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David H. Mathews, M.D., Ph.D.

David H. Mathews, M.D., Ph.D.

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About Me

Faculty Appointments

Professor - Department of Biochemistry and Biophysics (SMD)

Lynne E. Maquat Distinguished Professor - Department of Biochemistry and Biophysics (SMD)

Credentials

Education

MD | Univ Rochester Sch Med/Dent. Medicine. 2003

PhD | University of Rochester. Chemistry. 2002

BS | University of Rochester. Physics. 1994

Research

Our 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...
Our 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.

Publications

Journal Articles

Sequence Design Using RNAstructure.

Zhu M, Mathews DH

Methods in molecular biology.. 2025 2847 :17-31. Epub 1900 01 01.

Modeling and NMR Data Elucidate the Structure of a G-Quadruplex-Ligand Interaction for a Pu22T-Cyclometalated Iridium(III) System.

Reed CR, Kennedy SD, Horowitz RH, Keedakkatt Puthenpeedikakkal AM, Stern HA, Mathews DH

The journal of physical chemistry. B. 2024 November 19 Epub 11/19/2024.

Structural impact of 3-methylcytosine modification on the anticodon stem of a neuronally-enriched arginine tRNA.

Berger KD, Puthenpeedikakkal AMK, Mathews DH, Fu D

bioRxiv : the preprint server for biology.. 2024 November 18 Epub 11/18/2024.

Using the RNAstructure Software Package to Predict Conserved RNA Structures.

Mittal A, Ali SE, Mathews DH

Current protocols.. 2024 November 4 (11):e70054. Epub 1900 01 01.

memerna: Sparse RNA Folding Including Coaxial Stacking.

Courtney E, Datta A, Mathews DH, Ward M

Journal of molecular biology.. 2024 October 18 :168819. Epub 10/18/2024.

Two riboswitch classes that share a common ligand-binding fold show major differences in the ability to accommodate mutations.

Srivastava Y, Akinyemi O, Rohe TC, Pritchett EM, Baker CD, Sharma A, Jenkins JL, Mathews DH, Wedekind JE

Nucleic acids research.. 2024 October 16 Epub 10/16/2024.

DecoyFinder: Identification of Contaminants in Sets of Homologous RNA Sequences.

Zhu M, Zuber J, Tan Z, Sharma G, Mathews DH

bioRxiv : the preprint server for biology.. 2024 October 15 Epub 10/15/2024.

Comprehensive Profiling of Roquin Binding Preferences for RNA Stem-Loops.

Oberstrass L, Tants JN, Lichtenthaeler C, Ali SE, Koch L, Mathews DH, Schlundt A, Weigand J

Angewandte Chemie.. 2024 September 30 :e202412596. Epub 09/30/2024.

NNDB: An Expanded Database of Nearest Neighbor Parameters for Predicting Stability of Nucleic Acid Secondary Structures.

Mittal A, Turner DH, Mathews DH

Journal of molecular biology.. 2024 September 1436 (17):168549. Epub 03/24/2024.

LinearAlifold: Linear-time consensus structure prediction for RNA alignments.

Malik A, Zhang L, Gautam M, Dai N, Li S, Zhang H, Mathews DH, Huang L

Journal of molecular biology.. 2024 September 1436 (17):168694. Epub 07/04/2024.

Computational Resources for Molecular Biology 2024.

Casadio R, Mathews DH, Sternberg MJE

Journal of molecular biology.. 2024 September 1436 (17):168739. Epub 08/06/2024.

Estimating RNA Secondary Structure Folding Free Energy Changes with efn2.

Zuber J, Mathews DH

Methods in molecular biology.. 2024 2726 :1-13. Epub 1900 01 01.

LinearCoFold and LinearCoPartition: linear-time algorithms for secondary structure prediction of interacting RNA molecules.

Zhang H, Li S, Dai N, Zhang L, Mathews DH, Huang L

Nucleic acids research.. 2023 October 1351 (18):e94. Epub 1900 01 01.

Secondary structures that regulate mRNA translation provide insights for ASO-mediated modulation of cardiac hypertrophy.

Hedaya OM, Venkata Subbaiah KC, Jiang F, Xie LH, Wu J, Khor ES, Zhu M, Mathews DH, Proschel C, Yao P

Nature communications.. 2023 October 314 (1):6166. Epub 10/03/2023.

DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters.

Pham TM, Miffin T, Sun H, Sharp KK, Wang X, Zhu M, Hoshika S, Peterson RJ, Benner SA, Kahn JD, Mathews DH

ACS synthetic biology.. 2023 September 1512 (9):2750-2763. Epub 09/06/2023.

Algorithm for optimized mRNA design improves stability and immunogenicity.

Zhang H, Zhang L, Lin A, Xu C, Li Z, Liu K, Liu B, Ma X, Zhao F, Jiang H, Chen C, Shen H, Li H, Mathews DH, Zhang Y, Huang L

Nature.. 2023 September 621 (7978):396-403. Epub 05/02/2023.

Genome-Wide DNA Changes Acquired by Caspofungin-Adapted Mutants.

