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Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data

Journal of proteome research, 2019-02, Vol.18 (2), p.623-632

2019

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An efficient approach based on multi-sources information to predict circRNA–disease associations using deep convolutional neural network

Bioinformatics, 2020-07, Vol.36 (13), p.4038-4046

2020

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Dream: powerful differential expression analysis for repeated measures designs

Bioinformatics, 2021-04, Vol.37 (2), p.192-201

2021

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BP4RNAseq: a babysitter package for retrospective and newly generated RNA-seq data analyses using both alignment-based and alignment-free quantification method

Bioinformatics, 2021-06, Vol.37 (9), p.1319-1321

2021

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Special Issue: Computational Analysis of RNA Structure and Function

Genes, 2019-01, Vol.10 (1), p.55

Gorodkin, Jan

2019

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POKY: a software suite for multidimensional NMR and 3D structure calculation of biomolecules

Bioinformatics (Oxford, England), 2021-09, Vol.37 (18), p.3041-3042

2021

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CRISPR-Cas9 off-targeting assessment with nucleic acid duplex energy parameters

Genome Biology, 2018-10, Vol.19 (1), p.177-177, Article 177

2018

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Gene regulation inference from single-cell RNA-seq data with linear differential equations and velocity inference

Bioinformatics (Oxford, England), 2020-09, Vol.36 (18), p.4774-4780

2020

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Improved RNA secondary structure and tertiary base-pairing prediction using evolutionary profile, mutational coupling and two-dimensional transfer learning

Bioinformatics (Oxford, England), 2021-09, Vol.37 (17), p.2589-2600

2021

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Deep graph learning of inter-protein contacts

Bioinformatics, 2022-01, Vol.38 (4), p.947-953

2022

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Improving circRNA–disease association prediction by sequence and ontology representations with convolutional and recurrent neural networks

Bioinformatics, 2021-04, Vol.36 (24), p.5656-5664

2021

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RNAcentral 2021: secondary structure integration, improved sequence search and new member databases

Nucleic acids research, 2021-01, Vol.49 (D1), p.D212

RNAcentral Consortium

2021

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iCircDA-LTR: identification of circRNA–disease associations based on Learning to Rank

Bioinformatics (Oxford, England), 2021-10, Vol.37 (19), p.3302-3310

2021

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

Bioinformatics, 2020-02, Vol.36 (4), p.1107-1113

2020

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CRISPR/Cas9 gRNA activity depends on free energy changes and on the target PAM context

Nature communications, 2022-05, Vol.13 (1), p.3006-3006, Article 3006

2022

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STACAS: Sub-Type Anchor Correction for Alignment in Seurat to integrate single-cell RNA-seq data

Bioinformatics, 2021-05, Vol.37 (6), p.882-884

2021

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PSI-Sigma: a comprehensive splicing-detection method for short-read and long-read RNA-seq analysis

Bioinformatics, 2019-12, Vol.35 (23), p.5048-5054

2019

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alona: a web server for single-cell RNA-seq analysis

Bioinformatics, 2020-06, Vol.36 (12), p.3910-3912

2020

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RIsearch: fast RNA-RNA interaction search using a simplified nearest-neighbor energy model

Bioinformatics, 2012-11, Vol.28 (21), p.2738-2746

2012

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TISSUES 2.0: an integrative web resource on mammalian tissue expression

Database : the journal of biological databases and curation, 2018-01, Vol.2018

2018

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aPRBind: protein–RNA interface prediction by combining sequence and I-TASSER model-based structural features learned with convolutional neural networks

Bioinformatics, 2021-05, Vol.37 (7), p.937-942

2021

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PRISM: recovering cell-type-specific expression profiles from individual composite RNA-seq samples

Bioinformatics (Oxford, England), 2021-09, Vol.37 (18), p.2882-2888

2021

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TargetNet: functional microRNA target prediction with deep neural networks

Bioinformatics (Oxford, England), 2022-01, Vol.38 (3), p.671-677

2022

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TIMEx: tumor-immune microenvironment deconvolution web-portal for bulk transcriptomics using pan-cancer scRNA-seq signatures

Bioinformatics (Oxford, England), 2021-10, Vol.37 (20), p.3681-3683

2021

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NeoFuse: predicting fusion neoantigens from RNA sequencing data

Bioinformatics, 2020-04, Vol.36 (7), p.2260-2261

2020

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Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data

An efficient approach based on multi-sources information to predict circRNA–disease associations using deep convolutional neural network

Dream: powerful differential expression analysis for repeated measures designs

BP4RNAseq: a babysitter package for retrospective and newly generated RNA-seq data analyses using both alignment-based and alignment-free quantification method

Special Issue: Computational Analysis of RNA Structure and Function

POKY: a software suite for multidimensional NMR and 3D structure calculation of biomolecules

CRISPR-Cas9 off-targeting assessment with nucleic acid duplex energy parameters

Gene regulation inference from single-cell RNA-seq data with linear differential equations and velocity inference

Improved RNA secondary structure and tertiary base-pairing prediction using evolutionary profile, mutational coupling and two-dimensional transfer learning

Deep graph learning of inter-protein contacts

Improving circRNA–disease association prediction by sequence and ontology representations with convolutional and recurrent neural networks

RNAcentral 2021: secondary structure integration, improved sequence search and new member databases

iCircDA-LTR: identification of circRNA–disease associations based on Learning to Rank

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

CRISPR/Cas9 gRNA activity depends on free energy changes and on the target PAM context

STACAS: Sub-Type Anchor Correction for Alignment in Seurat to integrate single-cell RNA-seq data

PSI-Sigma: a comprehensive splicing-detection method for short-read and long-read RNA-seq analysis

alona: a web server for single-cell RNA-seq analysis

RIsearch: fast RNA-RNA interaction search using a simplified nearest-neighbor energy model

TISSUES 2.0: an integrative web resource on mammalian tissue expression

aPRBind: protein–RNA interface prediction by combining sequence and I-TASSER model-based structural features learned with convolutional neural networks

PRISM: recovering cell-type-specific expression profiles from individual composite RNA-seq samples

TargetNet: functional microRNA target prediction with deep neural networks

TIMEx: tumor-immune microenvironment deconvolution web-portal for bulk transcriptomics using pan-cancer scRNA-seq signatures

NeoFuse: predicting fusion neoantigens from RNA sequencing data

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