Computational & Systems Biology Dept. at Pitt
@csbpitt.bsky.social
Harnessing the power of computational & systems-level analyses to solve critical biological problems, and training the next generation of multidisciplinary scientists. Visit https://www.csb.pitt.edu/
Our department members had a frightfully fun time at the CSB Halloween party!
November 3, 2025 at 4:00 PM
Our department members had a frightfully fun time at the CSB Halloween party!
An international team of scientists led by CSB department chair Fritz Roth has created a first-of-its-kind resource to identify those with a genetic risk for elevated “bad” cholesterol—a major contributor to heart disease.
Read more about the research: tinyurl.com/RothScience
Read more about the research: tinyurl.com/RothScience
Study Links Genetic Variants to Higher "Bad" Cholesterol and Heart Attack Risk | School of Medicine | University of Pittsburgh
An international team led by a University of Pittsburgh School of Medicine scientist has created a first-of-its-kind resource to identify those with a genetic risk for elevated “bad” cholesterol—a maj...
tinyurl.com
October 31, 2025 at 4:24 PM
An international team of scientists led by CSB department chair Fritz Roth has created a first-of-its-kind resource to identify those with a genetic risk for elevated “bad” cholesterol—a major contributor to heart disease.
Read more about the research: tinyurl.com/RothScience
Read more about the research: tinyurl.com/RothScience
When Murat Can Cobanoglu was a child, he lost two grandparents to cancer. This early experience sparked his interest in cancer diagnosis.
Now, he works as a staff bioinformatics scientist. Using a blood sample, Cobanoglu’s team can tell whether a patient has cancer or not.
🔗 tinyurl.com/MuratCanC
Now, he works as a staff bioinformatics scientist. Using a blood sample, Cobanoglu’s team can tell whether a patient has cancer or not.
🔗 tinyurl.com/MuratCanC
CPCB Alumni Spotlight: Murat Can Cobanoglu, Staff Bioinformatics Scientist - Department of Computational and Systems Biology
Alumnus Murat Can Cobanoglu works as a staff bioinformatics scientist at Natera. Using a blood sample, Cobanoglu’s team can tell whether a patient has cancer or not.
tinyurl.com
October 29, 2025 at 5:35 PM
When Murat Can Cobanoglu was a child, he lost two grandparents to cancer. This early experience sparked his interest in cancer diagnosis.
Now, he works as a staff bioinformatics scientist. Using a blood sample, Cobanoglu’s team can tell whether a patient has cancer or not.
🔗 tinyurl.com/MuratCanC
Now, he works as a staff bioinformatics scientist. Using a blood sample, Cobanoglu’s team can tell whether a patient has cancer or not.
🔗 tinyurl.com/MuratCanC
The Department of Computational and Systems Biology welcomed leading genomics researchers from across the country to Pitt’s University Club for the 2025 Centers of Excellence in Genomic Science Annual Meeting.
Read more: tinyurl.com/CEGS2025
Read more: tinyurl.com/CEGS2025
University of Pittsburgh hosts 2025 Centers of Excellence in Genomic Science annual meeting - Department of Computational and Systems Biology
The University of Pittsburgh Department of Computational and Systems Biology welcomed leading genomics researchers from across the country to Pitt’s University Club on Oct. 7–8 for the 2025 Centers of...
tinyurl.com
October 24, 2025 at 3:50 PM
The Department of Computational and Systems Biology welcomed leading genomics researchers from across the country to Pitt’s University Club for the 2025 Centers of Excellence in Genomic Science Annual Meeting.
Read more: tinyurl.com/CEGS2025
Read more: tinyurl.com/CEGS2025
Whether he's in the classroom or in the sky, PhD student Swapnil Keshari is always aiming to achieve new heights.
After three years of hard work, Keshari earned his wings as a private pilot.
Read more: tinyurl.com/SwapnilPilot
After three years of hard work, Keshari earned his wings as a private pilot.
Read more: tinyurl.com/SwapnilPilot
October 23, 2025 at 3:05 PM
Whether he's in the classroom or in the sky, PhD student Swapnil Keshari is always aiming to achieve new heights.
After three years of hard work, Keshari earned his wings as a private pilot.
Read more: tinyurl.com/SwapnilPilot
After three years of hard work, Keshari earned his wings as a private pilot.
Read more: tinyurl.com/SwapnilPilot
Reposted by Computational & Systems Biology Dept. at Pitt
✨New preprint!✨
We built dLEM - a differentiable Loop Extrusion Model that bridges biophysics and machine learning for 3D genome folding.
dLEM makes loop extrusion learnable and interpretable—predicting how genomes fold and how they respond to perturbations.