Zuber J, Sah SK, Mathews DH, Rustchenko E

Microorganisms.. 2023 July 2511 (8)Epub 07/25/2023.

Computational Resources for Molecular Biology 2023.

Mathews DH, Casadio R, Sternberg MJE

Journal of molecular biology.. 2023 July 15435 (14):168160. Epub 05/25/2023.

RNA Secondary Structure Analysis Using RNAstructure.

Ali SE, Mittal A, Mathews DH

Current protocols.. 2023 July 3 (7):e846. Epub 1900 01 01.

RNA design via structure-aware multifrontier ensemble optimization.

Zhou T, Dai N, Li S, Ward M, Mathews DH, Huang L

Bioinformatics.. 2023 June 3039 (39 Suppl 1):i563-i571. Epub 1900 01 01.

Generation and Functional Analysis of Defective Viral Genomes during SARS-CoV-2 Infection.

Zhou T, Gilliam NJ, Li S, Spandau S, Osborn RM, Connor S, Anderson CS, Mariani TJ, Thakar J, Dewhurst S, Mathews DH, Huang L, Sun Y

mBio.. 2023 June 2714 (3):e0025023. Epub 04/19/2023.

Secondary structures that regulate mRNA translation provide insights for ASO-mediated modulation of cardiac hypertrophy.

Hedaya OM, Subbaiah KCV, Jiang F, Xie LH, Wu J, Khor E, Zhu M, Mathews DH, Proschel C, Yao P

bioRxiv : the preprint server for biology.. 2023 June 15 Epub 06/15/2023.

DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters.

Pham TM, Miffin T, Sun H, Sharp KK, Wang X, Zhu M, Hoshika S, Peterson RJ, Benner SA, Kahn JD, Mathews DH

bioRxiv : the preprint server for biology.. 2023 June 8 Epub 06/08/2023.

In vivo secondary structural analysis of Influenza A virus genomic RNA.

Mirska B, Wo?niak T, Lorent D, Ruszkowska A, Peterson JM, Moss WN, Mathews DH, Kierzek R, Kierzek E

Cellular and molecular life sciences : CMLS.. 2023 May 280 (5):136. Epub 05/02/2023.

A riboswitch separated from its ribosome-binding site still regulates translation.

Schroeder GM, Akinyemi O, Malik J, Focht CM, Pritchett EM, Baker CD, McSally JP, Jenkins JL, Mathews DH, Wedekind JE

Nucleic acids research.. 2023 March 2151 (5):2464-2484. Epub 1900 01 01.

LazySampling and LinearSampling: fast stochastic sampling of RNA secondary structure with applications to SARS-CoV-2.

Zhang H, Li S, Zhang L, Mathews DH, Huang L

Nucleic acids research.. 2023 January 2551 (2):e7. Epub 1900 01 01.

Isothermal Titration Calorimetry Analysis of a Cooperative Riboswitch Using an Interdependent-Sites Binding Model.

Cavender CE, Schroeder GM, Mathews DH, Wedekind JE

Methods in molecular biology.. 2023 2568 :53-73. Epub 1900 01 01.

Linear-Time Algorithms for RNA Structure Prediction.

Zhang H, Zhang L, Liu K, Li S, Mathews DH, Huang L

Methods in molecular biology.. 2023 2586 :15-34. Epub 1900 01 01.

Intrinsically Unstructured Sequences in the mRNA 3' UTR Reduce the Ability of Poly(A) Tail to Enhance Translation.

Lai WC, Zhu M, Belinite M, Ballard G, Mathews DH, Ermolenko DN

Journal of molecular biology.. 2022 December 30434 (24):167877. Epub 11/08/2022.

A Test and Refinement of Folding Free Energy Nearest Neighbor Parameters for RNA Including N-Methyladenosine.

Szabat M, Prochota M, Kierzek R, Kierzek E, Mathews DH

Journal of molecular biology.. 2022 September 30434 (18):167632. Epub 05/16/2022.

Deep learning models for RNA secondary structure prediction (probably) do not generalize across families.

Szikszai M, Wise M, Datta A, Ward M, Mathews DH

Bioinformatics.. 2022 August 1038 (16):3892-3899. Epub 1900 01 01.

Computational Resources for Molecular Biology 2022.

Casadio R, Mathews DH, Sternberg MJE

Journal of molecular biology.. 2022 June 15434 (11):167625. Epub 05/13/2022.

Quantitative prediction of variant effects on alternative splicing in using endogenous pre-messenger RNA structure probing.

Kumar J, Lackey L, Waldern JM, Dey A, Mustoe AM, Weeks K, Mathews DH, Laederach A

eLife.. 2022 June 1311 Epub 06/13/2022.

Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of nucleotide variants at the center of the pre-mRNA splice site signal.

Glasser E, Maji D, Biancon G, Puthenpeedikakkal AMK, Cavender CE, Tebaldi T, Jenkins JL, Mathews DH, Halene S, Kielkopf CL

Nucleic acids research.. 2022 May 2050 (9):5299-5312. Epub 1900 01 01.

