David H. Mathews

Also affiliated with University of Rochester

Biochemistry, Genetics and Molecular Biology

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 4%percentile

0.701Author DataRank

Indexed papers

1in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 1 indexed paper attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

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

Journal of Molecular Biology(2024)10.1016/j.jmb.2024.168549

Top 29%

0.701DataRank

Top 29%27 citations

Douglas H. Turner, David H. Mathews, Abhinav Mittal

Papers

Driven by 55 papers — median percentile 71. Top paper: “CRISPR-Cas9-based mutagenesis frequently provokes on-target mRNA misregulation”.

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

Nature Communications(2019)10.1038/s41467-019-12028-5

N/A

0.818DataRank · unranked

232 citations

Yunku Yeu, John Tyler Piazza, Zhen Tan, Jean Rene Clemenceau, Xiaofeng Wu +9 more

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

Journal of Molecular Biology(2024)10.1016/j.jmb.2024.168549

Top 29%

0.701DataRank

Top 29%27 citations

Douglas H. Turner, David H. Mathews, Abhinav Mittal

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

eLife(2022)10.7554/elife.73888

N/A

0.691DataRank · unranked

24 citations

Lela Lackey, Justin M. Waldern, Abhishek Dey, Anthony M. Mustoe, Kevin M. Weeks +3 more

Making ends meet: new functions of mRNA secondary structure

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.04.29.069203

N/A

0DataRank · unranked

0 citations

David H. Mathews, Dmitri N. Ermolenko

Principles for Understanding the Accuracy of SHAPE-Directed RNA Structure Modeling

UNC Libraries(2020)10.17615/wv1r-nd02

N/A

0DataRank · unranked

0 citations

Christine E. Hajdin, Kevin M. Weeks, Oleg V. Favorov, David H. Mathews, Christopher W. Leonard +2 more

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

UNC Libraries(2020)10.17615/fb5q-hd04

N/A

0DataRank · unranked

0 citations

Justin Ritz, Eric Gamache, Alain Laederach, Jung H. Doh, Stanislav Bellaousov +2 more

High-Throughput SHAPE Analysis Reveals Structures in HIV-1 Genomic RNA Strongly Conserved across Distinct Biological States

UNC Libraries(2020)10.17615/avxz-y611

N/A

0DataRank · unranked

0 citations

Robert J. Gorelick, David H. Mathews, Kevin A. Wilkinson, Alan Rein, Morgan C. Giddings +3 more

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

Proceedings of the National Academy of Sciences(2021)10.1073/pnas.2116269118

N/A

0DataRank · unranked

26 citations

He Zhang, Liang Zhang, Kaibo Liu, Boxiang Liu, David H. Mathews +2 more

Secondary Structure Prediction for RNA Sequences Including N 6 -methyladenosine

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.04.26.441443

N/A

0DataRank · unranked

1 citations

Xiaoju Zhang, Richard M. Watson, Ryszard Kierzek, David H. Mathews, Elżbieta Kierzek

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

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.09.13.460117

N/A

0DataRank · unranked

1 citations

Lela Lackey, Justin M. Waldern, Abhishek Dey, David H. Mathews, Alain Laederach +1 more

Secondary structure prediction for RNA sequences including N6-methyladenosine

Nature Communications(2022)10.1038/s41467-022-28817-4

N/A

0DataRank · unranked

95 citations

Xiaoju Zhang, Richard M. Watson, Scott D. Kennedy, Marta Szabat, Ryszard Kierzek +2 more

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

Bioinformatics(2022)10.1093/bioinformatics/btac415

N/A

0DataRank · unranked

90 citations

Michael J. Wise, Amitava Datta, Max Ward, David H. Mathews, Marcell Szikszai

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

Nucleic Acids Research(2022)10.1093/nar/gkac287

N/A

0DataRank · unranked

47 citations

Debanjana Maji, Giulia Biancon, Anees Mohammed Keedakkatt Puthenpeedikakkal, Chapin E. Cavender, Toma Tebaldi +5 more

