Pitt prepares to resume research

The University of Pittsburgh is making preparations to resume research activities on campus amidst the COVID-19 pandemic. On Friday, Chancellor Patrick Gallagher issued a statement outlining the goals of re-opening the university by saying, “we are seeking to adapt to a new reality: performing our vital mission and protecting our community in the midst of a pandemic.” In his message, he commented on the time-critical elements of Pitt’s mission and that “students can’t put their education and lives on hold, and our researchers and scholars can’t sit on the sidelines until the threat dissipates.” However, he also emphasized the importance of moving forward responsibly through infection prevention and control measures such as modifying building use, acquiring the technology needed to conduct remote and on-campus work, developing approaches for recognizing risks (e.g., testing, symptom tracking, temperature monitoring, etc.), and performing contact tracing. Gallagher concluded his message saying that the road ahead will be a complicated one, but one that he believes we can traverse safely while still performing Pitt’s mission–“It’s a strange new world. But I remain extremely proud to be your colleague and incredibly optimistic as we set out to tackle this next transition together.”

Biomedical Science Tower 3, where some of the Department of Computational & Systems Biology’s facilities are located, will be among one of the first research buildings to be adapted to the new rules and guidelines for resuming research.

Drs. Joseph Ayoob and Joshua Kangas publish in PLoS Computational Biology

Dr. Joseph Ayoob, Associate Professor, Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh; and Dr. Joshua Kangas, Assistant Teaching Professor, Computational Biology Department, School of Computer Science, Carnegie Mellon University have published “10 Simple Rules for Teaching Wet-Lab Experimentation to Computational Biology Students (aka, turning computer mice into lab rats)” in PLoS Computational Biology.

Joe and Josh first became involved with the Lab Methods for Computational Biology class, which is part of the Carnegie-Mellon University of Pittsburgh Computational Biology Ph.D. program, over ten years ago – with Josh as a student and then teaching assistant and Joe as a new instructor. For the past three years they have been teaching the course together and wanted to share their years of expertise with the broader computational biology community.

Abstract: “Graduate students in Computational Biology typically have strong computational backgrounds but are frequently limited in their understanding of the theory, approach, and practice of biological experimentation used to generate data. A thorough understanding of the techniques used to generate biological data is essential for computational biologists to effectively critique and incorporate data into their research efforts. Furthermore, students are more frequently generating their own data in their PhD research making this background knowledge crucial for their success.  To give students this knowledge, insight, and experience, the ‘Laboratory Methods for Computational Biologists’ (LMCB) course was established as a core course in the CPCB curriculum to provide a hands-on, research-oriented laboratory experience in four major areas: genomics, microscopy and bioimaging, high content screening, and X-ray crystallography.  The LMCB course provides foundational and experiential wet-lab training for the benefit of nascent computational scientists.  In this article, we provide some of the guiding principles and approaches that we have used to establish, evolve, and shape the LMCB course.”

Congratulations Drs. Ayoob and Kangas on your publication and thank you for your continued dedication to education!

Ayoob JC, Kangas JD. (2020) 10 simple rules for teaching wet-lab experimentation to computational biology students, i.e., turning computer mice into lab rats. PLoS Comput Biol 16(6): e1007911. https://doi.org/10.1371/journal.pcbi.1007911


Department Mourns the Passing of Dr. Bing Liu

It is with deep sadness and shock that we learned of the untimely passing of Dr. Bing Liu, Research Assistant Professor in our department on Saturday, May 2nd, 2020.

Dr. Bing Liu was an outstanding researcher, who has earned the respect and appreciation of many colleagues in the field, and made unique contributions to science. His area of expertise was computational modeling and analysis of biological systems dynamics. He had developed high-performance computing techniques and advanced machine-learning approaches for modeling the time evolution of complex cellular interactions, Bayesian network models and methods, and statistical model checking and sensitivity analyses.