Nearest neighbor rules for RNA helix folding thermodynamics: improved end effects.

Zuber J, Schroeder SJ, Sun H, Turner DH, Mathews DH

Nucleic acids research.. 2022 May 2050 (9):5251-5262. Epub 1900 01 01.

Secondary structure prediction for RNA sequences including N-methyladenosine.

Kierzek E, Zhang X, Watson RM, Kennedy SD, Szabat M, Kierzek R, Mathews DH

Nature communications.. 2022 March 1113 (1):1271. Epub 03/11/2022.

Secondary Structure of Influenza A Virus Genomic Segment 8 RNA Folded in a Cellular Environment.

Szutkowska B, Wieczorek K, Kierzek R, Zmora P, Peterson JM, Moss WN, Mathews DH, Kierzek E

International journal of molecular sciences.. 2022 February 2323 (5)Epub 02/23/2022.

Specific length and structure rather than high thermodynamic stability enable regulatory mRNA stem-loops to pause translation.

Bao C, Zhu M, Nykonchuk I, Wakabayashi H, Mathews DH, Ermolenko DN

Nature communications.. 2022 February 2113 (1):988. Epub 02/21/2022.

A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control.

Schroeder GM, Cavender CE, Blau ME, Jenkins JL, Mathews DH, Wedekind JE

Nature communications.. 2022 January 1113 (1):199. Epub 01/11/2022.

LinearTurboFold: Linear-time global prediction of conserved structures for RNA homologs with applications to SARS-CoV-2.

Li S, Zhang H, Zhang L, Liu K, Liu B, Mathews DH, Huang L

Proceedings of the National Academy of Sciences of the United States of America.. 2021 December 28118 (52)Epub 1900 01 01.

LazySampling and LinearSampling: Fast Stochastic Sampling of RNA Secondary Structure with Applications to SARS-CoV-2.

Zhang H, Zhang L, Li S, Mathews DH, Huang L

bioRxiv : the preprint server for biology.. 2021 November 24 Epub 11/24/2021.

Making ends meet: New functions of mRNA secondary structure.

Ermolenko DN, Mathews DH

Wiley interdisciplinary reviews. RNA.. 2021 March 12 (2):e1611. Epub 06/29/2020.

Inverse RNA Folding Workflow to Design and Test Ribozymes that Include Pseudoknots.

Kayedkhordeh M, Yamagami R, Bevilacqua PC, Mathews DH

Methods in molecular biology.. 2021 2167 :113-143. Epub 1900 01 01.

Arginine Forks Are a Widespread Motif to Recognize Phosphate Backbones and Guanine Nucleobases in the RNA Major Groove.

Chavali SS, Cavender CE, Mathews DH, Wedekind JE

Journal of the American Chemical Society.. 2020 November 25142 (47):19835-19839. Epub 11/10/2020.

Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation.

Schroeder GM, Dutta D, Cavender CE, Jenkins JL, Pritchett EM, Baker CD, Ashton JM, Mathews DH, Wedekind JE

Nucleic acids research.. 2020 August 2048 (14):8146-8164. Epub 1900 01 01.

LinearPartition: linear-time approximation of RNA folding partition function and base-pairing probabilities.

Zhang H, Zhang L, Mathews DH, Huang L

Bioinformatics.. 2020 July 136 (Suppl_1):i258-i267. Epub 1900 01 01.

Determining parameters for non-linear models of multi-loop free energy change.

Ward M, Sun H, Datta A, Wise M, Mathews DH

Bioinformatics.. 2019 November 135 (21):4298-4306. Epub 1900 01 01.

CRISPR-Cas9-based mutagenesis frequently provokes on-target mRNA misregulation.

Tuladhar R, Yeu Y, Tyler Piazza J, Tan Z, Rene Clemenceau J, Wu X, Barrett Q, Herbert J, Mathews DH, Kim J, Hyun Hwang T, Lum L

Nature communications.. 2019 September 610 (1):4056. Epub 09/06/2019.

LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search.

Huang L, Zhang H, Deng D, Zhao K, Liu K, Hendrix DA, Mathews DH

Bioinformatics.. 2019 July 1535 (14):i295-i304. Epub 1900 01 01.

How to benchmark RNA secondary structure prediction accuracy.

Mathews DH

Methods : a companion to Methods in enzymology.. 2019 June 1162-163 :60-67. Epub 04/02/2019.

Estimating uncertainty in predicted folding free energy changes of RNA secondary structures.

Zuber J, Mathews DH

RNA.. 2019 June 25 (6):747-754. Epub 04/05/2019.

Conservation of location of several specific inhibitory codon pairs in the Saccharomyces sensu stricto yeasts reveals translational selection.

Ghoneim DH, Zhang X, Brule CE, Mathews DH, Grayhack EJ

Nucleic acids research.. 2019 February 2047 (3):1164-1177. Epub 1900 01 01.

Design of highly active double-pseudoknotted ribozymes: a combined computational and experimental study.