🧵
We built dLEM - a differentiable Loop Extrusion Model that bridges biophysics and machine learning for 3D genome folding.
dLEM makes loop extrusion learnable and interpretable—predicting how genomes fold and how they respond to perturbations.
🧵
Mechanistic Genome Folding at Scale through the Differentiable Loop Extrusion Model https://www.biorxiv.org/content/10.1101/2025.10.17.682904v1
October 21, 2025 at 1:51 PM
✨New preprint!✨
We built dLEM - a differentiable Loop Extrusion Model that bridges biophysics and machine learning for 3D genome folding.
dLEM makes loop extrusion learnable and interpretable—predicting how genomes fold and how they respond to perturbations.
🧵
We built dLEM - a differentiable Loop Extrusion Model that bridges biophysics and machine learning for 3D genome folding.
dLEM makes loop extrusion learnable and interpretable—predicting how genomes fold and how they respond to perturbations.
🧵
The Gur Lab has created a computational method that brings a new lens to the study of attractive and repulsive interactions across protein interfaces.
“We built a tool that doesn’t just count close contacts; it captures the rhythm of motion between molecules,” Mert Gur said.
tinyurl.com/GurProtein
“We built a tool that doesn’t just count close contacts; it captures the rhythm of motion between molecules,” Mert Gur said.
tinyurl.com/GurProtein
New computational method spots both the “handshakes” and the “shoves” that shape protein partnerships - Department of Computational and Systems Biology
The Gur Lab has unveiled a fast, practical way to read molecular “movies” and pinpoint the forces that make proteins stick together or push apart.
tinyurl.com
October 20, 2025 at 4:18 PM
The Gur Lab has created a computational method that brings a new lens to the study of attractive and repulsive interactions across protein interfaces.
“We built a tool that doesn’t just count close contacts; it captures the rhythm of motion between molecules,” Mert Gur said.
tinyurl.com/GurProtein
“We built a tool that doesn’t just count close contacts; it captures the rhythm of motion between molecules,” Mert Gur said.
tinyurl.com/GurProtein
Congratulations to Professor Jianhua Xing, who was awarded a grant from National Institute of Dental and Craniofacial Research!
This grant will support his research team's project on outcomes of head and neck cancer using system biology modeling with experimental validation.
This grant will support his research team's project on outcomes of head and neck cancer using system biology modeling with experimental validation.
October 1, 2025 at 1:29 PM
Congratulations to Professor Jianhua Xing, who was awarded a grant from National Institute of Dental and Craniofacial Research!
This grant will support his research team's project on outcomes of head and neck cancer using system biology modeling with experimental validation.
This grant will support his research team's project on outcomes of head and neck cancer using system biology modeling with experimental validation.
New research from the Barton lab could inform the development of HIV cure strategies. The research team created a mathematical model of latently infected cells. HIV DNA can hide in a latent, inactive state and sometimes reactivate, making HIV controllable but not curable.
tinyurl.com/BartonArticle
tinyurl.com/BartonArticle
Clonal heterogeneity and antigenic stimulation shape persistence of the latent reservoir of HIV - PubMed
Drug treatment can control HIV-1 replication, but it cannot cure infection. This is because of a long-lived population of quiescent infected cells, known as the latent reservoir (LR), that can restart...
tinyurl.com
September 29, 2025 at 4:22 PM
New research from the Barton lab could inform the development of HIV cure strategies. The research team created a mathematical model of latently infected cells. HIV DNA can hide in a latent, inactive state and sometimes reactivate, making HIV controllable but not curable.
tinyurl.com/BartonArticle
tinyurl.com/BartonArticle
Are you a medical student eager to amplify your impact? Imagine a career where clinical expertise merges with data-driven innovation.
The machine learning skills you'll learn in the Computational Biomedicine and Biotechnology program make this possible. Read the blog: tinyurl.com/MachineLearn...
The machine learning skills you'll learn in the Computational Biomedicine and Biotechnology program make this possible. Read the blog: tinyurl.com/MachineLearn...
How machine learning is shaping the future of medicine and health care - Department of Computational and Systems Biology
Are you a health care student eager to amplify your impact? Imagine a career where clinical expertise merges with data-driven innovation—where you’re not just practicing medicine but shaping its futur...
tinyurl.com
September 25, 2025 at 5:01 PM
Are you a medical student eager to amplify your impact? Imagine a career where clinical expertise merges with data-driven innovation.
The machine learning skills you'll learn in the Computational Biomedicine and Biotechnology program make this possible. Read the blog: tinyurl.com/MachineLearn...