Bing was a prolific researcher. During his career he co-authored in 30+ publications, including four in 2020, in addition to a book.  He played a critical role in the Bahar Lab and was the leader in systems biology research for Ivet and her lab. He single-handedly helped all of us as well as many collaborators including clinicians here and in other institutions, understand and quantitatively model many complex processes, including immune signaling events,  apoptotic and ferroptotic cell death,  autophagy, redox lipid programming, response to radiation and radiation therapy, systems (poly)pharmacological treatments. In recent years, he had three publications in Nature Chem Biol, three in Radiation Research, two in Scientific Reports, one in Science Signaling,  one in International Journal of Molecular Sciences, and one in Frontiers in Pharmacology.

Liu was an excellent mentor. He had been generously sharing his time and knowledge with younger members of the Bahar lab, as well as students enrolled in our various programs, including our summer programs (TECBio REU and the UPMC Hillman Cancer Center Summer Academy. He was patient, intelligent, and extremely mature. We will miss him very much.

Dr. Liu received his BS and PhD in Computer Science, at the National University of Singapore, under the supervisions of Drs. P.S. Thiagarajan and David Hsu, and did his postdoctoral studies in the lab of Professor Dr. Edmund Clarke at  Carnegie Mellon University, after which he joined the Bahar lab, as a Research Associate, and was recently promoted to a Research Assistant Professor position within our department.

Bing was on the verge of making very significant findings toward understanding the cellular mechanisms that underlie SARS-CoV-2 infection and the cellular basis of the following complications. We will make an effort to complete what he started in an effort to pay homage to his scientific excellence.

His loss will be felt throughout the entire scientific community. Please keep his family, friends, and colleagues in your thoughts. Thank you.

DCSB Welcomes New Executive Administrator: Donald Bonidie

Please join us in welcoming our new Executive AdministratorDonald Bonidie, who joins us from the School of Computing and Information at the University of Pittsburgh where he was the Director of Business and Finance. He has been with the university for over 26 years.

We put together a brief interview with him below so that we all may get to know him a little better.

Are you from the Pittsburgh area?
I was born and raised in the Pittsburgh area. Lived in the inner city of Pittsburgh, East Liberty, with my 3 brothers and graduated from Peabody HS. I now reside outside of the city in Springdale with my wife of just about 25 years (on June 3rd!) Deanna, and my two daughters Victoria, a recent college graduate and in the fall a Pitt student pursuing her PhD in physics and astronomy and Haley, a soon to be senior in HS.

Where did you do your undergrad/masters and what did you study?
I did both my undergraduate (BS) and graduate (MS) degrees from the University of Pittsburgh, UG focus was in math and computer science while my masters was in Information Science.

What made you choose the University of Pittsburgh for your career?
I was always a big Pitt fan and always wanted to attend. However, funds were low so I got a job in the ID center at Pitt so I could take advantage of the tuition benefits. From there I took every opportunity to not only get my education but expand my resume by taking every staff training made available to me and every new task I could find. That has grown into a 28-year (this August) career.

Who is your mentor and who inspires you?
I have worked for the University for almost 28 years now and have been fortunate enough to have many mentors. However, Michele Montag of the Dietrich School stands out the most. She is incredibly bright, compassionate, and effective. As the Director of Administration, she demonstrated many of the qualities necessary to be an effective and inspirational leader.

What’s your most-used productivity hack?
Tackle must do and difficult tasks first. That’s when you will have the most energy to deal with them. Save the easier stuff for when you are the least energetic.

What’s something that you’re proud of?
That’s easy, I have two daughters and their accomplishments are what makes me most proud. I also love the fact that I was able to make them both feel and believe they are my favorite.

What motivates you at work?
Every job I have ever had I want to leave being the best that job has ever had. I want to set the bar and that’s a big task and a big motivator.

What are you hoping to achieve as the new Department Administrator?
My goal is to find operational efficiencies. I like taking a tedious task that takes a lot of time and effort and automating it to make it more efficient, accurate, and certainly less time.

Do you have any talents or hobbies?
My “hobby” if you will and my passion is teaching. I have been teaching as an adjunct faculty member here at Pitt for over 20 years.

Do you have any pets?
I have two wonderful pet piranhas.