for good open data management in her research. 👏🎊
Luisa is currently visiting @gamzeandgursoy.bsky.social lab at @columbiauniversity.bsky.social during her PhD in Cedric Notredame's Lab at @crg.eu
#OAWeek2025
Luisa is currently visiting @gamzeandgursoy.bsky.social lab at @columbiauniversity.bsky.social during her PhD in Cedric Notredame's Lab at @crg.eu
#OAWeek2025
Excited to share that our paper that was accepted to #CHIL2025 "KEEP: Integrating Medical Ontologies with Clinical Data for
Robust Code Embeddings" is now available at PMLR: raw.githubusercontent.com/mlresearch/v...
Robust Code Embeddings" is now available at PMLR: raw.githubusercontent.com/mlresearch/v...
August 4, 2025 at 1:32 PM
Excited to share that our paper that was accepted to #CHIL2025 "KEEP: Integrating Medical Ontologies with Clinical Data for
Robust Code Embeddings" is now available at PMLR: raw.githubusercontent.com/mlresearch/v...
Robust Code Embeddings" is now available at PMLR: raw.githubusercontent.com/mlresearch/v...
Super excited to share the first 3D genome paper from my lab @narjournal.bsky.social , led by my smart and hardworking student Carlos (joint with @LuLaboratory) with assists from a brilliant summer intern Narjis. (1/n) academic.oup.com/nar/article/...
pC-SAC: A method for high-resolution 3D genome reconstruction from low-resolution Hi-C data
Abstract. The three-dimensional (3D) organization of the genome is crucial for gene regulation, with disruptions linked to various diseases. High-throughpu
academic.oup.com
April 14, 2025 at 5:02 PM
Super excited to share the first 3D genome paper from my lab @narjournal.bsky.social , led by my smart and hardworking student Carlos (joint with @LuLaboratory) with assists from a brilliant summer intern Narjis. (1/n) academic.oup.com/nar/article/...
super excited to share the newest from my lab: a tool that can securely process RNA-seq reads to quantify gene expression. Huge congrats to the dream team Seungwan, @BioConorWalker, and Annie! We developed a new gene expression quantification algorithm 1/2 www.nature.com/articles/s41...
Secure and scalable gene expression quantification with pQuant - Nature Communications
RNA-seq data can expose private genotypes during computation. Here, the authors present pQuant, a privacy-preserving tool that uses homomorphic encryption to quantify gene expression securely, achievi...
www.nature.com
March 10, 2025 at 8:29 PM
super excited to share the newest from my lab: a tool that can securely process RNA-seq reads to quantify gene expression. Huge congrats to the dream team Seungwan, @BioConorWalker, and Annie! We developed a new gene expression quantification algorithm 1/2 www.nature.com/articles/s41...
Reposted by Gamze Gürsoy
Stop collaborate and listen! 😀Yesterday was a great day for science! Thank you @standupforscience.bsky.social !The real work begins now. People are listening! We need to challenge misunderstandings and show that investment in science is crucial for our health for our economy and for our future!
March 8, 2025 at 3:37 PM
Stop collaborate and listen! 😀Yesterday was a great day for science! Thank you @standupforscience.bsky.social !The real work begins now. People are listening! We need to challenge misunderstandings and show that investment in science is crucial for our health for our economy and for our future!
Reposted by Gamze Gürsoy
One of the most powerful moments of the day came from Emily Whitehead who told the story of how she was the first pediatric patient to receive CAR T-cell therapy for her leukemia at age 5: “I stand up for science because science saved my life. And that’s a fact.” @standupforscience.bsky.social
March 8, 2025 at 1:18 PM
One of the most powerful moments of the day came from Emily Whitehead who told the story of how she was the first pediatric patient to receive CAR T-cell therapy for her leukemia at age 5: “I stand up for science because science saved my life. And that’s a fact.” @standupforscience.bsky.social
Reposted by Gamze Gürsoy
🔷 📰 BLUETORIAL time! 📰 🔷
Excited to share recent work from our lab on noncoding genomics 🔎🧬: High-resolution CRISPR perturbations of the MYC TAD (~3 Mb) in 6 different human cancer cell lines
www.nature.com/articles/s41...
Excited to share recent work from our lab on noncoding genomics 🔎🧬: High-resolution CRISPR perturbations of the MYC TAD (~3 Mb) in 6 different human cancer cell lines
www.nature.com/articles/s41...
Comprehensive dissection of cis-regulatory elements in a 2.8 Mb topologically associated domain in six human cancers - Nature Communications
The oncogene MYC plays a key role in cancer initiation and progression. Using thousands of CRISPR perturbations, the authors investigate regulators of MYC in six different cancers. These tumor-specifi...
www.nature.com
March 3, 2025 at 2:40 AM
🔷 📰 BLUETORIAL time! 📰 🔷
Excited to share recent work from our lab on noncoding genomics 🔎🧬: High-resolution CRISPR perturbations of the MYC TAD (~3 Mb) in 6 different human cancer cell lines
www.nature.com/articles/s41...
