PubRank

Kenta Nakai

Author PubWeight™ 129.79‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 WoLF PSORT: protein localization predictor. Nucleic Acids Res 2007 10.14
2 Complete sequencing and characterization of 21,243 full-length human cDNAs. Nat Genet 2003 7.98
3 Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol 2004 7.17
4 Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Genome Res 2005 5.22
5 Extensive feature detection of N-terminal protein sorting signals. Bioinformatics 2002 5.16
6 The Jmjd3-Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection. Nat Immunol 2010 4.66
7 DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs. Nucleic Acids Res 2002 4.29
8 PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria. Nucleic Acids Res 2003 4.25
9 DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Res 2007 3.80
10 ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. Nucleic Acids Res 2006 3.74
11 DBTSS, DataBase of Transcriptional Start Sites: progress report 2004. Nucleic Acids Res 2004 3.73
12 DBTSS: database of transcription start sites, progress report 2008. Nucleic Acids Res 2007 3.11
13 T cell receptor stimulation-induced epigenetic changes and Foxp3 expression are independent and complementary events required for Treg cell development. Immunity 2012 2.78
14 DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics. Nucleic Acids Res 2004 2.61
15 Prediction of transcriptional terminators in Bacillus subtilis and related species. PLoS Comput Biol 2005 2.54
16 DBTSS: DataBase of Human Transcription Start Sites, progress report 2006. Nucleic Acids Res 2006 2.52
17 The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res 2007 2.07
18 PrognoScan: a new database for meta-analysis of the prognostic value of genes. BMC Med Genomics 2009 2.07
19 Massive transcriptional start site analysis of human genes in hypoxia cells. Nucleic Acids Res 2009 1.60
20 Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity. Gene 2005 1.57
21 Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis. Genome Res 2011 1.57
22 HitPredict: a database of quality assessed protein-protein interactions in nine species. Nucleic Acids Res 2010 1.50
23 Distinct class of putative "non-conserved" promoters in humans: comparative studies of alternative promoters of human and mouse genes. Genome Res 2007 1.37
24 DBTSS provides a tissue specific dynamic view of Transcription Start Sites. Nucleic Acids Res 2009 1.36
25 Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues. Nucleic Acids Res 2005 1.35
26 DBTSS: DataBase of Transcriptional Start Sites progress report in 2012. Nucleic Acids Res 2011 1.33
27 Comparative genomic analyses of Streptococcus mutans provide insights into chromosomal shuffling and species-specific content. BMC Genomics 2009 1.29
28 Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions. Genome Res 2004 1.25
29 Prediction of subcellular locations of proteins: where to proceed? Proteomics 2010 1.22
30 Sequence- and species-dependence of proteasomal processivity. ACS Chem Biol 2012 1.18
31 Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals. Nucleic Acids Res 2005 1.15
32 Inferring the choreography of parental genomes during fertilization from ultralarge-scale whole-transcriptome analysis. Genes Dev 2013 1.11
33 Genomic cis-regulatory networks in the early Ciona intestinalis embryo. Development 2010 1.10
34 Pseudocounts for transcription factor binding sites. Nucleic Acids Res 2008 1.06
35 Retrotransposition as a source of new promoters. Mol Biol Evol 2008 1.00
36 Small open reading frames in 5' untranslated regions of mRnas. C R Biol 2004 1.00
37 Comprehensive detection of human terminal oligo-pyrimidine (TOP) genes and analysis of their characteristics. Nucleic Acids Res 2008 0.99
38 Challenges of the next decade for the Asia Pacific region: 2010 International Conference in Bioinformatics (InCoB 2010). BMC Genomics 2010 0.98
39 Large-scale collection and characterization of promoters of human and mouse genes. In Silico Biol 2004 0.97
40 DBTGR: a database of tunicate promoters and their regulatory elements. Nucleic Acids Res 2006 0.93
41 Genome-wide demethylation during neural differentiation of P19 embryonal carcinoma cells. J Hum Genet 2008 0.93
42 Genome-wide analysis of DNA methylation and expression of microRNAs in breast cancer cells. Int J Mol Sci 2012 0.92
43 Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions. Nucleic Acids Res 2007 0.92