The machine learning skills you'll learn in the Computational Biomedicine and Biotechnology program make this possible. Read the blog: tinyurl.com/MachineLearn...
The second annual Pittsburgh Biological Physics Day showcased vibrant research in the Pittsburgh area that merged principles of physics and biology.
Read more about the event: tinyurl.com/BioPhysics2025
Read more about the event: tinyurl.com/BioPhysics2025
Second annual Pittsburgh Biological Physics Day showcases research - Department of Computational and Systems Biology
The second annual Pittsburgh Biological Physics Day was held on Sept. 16 at the Mellon Insitute. This event showcased vibrant research in the Pittsburgh area that merged principles of physics and biol...
tinyurl.com
September 19, 2025 at 4:10 PM
The second annual Pittsburgh Biological Physics Day showcased vibrant research in the Pittsburgh area that merged principles of physics and biology.
Read more about the event: tinyurl.com/BioPhysics2025
Read more about the event: tinyurl.com/BioPhysics2025
How is the decrease in awarded NIH research grants affecting society?
"The dismantling of the US research and innovation pipeline is causing economic and job losses nationwide. But it is not too late to act," Professor Jeremy Berg et al. write.
Read the article in Nature: tinyurl.com/NatureBerg
"The dismantling of the US research and innovation pipeline is causing economic and job losses nationwide. But it is not too late to act," Professor Jeremy Berg et al. write.
Read the article in Nature: tinyurl.com/NatureBerg
Impoundment of funds endangers US investment in science and medical research
Letter to the Editor
tinyurl.com
September 17, 2025 at 1:58 PM
How is the decrease in awarded NIH research grants affecting society?
"The dismantling of the US research and innovation pipeline is causing economic and job losses nationwide. But it is not too late to act," Professor Jeremy Berg et al. write.
Read the article in Nature: tinyurl.com/NatureBerg
"The dismantling of the US research and innovation pipeline is causing economic and job losses nationwide. But it is not too late to act," Professor Jeremy Berg et al. write.
Read the article in Nature: tinyurl.com/NatureBerg
🔬 New publication alert! The Roth lab has published new research that could improve Amyotrophic lateral sclerosis (ALS) diagnosis. By creating a missense variant-effects map, they gained new insights into ALS caused by variations in superoxide dismutase 1.
Read more: tinyurl.com/ALSVariant
#Science
Read more: tinyurl.com/ALSVariant
#Science
Landscapes of missense variant impact for human superoxide dismutase 1
Amyotrophic lateral sclerosis (ALS) is a progressive motor neuron disease for which important subtypes are caused by variation in superoxide dismutase…
tinyurl.com
September 15, 2025 at 5:28 PM
🔬 New publication alert! The Roth lab has published new research that could improve Amyotrophic lateral sclerosis (ALS) diagnosis. By creating a missense variant-effects map, they gained new insights into ALS caused by variations in superoxide dismutase 1.
Read more: tinyurl.com/ALSVariant
#Science
Read more: tinyurl.com/ALSVariant
#Science
Calling all aspiring bioimaging specialists!
Chakra Chennubhotla, chief of AI at PredxBio, explains how he launched a career in spatial biology.
“A strong understanding of how to analyze biological images is becoming essential across the life sciences," he said.
Read more: tinyurl.com/ChakraCareer
Chakra Chennubhotla, chief of AI at PredxBio, explains how he launched a career in spatial biology.
“A strong understanding of how to analyze biological images is becoming essential across the life sciences," he said.
Read more: tinyurl.com/ChakraCareer
September 8, 2025 at 3:26 PM
Calling all aspiring bioimaging specialists!
Chakra Chennubhotla, chief of AI at PredxBio, explains how he launched a career in spatial biology.
“A strong understanding of how to analyze biological images is becoming essential across the life sciences," he said.
Read more: tinyurl.com/ChakraCareer
Chakra Chennubhotla, chief of AI at PredxBio, explains how he launched a career in spatial biology.
“A strong understanding of how to analyze biological images is becoming essential across the life sciences," he said.
Read more: tinyurl.com/ChakraCareer
Save the date for Pittsburgh Biological Physics Day on Tuesday, September 16!
Join us for a day of science featuring a keynote talk from Yuhai Tu of Flatiron Institute, lightning talks and poster presentations.
To register and learn more, visit: tinyurl.com/PittBioPhysics
Join us for a day of science featuring a keynote talk from Yuhai Tu of Flatiron Institute, lightning talks and poster presentations.
To register and learn more, visit: tinyurl.com/PittBioPhysics
August 26, 2025 at 1:49 PM
Save the date for Pittsburgh Biological Physics Day on Tuesday, September 16!
