David H. Mathews

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Michael ZukerRensselaer Polytechnic InstituteVerified email at alum.mit.edu
Stanislav BellaousovUniversity of RochesterVerified email at urmc.rochester.edu
Liang HuangProfessor of Computer Science and (by courtesy) Biochemistry/Biophysics, Oregon State UniversityVerified email at oregonstate.edu
Kevin M WeeksKenan Distinguished Professor, University of North Carolina - Chapel HillVerified email at unc.edu
He ZhangRaina Biosciences, Baidu Research USA (previously), Oregon State University (previously)Verified email at rainabio.com
Gaurav SharmaUniversity of RochesterVerified email at rochester.edu
Liang ZhangZhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of SciencesVerified email at him.cas.cn
Joseph WedekindUniversity of Rochester School of Medicine and DentistryVerified email at rochester.edu
Zhi John LuAssociate Professor, Tsinghua UniversityVerified email at tsinghua.edu.cn
Zhenjiang Zech Xustate key lab of food science and resources, nuVerified email at ucsd.edu
Arif Ozgun HarmanciUniversity of Texas Health Science Center at HoustonVerified email at harmancilab.org
Chapin E. CavenderOpen Force Field Initiative, University of California San Diego, Skaggs School of PharmacyVerified email at health.ucsd.edu
Zhen TanYale UniversityVerified email at yale.edu
Aleksandar SpasicWuXi AppTec, Natick, MAVerified email at wuxiapptec.com
Xiaoju ZhangMETiS TherapeuticsVerified email at metispharma.com
Philip BevilacquaProfessor of Chemistry, The Pennsylvania State UniversityVerified email at psu.edu
Alan GrossfieldBiochemistry and Biophysics, University of Rochester Medical CenterVerified email at urmc.rochester.edu
Hongying SunUniversity of RochesterVerified email at rochester.edu
Sizhen LiOregon State UniversityVerified email at oregonstate.edu
Anne CondonProfessor of Computer Science, University of British ColumbiaVerified email at cs.ubc.ca

David H. Mathews

Department of Biochemistry and Biophysics, University of Rochester Medical Center

Verified email at urmc.rochester.edu - Homepage

Computational Biology RNA RNA Biology


Title Sort by citations Sort by year Sort by title	Cited by Cited by	Year
Amber 10 DA Case, TA Darden, TE Cheatham, CL Simmerling, J Wang, RE Duke, ... University of California, 2008	12254*	2008
Amber 2023 DA Case, HM Aktulga, K Belfon, IY Ben-Shalom, JT Berryman, SR Brozell, ... University of California, San Francisco, 2023	5973	2023
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure DH Mathews, J Sabina, M Zuker, DH Turner Journal of molecular biology 288 (5), 911-940, 1999	4887	1999
RNAstructure: software for RNA secondary structure prediction and analysis JS Reuter, DH Mathews BMC bioinformatics 11, 1-9, 2010	2119	2010
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure DH Mathews, MD Disney, JL Childs, SJ Schroeder, M Zuker, DH Turner Proceedings of the National Academy of Sciences 101 (19), 7287-7292, 2004	1932	2004
Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide M Zuker, DH Mathews, DH Turner RNA biochemistry and biotechnology, 11-43, 1999	1458	1999
Accurate SHAPE-directed RNA structure determination KE Deigan, TW Li, DH Mathews, KM Weeks Proceedings of the National Academy of Sciences 106 (1), 97-102, 2009	804	2009
NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure DH Turner, DH Mathews Nucleic acids research 38 (suppl_1), D280-D282, 2010	666	2010
Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. AE Walter, DH Turner, J Kim, MH Lyttle, P Müller, DH Mathews, M Zuker Proceedings of the National Academy of Sciences 91 (20), 9218-9222, 1994	643	1994
Prediction of RNA secondary structure by free energy minimization DH Mathews, DH Turner Current opinion in structural biology 16 (3), 270-278, 2006	536	2006
Dynalign: an algorithm for finding the secondary structure common to two RNA sequences DH Mathews, DH Turner Journal of molecular biology 317 (2), 191-203, 2002	535	2002
AMBER 10; University of California: San Francisco, 2008 DA Case, TA Darden, TE Cheatham III, CL Simmerling, J Wang, RE Duke, ... Academic Search There is no corresponding record for this reference, 2008	508	2008
High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states KA Wilkinson, RJ Gorelick, SM Vasa, N Guex, A Rein, DH Mathews, ... PLoS biology 6 (4), e96, 2008	481	2008
Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization DH Mathews Rna 10 (8), 1178-1190, 2004	469	2004
RNAstructure: web servers for RNA secondary structure prediction and analysis S Bellaousov, JS Reuter, MG Seetin, DH Mathews Nucleic acids research 41 (W1), W471-W474, 2013	459	2013
FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing JG Underwood, AV Uzilov, S Katzman, CS Onodera, JE Mainzer, ... Nature methods 7 (12), 995-1001, 2010	393	2010
Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots CE Hajdin, S Bellaousov, W Huggins, CW Leonard, DH Mathews, ... Proceedings of the National Academy of Sciences 110 (14), 5498-5503, 2013	366	2013
Predicting oligonucleotide affinity to nucleic acid targets DH Mathews, ME Burkard, SM Freier, JR Wyatt, DH Turner Rna 5 (11), 1458-1469, 1999	315	1999
Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change AV Uzilov, JM Keegan, DH Mathews BMC bioinformatics 7, 1-30, 2006	287	2006
Revolutions in RNA secondary structure prediction DH Mathews Journal of molecular biology 359 (3), 526-532, 2006	275	2006

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