PubRank

Satoru Miyano

Author PubWeight™ 208.22‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 International network of cancer genome projects. Nature 2010 20.35
2 Frequent pathway mutations of splicing machinery in myelodysplasia. Nature 2011 11.44
3 Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers. Cancer Res 2011 6.02
4 Extensive feature detection of N-terminal protein sorting signals. Bioinformatics 2002 5.16
5 Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators. Nat Genet 2012 4.84
6 Integrated molecular analysis of clear-cell renal cell carcinoma. Nat Genet 2013 4.61
7 Somatic Mutations and Clonal Hematopoiesis in Aplastic Anemia. N Engl J Med 2015 3.42
8 Identification of genes upregulated in ALK-positive and EGFR/KRAS/ALK-negative lung adenocarcinomas. Cancer Res 2011 2.81
9 Prediction of transcriptional terminators in Bacillus subtilis and related species. PLoS Comput Biol 2005 2.54
10 Estimation of genetic networks and functional structures between genes by using Bayesian networks and nonparametric regression. Pac Symp Biocomput 2002 2.30
11 Recurrent mutations in multiple components of the cohesin complex in myeloid neoplasms. Nat Genet 2013 2.14
12 Somatic SETBP1 mutations in myeloid malignancies. Nat Genet 2013 2.12
13 Whole-genome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing. Nat Genet 2010 2.08
14 Inferring gene networks from time series microarray data using dynamic Bayesian networks. Brief Bioinform 2003 2.08
15 Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection. Bioinformatics 2003 1.95
16 Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks. Proc IEEE Comput Soc Bioinform Conf 2003 1.89
17 Variant ALDH2 is associated with accelerated progression of bone marrow failure in Japanese Fanconi anemia patients. Blood 2013 1.79
18 Exome sequencing identifies secondary mutations of SETBP1 and JAK3 in juvenile myelomonocytic leukemia. Nat Genet 2013 1.71
19 Modeling gene expression regulatory networks with the sparse vector autoregressive model. BMC Syst Biol 2007 1.69
20 The tumor-suppressive miR-497-195 cluster targets multiple cell-cycle regulators in hepatocellular carcinoma. PLoS One 2013 1.69
21 ACTN1 mutations cause congenital macrothrombocytopenia. Am J Hum Genet 2013 1.49
22 Dynamic Bayesian network and nonparametric regression for nonlinear modeling of gene networks from time series gene expression data. Biosystems 2004 1.47
23 Bayesian network and nonparametric heteroscedastic regression for nonlinear modeling of genetic network. J Bioinform Comput Biol 2003 1.44
24 A neural network method for identification of RNA-interacting residues in protein. Genome Inform 2004 1.42
25 Identification of novel adrenomedullin in mammals: a potent cardiovascular and renal regulator. FEBS Lett 2004 1.40
26 Inferring the global structure of chromosomes from structural variations. BMC Genomics 2015 1.37
27 Biopathways representation and simulation on hybrid functional Petri net. In Silico Biol 2003 1.37
28 Inferring gene regulatory networks from time-ordered gene expression data of Bacillus subtilis using differential equations. Pac Symp Biocomput 2003 1.34
29 Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models. Bioinformatics 2008 1.33
30 The landscape of somatic mutations in Down syndrome-related myeloid disorders. Nat Genet 2013 1.31
31 Plastin3 is a novel marker for circulating tumor cells undergoing the epithelial-mesenchymal transition and is associated with colorectal cancer prognosis. Cancer Res 2013 1.29
32 Genomic Object Net: I. A platform for modelling and simulating biopathways. Appl Bioinformatics 2003 1.26
33 A top-r feature selection algorithm for microarray gene expression data. IEEE/ACM Trans Comput Biol Bioinform 2012 1.25
34 An empirical Bayesian framework for somatic mutation detection from cancer genome sequencing data. Nucleic Acids Res 2013 1.24
35 Cell system ontology: representation for modeling, visualizing, and simulating biological pathways. In Silico Biol 2007 1.20
36 BCOR and BCORL1 mutations in myelodysplastic syndromes and related disorders. Blood 2013 1.16
37 Combining microarrays and biological knowledge for estimating gene networks via bayesian networks. J Bioinform Comput Biol 2004 1.16
38 ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information. BMC Bioinformatics 2011 1.15