Join us for a day of science featuring a keynote talk from Yuhai Tu of Flatiron Institute, lightning talks and poster presentations.
To register and learn more, visit: tinyurl.com/PittBioPhysics
Join us for a day of science featuring a keynote talk from Yuhai Tu of Flatiron Institute, lightning talks and poster presentations.
To register and learn more, visit: tinyurl.com/PittBioPhysics
RNA velocities provide powerful insights into cell dynamics.
To address current limitations, Jianhua Xing and his lab created GraphVelo, a machine learning framework that extends RNA velocity to multimodal data.
Read the full paper in Nature Communications: tinyurl.com/GraphVelo
To address current limitations, Jianhua Xing and his lab created GraphVelo, a machine learning framework that extends RNA velocity to multimodal data.
Read the full paper in Nature Communications: tinyurl.com/GraphVelo
GraphVelo allows for accurate inference of multimodal velocities and molecular mechanisms for single cells - Nature Communications
RNA velocity offers insight into cell dynamics but faces key limitations across modalities. Here, authors present GraphVelo, a machine learning framework that refines and extends RNA velocity to multi...
tinyurl.com
August 25, 2025 at 6:04 PM
RNA velocities provide powerful insights into cell dynamics.
To address current limitations, Jianhua Xing and his lab created GraphVelo, a machine learning framework that extends RNA velocity to multimodal data.
Read the full paper in Nature Communications: tinyurl.com/GraphVelo
To address current limitations, Jianhua Xing and his lab created GraphVelo, a machine learning framework that extends RNA velocity to multimodal data.
Read the full paper in Nature Communications: tinyurl.com/GraphVelo
📚 Happy first day of classes! If this is your first semester, you may have some questions about life at Pitt. We’ve assembled a list of frequently asked questions to make your transition to campus a little easier.
Check it out: tinyurl.com/NewCSBStudents
Check it out: tinyurl.com/NewCSBStudents
New Student Survival Guide - Department of Computational and Systems Biology
We’re so glad you’ve found your way to the University of Pittsburgh Department of Computational and Systems Biology! We’re sure you have many questions about life at Pitt, so we’ve assembled a list of...
tinyurl.com
August 25, 2025 at 2:43 PM
📚 Happy first day of classes! If this is your first semester, you may have some questions about life at Pitt. We’ve assembled a list of frequently asked questions to make your transition to campus a little easier.
Check it out: tinyurl.com/NewCSBStudents
Check it out: tinyurl.com/NewCSBStudents
We had a great orientation yesterday with the new class of Computational Biomedicine and Biotechnology MS students!
We can't wait to see what you accomplish during your time at Pitt.
We can't wait to see what you accomplish during your time at Pitt.
August 20, 2025 at 5:39 PM
We had a great orientation yesterday with the new class of Computational Biomedicine and Biotechnology MS students!
We can't wait to see what you accomplish during your time at Pitt.
We can't wait to see what you accomplish during your time at Pitt.
In the complex world inside our bodies, timing can be everything.
A new study from Steven Smeal and Robin E.C. Lee reveals the timing of molecular signals can change how cells respond to their environment, with implications for cancer treatment and drug discovery.
Read more: rdcu.be/ezTxF
A new study from Steven Smeal and Robin E.C. Lee reveals the timing of molecular signals can change how cells respond to their environment, with implications for cancer treatment and drug discovery.
Read more: rdcu.be/ezTxF
Time-varying stimuli that prolong IKK activation promote nuclear remodeling and mechanistic switching of NF-κB dynamics
Nature Communications - Cells rely on limited numbers of transmembrane receptors to process signals from dynamic microenvironments. Using microfluidics and endogenous reporters, the authors track...
rdcu.be
August 15, 2025 at 4:15 PM
In the complex world inside our bodies, timing can be everything.
A new study from Steven Smeal and Robin E.C. Lee reveals the timing of molecular signals can change how cells respond to their environment, with implications for cancer treatment and drug discovery.
Read more: rdcu.be/ezTxF
A new study from Steven Smeal and Robin E.C. Lee reveals the timing of molecular signals can change how cells respond to their environment, with implications for cancer treatment and drug discovery.
Read more: rdcu.be/ezTxF
📣New research alert! The Chikina lab has published an article in Annual Review of Biomedical Data Science.
