Research Summaries/Scholarly Activities……………………….12 Grants Awarded……………………………………………..…….100 CPCB Seminar Series………………….……………………….118 Training Grant Publications…………………………………….116 Administrative Duties……………………………………………117 Postdoctoral Associates………………………………………...121 Graduate Students………………………….…………….…..…122 Department Seminar Series……………………...……..….…..125 Primary Faculty…….……………………………...……..…........126 Joint Appointments...……………………………...……...….…..127 U of Pitt School of Medicine Committee Service….…..………128 University of Pittsburgh Committee Service..……….…...…....130 Other Services Outside of the University of Pittsburgh.….…..131 Tenure Track Faculty……………………………...……..….......138 Non-Tenure Track Faculty.………………………...……......….152 Executive Summary...……………………………...……..…......160 Resources..…………...……………………………...……...…...162 Budget………………...……………………………...……...…....164 Computational and Systems Biology – Who We Are The Department of Computational and Systems Biology (CSB) has continued to be a leader in the field. Our increasing focus on multi-scale interactions in biological systems enabled us to tackle more research at an integrated, Systems level. The post-genomic and big data era has brought a new excitement to science. With this excitement also comes new challenges that require new and innovative approaches with which to tackle them. CSB continues to play a leading role in driving discovery through continued interdisciplinary efforts to answer the research challenges of today and define the new approaches to address the questions of tomorrow. Concomitant, with our research foci, we also make concerted efforts in educating the next generation of scientists, who will continue this work. The unique, hands-on research opportunities that we provide to students at the graduate, undergraduate, and even high school levels provide these students with the necessary interdisciplinary and hands-on training to prepare them for careers in these fields. At the same time, these efforts provide numerous opportunities for our postdoctoral fellows and junior faculty to serve as mentors for our scientists-in-training, especially those at the undergraduate and high school level. These early experiences in mentoring are valuable opportunities that allow these scientists to hone their mentoring skills, while working together with some of the best and brightest in the next generation. A Brief History Computational biology was established as a research discipline at the University of Pittsburgh with the vision of the Senior Vice Chancellor, Dr. Arthur S. Levine, who recruited Dr. Bahar to create a new Center for Computational Biology and Bioinformatics in March 2001, which soon became a highly visible center. The creation of the Department of Computational Biology within the School of Medicine followed in October 2004. Built on the premise of the founding Center for Computational Biology and Bioinformatics, the department was created with Dr. Ivet Bahar as the Founding Chair, to establish a home uniquely welcoming to highly interdisciplinary faculty, and to firmly establish the University of Pittsburgh in a nationally recognized leadership role in a field of tremendous growth and excitement. The department name was changed to Department of Computational and Systems Biology in 2009, to reflect the expansion in research and educational goals and activities of the department. In 2020, the contributions of our Faculty were highlighted by various awards and promotions. Within our department: Dr. Ivet Bahar was elected to the National Academy of Sciences Dr. Ivet Bahar and she and her colleagues were named recipients of awards by the 2020 Human Frontier Science Program (HFSP); Dr. Robin Lee was promoted to Associate Professor with Tenure and was named one of the 126 Sloan Research Fellows for 2020.; Dr. Nathan Lord from Harvard Medical School joined the department as an Assistant Professor in the Tenure Stream; Dr. Maria Chikina to receive 2020 Chancellor’s Distinguished Research Award that annually recognizes outstanding scholarly accomplishments of members of the University of Pittsburgh’s faculty; Dr. Anne-Ruxandra Carvunis was featured in Nature and Science magazine articles which highlighted her work on de novo gene birth, was named one of the awardees of the highly prestigious NIH Director’s New Innovator Award for 2019 and was nominated Outstanding New PI of the Month by New PI Slack (NPIS), an international group of early stage faculty.; Dr. Jianhua Xing co- authored a paper published in PNAS. We are committed to providing a home that welcomes highly interdisciplinary faculty, and that firmly establishes the University of Pittsburgh in nationally recognized leadership roles in rapidly growing and evolving fields that are driving the next wave of scientific discovery. 6 CSB Research – Leading the Field with Cutting-edge Science Increasingly complex biological problems and extremely large biological data sets have necessitated new approaches to answer many of today’s current research challenges. As one of the fields in what are now being called the “New Biologies”, Computational and Systems Biology encompasses an interdisciplinary approach to harness the power of computation to tackle the emerging big data challenges and to answer questions in biology not amenable to traditional approaches. Thus, to rise to these challenges and to continue to be a leader in this newly emerging field, CSB has set our research mission to: Advance the scientific understanding of biological systems through computational tools and theoretical approaches based on the fundamental principles of physical sciences. Design new computational/mathematical models and methods for simulating complex biological processes and for extracting useful information from accumulating data. CSB Educational Endeavors – Training the Next Generation of Scientists As one of the first departments in computational and systems biology in the nation, the faculty and staff of the department strive to establish a successful model for inter-disciplinary research by collaborating with experimentalists and theoreticians alike and training a new generation of researchers capable of meeting the next wave of scientific challenges and thereby propagating scientific advances and breakthroughs. To this end, we have also set forth the educational goals of offering first-class programs at the graduate, undergraduate, and high school levels in computational biology, all of which serve multiple purposes: (i) to introduce computational biology problems and methods to students from chemistry, physics, engineering, mathematics, and computer sciences, (ii) to teach fundamental concepts of the quantitative and physical sciences to biology and biomedical sciences students, (iii) to prepare and encourage students at all levels for a career in computational biology research, and (iv) to reach out to and recruit students from backgrounds that are underrepresented in the sciences. In all cases, the aim is to train students and postdoctoral researchers to identify and tackle complex biological problems that are beyond the reach of traditional approaches. Joint CMU-Pitt Ph.D. Program in Computational Biology To support this educational mission, the Joint CMU-Pitt Ph.D. Program in Computational Biology (CPCB) was developed as a collaborative effort between the University of Pittsburgh and Carnegie Mellon University. This program was conceived as a cross-institutional (Pitt and CMU) and cross-campus (Pitt SOM and SAS) Ph.D. program that would exploit the complementing strengths of the different universities or schools. (For additional details about this program please refer to the Teaching Activities section of the department’s Annual Report.) The CPCB is supported through the Graduate Studies Office of the School of Medicine. In the first year of the program, students’ stipends and tuition expenses are covered by their respective universities. Beginning in their second year, students’ stipend costs are supported by their respective mentors through research dollars and/or other funding sources. Tuition costs for those students enrolled in the University of Pittsburgh are allocated to their respective departments via the university’s annual step-down cost model. In its first year, the CPCB enrolled six students (4 at Pitt and 2 at CMU). Including the 13 students who joined the program in Fall 2020, the program has a total of 84 students, of which 50% are domestic. About 37% of our students are female. Through aggressive recruiting efforts and wide dissemination of program information, CPCB expects to steadily increase enrollment each year. In FY20, the following activities are planned: Creation and distribution of a more dynamic program flyer; attendance at SACNAS and ABRCMS conferences to reach out to students underrepresented in the sciences; increased recruitment at research conferences and workshops; complete overhaul of program website; social networking, and a virtual fall open house. In FY21, we anticipate that 5-6students will apply for graduation to complete their thesis requirements. In November 2005, Carnegie Mellon University, in partnership with the University of Pittsburgh, was selected to receive a $1 million grant from the Howard Hughes Medical Institute (HHMI) to support the development of the CPCB. In FY09, our program was awarded an NIBIB T32 Training Grant: Integrated, Interdisciplinary, Inter-University Ph.D. Program in Computational Biology (PIs: Ivet Bahar and Robert Murphy). This training grant was