🎓Congratulations to Murdo Chiknas, who graduated from the Computational Biomedicine and Biotechnology master’s degree program! His next step is becoming the first person in his family to earn a PhD. Read more in our grad spotlight tinyurl.com/MurdoChiknas

🎓 A big shout out to Steven Smeal, who graduated from the Joint Carnegie Mellon-University of Pittsburgh PhD Program in Computational Biology! His next adventure is working as a postdoctoral associate at Carnegie Mellon University. Read more in this grad spotlight story: tinyurl.com/StevenSmeal

Congratulations to Jessie Weng, a 2025 graduate! She leaves students with some advice: “Trust the process. Some of you might just be waiting on graduation to be done, but be curious about what you’re doing now, too. At the end of the day, curiosity pays off.” Read more: tinyurl.com/JessieWeng

New research alert from the Lee lab! CPCB students Annie Kim and Ben Krummenacher, with ISB’s Jason Yeung, leverage naturally occurring variations of interleukin (IL)-1β from multiple species to determine the impact of affinity on human IL-1 receptor signaling. Read more: tinyurl.com/LeeLabResearch

Donating a little bit of time can make a big impact. On Nov. 21, members of the Department of Computational and Systems Biology spent the day volunteering at Cribs for Kids, assembling 1,000 safe-sleep survival kits for infants. Read more about our volunteering event: tinyurl.com/CribsforKids...

Emeritus Professor Hagai Meirovitch returned to the University of Pittsburgh for a visit last week. “I see many new people, so I think this a good sign that the place is growing and breathing,” he said. “I see progress and a future for the department that we worked to create.” tinyurl.com/HagaiM

How does HIV-1, the virus that causes AIDS, evolve to outsmart the immune system? A new study by Kai Shimagaki and John Barton uncovers striking parallels in HIV-1 evolution between humans and rhesus macaques. pubmed.ncbi.nlm.nih.gov/41212071/ #Biology #AIDSResearch

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

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

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

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

✨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. 🧵

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

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.

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

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 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

🔬 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

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

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

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

📚 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

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.

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

📣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

👏 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 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

👏 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.

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

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

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

📚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. . Read more: tinyurl.com/BioimagingAn...

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...

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 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...

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

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

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...

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

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

Congratulations to Roshni Bhatt, CPCB graduate! 🎓“Getting my PhD has been a goal of mine for so long and being a grad student has been my life for so long, so I’m grateful for the opportunity to figure out what the next big thing is,” she said. Read more: tinyurl.com/RoshniBhatt

🎓As David Antolick nears the finish line of his Computational Biomedicine and Biotechnology master’s degree, he reflects on a whirlwind journey—one filled with hours of coding, valuable lessons in machine learning, and a genuine love for the field. Read more: tinyurl.com/DavidAntolick

PhD student Gaohan Yu delivered a talk at the American Physical Society Global Physics Summit. “It’s really opened my mind to see how a conference works, how I should present my work, and how I should advertise my work and myself. It’s a really good experience," he said. 🔗 tinyurl.com/GaohanYu

Mark your calendars for the CSB Seminar Series on Monday, April 14! Jian Zhou, Assistant Professor at UT Southwestern Medical Center, will deliver a talk titled "Decoding the sequence-basis of genome regulation." The event will be held in BST3 room 6014 and on Zoom. We hope to see you there.

Postdoctoral associate Anuraag Bukkuri was recognized with the Scott H. Williamson Award from the Society for Modeling and Theory in Population Biology. This international award honors the achievements and promise of one outstanding early-career researcher. Congratulations! tinyurl.com/AnuraagB

How do you analyze millions of papers in the life sciences and physical sciences that have been published in the past 25 years? Jishnu Das and Swapnil Keshari developed the #MachineLearning tool DISCo-Net and used it to analyze papers from over 200 countries. Read more: tinyurl.com/CSBMachineLe...