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

Nucleic Acids Research(2022)10.1093/nar/gkac261

N/A

0DataRank · unranked

41 citations

Susan J. Schroeder, Hongying Sun, Douglas H. Turner, David H. Mathews, Jeffrey Zuber

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

Nature Communications(2022)10.1038/s41467-021-27790-8

N/A

0DataRank · unranked

28 citations

Chapin E. Cavender, Maya E. Blau, Jermaine L. Jenkins, David H. Mathews, Joseph E. Wedekind +1 more

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

Journal of Molecular Biology(2022)10.1016/j.jmb.2022.167877

N/A

0DataRank · unranked

25 citations

Mingyi Zhu, Margarita Belinite, Gregory P. Ballard, David H. Mathews, Dmitri N. Ermolenko +1 more

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

Nucleic Acids Research(2022)10.1093/nar/gkac1029

N/A

0DataRank · unranked

14 citations

Sizhen Li, Liang Zhang, David H. Mathews, Liang Huang, He Zhang

A Test and Refinement of Folding Free Energy Nearest Neighbor Parameters for RNA Including N6-Methyladenosine

Journal of Molecular Biology(2022)10.1016/j.jmb.2022.167632

N/A

0DataRank · unranked

11 citations

Martina Prochota, Ryszard Kierzek, Elżbieta Kierzek, David H. Mathews, Marta Szabat

Computational Resources for Molecular Biology 2022

Journal of Molecular Biology(2022)10.1016/j.jmb.2022.167625

N/A

0DataRank · unranked

2 citations

David H. Mathews, Michael J.E. Sternberg, Rita Casadio

Generation and functional analysis of defective viral genomes during SARS-CoV-2 infection

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.09.22.509123

N/A

0DataRank · unranked

10 citations

Nora J. Gilliam, Sizhen Li, Simone Spaudau, Raven M. Osborn, Christopher Anderson +7 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.03.21.485135

N/A

0DataRank · unranked

4 citations

Michael J. Wise, Amitava Datta, Max Ward, David H. Mathews, Marcell Szikszai

LinearAlifold: Linear-Time Consensus Structure Prediction for RNA Alignments

arXiv (Cornell University)(2022)10.48550/arxiv.2206.14794

N/A

0DataRank · unranked

1 citations

Liang Zhang, Gautam, Milan, Dai, Ning, Sizhen Li, He Zhang +3 more

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

UNC Libraries(2022)10.17615/n0h1-jc89

N/A

0DataRank · unranked

0 citations

Abhishek Dey, Alain Laederach, Anthony M. Mustoe, Lela Lackey, Kevin M. Weeks +3 more

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

mBio(2023)10.1128/mbio.00250-23

N/A

0DataRank · unranked

42 citations

Nora J. Gilliam, Sizhen Li, Simone Spandau, Raven M. Osborn, Sarah E. Connor +8 more

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

Nature Communications(2023)10.1038/s41467-023-41799-1

N/A

0DataRank · unranked

37 citations

Kadiam C. Venkata Subbaiah, Feng Jiang, Li Xie, Jiangbin Wu, Eng-Soon Khor +5 more

RNA Secondary Structure Analysis Using RNAstructure

Current Protocols(2023)10.1002/cpz1.846

N/A

0DataRank · unranked

30 citations

Abhinav Mittal, David H. Mathews, Sara E. Ali

RNA design via structure-aware multifrontier ensemble optimization

Bioinformatics(2023)10.1093/bioinformatics/btad252

N/A

0DataRank · unranked

23 citations

Ning Dai, Sizhen Li, Max Ward, David H. Mathews, Liang Huang +1 more

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

Nucleic Acids Research(2023)10.1093/nar/gkad056

N/A

0DataRank · unranked

12 citations

Olayinka Akinyemi, Jeffrey Malik, Caroline M. Focht, Elizabeth M. Pritchett, Cameron Baker +5 more

