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A putative scenario of how de novo protein-coding genes originate in the Saccharomyces cerevisiae lineage

BMC genomics, 2024-09, Vol.25 (Suppl 3), p.834-10, Article 834

2024

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Micropeptides Encoded in Transcripts Previously Identified as Long Noncoding RNAs: A New Chapter in Transcriptomics and Proteomics

Frontiers in genetics, 2018-04, Vol.9, p.144-144

2018

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Long Noncoding RNA NEAT1-Dependent SFPQ Relocation from Promoter Region to Paraspeckle Mediates IL8 Expression upon Immune Stimuli

Molecular cell, 2014-02, Vol.53 (3), p.393-406

2014

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Dynamical robustness and its structural dependence in biological networks

Journal of theoretical biology, 2021-10, Vol.526, p.110808-110808, Article 110808

2021

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Identification and analysis of short open reading frames (sORFs) in the initially annotated noncoding RNA LINC00493 from human cells

Journal of biochemistry (Tokyo), 2021-04, Vol.169 (4), p.421-434

2021

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miRNA-target prediction based on transcriptional regulation

BMC genomics, 2013, Vol.14 Suppl 2 (Suppl 2), p.S3-S3, Article S3

2013

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Estimating optimal sparseness of developmental gene networks using a semi-quantitative model

PloS one, 2017-04, Vol.12 (4), p.e0176492-e0176492

2017

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Identification of Minimal p53 Promoter Region Regulated by MALAT1 in Human Lung Adenocarcinoma Cells

Frontiers in genetics, 2018-03, Vol.8, p.208-208

2018

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Analysis of RNA decay factor mediated RNA stability contributions on RNA abundance

BMC genomics, 2015-03, Vol.16 (1), p.154-154, Article 154

2015

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Tetrahedral gray code for visualization of genome information

PloS one, 2014-01, Vol.9 (1), p.e86133-e86133

2014

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Large-scale motif discovery using DNA Gray code and equiprobable oligomers

Bioinformatics, 2012-01, Vol.28 (1), p.25-31

2012

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Asymmetry in indegree and outdegree distributions of gene regulatory networks arising from dynamical robustness

Physical review. E, 2018-06, Vol.97 (6), Article 062315

2018

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Discrimination between Dementia Groups and Healthy Elderlies Using Scalp-Recorded-EEG-Based Brain Functional Connectivity Networks

Journal of biomedical science and engineering, 2020, Vol.13 (7), p.153-167

2020

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Long Noncoding RNA NEAT1-Dependent SFPQ Relocation from Promoter Region to Paraspeckle Mediates IL8 Expression upon Immune Stimuli

Molecular cell, 2014-06, Vol.54 (6), p.1055-1055

2014

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Predicting promoter activities of primary human DNA sequences

Nucleic acids research, 2011-06, Vol.39 (11), p.e75-e75

2011

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A new computational method to predict transcriptional activity of a DNA sequence from diverse datasets of massively parallel reporter assays

Nucleic acids research, 2017-07, Vol.45 (13), p.e124-e124

2017

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S2d2-5 A motif-based framework for constructing promoter models(S2-d2: "Bioinformatics of Transcriptional Regulation",Symposia,Abstract,Meeting Program of EABS & BSJ 2006)

Seibutsu Butsuri, 2006/10/01, Vol.46(supplement2), pp.S130

Yada, Tetsushi

2006

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Identification of hundreds of novel UPF1 target transcripts by direct determination of whole transcriptome stability

RNA biology, 2012-11, Vol.9 (11), p.1370-1379

2012

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Asymmetry in indegree and outdegree distributions of gene regulatory networks arising from dynamical robustness

Physical review. E, 2018-06, Vol.97 (6-1), p.062315-062315

2018

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LINEAR REGRESSION MODELS PREDICTING STRENGTH OF TRANSCRIPTIONAL ACTIVITY OF PROMOTERS

Genome Informatics, 2011, Vol.25(1), pp.53-60

2011

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Differential display analysis of mutants for the transcription factor Pdr1p regulating multidrug resistance in the budding yeast

FEBS letters, 2001-09, Vol.505 (1), p.103-108

2001

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Analysis of the promoter of mutated human whey acidic protein (WAP) gene

Journal of Reproduction and Development, 2006, Vol.52(2), pp.315-320

2006

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Guide to HGREP (Human Genome REconstruction Project)

Trends in Glycoscience and Glycotechnology, 2002/05/02, Vol.14(77), pp.189-197

2002

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Chromosome-wide assessment of replication timing for human chromosomes 11q and 21q: disease-related genes in timing-switch regions

Human molecular genetics, 2002, Vol.11 (1), p.13-21

2002

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Modeling and predicting transcriptional units of Escherichia coli genes using hidden Markov models

Bioinformatics (Oxford, England), 1999-12, Vol.15 (12), p.987-993

1999

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A putative scenario of how de novo protein-coding genes originate in the Saccharomyces cerevisiae lineage

Micropeptides Encoded in Transcripts Previously Identified as Long Noncoding RNAs: A New Chapter in Transcriptomics and Proteomics

Long Noncoding RNA NEAT1-Dependent SFPQ Relocation from Promoter Region to Paraspeckle Mediates IL8 Expression upon Immune Stimuli

Dynamical robustness and its structural dependence in biological networks

Identification and analysis of short open reading frames (sORFs) in the initially annotated noncoding RNA LINC00493 from human cells

miRNA-target prediction based on transcriptional regulation

Estimating optimal sparseness of developmental gene networks using a semi-quantitative model

Identification of Minimal p53 Promoter Region Regulated by MALAT1 in Human Lung Adenocarcinoma Cells

Analysis of RNA decay factor mediated RNA stability contributions on RNA abundance

Tetrahedral gray code for visualization of genome information

Large-scale motif discovery using DNA Gray code and equiprobable oligomers

Asymmetry in indegree and outdegree distributions of gene regulatory networks arising from dynamical robustness

Discrimination between Dementia Groups and Healthy Elderlies Using Scalp-Recorded-EEG-Based Brain Functional Connectivity Networks

Long Noncoding RNA NEAT1-Dependent SFPQ Relocation from Promoter Region to Paraspeckle Mediates IL8 Expression upon Immune Stimuli

Predicting promoter activities of primary human DNA sequences

A new computational method to predict transcriptional activity of a DNA sequence from diverse datasets of massively parallel reporter assays

S2d2-5 A motif-based framework for constructing promoter models(S2-d2: "Bioinformatics of Transcriptional Regulation",Symposia,Abstract,Meeting Program of EABS & BSJ 2006)

Identification of hundreds of novel UPF1 target transcripts by direct determination of whole transcriptome stability

Asymmetry in indegree and outdegree distributions of gene regulatory networks arising from dynamical robustness

LINEAR REGRESSION MODELS PREDICTING STRENGTH OF TRANSCRIPTIONAL ACTIVITY OF PROMOTERS

Differential display analysis of mutants for the transcription factor Pdr1p regulating multidrug resistance in the budding yeast

Analysis of the promoter of mutated human whey acidic protein (WAP) gene

Guide to HGREP (Human Genome REconstruction Project)

Chromosome-wide assessment of replication timing for human chromosomes 11q and 21q: disease-related genes in timing-switch regions

Modeling and predicting transcriptional units of Escherichia coli genes using hidden Markov models

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