44 Chemical composition is maintained in poorly conserved intrinsically disordered regions and suggests a means for their classification. Mol Biosyst 2012 0.92
45 Effects of Alu elements on global nucleosome positioning in the human genome. BMC Genomics 2010 0.91
46 Diverse DNA methylation statuses at alternative promoters of human genes in various tissues. DNA Res 2006 0.89
47 RANK signaling induces interferon-stimulated genes in the fetal thymic stroma. Biochem Biophys Res Commun 2011 0.88
48 A regression analysis of gene expression in ES cells reveals two gene classes that are significantly different in epigenetic patterns. BMC Bioinformatics 2011 0.87
49 Modeling tissue-specific structural patterns in human and mouse promoters. Nucleic Acids Res 2009 0.86
50 Global gene expression of the inner cell mass and trophectoderm of the bovine blastocyst. BMC Dev Biol 2012 0.85
51 Assessing the utility of gene co-expression stability in combination with correlation in the analysis of protein-protein interaction networks. BMC Genomics 2011 0.85
52 Melina: motif extraction from promoter regions of potentially co-regulated genes. Bioinformatics 2003 0.85
53 An assessment of prediction algorithms for nucleosome positioning. Genome Inform 2009 0.85
54 Identification of novel motif patterns to decipher the promoter architecture of co-expressed genes in Arabidopsis thaliana. BMC Syst Biol 2013 0.85
55 Intrinsic promoter activities of primary DNA sequences in the human genome. DNA Res 2007 0.84
56 Linking transcriptional changes over time in stimulated dendritic cells to identify gene networks activated during the innate immune response. PLoS Comput Biol 2013 0.83
57 Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs. BMC Genomics 2008 0.82
58 InCoB2010 - 9th International Conference on Bioinformatics at Tokyo, Japan, September 26-28, 2010. BMC Bioinformatics 2010 0.82
59 Predicting promoter activities of primary human DNA sequences. Nucleic Acids Res 2011 0.81
60 Gradual transition from mosaic to global DNA methylation patterns during deuterostome evolution. BMC Bioinformatics 2010 0.81
61 Characterization of the compact bicistronic microRNA precursor, miR-1/miR-133, expressed specifically in Ciona muscle tissues. Gene Expr Patterns 2012 0.81
62 Sequence-based approach for identification of cell wall proteins in Saccharomyces cerevisiae. Curr Genet 2002 0.81
63 Markov chain-based promoter structure modeling for tissue-specific expression pattern prediction. DNA Res 2008 0.81
64 TimeXNet: identifying active gene sub-networks using time-course gene expression profiles. BMC Syst Biol 2014 0.80
65 Functional annotation of intrinsically disordered domains by their amino acid content using IDD Navigator. Pac Symp Biocomput 2012 0.80
66 A novel strategy to search conserved transcription factor binding sites among coexpressing genes in human. Genome Inform 2008 0.80
67 Cross-validated methods for promoter/transcription start site mapping in SL trans-spliced genes, established using the Ciona intestinalis troponin I gene. Nucleic Acids Res 2010 0.79
68 Two different classes of co-occurring motif pairs found by a novel visualization method in human promoter regions. BMC Genomics 2008 0.79
69 Profiling ascidian promoters as the primordial type of vertebrate promoter. BMC Genomics 2011 0.79
70 Characterization of transcription start sites of putative non-coding RNAs by multifaceted use of massively paralleled sequencer. DNA Res 2010 0.78
71 Using simple rules on presence and positioning of motifs for promoter structure modeling and tissue-specific expression prediction. Genome Inform 2008 0.78
72 Genome-wide analysis of Chlamydophila pneumoniae gene expression at the late stage of infection. DNA Res 2008 0.78
73 Spatial and temporal preferences for trans-splicing in Ciona intestinalis revealed by EST-based gene expression analysis. Gene 2008 0.77
74 Positional variations among heterogeneous nucleosome maps give dynamical information on chromatin. Chromosoma 2010 0.76
75 A bit-parallel dynamic programming algorithm suitable for DNA sequence alignment. J Bioinform Comput Biol 2012 0.75
76 An O(N2) algorithm for discovering optimal Boolean pattern pairs. IEEE/ACM Trans Comput Biol Bioinform 2006 0.75
77 [Transcriptome analyses and transcriptome databases]. Tanpakushitsu Kakusan Koso 2004 0.75
78 Design and utility of CCN2 anchor peptide aptamers. Biochimie 2010 0.75