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

Nucleic Acids Research(2023)10.1093/nar/gkad664

N/A

0DataRank · unranked

8 citations

Sizhen Li, Ning Dai, Liang Zhang, David H. Mathews, Liang Huang +1 more

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

ACS Synthetic Biology(2023)10.1021/acssynbio.3c00358

N/A

0DataRank · unranked

7 citations

Terrel Miffin, Hongying Sun, Kenneth K. Sharp, Xiaoyu Wang, Mingyi Zhu +6 more

Genome-Wide DNA Changes Acquired by Candida albicans Caspofungin-Adapted Mutants

Microorganisms(2023)10.3390/microorganisms11081870

N/A

0DataRank · unranked

6 citations

Sudisht K. Sah, David H. Mathews, Elena Rustchenko, Jeffrey Zuber

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

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.06.15.545153

N/A

0DataRank · unranked

2 citations

Kadiam C. Venkata Subbaiah, Feng Jiang, Li Xie, Jiangbin Wu, Eng-Soon Khor +5 more

Computational Resources for Molecular Biology 2023

Journal of Molecular Biology(2023)10.1016/j.jmb.2023.168160

N/A

0DataRank · unranked

0 citations

Rita Casadio, Michael J.E. Sternberg, David H. Mathews

Undesignable RNA Structure Identification via Rival Structure Generation and Structure Decomposition

arXiv (Cornell University)(2023)10.48550/arxiv.2311.08339

N/A

0DataRank · unranked

0 citations

Wei Yu Tang, David H. Mathews, Liang Huang, Tianshuo Zhou

LinearAlifold: Linear-time consensus structure prediction for RNA alignments

Journal of Molecular Biology(2024)10.1016/j.jmb.2024.168694

N/A

0DataRank · unranked

9 citations

Liang Zhang, Milan Gautam, Ning Dai, Sizhen Li, He Zhang +3 more

Using the RNAstructure Software Package to Predict Conserved RNA Structures

Current Protocols(2024)10.1002/cpz1.70054

N/A

0DataRank · unranked

12 citations

Sara E. Ali, David H. Mathews, Abhinav Mittal

memerna: Sparse RNA folding including coaxial stacking

Journal of Molecular Biology(2024)10.1016/j.jmb.2024.168819

N/A

0DataRank · unranked

2 citations

Amitava Datta, David H. Mathews, Max Ward, Eliot Courtney

Comprehensive Profiling of Roquin Binding Preferences for RNA Stem‐Loops

Angewandte Chemie International Edition(2024)10.1002/anie.202412596

N/A

0DataRank · unranked

3 citations

Jan‐Niklas Tants, Chiara Lichtenthaeler, Sara E. Ali, Louisa Koch, David H. Mathews +3 more

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

Nucleic Acids Research(2024)10.1093/nar/gkae886

N/A

0DataRank · unranked

3 citations

Olayinka Akinyemi, Tiana C Rohe, Elizabeth M. Pritchett, Cameron Baker, Akshara Sharma +4 more

Computational Resources for Molecular Biology 2024

Journal of Molecular Biology(2024)10.1016/j.jmb.2024.168739

N/A

0DataRank · unranked

1 citations

David H. Mathews, Michael J.E. Sternberg, Rita Casadio

Scalable and Interpretable Identification of Minimal Undesignable RNA Structure Motifs with Rotational Invariance

arXiv (Cornell University)(2024)10.48550/arxiv.2402.17206

N/A

0DataRank · unranked

0 citations

Wei Yu Tang, Malik, Apoorv, David H. Mathews, Liang Huang, Tianshuo Zhou

Detaillierte Analyse der Bindepräferenz von Roquin an RNA‐Stammschleifen

Angewandte Chemie(2024)10.1002/ange.202412596

N/A

0DataRank · unranked

0 citations

Jan‐Niklas Tants, Chiara Lichtenthaeler, Sara E. Ali, Louisa Koch, David H. Mathews +3 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.11.18.624017

