Computational & Systems Biology Dept. at Pitt

Jianhua Xing, Professor

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.

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...

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

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...

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...

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...

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

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

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…

🔬 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

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

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

Pittsburgh Biological Physics Day

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

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...

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

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...

📚 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

Computational Biomedicine and Biotechnology orientation 2025

Computational Biomedicine and Biotechnology orientation 2025

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.

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...

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

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...

📣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

Alison Guyer

👏 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.”

PhD student Ananksha Sachan

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

Fareeda Abu-Juam

👏 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.

✨ 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.

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.

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

school of medicine graduate student research symposium

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

mosquito on an arm

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

bioimaging analysis lab image

📚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...

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.

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...

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...

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

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.

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...

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.

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

Graduate Spotlight: Haiyi Mao, PhD ‘25 - Department of Computational and Systems Biology As Haiyi Mao graduates from the Joint Carnegie Mellon-University of Pittsburgh PhD Program in Computational Biology (CPCB), he reflects on an experience that has enriched his life personally and profe...

Congratulations to Haiyi Mao, who graduated from CPCB on Sunday! “I think the most rewarding part of my PhD experience has been overcoming self-doubt by thinking hard about how to theoretically and biologically solve the problem,” he said.

Read more in our graduate spotlight: tinyurl.com/HaiyiMao

David Koes, BaDoi Phan, Andrew McNutt, Tyler Lovelace, Takis Benos, Haiyi Mao and Minxue Jia

Congratulations to our graduates who attended the School of Medicine Class of 2025 Graduation yesterday! 🎓 💛

When a bovine cytokine talks to a human cell: Lessons from cross-species signaling experiments. 😊 🐱 🐰 🐁 🐀 🐄
www.biorxiv.org/content/10.1...

Optogenetic control of Nodal signaling patterns - PubMed A crucial step in early embryogenesis is the establishment of spatial patterns of signaling activity. Tools to perturb morphogen signals with high resolution in space and time can help reveal how embr...

A new tool from Assistant Professor Nate Lord uses light to precisely control Nodal signaling in zebrafish embryos—revealing how cells make fate decisions during development. 🔬🐟
Read more about this powerful new approach to studying embryogenesis:
tinyurl.com/LordZebrafish

PhD students earn recognition from National Science Foundation fellowship - Department of Computational and Systems Biology Two students in the Joint Carnegie Mellon-University of Pittsburgh PhD Program in Computational Biology have received honorable mentions from the National Science Foundation’s Graduate Research Fellow...

Two students in the Joint Carnegie Mellon-University of Pittsburgh PhD Program in Computational Biology have received honorable mentions from the National Science Foundation’s Graduate Research Fellowship Program. Congratulations to Anamarie Martinez and Emma Flynn!

Read more: tinyurl.com/GRFPPitt