Yamagami R, Kayedkhordeh M, Mathews DH, Bevilacqua PC

Nucleic acids research.. 2019 January 1047 (1):29-42. Epub 1900 01 01.

Identification of new high affinity targets for Roquin based on structural conservation.

Braun J, Fischer S, Xu ZZ, Sun H, Ghoneim DH, Gimbel AT, Plessmann U, Urlaub H, Mathews DH, Weigand JE

Nucleic acids research.. 2018 December 1446 (22):12109-12125. Epub 1900 01 01.

Chemically Accurate Relative Folding Stability of RNA Hairpins from Molecular Simulations.

Smith LG, Tan Z, Spasic A, Dutta D, Salas-Estrada LA, Grossfield A, Mathews DH

Journal of chemical theory and computation.. 2018 December 1114 (12):6598-6612. Epub 11/27/2018.

Accelerated RNA secondary structure design using preselected sequences for helices and loops.

Bellaousov S, Kayedkhordeh M, Peterson RJ, Mathews DH

RNA.. 2018 November 24 (11):1555-1567. Epub 08/10/2018.

Analysis of RNA nearest neighbor parameters reveals interdependencies and quantifies the uncertainty in RNA secondary structure prediction.

Zuber J, Cabral BJ, McFadyen I, Mauger DM, Mathews DH

RNA.. 2018 November 24 (11):1568-1582. Epub 08/13/2018.

mRNAs and lncRNAs intrinsically form secondary structures with short end-to-end distances.

Lai WC, Kayedkhordeh M, Cornell EV, Farah E, Bellaousov S, Rietmeijer R, Salsi E, Mathews DH, Ermolenko DN

Nature communications.. 2018 October 189 (1):4328. Epub 10/18/2018.

Structure of HIV TAR in complex with a Lab-Evolved RRM provides insight into duplex RNA recognition and synthesis of a constrained peptide that impairs transcription.

Belashov IA, Crawford DW, Cavender CE, Dai P, Beardslee PC, Mathews DH, Pentelute BL, McNaughton BR, Wedekind JE

Nucleic acids research.. 2018 July 2746 (13):6401-6415. Epub 1900 01 01.

Improving RNA nearest neighbor parameters for helices by going beyond the two-state model.

Spasic A, Berger KD, Chen JL, Seetin MG, Turner DH, Mathews DH

Nucleic acids research.. 2018 June 146 (10):4883-4892. Epub 1900 01 01.

Molecular dynamics correctly models the unusual major conformation of the GAGU RNA internal loop and with NMR reveals an unusual minor conformation.

Spasic A, Kennedy SD, Needham L, Manoharan M, Kierzek R, Turner DH, Mathews D

RNA.. 2018 May 24 (5):656-672. Epub 02/06/2018.

Surprising Sequence Effects on GU Closure of Symmetric 2 × 2 Nucleotide RNA Internal Loops.

Berger KD, Kennedy SD, Schroeder SJ, Znosko BM, Sun H, Mathews DH, Turner DH

Biochemistry.. 2018 April 1057 (14):2121-2131. Epub 03/23/2018.

Widespread temperature sensitivity and tRNA decay due to mutations in a yeast tRNA.

Payea MJ, Sloma MF, Kon Y, Young DL, Guy MP, Zhang X, De Zoysa T, Fields S, Mathews DH, Phizicky EM

RNA.. 2018 March 24 (3):410-422. Epub 12/19/2017.

Modeling RNA secondary structure folding ensembles using SHAPE mapping data.

Spasic A, Assmann SM, Bevilacqua PC, Mathews DH

Nucleic acids research.. 2018 January 946 (1):314-323. Epub 1900 01 01.

TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs.

Tan Z, Fu Y, Sharma G, Mathews DH

Nucleic acids research.. 2017 November 1645 (20):11570-11581. Epub 1900 01 01.

Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs.

Sloma MF, Mathews DH

PLoS computational biology.. 2017 November 13 (11):e1005827. Epub 11/06/2017.

Physics-based all-atom modeling of RNA energetics and structure.

Smith LG, Zhao J, Mathews DH, Turner DH

Wiley interdisciplinary reviews. RNA.. 2017 September 8 (5)Epub 1900 01 01.

Advanced multi-loop algorithms for RNA secondary structure prediction reveal that the simplest model is best.

Ward M, Datta A, Wise M, Mathews DH

Nucleic acids research.. 2017 August 2145 (14):8541-8550. Epub 1900 01 01.

Modeling RNA Secondary Structure with Sequence Comparison and Experimental Mapping Data.

Tan Z, Sharma G, Mathews DH

Biophysical journal.. 2017 July 25113 (2):330-338. Epub 07/20/2017.

A sensitivity analysis of RNA folding nearest neighbor parameters identifies a subset of free energy parameters with the greatest impact on RNA secondary structure prediction.

Zuber J, Sun H, Zhang X, McFadyen I, Mathews DH

Nucleic acids research.. 2017 June 245 (10):6168-6176. Epub 1900 01 01.

Structure-Function Model for Kissing Loop Interactions That Initiate Dimerization of Ty1 RNA.

