CONTACT INFORMATIONCREDENTIALSPUBLICATIONSDavid H. Mathews, M.D., Ph.D.Contact InformationPhone NumbersOffice: (585) 275-1734Fax: (585) 271-2683Research LabsVisit Lab WebsiteLocationsUniversity of Rochester Medical CenterSchool of Medicine and Dentistry601 Elmwood Ave, Box 712Rochester, NY 14642Faculty AppointmentsProfessor - Department of Biochemistry and Biophysics (SMD) Lynne E. Maquat Distinguished Professor - Department of Biochemistry and Biophysics (SMD) BiographyResearchOur understanding of the role of RNA in cellular processes has expanded enormously over the last two decades. Originally, RNA was understood to participate in protein expression as a carrier of genetic information (mRNA) and as an adapter molecule (tRNA) for reading the code. Then RNA was discovered to catalyze reactions, including self-splicing, phosphodiester bond cleavage, and peptide bond formation. RNA is now known to play functions in diverse cellular processes, such as development, immunity, RNA editing and modification, and post-transcriptional gene regulation. RNA is also an important player in many diseases, including Prader-Willi, b-thalassemia, and myotonic dystrophy. RNA sequences can be evolved in vitro to catalyze many reactions that are not part of the natural repertoire. Antisense and RNAi can be used to modulate gene expression. Research in the Mathews lab spans the fields of Computational Biology and Bioinformatics. We are interested in predicting RNA structure and we develop computational tools for targeting RNA with pharmaceuticals and for using RNA as a pharmaceutical (Mathews et al., 1999a). In collaboration with Doug Turner (University of Rochester) and Michael Zuker (RPI), we have developed software that predicts secondary structure, i.e. the canonical base pairs (Mathews et al., 2004; Mathews et al., 1999b). On average, 73% of base pairs are correctly predicted in a set of diverse sequences with known structures. This accuracy can be improved by constraining the structure prediction using data derived from experiments. We have also developed software that uses a partition function to predict base pairing probabilities (Mathews, 2004). Using this algorithm, secondary structures can be color annotated according to pairing probability to graphically demonstrate both high probability pairs and low probability pairs that are, on average, not as accurate. Finally, we are developing methods to predict a secondary structure common to multiple sequences (Mathews & Turner, 2002). The accuracy of structure predictions is dramatically improved by using the information contained in multiple sequences. For example, for a set of poorly predicted 5S rRNA sequences, the average accuracy of base pair prediction improves from 47.8% to 86.4% when the structure common to two sequences is determined.CredentialsEducation1994BS | University of RochesterPhysics2002PhD | University of RochesterChemistry2003MD | Univ Rochester Sch Med/DentMedicinePublicationsJournal Articles2/10/2023Schroeder GM, Akinyemi O, Malik J, Focht CM, Pritchett EM, Baker CD, McSally JP, Jenkins JL, Mathews DH, Wedekind JE. "A riboswitch separated from its ribosome-binding site still regulates translation." Nucleic acids research.. 2023 Feb 10; Epub 2023 Feb 10. 2023Cavender CE, Schroeder GM, Mathews DH, Wedekind JE. "Isothermal Titration Calorimetry Analysis of a Cooperative Riboswitch Using an Interdependent-Sites Binding Model." Methods in molecular biology.. 2023 2568:53-73. 2023Zhang H, Zhang L, Liu K, Li S, Mathews DH, Huang L. "Linear-Time Algorithms for RNA Structure Prediction." Methods in molecular biology.. 2023 2586:15-34. VIEW ALL PUBLICATIONSClose WindowSchedule an appointment with David H. Mathews, M.D., Ph.D.Please answer the following questions to help us find the right appointment for you.Important: If you believe that you have a medical or psychiatric emergency, please call 911 or go to the nearest hospital. This website is not intended for emergency care.Have you seen this provider in the last 2 years?YesNoExisting Patient Schedule or request a follow up appointment online through MyChart. If you do not have a MyChart account, please close this window and call the appointment phone number. David H. Mathews, M.D., Ph.D. is currently scheduling for the following appointment type(s): Our policy does not permit patients to establish care with multiple providers within the same practice or specialty without prior approval. If you choose a new provider in the same office, we will cancel the appointment. Please contact the office directly with questions on this policy.