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PureCLIP: capturing target-specific protein-RNA interaction footprints from single-nucleotide CLIP-seq data

Genome Biology, 2017-12, Vol.18 (1), p.240-240, Article 240

2017

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Integrated analysis of Xist upregulation and X-chromosome inactivation with single-cell and single-allele resolution

Nature communications, 2021-06, Vol.12 (1), p.3638-3638, Article 3638

2021

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ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data

Nucleic acids research, 2017-11, Vol.45 (19), p.11004

2017

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Towards in silico CLIP-seq: predicting protein-RNA interaction via sequence-to-signal learning

Genome Biology, 2023-08, Vol.24 (1), p.180-180, Article 180

2023

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Microprocessor Activity Controls Differential miRNA Biogenesis In Vivo

Cell reports (Cambridge), 2014-10, Vol.9 (2), p.542-554

2014

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pysster: classification of biological sequences by learning sequence and structure motifs with convolutional neural networks

Bioinformatics, 2018-09, Vol.34 (17), p.3035-3037

2018

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Identifying lncRNA-mediated regulatory modules via ChIA-PET network analysis

BMC bioinformatics, 2019-05, Vol.20 (1), p.292-292, Article 292

2019

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A Data-Mining Approach to Identify NF-kB-Responsive microRNAs in Tissues Involved in Inflammatory Processes: Potential Relevance in Age-Related Diseases

International journal of molecular sciences, 2023-03, Vol.24 (6), p.5123

2023

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Network Embedding Across Multiple Tissues and Data Modalities Elucidates the Context of Host Factors Important for COVID-19 Infection

Frontiers in genetics, 2022-07, Vol.13, p.909714

2022

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Screening for eukaryotic motifs in Legionella pneumophila reveals Smh1 as bacterial deacetylase of host histones

Virulence, 2022-12, Vol.13 (1), p.2042-2058

2022

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Microprocessor Activity Controls Differential miRNA Biogenesis In Vivo

Cell reports (Cambridge), 2015-02, Vol.10 (6), p.1020-1020

2015

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Network-Based Methods and Other Approaches for Predicting lncRNA Functions and Disease Associations

Methods in molecular biology (Clifton, N.J.), 2019, Vol.1912, p.301

2019

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Structural fragment clustering reveals novel structural and functional motifs in alpha-helical transmembrane proteins

BMC bioinformatics, 2010-04, Vol.11 (1), p.204-204, Article 204

2010

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In Silico Promoter Recognition from deepCAGE Data

Methods in molecular biology (Clifton, N.J.), 2017-01, Vol.1468, p.171

2017

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Zebrafish Expression Ontology of Gene Sets (ZEOGS): A Tool to Analyze Enrichment of Zebrafish Anatomical Terms in Large Gene Sets

Zebrafish, 2013-09, Vol.10 (3), p.33-315

2013

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Principles of microRNA Regulation Revealed Through Modeling microRNA Expression Quantitative Trait Loci

Genetics (Austin), 2016-08, Vol.203 (4), p.1629-1640

2016

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A systematic benchmark of machine learning methods for protein–RNA interaction prediction

Briefings in bioinformatics, 2023-09, Vol.24 (5)

2023

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TriPepSVM: de novo prediction of RNA-binding proteins based on short amino acid motifs

Nucleic acids research, 2019-05, Vol.47 (9), p.4406

2019

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PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs

Genome biology, 2013-08, Vol.14 (8), p.R84-R84

2013

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Effect of Atmospheric Aging on Soot Particle Toxicity in Lung Cell Models at the Air-Liquid Interface: Differential Toxicological Impacts of Biogenic and Anthropogenic Secondary Organic Aerosols (SOAs)

Environmental health perspectives, 2022-02, Vol.130 (2), p.27003-27003

2022

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Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy

Genome research, 2024-05, Vol.34 (4), p.572

2024

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Single-cell RNA sequencing uncovers the nuclear decoy lincRNA PIRAT as a regulator of systemic monocyte immunity during COVID-19

Proceedings of the National Academy of Sciences - PNAS, 2022-09, Vol.119 (36), p.1-e2120680119

2022

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Distal and proximal cis-regulatory elements sense X chromosome dosage and developmental state at the Xist locus

Molecular cell, 2022-01, Vol.82 (1), p.190-208.e17

2022

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Kinetics of Xist -induced gene silencing can be predicted from combinations of epigenetic and genomic features

Genome research, 2019-07, Vol.29 (7), p.1087

2019

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Graph Convolutional Networks Improve the Prediction of Cancer Driver Genes

Artificial Neural Networks and Machine Learning – ICANN 2019: Workshop and Special Sessions, p.658-668

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PureCLIP: capturing target-specific protein-RNA interaction footprints from single-nucleotide CLIP-seq data

Integrated analysis of Xist upregulation and X-chromosome inactivation with single-cell and single-allele resolution

ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data

Towards in silico CLIP-seq: predicting protein-RNA interaction via sequence-to-signal learning

Microprocessor Activity Controls Differential miRNA Biogenesis In Vivo

pysster: classification of biological sequences by learning sequence and structure motifs with convolutional neural networks

Identifying lncRNA-mediated regulatory modules via ChIA-PET network analysis

A Data-Mining Approach to Identify NF-kB-Responsive microRNAs in Tissues Involved in Inflammatory Processes: Potential Relevance in Age-Related Diseases

Network Embedding Across Multiple Tissues and Data Modalities Elucidates the Context of Host Factors Important for COVID-19 Infection

Screening for eukaryotic motifs in Legionella pneumophila reveals Smh1 as bacterial deacetylase of host histones

Microprocessor Activity Controls Differential miRNA Biogenesis In Vivo

Network-Based Methods and Other Approaches for Predicting lncRNA Functions and Disease Associations

Structural fragment clustering reveals novel structural and functional motifs in alpha-helical transmembrane proteins

In Silico Promoter Recognition from deepCAGE Data

Zebrafish Expression Ontology of Gene Sets (ZEOGS): A Tool to Analyze Enrichment of Zebrafish Anatomical Terms in Large Gene Sets

Principles of microRNA Regulation Revealed Through Modeling microRNA Expression Quantitative Trait Loci

A systematic benchmark of machine learning methods for protein–RNA interaction prediction

TriPepSVM: de novo prediction of RNA-binding proteins based on short amino acid motifs

PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs

Effect of Atmospheric Aging on Soot Particle Toxicity in Lung Cell Models at the Air-Liquid Interface: Differential Toxicological Impacts of Biogenic and Anthropogenic Secondary Organic Aerosols (SOAs)

Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy

Single-cell RNA sequencing uncovers the nuclear decoy lincRNA PIRAT as a regulator of systemic monocyte immunity during COVID-19

Distal and proximal cis-regulatory elements sense X chromosome dosage and developmental state at the Xist locus

Kinetics of Xist -induced gene silencing can be predicted from combinations of epigenetic and genomic features

Graph Convolutional Networks Improve the Prediction of Cancer Driver Genes

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