Gamache ER, Doh JH, Ritz J, Laederach A, Bellaousov S, Mathews DH, Curcio MJ

Viruses.. 2017 April 269 (5)Epub 04/26/2017.

Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular Dynamics.

Aytenfisu AH, Spasic A, Grossfield A, Stern HA, Mathews DH

Journal of chemical theory and computation.. 2017 February 1413 (2):900-915. Epub 01/24/2017.

RNA Secondary Structure Prediction.

Mathews DH, Turner DH, Watson RM

Current protocols in nucleic acid chemistry. 2016 December 167 :11.2.1-11.2.19. Epub 12/01/2016.

Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures.

Sloma MF, Mathews DH

RNA.. 2016 December 22 (12):1808-1818. Epub 10/19/2016.

AccessFold: predicting RNA-RNA interactions with consideration for competing self-structure.

DiChiacchio L, Sloma MF, Mathews DH

Bioinformatics.. 2016 April 132 (7):1033-9. Epub 11/20/2015.

Bridging the gap between in vitro and in vivo RNA folding.

Leamy KA, Assmann SM, Mathews DH, Bevilacqua PC

Quarterly reviews of biophysics.. 2016 January 49 :e10. Epub 06/24/2016.

Secondary Structure Prediction of Single Sequences Using RNAstructure.

Xu ZZ, Mathews DH

Methods in molecular biology.. 2016 1490 :15-34. Epub 1900 01 01.

Prediction of Secondary Structures Conserved in Multiple RNA Sequences.

Xu ZZ, Mathews DH

Methods in molecular biology.. 2016 1490 :35-50. Epub 1900 01 01.

Predicting RNA-RNA Interactions Using RNAstructure.

DiChiacchio L, Mathews DH

Methods in molecular biology.. 2016 1490 :51-62. Epub 1900 01 01.

Experiment-Assisted Secondary Structure Prediction with RNAstructure.

Xu ZZ, Mathews DH

Methods in molecular biology.. 2016 1490 :163-76. Epub 1900 01 01.

Nuclear Magnetic Resonance-Assisted Prediction of Secondary Structure for RNA: Incorporation of Direction-Dependent Chemical Shift Constraints.

Chen JL, Bellaousov S, Tubbs JD, Kennedy SD, Lopez MJ, Mathews DH, Turner DH

Biochemistry.. 2015 November 1754 (45):6769-82. Epub 11/03/2015.

Molecular mechanism for preQ1-II riboswitch function revealed by molecular dynamics.

Aytenfisu AH, Liberman JA, Wedekind JE, Mathews DH

RNA.. 2015 November 21 (11):1898-907. Epub 09/14/2015.

Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data.

Wu Y, Shi B, Ding X, Liu T, Hu X, Yip KY, Yang ZR, Mathews DH, Lu ZJ

Nucleic acids research.. 2015 September 343 (15):7247-59. Epub 07/13/2015.

Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics.

Liberman JA, Suddala KC, Aytenfisu A, Chan D, Belashov IA, Salim M, Mathews DH, Spitale RC, Walter NG, Wedekind JE

Proceedings of the National Academy of Sciences of the United States of America.. 2015 July 7112 (27):E3485-94. Epub 06/23/2015.

Improving RNA secondary structure prediction with structure mapping data.

Sloma MF, Mathews DH

Methods in enzymology.. 2015 553 :91-114. Epub 02/03/2015.

Discovery of Novel ncRNA Sequences in Multiple Genome Alignments on the Basis of Conserved and Stable Secondary Structures.

Fu Y, Xu ZZ, Lu ZJ, Zhao S, Mathews DH

PloS one.. 2015 10 (6):e0130200. Epub 06/15/2015.

Dynalign II: common secondary structure prediction for RNA homologs with domain insertions.

Fu Y, Sharma G, Mathews DH

Nucleic acids research.. 2014 December 1642 (22):13939-48. Epub 1900 01 01.

Influence of Sequence and Covalent Modifications on Yeast tRNA Dynamics.

Zhang X, Walker RC, Phizicky EM, Mathews DH

Journal of chemical theory and computation.. 2014 August 1210 (8):3473-3483. Epub 05/28/2014.

Identification of the determinants of tRNA function and susceptibility to rapid tRNA decay by high-throughput in vivo analysis.

Guy MP, Young DL, Payea MJ, Zhang X, Kon Y, Dean KM, Grayhack EJ, Mathews DH, Fields S, Phizicky EM

Genes & development.. 2014 August 128 (15):1721-32. Epub 1900 01 01.

Using the RNAstructure Software Package to Predict Conserved RNA Structures.

Mathews DH

Current protocols in bioinformatics. 2014 June 1746 :12.4.1-12.4.22. Epub 06/17/2014.

RNA Secondary Structure Analysis Using RNAstructure.

Mathews DH

Current protocols in bioinformatics. 2014 June 1746 :12.6.1-12.6.25. Epub 06/17/2014.

Modified Amber Force Field Correctly Models the Conformational Preference for Tandem GA pairs in RNA.

