Congratulations Swapnil Keshari

PhD candidate Swapnil Keshari was recognized with two leadership awards!

Keshari received the Leadership & Service Award from Graduate and Professional Student Government and was also honored as a Student Sustainability Champion for 2026.

Fifth and Halket building

Fifth and Halket building

The Department of Computational and Systems Biology has a new home! CSB will relocate to the top floor of a newly constructed 10-story building on Fifth Avenue and Halket Street. The move has already begun and should conclude by April 22.

Read more: tinyurl.com/CSBFifthHalket

Chronic infections can generate SARS-CoV-2-like bursts of viral evolution without epistasis Multiple SARS-CoV-2 variants have arisen during the first years of the pandemic, often bearing many new mutations. Several explanations have been offered for the surprisingly sudden emergence of multiple mutations that enhance viral fitness, ...

How did SARS-CoV-2 variants acquire dozens of mutations during the pandemic?

New research from the Barton Lab investigates how such divergent, highly mutated variants could arise.

Read the full research in Virus Evolution: tinyurl.com/BartonSARS2

5 benefits of earning a master’s degree in Computational Biomedicine and Biotechnology - Department of Computational and Systems Biology What is it about a master’s degree that can set you apart from other candidates in the job market? Beyond the personal fulfilment of earning your diploma, there are tangible career benefits to pursuin...

What is it about a master’s degree that can set you apart from other job candidates?

Beyond the personal fulfilment of earning your diploma, there are tangible career benefits to pursuing a master’s degree in Computational Biomedicine and Biotechnology.

www.csb.pitt.edu/2026/03/25/5...

protein phosphate 2A

The Gur lab has published a new article in JACS Au, a journal of the American Chemical Society, that sheds light on how a promising class of cancer-fighting molecules works at the atomic level.

Read more about the research on protein phosphate 2A, an "off-switch" for cancer:
tinyurl.com/JACSPP2A

Jennifer Watt on the Appalachian Trail

Jennifer Watt on the Appalachian Trail

What word would Jennifer Watt use to describe herself? Resilient. This word perfectly captures how the administrative manager has overcome setbacks to thrive in all aspects of her life, from running ultramarathons to building a new career.
Read more in our staff spotlight: tinyurl.com/JenniferWatt

Faculty Spotlight: Warren van Loggerenberg - Department of Computational and Systems Biology From a young age, Warren van Loggerenberg dreamed of becoming a professor. That dream is now becoming reality as he transitions from a research scientist to an assistant professor in the Department of...

From a young age, Warren van Loggerenberg dreamed of becoming a professor. That dream is now becoming reality as he transitions from a research scientist to an assistant professor.

Learn more about Warren in our faculty spotlight: tinyurl.com/WarrenSpotli...

Computational and Systems Biology Fund - Pitt Day of Giving The pipeline of new medical breakthroughs begins upstream, with fundamental discoveries. The Department of Computational and Systems Biology (CSB) is harnessing advanced computational methods and syst...

Today's the day for Pitt Day of Giving!

Join us in making an impact to ensure that we have the latest tools and resources to stay at the forefront of research, discovery, and training.

⏰ Giving ends at midnight.
➡️ Donate today: tinyurl.com/CSBGive

How a master’s degree can jump-start your bioinformatics career - Department of Computational and Systems Biology Have you ever wondered where a master’s degree in Computational Biomedicine and Biotechnology (CoBB) will take you? Read on to learn more about the bioinformatics scientist profession.

There is a growing need for bioinformatics professionals who can manage and interpret extensive genetic datasets.

Have you ever wondered how to become a bioinformatics scientist? Check out this blog post:

tinyurl.com/Bioinformati...

Kate Rubins

Sylvain Costes

Join us in welcoming Professor Kate Rubins and Professor Sylvain Costes to the CSB faculty!

Rubins and Costes are founding members of the Trivedi Institute for Space and Global Biomedicine.

We can't wait to see what these two will accomplish at Pitt!

High-throughput drug screening for targeting polyploid cancer cells with an interactive web portal

Assistant Professor Yu-Chih Chen's new research is enabling more precise detection of cells that are resistant to cancer treatment (PGCCs).

They also made these findings accessible via their PGCC Explorer, an interactive web tool for drug discovery.

Read more: tinyurl.com/PGCCExplorer

New study reveals cells take two different paths during EMT - Department of Computational and Systems Biology PhD student Sophia Hu and Professor Jianhua Xing’s lab have developed a computational method to demystify what happens when cells go through epithelial-to-mesenchymal transition (EMT).

PhD student Sophia Hu and Professor Jianhua Xing’s lab have developed a computational method to demystify what happens when cells go through epithelial-to-mesenchymal transition (EMT).

Read more: tinyurl.com/HuEMT

#BiologyResearch

Pitt’s new Trivedi Institute will translate space science into human health breakthroughs Former NASA astronaut and Professor Kate Rubins will lead the $25 million institute, funded by the Trivedi Family Foundation.