In this review, they break down how DNA methylation, a fundamental epigenetic mark, shapes gene regulation and cellular identity. Read more: tinyurl.com/Chikina
In this review, they break down how DNA methylation, a fundamental epigenetic mark, shapes gene regulation and cellular identity. Read more: tinyurl.com/Chikina
Methylation Data Analysis and Interpretation - PubMed
DNA methylation, a covalent modification, fundamentally shapes mammalian gene regulation and cellular identity. This review examines methylation's biochemical underpinnings, genomic distribution patte...
tinyurl.com
August 14, 2025 at 7:33 PM
📣New research alert! The Chikina lab has published an article in Annual Review of Biomedical Data Science.
In this review, they break down how DNA methylation, a fundamental epigenetic mark, shapes gene regulation and cellular identity. Read more: tinyurl.com/Chikina
In this review, they break down how DNA methylation, a fundamental epigenetic mark, shapes gene regulation and cellular identity. Read more: tinyurl.com/Chikina
👏 Congratulations to PhD candidate Alison Guyer, who has been awarded the Ruth L. Kirschstein National Research Service Award!
This grant is awarded to promising predoctoral students and will fund Guyer's project titled "Morphogen signaling feedback and dynamics in embryonic patterning.”
This grant is awarded to promising predoctoral students and will fund Guyer's project titled "Morphogen signaling feedback and dynamics in embryonic patterning.”
August 6, 2025 at 3:55 PM
👏 Congratulations to PhD candidate Alison Guyer, who has been awarded the Ruth L. Kirschstein National Research Service Award!
This grant is awarded to promising predoctoral students and will fund Guyer's project titled "Morphogen signaling feedback and dynamics in embryonic patterning.”
This grant is awarded to promising predoctoral students and will fund Guyer's project titled "Morphogen signaling feedback and dynamics in embryonic patterning.”
PhD student Akanksha Sachan has been awarded the Diana Jacobs Kalman/AFAR Scholarship for Research in the Biology of Aging. This scholarship will support Sachan's work in building machine learning methods to interpret cellular dynamics and reprogramming.
Read more: tinyurl.com/AkankshaSachan
Read more: tinyurl.com/AkankshaSachan
August 5, 2025 at 2:15 PM
PhD student Akanksha Sachan has been awarded the Diana Jacobs Kalman/AFAR Scholarship for Research in the Biology of Aging. This scholarship will support Sachan's work in building machine learning methods to interpret cellular dynamics and reprogramming.
Read more: tinyurl.com/AkankshaSachan
Read more: tinyurl.com/AkankshaSachan
👏 Congratulations to PhD student Fareeda Abu-Juam, who has been selected to receive an ACM SIGHPC Computational & Data Science Fellowship!
This award recognizes potential research contributions in computational science or data science and leadership capabilities.
This award recognizes potential research contributions in computational science or data science and leadership capabilities.
August 1, 2025 at 6:26 PM
👏 Congratulations to PhD student Fareeda Abu-Juam, who has been selected to receive an ACM SIGHPC Computational & Data Science Fellowship!
This award recognizes potential research contributions in computational science or data science and leadership capabilities.
This award recognizes potential research contributions in computational science or data science and leadership capabilities.
✨ That's a wrap on TECBio 2025!
Thank you to the amazing undergraduate students who spent 10 weeks at Pitt engaging in graduate-level research in computational biology.
Thank you to the amazing undergraduate students who spent 10 weeks at Pitt engaging in graduate-level research in computational biology.
July 30, 2025 at 5:41 PM
✨ That's a wrap on TECBio 2025!
Thank you to the amazing undergraduate students who spent 10 weeks at Pitt engaging in graduate-level research in computational biology.
Thank you to the amazing undergraduate students who spent 10 weeks at Pitt engaging in graduate-level research in computational biology.
A team of researchers in Assistant Professor Jishnu Das’s lab has developed a new language model that could revolutionize how scientists understand protein interactions.
This model, Sliding Window Interaction Grammar, captures the nuances of interactions.
Read more: tinyurl.com/DasLabModel
This model, Sliding Window Interaction Grammar, captures the nuances of interactions.
Read more: tinyurl.com/DasLabModel
Das lab creates language model for protein interactions - Department of Computational and Systems Biology
A team of researchers in Assistant Professor Jishnu Das’s lab has developed a new language model that could revolutionize how scientists understand protein interactions.
tinyurl.com
July 29, 2025 at 4:24 PM
A team of researchers in Assistant Professor Jishnu Das’s lab has developed a new language model that could revolutionize how scientists understand protein interactions.
This model, Sliding Window Interaction Grammar, captures the nuances of interactions.
Read more: tinyurl.com/DasLabModel
This model, Sliding Window Interaction Grammar, captures the nuances of interactions.
Read more: tinyurl.com/DasLabModel