Aytenfisu AH, Spasic A, Seetin MG, Serafini J, Mathews DH

Journal of chemical theory and computation.. 2014 March 1110 (3):1292-1301. Epub 01/22/2014.

Accelerating calculations of RNA secondary structure partition functions using GPUs.

Stern HA, Mathews DH

Algorithms for molecular biology : AMB.. 2013 November 18 (1):29. Epub 11/01/2013.

RNAstructure: Web servers for RNA secondary structure prediction and analysis.

Bellaousov S, Reuter JS, Seetin MG, Mathews DH

Nucleic acids research.. 2013 July 41 (Web Server issue):W471-4. Epub 04/24/2013.

Pyrvinium pamoate changes alternative splicing of the serotonin receptor 2C by influencing its RNA structure.

Shen M, Bellaousov S, Hiller M, de La Grange P, Creamer TP, Malina O, Sperling R, Mathews DH, Stoilov P, Stamm S

Nucleic acids research.. 2013 April 141 (6):3819-32. Epub 02/07/2013.

Air proteins control differential TRAMP substrate specificity for nuclear RNA surveillance.

Schmidt K, Xu Z, Mathews DH, Butler JS

RNA.. 2012 October 18 (10):1934-45. Epub 08/24/2012.

The Amber ff99 Force Field Predicts Relative Free Energy Changes for RNA Helix Formation.

Spasic A, Serafini J, Mathews DH

Journal of chemical theory and computation.. 2012 July 108 (7):2497-2505. Epub 06/05/2012.

TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots.

Seetin MG, Mathews DH

Bioinformatics.. 2012 March 1528 (6):792-8. Epub 01/27/2012.

Statistical evaluation of improvement in RNA secondary structure prediction.

Xu Z, Almudevar A, Mathews DH

Nucleic acids research.. 2012 February 40 (4):e26. Epub 12/01/2011.

RNA structure prediction: an overview of methods.

Seetin MG, Mathews DH

Methods in molecular biology.. 2012 905 :99-122. Epub 1900 01 01.

Molecular Mechanics Investigation of an Adenine-Adenine Non-Canonical Pair Conformational Change.

Van Nostrand KP, Kennedy SD, Turner DH, Mathews DH

Journal of chemical theory and computation.. 2011 November 87 (11):3779-3792. Epub 1900 01 01.

Automated RNA tertiary structure prediction from secondary structure and low-resolution restraints.

Seetin MG, Mathews DH

Journal of computational chemistry.. 2011 July 3032 (10):2232-44. Epub 04/21/2011.

Biophysical analysis of influenza A virus RNA promoter at physiological temperatures.

Noble E, Mathews DH, Chen JL, Turner DH, Takimoto T, Kim B

The Journal of biological chemistry.. 2011 July 1286 (26):22965-70. Epub 05/09/2011.

TurboFold: iterative probabilistic estimation of secondary structures for multiple RNA sequences.

Harmanci AO, Sharma G, Mathews DH

BMC bioinformatics.. 2011 April 2012 :108. Epub 04/20/2011.

Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences.

Xu Z, Mathews DH

Bioinformatics.. 2011 March 127 (5):626-32. Epub 12/30/2010.

Fluorescence competition and optical melting measurements of RNA three-way multibranch loops provide a revised model for thermodynamic parameters.

Liu B, Diamond JM, Mathews DH, Turner DH

Biochemistry.. 2011 February 850 (5):640-53. Epub 01/14/2011.

Folding and finding RNA secondary structure.

Mathews DH, Moss WN, Turner DH

Cold Spring Harbor perspectives in biology.. 2010 December 2 (12):a003665. Epub 08/04/2010.

ProbKnot: fast prediction of RNA secondary structure including pseudoknots.

Bellaousov S, Mathews DH

RNA.. 2010 October 16 (10):1870-80. Epub 08/10/2010.

RNAstructure: software for RNA secondary structure prediction and analysis.

Reuter JS, Mathews DH

BMC bioinformatics.. 2010 March 1511 :129. Epub 03/15/2010.

An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5'-UAA/5'-GAN Internal Loops Studied by Molecular Dynamics Methods.

Réblová K, St?elcová Z, Kulhánek P, Beššeová I, Mathews DH, Van Nostrand K, Yildirim I, Turner DH, Šponer J

Journal of chemical theory and computation.. 2010 March 96 (3):910-29. Epub 1900 01 01.

RNA pseudoknots: folding and finding.

Liu B, Mathews DH, Turner DH

F1000 biology reports. 2010 January 272 :8. Epub 01/27/2010.

NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure.

Turner DH, Mathews DH

Nucleic acids research.. 2010 January 38 (Database issue):D280-2. Epub 10/30/2009.

A sequence similar to tRNA 3 Lys gene is embedded in HIV-1 U3-R and promotes minus-strand transfer.

Piekna-Przybylska D, Dichiacchio L, Mathews DH, Bambara RA

Nature structural & molecular biology.. 2010 January 17 (1):83-9. Epub 12/06/2009.

Using OligoWalk to identify efficient siRNA sequences.

