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Computational & Systems Biology Computational & Systems Biology Menu Home About Annual Report 2019 Acknowledgements News News Archive Job Opportunities School of Medicine University of Pittsburgh Research Research Overview 2019 Publications Previous Publications Bahar Lab Ayoob Lab Benos Lab Camacho Lab Carvunis Lab Chennubhotla Lab Chikina Lab Clark Lab Faeder Lab Koes Lab Lee Lab Lezon Lab Shrivastava Lab Uttam Lab Xing Lab Drug Discovery Institute MMBioS Center Education Education Overview CoBB Masters Program Computational Biology Ph.D. TECBio REU @ Pitt UPMC Hillman Cancer Center Summer Academy Workshops People Faculty Ivet Bahar (Chair) Joseph C. Ayoob Takis Benos Jeremy Berg Carlos Camacho Anne-Ruxandra Carvunis Chakra Chennubhotla Maria Chikina James R. Faeder David Koes Robin E. C. Lee Tim Lezon Hagai Meirovitch Jacob Stewart-Ornstein D. Lansing Taylor Andreas Vogt John Vries Jianhua Xing Research Faculty Yi-Jiun Chen Mary Hongying Cheng Albert Gough Bing Liu Mark Miedel Mark Schurdak Indira Shrivastava Andrew Stern Shikhar Uttam Larry Vernetti Research Personnel Students Current Students CPCB Alumni Administration Joint/Adjunct Faculty Events Calendar CSB Seminar Series CPCB Seminar Series Distinguished Seminars External Seminar Calendars Molecular Biophysics + Structural Biology Microbiology & Molecular Genetics Biological Sciences Photo Gallery Resources Using the Cluster Departmental Hardware Web Applications AnchorQuery ANM Domain Split enoLOGOS enoLOGOS C2H2 FastContact 2.0 FOOTER 2.0 iGNM NPLA NucleoQuery oGNM P2P Pharmit PocketQuery ZINCPharmer Software 3Dmol.js aANM coMD GNM NMWiz Pharmer ProDy smina WESTPA Databases Docking Decoys Ensemble Protein D. iGNM Workshops Secure VPN Tunnel Contact Pharmacology & Drug Design Computational and theoretical approaches are revolutionizing Pharmacology and Drug Discovery. Predicting, modeling, and simulating potential therapeutic agents and their interactions with target molecules is a powerful new first step in the drug discovery process... (Read more) Cellular & Systems Biology Systems biology seeks to integrate different levels of information to understand how biological systems function at multiple scales, with the goal of developing an understandable model of a whole system. This is accomplished by studying the relationships and interactions between various parts of the particular system of interest which could... (Read more) Molecular & Structural Biology Studying the architecture, shape, and dynamics of biological macromolecules is paramount to understanding the basic mechanisms that drive the essential processes of all life. Macromolecules such as proteins and nucleic acids carry out most of the functions of a cell... (Read more) Comp Genomics & Bioinformatics These advances have enabled scientists to break new ground in the realms of genome assembly, analysis, alignment, computational evolutionary biology, protein structural alignment, interaction network analyses, small RNA species identification and characterization, and many other areas in genomics and proteomics. (Read more) Pharmacology & Drug Design Cellular & Systems Biology Molecular & Structural Biology Comp Genomics & Bioinformatics Home Increasingly complex biological problems and extremely large biological data sets have necessitated new approaches to answer many of today’s current research challenges and tackle emerging questions in biology not amenable to traditional approaches. As one of the fields in the New Biologies”, Computational and Systems Biology (CSB) encompasses an interdisciplinary approach that harnesses the power of computation and systems-level analyses to formulate and solve critical biological problems. These research programs within CSB also synergize and collaborate with the extensive basic and clinical research programs at the University of Pittsburgh and across the globe. Concomitant with our research foci, CSB is also a leader in educating and training all levels of emerging and nascent scientists, who will continue this work and identify and tackle new biological problems of the next generation. Robin Lee, Rachel Gottschalk, and Agustin Cruz Awarded AAI Intersect Fellowship The American Association of Immunologists(AAI) awarded Drs. J. Agustin Cruz and Robin E.C. Lee the Intersect Fellowship 2020. Dr. Cruz holds a PhD in Immunology and has been working for the past two years as a postdoctoral associate... (read more) James Krieger received the DCSB Best Postdoctoral Associate Award of the Year 2019 Dr. James Krieger received the DCSB Best Postdoctoral Associate Award of the Year 2019. He was nominated by his mentor, Dr. Ivet Bahar. Over the past year, he has contributed to 6 articles listed below. James is the one of three... (read more) Sanjana Gupta received the DCSB Best Student of the Year Award for 2019 at the CSB Annual Appreciation lunch Sanjana Gupta received the DCSB Best PhD Student of the Year Award for 2019 at the CSB Annual Appreciation lunch held at the University Club on Pitt’s Oakland campus, December 4, 2019. She was nominated by her co-advisors, Dr. James R. Faeder and Dr. Robin E.C. Lee for her current work on addressing the question of parameterization... (read more) Koes Lab Members Win NCATS ASPIRE Challenge Dr. Koes and his lab members were among the winners of the NCATS ASPIRE 2018 Award for the following project... (read more) The Lee lab develop a dynamic stimulation system to probe signal transduction networks in single cells Using open-source parts and 3D-printed components, the Lee lab develops a robotic system for mammalian cell cultures that accurately reproduces user-defined... (read more) Weiguang Mao and Dr. Maria Chikina Publish in Nature Methods We present pathway-level information extractor (PLIER), a broadly applicable solution for this problem that outperforms available cell proportion inference algorithms... (read more) Dr. Joseph Ayoob Named NRMN Mentor of the Month Dr. Joeseph Ayoob was named as the National Research Mentoring Network Mentor of the Month for July 2019, where he is also one of only four NRMN’s Master Mentors. Dr. Ayoob is an... (read more) Carvunis Lab publishes review on De Novo Gene Birth in PLOS Genetics Drs. Branden Van Oss and Anne-Ruxandra Carvunis review the field of de novo gene birth in their new PLOS Genetics Topic Page article. As part of the Topic Page initiative, the journal article also seeds a new Wikipedia page on the topic. (read more) A collaboration betwen the labs of Drs. Xing and Sant (Pharmacy) leads to publication in Cancer Research Targeting microenvironmental factors that foster migratory cell phenotypes is a promising strategy for halting tumor migration. However, lack of mechanistic understanding of the emergence of migratory phenotypes impedes pharmaceutical drug (read more) Machine learning model can help reduce follow up screenings to 28% of people with benign nodules A new machine learning model, developed in the Benos lab, can help reduce the unnecessary follow up screenings to people with benign nodules detected in low-dose CT scans by 28%. (read more) News & Highlights Robin Lee, Rachel Gottschalk, and Agustin Cruz Awarded AAI Intersect Fellowship James Krieger received the DCSB Best Postdoctoral Associate Award of the Year 2019 Sanjana Gupta received the DCSB Best Student of the Year Award for 2019 at the CSB Annual Appreciation lunch See more Click here to view full calendar © Department of Computational and Systems Biology | 3501 Fifth Avenue, 3064 BST3, Pittsburgh, PA 15260 | p: (412) 648-3333 f: (412)...