🚀 Now launching: the Trivedi Institute for Space and Global Biomedicine!

Professor Kate Rubins, a former NASA astronaut, will lead this institute. It will focus on applying insights from spaceflight to improve human health on Earth.

Read more: tinyurl.com/TrivediPitt

Alumnus Sahil Ganatra is bridging the gap between technology and clinical care - Department of Computational and Systems Biology Sahil Ganatra, a graduate of the Computational Biomedicine and Biotechnology (CoBB) master’s degree program, is bridging the gap between technology and clinical care.

CoBB alumnus Sahil Ganatra is stepping into a new role as a clinical study manager for Philips. He will oversee clinical trials that are focused on validating and testing medical devices for sleep and respiratory care diseases.

Read more in our alumni spotlight: tinyurl.com/SahilGanatra

Community benchmarking and evaluation of human unannotated microprotein detection by mass spectrometry based proteomics - PubMed Thousands of short open reading frames (sORFs) are translated outside of annotated coding sequences. Recent studies have pioneered searching for sORF-encoded microproteins in mass spectrometry (MS)-based proteomics and peptidomics datasets. Here, we assessed literature-reported MS-based identificati …

Pitt researchers are raising the bar for microprotein discovery.

By reassessing detection methods, Aaron Wacholder and Anne-Ruxandra Carvunis reveal why standardized protocols are essential for uncovering these elusive proteins' roles in health and disease.

tinyurl.com/NatureWachol...

Emergence and tandem repeat-mediated elongation of a translated de novo open reading frame in human oncogenic RNA gene VPS9D1-AS1 (MYU) - PubMed New protein-coding genes can arise de novo from ancestrally noncoding regions when open reading frames (ORFs) outside annotated genes are exposed to selection via pervasive translation. These ORFs are usually born short, and their elongation is considered a key step in de novo gene birth. However, m …

A new study reveals how gene orf143 emerged "from scratch" in primate ancestors and may now protect against cancer. Led by Lin Chou and Anne Carvunis, this research shows evolution creating new genes in real time—with implications for cancer biology.

Read more: tinyurl.com/ChouCarvunis

Year in review: 4 impactful moments for CSB in 2025 - Department of Computational and Systems Biology In 2025, the Department of Computational and Systems Biology tackled complex problems at the intersection of biology and technology. As we reflect on the impact of the last year, we’ve compiled our fa...

In 2025, the CSB department tackled complex problems at the intersection of biology and technology. We came together in a mission of education and discovery.

As we reflect on the impact of the last year, we’ve compiled our favorite stories from 2025. Read more: tinyurl.com/CSB2025Review

Graduate Spotlight: Peter Murdo Chiknas, MS ‘25 - Department of Computational and Systems Biology Peter Murdo Chiknas reflects on his experiences in the Computational Biomedicine and Biotechnology master's program and his next steps after graduation.

🎓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

Graduate Spotlight: Steven Smeal, PhD ‘25 - Department of Computational and Systems Biology Steven Smeal, a recent graduate of the Joint Carnegie Mellon-University of Pittsburgh PhD Program in Computational Biology (CPCB), reflects on the graduate school experiences that have helped to jumps...

🎓 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

Graduate Spotlight: Jessie Weng, MS '25 - Department of Computational and Systems Biology Jessie Weng always knew she wanted to work in the health care industry, but she wasn’t sure which direction her career would go. The Computational Biomedicine and Biotechnology (CoBB) master’s degree ...

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

NEMO recruitment at single cytokine-receptor complexes shows quantized dynamics independent of ligand affinity Kim et al. leverage natural variation in IL-1β affinity across species to show that while ligand affinity sets activation thresholds, each IL-1 receptor signaling complex outputs a fixed, quantized bu...

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

CSB members assemble 1,000 safe-sleep kits for infants at Cribs for Kids - Department of Computational and Systems Biology Donating a little bit of time can make a big impact. On Nov. 21, members of the Department of Computational and Systems Biology (CSB) spent the day volunteering at Cribs for Kids.

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 reflects on time at Pitt - Department of Computational and Systems Biology Emeritus Professor Hagai Meirovitch returned to the University of Pittsburgh for a visit last week.

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

Parallel HIV-1 fitness landscapes shape viral dynamics in humans and macaques that develop broadly neutralizing antibodies - PubMed HIV-1 evolves within individual hosts to escape adaptive immune responses while maintaining its capacity for replication. Coevolution between HIV-1 and the immune system generates extraordinary viral genetic diversity. In some individuals, this process also results in the development of broadly neut …

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

Students faculty and staff at a Halloween party

Students faculty and staff at a Halloween party

Students faculty and staff at a Halloween party

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

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.

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

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...

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

Swapnil Keshari stands in front of airplane

aerial view of Philadelphia

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.

🧵