Mathews DH

Methods in molecular biology.. 2010 629 :109-21. Epub 1900 01 01.

Factors that determine the efficiency of HIV-1 strand transfer initiated at a specific site.

Rigby ST, Van Nostrand KP, Rose AE, Gorelick RJ, Mathews DH, Bambara RA

Journal of molecular biology.. 2009 December 11394 (4):694-707. Epub 10/21/2009.

Improved RNA secondary structure prediction by maximizing expected pair accuracy.

Lu ZJ, Gloor JW, Mathews DH

RNA.. 2009 October 15 (10):1805-13. Epub 08/24/2009.

Stochastic sampling of the RNA structural alignment space.

Harmanci AO, Sharma G, Mathews DH

Nucleic acids research.. 2009 July 37 (12):4063-75. Epub 05/08/2009.

Accurate SHAPE-directed RNA structure determination

Deigan, K. E.; Li, T. W.; Mathews, D. H.; Weeks, K. M.;.

Proc Natl Acad Sci U S A. 2009; 106(31): 97-102.

NMR-assisted prediction of RNA secondary structure: identification of a probable pseudoknot in the coding region of an R2 retrotransposon.

Hart JM, Kennedy SD, Mathews DH, Turner DH

Journal of the American Chemical Society.. 2008 August 6130 (31):10233-9. Epub 07/10/2008.

OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics.

Lu ZJ, Mathews DH

Nucleic acids research.. 2008 July 136 (Web Server issue):W104-8. Epub 05/19/2008.

Fundamental differences in the equilibrium considerations for siRNA and antisense oligodeoxynucleotide design.

Lu ZJ, Mathews DH

Nucleic acids research.. 2008 June 36 (11):3738-45. Epub 05/15/2008.

PARTS: probabilistic alignment for RNA joinT secondary structure prediction.

Harmanci AO, Sharma G, Mathews DH

Nucleic acids research.. 2008 April 36 (7):2406-17. Epub 02/26/2008.

Efficient siRNA selection using hybridization thermodynamics.

Lu ZJ, Mathews DH

Nucleic acids research.. 2008 February 36 (2):640-7. Epub 12/10/2007.

High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states

Wilkinson, K. A.; Gorelick, R. J.; Vasa, S. M.; Guex, N.; Rein, A.; Mathews, D. H.; Giddings, M. C.; Weeks, K. M.;.

PLoS Biol. 2008; 6(34): e96.

NMR reveals the absence of hydrogen bonding in adjacent UU and AG mismatches in an isolated internal loop from ribosomal RNA.

Shankar N, Xia T, Kennedy SD, Krugh TR, Mathews DH, Turner DH

Biochemistry.. 2007 November 646 (44):12665-78. Epub 10/11/2007.

Efficient parameter estimation for RNA secondary structure prediction.

Andronescu M, Condon A, Hoos HH, Mathews DH, Murphy KP

Bioinformatics.. 2007 July 123 (13):i19-28. Epub 1900 01 01.

Predicting helical coaxial stacking in RNA multibranch loops.

Tyagi R, Mathews DH

RNA.. 2007 July 13 (7):939-51. Epub 05/16/2007.

Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign.

Harmanci AO, Sharma G, Mathews DH

BMC bioinformatics.. 2007 April 198 :130. Epub 04/19/2007.

RNA secondary structure prediction.

Mathews DH, Turner DH, Zuker M

Current protocols in nucleic acid chemistry. 2007 March Chapter 11 :Unit 11.2. Epub 1900 01 01.

Interpreting oligonucleotide microarray data to determine RNA secondary structure: application to the 3' end of Bombyx mori R2 RNA.

Duan S, Mathews DH, Turner DH

Biochemistry.. 2006 August 1545 (32):9819-32. Epub 1900 01 01.

Revolutions in RNA secondary structure prediction.

Mathews DH

Journal of molecular biology.. 2006 June 9359 (3):526-32. Epub 02/06/2006.

Prediction of RNA secondary structure by free energy minimization.

Mathews DH, Turner DH

Current opinion in structural biology.. 2006 June 16 (3):270-8. Epub 05/19/2006.

Nudged elastic band calculation of minimal energy paths for the conformational change of a GG non-canonical pair.

Mathews DH, Case DA

Journal of molecular biology.. 2006 April 14357 (5):1683-93. Epub 02/03/2006.

The RNA Ontology Consortium: an open invitation to the RNA community.

Leontis NB, Altman RB, Berman HM, Brenner SE, Brown JW, Engelke DR, Harvey SC, Holbrook SR, Jossinet F, Lewis SE, Major F, Mathews DH, Richardson JS, Williamson JR, Westhof E

RNA.. 2006 April 12 (4):533-41. Epub 02/16/2006.

Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change.

Uzilov AV, Keegan JM, Mathews DH

BMC bioinformatics.. 2006 March 277 :173. Epub 03/27/2006.

RNA secondary structure analysis using RNAstructure.

Mathews DH

Current protocols in bioinformatics. 2006 March Chapter 12 :Unit 12.6. Epub 1900 01 01.

