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Computational & Systems Biology Dept. at Pitt @csbpitt.bsky.social · 7d

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.

Computational & Systems Biology Dept. at Pitt @csbpitt.bsky.social · 9d

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

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...

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Computational & Systems Biology Dept. at Pitt @csbpitt.bsky.social · 13d

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...

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...

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Computational & Systems Biology Dept. at Pitt @csbpitt.bsky.social · 19d

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

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...

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Computational & Systems Biology Dept. at Pitt @csbpitt.bsky.social · 21d

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

Impoundment of funds endangers US investment in science and medical research

Letter to the Editor

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Computational & Systems Biology Dept. at Pitt @csbpitt.bsky.social · 23d

🔬 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

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

Computational & Systems Biology Dept. at Pitt @csbpitt.bsky.social · Sep 8

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

Chief of AI at PredxBio explains how to launch a career in bioimaging

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Computational & Systems Biology Dept. at Pitt @csbpitt.bsky.social · Aug 26

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

Computational & Systems Biology Dept. at Pitt @csbpitt.bsky.social · Aug 25

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

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...

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Computational & Systems Biology Dept. at Pitt @csbpitt.bsky.social · Aug 25

📚 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

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...

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Computational & Systems Biology Dept. at Pitt @csbpitt.bsky.social · Aug 20

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.

Computational Biomedicine and Biotechnology orientation 2025

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Computational & Systems Biology Dept. at Pitt @csbpitt.bsky.social · Aug 15

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

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...

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Computational & Systems Biology Dept. at Pitt @csbpitt.bsky.social · Aug 14

📣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

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...

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Computational & Systems Biology Dept. at Pitt @csbpitt.bsky.social · Aug 6

👏 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.”

Computational & Systems Biology Dept. at Pitt @csbpitt.bsky.social · Aug 5

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

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Computational & Systems Biology Dept. at Pitt @csbpitt.bsky.social · Aug 1

👏 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.

Computational & Systems Biology Dept. at Pitt @csbpitt.bsky.social · Jul 30

✨ 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.

Computational & Systems Biology Dept. at Pitt @csbpitt.bsky.social · Jul 29

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

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.

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Computational & Systems Biology Dept. at Pitt @csbpitt.bsky.social · Jul 24

Mark your calendars for the 30th Annual SOM Graduate Student Research Symposium!

Join us in celebrating the research and scholarly achievements of graduate students across all School of Medicine programs.

Register here: tinyurl.com/SOMSymposium

#PittGradResearch #SOMSymposium2025

school of medicine graduate student research symposium

Computational & Systems Biology Dept. at Pitt @csbpitt.bsky.social · Jul 15

Pitt virologists and computational biologists are combining their expertise to understand the replication cycle of a deadly mosquito-borne alphavirus. Read more about how they created a kinetic model of Eastern equine encephalitis virus.
🔗 tinyurl.com/EEEVModel

Computational & Systems Biology Dept. at Pitt @csbpitt.bsky.social · Jul 2

📚New course alert! Assistant Professor Shikhar Uttam has launched a new graduate-level course: Bioimaging, Analysis and Spatial Biology.

Students learn how imaging data are generated and analyzed to uncover biological insights.
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Read more: tinyurl.com/BioimagingAn...

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Computational & Systems Biology Dept. at Pitt @csbpitt.bsky.social · Jun 17

Congratulations to Assistant Professor Keisuke Ishihara, who has received the American Heart Association Career Development Award!

This grant will support Ishihara’s project titled “The physical role of the cardiac jelly in human cardiac organoids.”

Read more: tinyurl.com/KeisukeIshih...

Keisuke Ishihara receives American Heart Association research funding - Department of Computational and Systems Biology

Assistant Professor Keisuke Ishihara has received the American Heart Association Career Development Award, a three-year grant that began in April 2025.

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Computational & Systems Biology Dept. at Pitt @csbpitt.bsky.social · Jun 11

New publication alert! 🧬 A team of Pitt computational biologists and virologists built a detailed model of how Eastern equine encephalitis virus rapidly hijacks host cells to replicate. Check it out in PLOS Computational Biology.

🔗 tinyurl.com/EasternEquine

#virology #computationalbiology

A detailed kinetic model of Eastern equine encephalitis virus replication in a susceptible host cell

Author summary Eastern equine encephalitis virus (EEEV) is a positive-sense RNA virus transmitted via mosquitoes. It can cause lethal disease in humans with a high mortality rate, exceeding 30%. There...

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Computational & Systems Biology Dept. at Pitt @csbpitt.bsky.social · Jun 9

How you ever wondered how to build software solutions for today's technology-driven world? Software engineers have a front seat to the creation of everything from health care apps to video games.

Read more about how a master's degree can prepare you for this role:
tinyurl.com/CoBBSoftware...

How a master’s degree can launch your software engineering career - Department of Computational and Systems Biology

Have you ever wondered where a master’s degree in Computational Biomedicine and Biotechnology will take you? Read more about becoming a software engineer.

tinyurl.com

Computational & Systems Biology Dept. at Pitt @csbpitt.bsky.social · May 23

That's a wrap on the CSB retreat!

Last week, we held our annual department retreat at the Carnegie Science Center. It was a day filled with meaningful discussions, research presentations, and opportunities to explore.
tinyurl.com/CSBRetreat2025

Department of Computational and Systems Biology hosts 2025 annual retreat at Carnegie Science Center - Department of Computational and Systems Biology

The Department of Computational and Systems Biology hosted its annual retreat at the Carnegie Science Center on May 15.

tinyurl.com