RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning

Comparison of the Structures and Mechanisms of the Pistol and Hammerhead Ribozymes

(2019) Timothy J. Wilson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structure and functional reselection of the Mango-III fluorogenic RNA aptamer

(2019) Robert J. Trachman et al.   Nature Chemical Biology

Hatchet ribozyme structure and implications for cleavage mechanism

(2019) Luqian Zheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure and ligand binding of the glutamine-II riboswitch

(2019) Lin Huang et al.   NUCLEIC ACIDS RESEARCH

Crystal structure of an adenovirus virus-associated RNA

(2019) Iris V. Hood et al.   Nature Communications

Identifying molecular recognition features in intrinsically disordered regions of proteins by transfer learning

(2019) Jack Hanson et al.   BIOINFORMATICS

Computational design of three-dimensional RNA structure and function

(2019) Joseph D. Yesselman et al.   Nature Nanotechnology

Knotty: efficient and accurate prediction of complex RNA pseudoknot structures

(2018) Hosna Jabbari et al.   BIOINFORMATICS

bpRNA: large-scale automated annotation and analysis of RNA secondary structure

(2018) Padideh Danaee et al.   NUCLEIC ACIDS RESEARCH

Accurate Single-Sequence Prediction of Protein Intrinsic Disorder by an Ensemble of Deep Recurrent and Convolutional Architectures

(2018) Jack Hanson et al.   Journal of Chemical Information and Modeling

Single-sequence-based prediction of protein secondary structures and solvent accessibility by deep whole-sequence learning

(2018) Rhys Heffernan et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

A max-margin training of RNA secondary structure prediction integrated with the thermodynamic model

(2018) Manato Akiyama et al.   Journal of Bioinformatics and Computational Biology

B -factor profile prediction for RNA flexibility using support vector machines

(2017) Ivantha Guruge et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

(2017) Zhichao Miao et al.   RNA

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

(2017) Michael F. Sloma et al.   PLoS Computational Biology

Genome-Wide Analysis of RNA Secondary Structure

(2016) Philip C. Bevilacqua et al.   Annual Review of Genetics

RNAcentral: a comprehensive database of non-coding RNA sequences

(2016)   NUCLEIC ACIDS RESEARCH

RNA structure through multidimensional chemical mapping

(2016) Siqi Tian et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Genome-scale characterization of RNA tertiary structures and their functional impact by RNA solvent accessibility prediction

(2016) Yuedong Yang et al.   RNA

RNA motif discovery: a computational overview

(2015) Avinash Achar et al.   Biology Direct

Gene target specificity of the Super Elongation Complex (SEC) family: how HIV-1 Tat employs selected SEC members to activate viral transcription

(2015) Huasong Lu et al.   NUCLEIC ACIDS RESEARCH

The RNA shapes studio

(2014) S. Janssen et al.   BIOINFORMATICS

Describing the Structural Diversity within an RNA’s Ensemble

(2014) Joshua Martin   Entropy

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Structure of a class II preQ1 riboswitch reveals ligand recognition by a new fold

(2013) Joseph A Liberman et al.   Nature Chemical Biology

The four ingredients of single-sequence RNA secondary structure prediction. A unifying perspective

(2013) Elena Rivas   RNA Biology

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

A folding algorithm for extended RNA secondary structures

(2011) C. H. zu Siederdissen et al.   BIOINFORMATICS

IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming

(2011) Kengo Sato et al.   BIOINFORMATICS

Rich Parameterization Improves RNA Structure Prediction

(2011) Shay Zakov et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

ProbKnot: Fast prediction of RNA secondary structure including pseudoknots

(2010) S. Bellaousov et al.   RNA

VARNA: Interactive drawing and editing of the RNA secondary structure

(2009) Kévin Darty et al.   BIOINFORMATICS

A Survey on Transfer Learning

(2009) Sinno Jialin Pan et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING

Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation

(2009) Sakurako Goto-Ito et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

CENTROIDFOLD: a web server for RNA secondary structure prediction

(2009) K. Sato et al.   NUCLEIC ACIDS RESEARCH

The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data

(2008) Marc Parisien et al.   NATURE