N/A

0DataRank · unranked

0 citations

Anees Mohammed Keedakkatt Puthenpeedikakkal, David H. Mathews, Dragony Fu, Kyle D. Berger

Sampling-based Continuous Optimization with Coupled Variables for RNA Design

PubMed(2024)10.48550/arxiv.2412.08751

N/A

0DataRank · unranked

0 citations

Ning Dai, Tianshuo Zhou, David H. Mathews, Liang Huang, Wei Tang

Structural Impact of 3-methylcytosine Modification on the Anticodon Stem-loop of a Neuronally-enriched Arginine tRNA

Journal of Molecular Biology(2025)10.1016/j.jmb.2025.169096

N/A

0DataRank · unranked

6 citations

Anees Mohammed Keedakkatt Puthenpeedikakkal, David H. Mathews, Dragony Fu, Kyle D. Berger

A Ψ–Ψ codon–anticodon pairing in nonsense suppression and translational recoding

Nature Chemical Biology(2025)10.1038/s41589-025-02025-9

N/A

0DataRank · unranked

4 citations

Elzbieta Kierzek, Ryszard Kierzek, David H. Mathews, Yi‐Tao Yu, Yi Pan

Schizosaccharomyces pombe pus1mutants are temperature sensitive due to decay of tRNAIle(UAU)by the 5′-3′ exonuclease Dhp1, primarily targeting the unspliced pre-tRNA

RNA(2025)10.1261/rna.080315.124

N/A

0DataRank · unranked

2 citations

Erin Marcus, Savanah Neupert, Sarah M. Ostrowski, David H. Mathews, Eric M. Phizicky +1 more

Structural determinants of inverted Alu-mediated backsplicing revealed by -MaP and -JuMP

Nucleic Acids Research(2025)10.1093/nar/gkaf433

N/A

0DataRank · unranked

2 citations

Colin D. Taylor, Catherine A. Giannetti, Patrick S. Irving, Scott R. Allen, Mingyi Zhu +5 more

NMR and molecular dynamics demonstrate the RNA internal loop GAGU is dynamic and adjacent basepairs determine conformational preference

Biophysical Journal(2025)10.1016/j.bpj.2025.11.026

N/A

0DataRank · unranked

1 citations

Scott D. Kennedy, James P McSally, David H. Mathews, Olayinka Akinyemi

NMR and molecular dynamics demonstrate the RNA internal loop GAGU is dynamic and adjacent base pairs determine conformational preference

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.04.14.648754

N/A

0DataRank · unranked

0 citations

Scott D. Kennedy, James P McSally, David H. Mathews, Olayinka Akinyemi

Computational Resources for Molecular Biology 2025

Journal of Molecular Biology(2025)10.1016/j.jmb.2025.169222

N/A

0DataRank · unranked

0 citations

Rita Casadio, Michael J.E. Sternberg, David H. Mathews

40S ribosomal subunits scan mRNA for the start codon by one-dimensional diffusion

RNA(2025)10.1261/rna.080493.125

N/A

0DataRank · unranked

0 citations

Mingyi Zhu, Elizabeth J. Grayhack, David H. Mathews, Dmitri N. Ermolenko, Hironao Wakabayashi

Deep Learning for RNA Secondary Structure Determination: Gauging Generalizability and Broadening the Scope of Traditional Methods

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.11.04.686644

N/A

0DataRank · unranked

0 citations

Ting-Yuan Wang, Ryan Krueger, David H. Mathews, Max Ward, Sharon Aviran +1 more

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

Bioinformatics(2020)10.1093/bioinformatics/btaa460

N/A

0DataRank · unranked

93 citations

Liang Zhang, David H. Mathews, Liang Huang, He Zhang

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

Nucleic Acids Research(2020)10.1093/nar/gkaa546

N/A

0DataRank · unranked

39 citations

Debapratim Dutta, Chapin E. Cavender, Jermaine L. Jenkins, Elizabeth M. Pritchett, Cameron Baker +4 more

David H. Mathews

Indexed papers

Top data-sharing exemplar

Papers