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Design of RNAs: comparing programs for inverse RNA folding

Briefings in bioinformatics, 2018-03, Vol.19 (2), p.350-358

2018

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On the predictibility of A-minor motifs from their local contexts

RNA biology, 2022-12, Vol.19 (1), p.1208-1227

2022

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Finding recurrent RNA structural networks with fast maximal common subgraphs of edge-colored graphs

PLoS computational biology, 2021-05, Vol.17 (5), p.e1008990-e1008990

2021

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Understanding Hepatitis B Virus Dynamics and the Antiviral Effect of Interferon Alpha Treatment in Humanized Chimeric Mice

Journal of virology, 2021-06, Vol.95 (14), p.e0049220-e0049220

2021

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Advances in Parameter Estimation and Learning from Data for Mathematical Models of Hepatitis C Viral Kinetics

Mathematics (Basel), 2022-06, Vol.10 (12), p.2136

2022

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Concurrent prediction of RNA secondary structures with pseudoknots and local 3D motifs in an integer programming framework

Bioinformatics (Oxford, England), 2024-02, Vol.40 (2)

2024

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Reconstruction of ancestral RNA sequences under multiple structural constraints

BMC genomics, 2016-11, Vol.17 (Suppl 10), p.862-862, Article 862

2016

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Efficient Methods for Parameter Estimation of Ordinary and Partial Differential Equation Models of Viral Hepatitis Kinetics

Mathematics (Basel), 2020-09, Vol.8 (9), p.1483

2020

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αβDCA method identifies unspecific binding but specific disruption of the group I intron by the StpA chaperone

RNA (Cambridge), 2020-11, Vol.26 (11), p.1530-1540

2020

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Modeling the Interplay between HDV and HBV in Chronic HDV/HBV Patients

Mathematics (Basel), 2022-10, Vol.10 (20), p.3917

2022

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A Robust and Efficient Numerical Method for RNA-Mediated Viral Dynamics

Frontiers in applied mathematics and statistics, 2017-10, Vol.3

2017

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AlphaFold2 Can Predict Single-Mutation Effects

Physical review letters, 2023-11, Vol.131 (21), p.218401-218401, Article 218401

2023

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Numerical schemes for solving and optimizing multiscale models with age of hepatitis C virus dynamics

Mathematical biosciences, 2018-06, Vol.300, p.1-13

2018

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Advances in parameter estimation for mathematical models of hepatitis C viral kinetics

AIP Conference Proceedings, 2023, Vol.2849 (1)

2023

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Mining for recurrent long-range interactions in RNA structures reveals embedded hierarchies in network families

Nucleic acids research, 2018-05, Vol.46 (8), p.3841-3851

2018

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On the predictibility of A-minor motifs from their local contexts

RNA biology, 2022-12, Vol.19 (1), p.1208-1227

2022

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Classification and Identification of Non-canonical Base Pairs and Structural Motifs

Methods in molecular biology (Clifton, N.J.), 2024, Vol.2726, p.143

2024

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A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution

Bioinformatics, 2013-07, Vol.29 (13), p.i308-i315

2013

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A Parameter Estimation Method for Multiscale Models of Hepatitis C Virus Dynamics

Bulletin of mathematical biology, 2019-10, Vol.81 (10), p.3675-3721

2019

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Augmented base pairing networks encode RNA-small molecule binding preferences

Nucleic acids research, 2020-08, Vol.48 (14), p.7690-7699

2020

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RNA-MoIP: prediction of RNA secondary structure and local 3D motifs from sequence data

Nucleic acids research, 2017-07, Vol.45 (W1), p.W440-W444

2017

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incaRNAfbinv 2.0: a webserver and software with motif control for fragment-based design of RNAs

Bioinformatics, 2020-05, Vol.36 (9), p.2920-2922

2020

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Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure

Bioinformatics (Oxford, England), 2012-06, Vol.28 (12), p.i207-i214

2012

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On the emergence of structural complexity in RNA replicators

RNA (Cambridge), 2019-12, Vol.25 (12), p.1579-1591

2019

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Automated, customizable and efficient identification of 3D base pair modules with BayesPairing

Nucleic acids research, 2019-04, Vol.47 (7), p.3321-3332

2019

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Design of RNAs: comparing programs for inverse RNA folding

On the predictibility of A-minor motifs from their local contexts

Finding recurrent RNA structural networks with fast maximal common subgraphs of edge-colored graphs

Understanding Hepatitis B Virus Dynamics and the Antiviral Effect of Interferon Alpha Treatment in Humanized Chimeric Mice

Advances in Parameter Estimation and Learning from Data for Mathematical Models of Hepatitis C Viral Kinetics

Concurrent prediction of RNA secondary structures with pseudoknots and local 3D motifs in an integer programming framework

Reconstruction of ancestral RNA sequences under multiple structural constraints

Efficient Methods for Parameter Estimation of Ordinary and Partial Differential Equation Models of Viral Hepatitis Kinetics

αβDCA method identifies unspecific binding but specific disruption of the group I intron by the StpA chaperone

Modeling the Interplay between HDV and HBV in Chronic HDV/HBV Patients

A Robust and Efficient Numerical Method for RNA-Mediated Viral Dynamics

AlphaFold2 Can Predict Single-Mutation Effects

Numerical schemes for solving and optimizing multiscale models with age of hepatitis C virus dynamics

Advances in parameter estimation for mathematical models of hepatitis C viral kinetics

Mining for recurrent long-range interactions in RNA structures reveals embedded hierarchies in network families

On the predictibility of A-minor motifs from their local contexts

Classification and Identification of Non-canonical Base Pairs and Structural Motifs

A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution

A Parameter Estimation Method for Multiscale Models of Hepatitis C Virus Dynamics

Augmented base pairing networks encode RNA-small molecule binding preferences

RNA-MoIP: prediction of RNA secondary structure and local 3D motifs from sequence data

incaRNAfbinv 2.0: a webserver and software with motif control for fragment-based design of RNAs

Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure

On the emergence of structural complexity in RNA replicators

Automated, customizable and efficient identification of 3D base pair modules with BayesPairing

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