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Biopython: freely available Python tools for computational molecular biology and bioinformatics

Bioinformatics, 2009-06, Vol.25 (11), p.1422-1423

2009

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Hierarchical Evolution of the Bacterial Sporulation Network

Current biology, 2010-09, Vol.20 (17), p.R735-R745

2010

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A comprehensive survey of 3' animal miRNA modification events and a possible role for 3' adenylation in modulating miRNA targeting effectiveness

Genome research, 2010-10, Vol.20 (10), p.1398

2010

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Update of the FANTOM web resource: expansion to provide additional transcriptome atlases

Nucleic acids research, 2019-01, Vol.47 (D1), p.D752

2019

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Annotation of nuclear lncRNAs based on chromatin interactions

PloS one, 2024-05, Vol.19 (5), p.e0295971-e0295971

2024

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Site-specific DICER and DROSHA RNA products control the DNA―damage response

Nature (London), 2012-08, Vol.488 (7410), p.231-235

2012

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An integrated expression atlas of miRNAs and their promoters in human and mouse

Nature biotechnology, 2017-09, Vol.35 (9), p.872-878

2017

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Batf2/Irf1 induces inflammatory responses in classically activated macrophages, lipopolysaccharides, and mycobacterial infection

The Journal of immunology (1950), 2015-06, Vol.194 (12), p.6035-6044

2015

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LETR1 is a lymphatic endothelial-specific lncRNA governing cell proliferation and migration through KLF4 and SEMA3C

Nature communications, 2021-02, Vol.12 (1), p.925-925, Article 925

2021

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Transcriptome analysis of controlled and therapy-resistant childhood asthma reveals distinct gene expression profiles

Journal of allergy and clinical immunology, 2015-09, Vol.136 (3), p.638-648

2015

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Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics

Nucleic acids research, 2015-08, Vol.43 (14), p.6969

2015

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PAPD5-mediated 3′ adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease

Proceedings of the National Academy of Sciences - PNAS, 2014-08, Vol.111 (31), p.11467-11472

2014

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Functional annotation of the vlinc class of non-coding RNAs using systems biology approach

Nucleic acids research, 2016-04, Vol.44 (7), p.3233

2016

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FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs

Nucleic acids research, 2021-01, Vol.49 (D1), p.D892

2021

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Optimization of turn-back primers in isothermal amplification

Nucleic acids research, 2011-05, Vol.39 (9), p.e59

2011

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Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries

Genome research, 2010-02, Vol.20 (2), p.257

2010

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Deep-sequencing of human Argonaute-associated small RNAs provides insight into miRNA sorting and reveals Argonaute association with RNA fragments of diverse origin

RNA biology, 2011-01, Vol.8 (1), p.158-177

2011

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Recent advances in functional genome analysis [version 1; peer review: 2 approved]

F1000 research, 2018, Vol.7, p.1968

2018

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Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite

Bioinformatics, 2009-10, Vol.25 (19), p.2613-2614

2009

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Prediction of transcriptional terminators in Bacillus subtilis and related species

PLoS computational biology, 2005-08, Vol.1 (3), p.e25-e25

2005

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Effect of Thiazole Orange Doubly Labeled Thymidine on DNA Duplex Formation

Biochemistry (Easton), 2012-08, Vol.51 (31), p.6056-6067

2012

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The choice of negative control antisense oligonucleotides dramatically impacts downstream analysis depending on the cellular background

BMC genomic data, 2021-09, Vol.22 (1), p.33-33, Article 33

2021

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FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions

Genome biology, 2009-01, Vol.10 (4), p.R39-R39

2009

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Hon-yaku: a biology-driven Bayesian methodology for identifying translation initiation sites in prokaryotes

BMC bioinformatics, 2007-02, Vol.8 (1), p.47-47, Article 47

2007

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Biopython: freely available Python tools for computational molecular biology and bioinformatics

Hierarchical Evolution of the Bacterial Sporulation Network

A comprehensive survey of 3' animal miRNA modification events and a possible role for 3' adenylation in modulating miRNA targeting effectiveness

Update of the FANTOM web resource: expansion to provide additional transcriptome atlases

An atlas of human long non-coding RNAs with accurate 5' ends

Annotation of nuclear lncRNAs based on chromatin interactions

Site-specific DICER and DROSHA RNA products control the DNA―damage response

An integrated expression atlas of miRNAs and their promoters in human and mouse

Batf2/Irf1 induces inflammatory responses in classically activated macrophages, lipopolysaccharides, and mycobacterial infection

LETR1 is a lymphatic endothelial-specific lncRNA governing cell proliferation and migration through KLF4 and SEMA3C

Transcriptome analysis of controlled and therapy-resistant childhood asthma reveals distinct gene expression profiles

Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics

PAPD5-mediated 3′ adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease

Functional annotation of the vlinc class of non-coding RNAs using systems biology approach

FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs

Optimization of turn-back primers in isothermal amplification

Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries

Deep-sequencing of human Argonaute-associated small RNAs provides insight into miRNA sorting and reveals Argonaute association with RNA fragments of diverse origin

Recent advances in functional genome analysis [version 1; peer review: 2 approved]

Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite

Prediction of transcriptional terminators in Bacillus subtilis and related species

Effect of Thiazole Orange Doubly Labeled Thymidine on DNA Duplex Formation

The choice of negative control antisense oligonucleotides dramatically impacts downstream analysis depending on the cellular background

FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions

Hon-yaku: a biology-driven Bayesian methodology for identifying translation initiation sites in prokaryotes

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