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A DEEP LEARNING APPROACH FOR CANCER DETECTION AND RELEVANT GENE IDENTIFICATION

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2017-01, Vol.22, p.219

2017

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LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search

Bioinformatics, 2019-07, Vol.35 (14), p.i295-i304

2019

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bpRNA-align: improved RNA secondary structure global alignment for comparing and clustering RNA structures

RNA (Cambridge), 2023-05, Vol.29 (5), p.584-595

2023

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Improving deep models of protein-coding potential with a Fourier-transform architecture and machine translation task

PLoS computational biology, 2023-10, Vol.19 (10), p.e1011526-e1011526

2023

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A deep recurrent neural network discovers complex biological rules to decipher RNA protein-coding potential

Nucleic acids research, 2018-09, Vol.46 (16), p.8105-8113

2018

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

Nucleic acids research, 2018-06, Vol.46 (11), p.5381-5394

2018

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The lncRNA Locus Handsdown Regulates Cardiac Gene Programs and Is Essential for Early Mouse Development

Developmental cell, 2019-09, Vol.50 (5), p.644-657.e8

2019

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Shadow Enhancers as a Source of Evolutionary Novelty

Science (American Association for the Advancement of Science), 2008-09, Vol.321 (5894), p.1314-1314

2008

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Circadian deep sequencing reveals stress-response genes that adopt robust rhythmic expression during aging

Nature communications, 2017-02, Vol.8 (1), p.14529-14529, Article 14529

2017

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Crowdsourcing to predict RNA degradation and secondary structure

Nature machine intelligence, 2023-02, Vol.5 (2), p.101-103

Hendrix, David A.

2023

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MicroRNA and gene expression changes in unruptured human cerebral aneurysms

Journal of neurosurgery, 2016-12, Vol.125 (6), p.1390-1399

2016

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In Vivo Characterization of an AHR-Dependent Long Noncoding RNA Required for Proper Sox9b Expression

Molecular pharmacology, 2017-06, Vol.91 (6), p.609-619

2017

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A distinct class of small RNAs arises from pre-miRNA-proximal regions in a simple chordate

Nature structural & molecular biology, 2009-02, Vol.16 (2), p.183-189

2009

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Transcription Factor CTIP1/ BCL11A Regulates Epidermal Differentiation and Lipid Metabolism During Skin Development

Scientific reports, 2017-10, Vol.7 (1), p.13427-16, Article 13427

2017

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miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data

Genome biology, 2010-04, Vol.11 (4), p.R39-R39, Article R39

2010

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PRC2 Is Required to Maintain Expression of the Maternal Gtl2-Rian-Mirg Locus by Preventing De Novo DNA Methylation in Mouse Embryonic Stem Cells

Cell reports (Cambridge), 2015-09, Vol.12 (9), p.1456-1470

2015

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Predicting Drosha and Dicer Cleavage Sites with DeepMirCut

Frontiers in molecular biosciences, 2022-01, Vol.8, p.799056

2022

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Sulforaphane Bioavailability and Chemopreventive Activity in Men Presenting for Biopsy of the Prostate Gland: A Randomized Controlled Trial

Nutrition and cancer, 2020-01, Vol.72 (1), p.74-87

2020

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Long noncoding RNAs and sulforaphane: a target for chemoprevention and suppression of prostate cancer

The Journal of nutritional biochemistry, 2017-04, Vol.42, p.72-83

2017

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DELAY OF GERMINATION 1‐LIKE 4 acts as an inducer of seed reserve accumulation

The Plant journal : for cell and molecular biology, 2019-10, Vol.100 (1), p.7-19

2019

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Promoter elements associated with RNA Pol II stalling in the Drosophila embryo

Proceedings of the National Academy of Sciences - PNAS, 2008-06, Vol.105 (22), p.7762-7767

2008

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Lactate dehydrogenase expression modulates longevity and neurodegeneration in Drosophila melanogaster

Aging (Albany, NY.), 2020-06, Vol.12 (11), p.10041-10058

2020

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How the Dorsal gradient works: Insights from postgenome technologies

Proceedings of the National Academy of Sciences - PNAS, 2008-12, Vol.105 (51), p.20072-20076

2008

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Neural-specific elongation of 3' UTRs during Drosophila development

Proceedings of the National Academy of Sciences - PNAS, 2011-09, Vol.108 (38), p.15864-15869

2011

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The Polycomb Group Mutant esc Leads to Augmented Levels of Paused Pol II in the Drosophila Embryo

Molecular cell, 2011-06, Vol.42 (6), p.837-844

2011

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A DEEP LEARNING APPROACH FOR CANCER DETECTION AND RELEVANT GENE IDENTIFICATION

LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search

bpRNA-align: improved RNA secondary structure global alignment for comparing and clustering RNA structures

Improving deep models of protein-coding potential with a Fourier-transform architecture and machine translation task

A deep recurrent neural network discovers complex biological rules to decipher RNA protein-coding potential

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

The lncRNA Locus Handsdown Regulates Cardiac Gene Programs and Is Essential for Early Mouse Development

Shadow Enhancers as a Source of Evolutionary Novelty

Circadian deep sequencing reveals stress-response genes that adopt robust rhythmic expression during aging

Crowdsourcing to predict RNA degradation and secondary structure

MicroRNA and gene expression changes in unruptured human cerebral aneurysms

In Vivo Characterization of an AHR-Dependent Long Noncoding RNA Required for Proper Sox9b Expression

A distinct class of small RNAs arises from pre-miRNA-proximal regions in a simple chordate

Transcription Factor CTIP1/ BCL11A Regulates Epidermal Differentiation and Lipid Metabolism During Skin Development

miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data

PRC2 Is Required to Maintain Expression of the Maternal Gtl2-Rian-Mirg Locus by Preventing De Novo DNA Methylation in Mouse Embryonic Stem Cells

Predicting Drosha and Dicer Cleavage Sites with DeepMirCut

Sulforaphane Bioavailability and Chemopreventive Activity in Men Presenting for Biopsy of the Prostate Gland: A Randomized Controlled Trial

Long noncoding RNAs and sulforaphane: a target for chemoprevention and suppression of prostate cancer

DELAY OF GERMINATION 1‐LIKE 4 acts as an inducer of seed reserve accumulation

Promoter elements associated with RNA Pol II stalling in the Drosophila embryo

Lactate dehydrogenase expression modulates longevity and neurodegeneration in Drosophila melanogaster

How the Dorsal gradient works: Insights from postgenome technologies

Neural-specific elongation of 3' UTRs during Drosophila development

The Polycomb Group Mutant esc Leads to Augmented Levels of Paused Pol II in the Drosophila Embryo

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