Nearest neighbor parameters for Watson-Crick complementary heteroduplexes formed between 2'-O-methyl RNA and RNA oligonucleotides.

Kierzek E, Mathews DH, Ciesielska A, Turner DH, Kierzek R

Nucleic acids research.. 2006 34 (13):3609-14. Epub 07/26/2006.

A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation.

Lu ZJ, Turner DH, Mathews DH

Nucleic acids research.. 2006 34 (17):4912-24. Epub 09/18/2006.

Predicting a set of minimal free energy RNA secondary structures common to two sequences.

Mathews DH

Bioinformatics.. 2005 May 1521 (10):2246-53. Epub 02/24/2005.

The influence of locked nucleic acid residues on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexes.

Kierzek E, Ciesielska A, Pasternak K, Mathews DH, Turner DH, Kierzek R

Nucleic acids research.. 2005 33 (16):5082-93. Epub 09/09/2005.

Predicting the secondary structure common to two RNA sequences with Dynalign.

Mathews D

Current protocols in bioinformatics. 2004 December Chapter 12 :Unit 12.4. Epub 1900 01 01.

Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization.

Mathews DH

RNA.. 2004 August 10 (8):1178-90. Epub 1900 01 01.

Secondary structure models of the 3' untranslated regions of diverse R2 RNAs.

Ruschak AM, Mathews DH, Bibillo A, Spinelli SL, Childs JL, Eickbush TH, Turner DH

RNA.. 2004 June 10 (6):978-87. Epub 1900 01 01.

Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure.

Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH

Proceedings of the National Academy of Sciences of the United States of America.. 2004 May 11101 (19):7287-92. Epub 05/03/2004.

Thermodynamic criteria for high hit rate antisense oligonucleotide design.

Matveeva OV, Mathews DH, Tsodikov AD, Shabalina SA, Gesteland RF, Atkins JF, Freier SM

Nucleic acids research.. 2003 September 131 (17):4989-94. Epub 1900 01 01.

Use of chemical modification to elucidate RNA folding pathways.

Mathews DH, Turner DH

Current protocols in nucleic acid chemistry. 2002 August Chapter 11 :Unit 11.9. Epub 1900 01 01.

Dynalign: an algorithm for finding the secondary structure common to two RNA sequences.

Mathews DH, Turner DH

Journal of molecular biology.. 2002 March 22317 (2):191-203. Epub 1900 01 01.

Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops.

Mathews DH, Turner DH

Biochemistry.. 2002 January 2241 (3):869-80. Epub 1900 01 01.

Thermodynamics of three-way multibranch loops in RNA.

Diamond JM, Turner DH, Mathews DH

Biochemistry.. 2001 June 1240 (23):6971-81. Epub 1900 01 01.

Predicting oligonucleotide affinity to nucleic acid targets.

Mathews DH, Burkard ME, Freier SM, Wyatt JR, Turner DH

RNA.. 1999 November 5 (11):1458-69. Epub 1900 01 01.

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.

Mathews DH, Sabina J, Zuker M, Turner DH

Journal of molecular biology.. 1999 May 21288 (5):911-40. Epub 1900 01 01.

Secondary structure model of the RNA recognized by the reverse transcriptase from the R2 retrotransposable element.

Mathews DH, Banerjee AR, Luan DD, Eickbush TH, Turner DH

RNA.. 1997 January 3 (1):1-16. Epub 1900 01 01.

Thermodynamic and activation parameters for binding of a pyrene-labeled substrate by the Tetrahymena ribozyme: docking is not diffusion-controlled and is driven by a favorable entropy change.

Li Y, Bevilacqua PC, Mathews D, Turner DH

Biochemistry.. 1995 November 734 (44):14394-9. Epub 1900 01 01.

Elastic scattering and quasielastic transfer for 32S+96,100Mo at Elab=180 MeV.

Herrick DM, Wolfs FL, Bryan DC, Freeman CG, Kurz KL, Mathews DH, Perera PA, Zanni MT

Physical review. C, Nuclear physics.. 1995 August 52 (2):744-754. Epub 1900 01 01.

New Focal Plane Detector System for the Rochester Recoil Mass Spectrometer

Freeman, C. G.; Herrick, D. M.; Bryan, D. C.; Kurtz, K. L.; Mathews, D. H.; Perera, P. A. A.; Wolfs, F. L. H.; Zanni, M. T. ;.

Nuclear Instruments and Methods. 1995; 357(3): 450-457.

Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding.

Walter AE, Turner DH, Kim J, Lyttle MH, Müller P, Mathews DH, Zuker M

Proceedings of the National Academy of Sciences of the United States of America.. 1994 September 2791 (20):9218-22. Epub 1900 01 01.

Breakup of 87 MeV 11B.

Wolfs FL, White CA, Bryan DC, Freeman CG, Herrick DM, Kurz KL, Mathews DH, Perera PA, Zanni MT

Physical review. C, Nuclear physics.. 1994 May 49 (5):2538-2548. Epub 1900 01 01.