Excited to share recent work from our lab on noncoding genomics 🔎🧬: High-resolution CRISPR perturbations of the MYC TAD (~3 Mb) in 6 different human cancer cell lines
www.nature.com/articles/s41...
More science! We have a new pre-print - more on non-IID federated learning: We (well my student Ahmed) were inspired by model pruning and developed a new metric called federation sensitivity. (1/2) www.arxiv.org/abs/2502.08829
PLayer-FL: A Principled Approach to Personalized Layer-wise Cross-Silo Federated Learning
Non-identically distributed data is a major challenge in Federated Learning (FL). Personalized FL tackles this by balancing local model adaptation with global model consistency. One variant, partial F...
www.arxiv.org
February 15, 2025 at 9:57 PM
More science! We have a new pre-print - more on non-IID federated learning: We (well my student Ahmed) were inspired by model pruning and developed a new metric called federation sensitivity. (1/2) www.arxiv.org/abs/2502.08829
The world is on fire but we must continue doing science! With immense pride, I share the latest from my lab: privateQTL - a method for federated and secure eQTL mapping, led by my brilliant student Annie from @ColumbiaDBMI www.cell.com/cell-genomic...
(1/n)
(1/n)
Secure and federated quantitative trait loci mapping with privateQTL
Choi et al. developed a novel tool for privacy-preserving cross-institutional eQTL
mapping studies. The authors benchmarked their tool against meta-analysis and demonstrated
that it achieves higher ac...
www.cell.com
February 12, 2025 at 4:17 PM
The world is on fire but we must continue doing science! With immense pride, I share the latest from my lab: privateQTL - a method for federated and secure eQTL mapping, led by my brilliant student Annie from @ColumbiaDBMI www.cell.com/cell-genomic...
(1/n)
(1/n)
Call for submission to 2025 @recombconf.bsky.social Satellite Conference on Biomedical Privacy and Equity (RECOMB P&E) is open! For more info please see recomb-privacy-equity.github.io/papers/ or reach out to our wonderful chairs (Hoon Cho and Shalmali Joshi! )
Call for Papers
RECOMB Satellite Conference on Biomedical Privacy and Equity
recomb-privacy-equity.github.io
January 14, 2025 at 12:15 PM
Call for submission to 2025 @recombconf.bsky.social Satellite Conference on Biomedical Privacy and Equity (RECOMB P&E) is open! For more info please see recomb-privacy-equity.github.io/papers/ or reach out to our wonderful chairs (Hoon Cho and Shalmali Joshi! )
Reposted by Gamze Gürsoy
🎇🎄Some holiday reading: Overdue TWEETORIAL on the latest preprint from our lab 🎇🎄
In this work, superstar postdoc @xinhexue.bsky.social combined 2 kinds of pooled CRISPR screens to pinpoint noncoding regulatory elements and the transcription factors that activate these elements.
In this work, superstar postdoc @xinhexue.bsky.social combined 2 kinds of pooled CRISPR screens to pinpoint noncoding regulatory elements and the transcription factors that activate these elements.
December 26, 2024 at 3:01 AM
🎇🎄Some holiday reading: Overdue TWEETORIAL on the latest preprint from our lab 🎇🎄
In this work, superstar postdoc @xinhexue.bsky.social combined 2 kinds of pooled CRISPR screens to pinpoint noncoding regulatory elements and the transcription factors that activate these elements.
In this work, superstar postdoc @xinhexue.bsky.social combined 2 kinds of pooled CRISPR screens to pinpoint noncoding regulatory elements and the transcription factors that activate these elements.
New paper alert! 🚨 SQUiD: Our secure and queryable genotype-phenotype database prototype with many secure analysis functionalities is out
@genomebiologyunit.bsky.social link.springer.com/article/10.1...
@genomebiologyunit.bsky.social link.springer.com/article/10.1...
SQUiD: ultra-secure storage and analysis of genetic data for the advancement of precision medicine - Genome Biology
Cloud computing allows storing the ever-growing genotype-phenotype datasets crucial for precision medicine. Due to the sensitive nature of this data and varied laws and regulations, additional securit...
link.springer.com
December 18, 2024 at 7:29 PM
New paper alert! 🚨 SQUiD: Our secure and queryable genotype-phenotype database prototype with many secure analysis functionalities is out
@genomebiologyunit.bsky.social link.springer.com/article/10.1...
@genomebiologyunit.bsky.social link.springer.com/article/10.1...
Super excited for my lab's first paper at @recombconf.bsky.social. See you all in South Korea!
December 18, 2024 at 1:03 AM
Super excited for my lab's first paper at @recombconf.bsky.social. See you all in South Korea!