39 Deep sequencing reveals stepwise mutation acquisition in paroxysmal nocturnal hemoglobinuria. J Clin Invest 2014 1.09
40 Gene network inference and visualization tools for biologists: application to new human transcriptome datasets. Nucleic Acids Res 2011 1.08
41 Recursive regularization for inferring gene networks from time-course gene expression profiles. BMC Syst Biol 2009 1.06
42 Cell fate simulation model of gustatory neurons with MicroRNAs double-negative feedback loop by hybrid functional Petri net with extension. Genome Inform 2006 1.04
43 Constructing biological pathway models with hybrid functional Petri nets. In Silico Biol 2004 1.01
44 Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension. BMC Syst Biol 2009 1.00
45 Kernel mixture survival models for identifying cancer subtypes, predicting patient's cancer types and survival probabilities. Genome Inform 2004 1.00
46 Inhibition of histone demethylase JMJD1A improves anti-angiogenic therapy and reduces tumor-associated macrophages. Cancer Res 2013 0.99
47 Modelling and simulation of signal transductions in an apoptosis pathway by using timed Petri nets. J Biosci 2007 0.99
48 An efficient grid layout algorithm for biological networks utilizing various biological attributes. BMC Bioinformatics 2007 0.99
49 Ontology-based instance data validation for high-quality curated biological pathways. BMC Bioinformatics 2011 0.98
50 Association between single-nucleotide polymorphisms in selectin genes and immunoglobulin A nephropathy. Am J Hum Genet 2002 0.98
51 Association of single-nucleotide polymorphisms in the polymeric immunoglobulin receptor gene with immunoglobulin A nephropathy (IgAN) in Japanese patients. J Hum Genet 2003 0.98
52 Estimating gene regulatory networks and protein-protein interactions of Saccharomyces cerevisiae from multiple genome-wide data. Bioinformatics 2005 0.96
53 Online model checking approach based parameter estimation to a neuronal fate decision simulation model in Caenorhabditis elegans with hybrid functional Petri net with extension. Mol Biosyst 2011 0.95
54 Epidermal growth factor receptor tyrosine kinase defines critical prognostic genes of stage I lung adenocarcinoma. PLoS One 2012 0.95
55 Ligand-based gene expression profiling reveals novel roles of glucocorticoid receptor in cardiac metabolism. Am J Physiol Endocrinol Metab 2009 0.94
56 MIRACH: efficient model checker for quantitative biological pathway models. Bioinformatics 2011 0.94
57 A versatile petri net based architecture for modeling and simulation of complex biological processes. Genome Inform 2004 0.94
58 Cell Illustrator 4.0: a computational platform for systems biology. In Silico Biol 2010 0.94
59 Modeling and estimation of dynamic EGFR pathway by data assimilation approach using time series proteomic data. Genome Inform 2006 0.93
60 A state space representation of VAR models with sparse learning for dynamic gene networks. Genome Inform 2010 0.92
61 Genomic Object Net: II. Modelling biopathways by hybrid functional Petri net with extension. Appl Bioinformatics 2003 0.91
62 Parameter estimation of in silico biological pathways with particle filtering towards a petascale computing. Pac Symp Biocomput 2009 0.91
63 Single-nucleotide polymorphisms in the class II region of the major histocompatibility complex in Japanese patients with immunoglobulin A nephropathy. J Hum Genet 2002 0.91
64 Automatic drawing of biological networks using cross cost and subcomponent data. Genome Inform 2005 0.91
65 Molecular features of triple negative breast cancer cells by genome-wide gene expression profiling analysis. Int J Oncol 2012 0.91
66 The rs6983267 SNP is associated with MYC transcription efficiency, which promotes progression and worsens prognosis of colorectal cancer. Ann Surg Oncol 2012 0.90
67 A statistical framework for genome-wide discovery of biomarker splice variations with GeneChip Human Exon 1.0 ST Arrays. Genome Inform 2006 0.89
68 Phosphoproteomics-based modeling defines the regulatory mechanism underlying aberrant EGFR signaling. PLoS One 2010 0.89
69 Inferring dynamic gene networks under varying conditions for transcriptomic network comparison. Bioinformatics 2010 0.89
70 Understanding endothelial cell apoptosis: what can the transcriptome, glycome and proteome reveal? Philos Trans R Soc Lond B Biol Sci 2007 0.89
71 AYUMS: an algorithm for completely automatic quantitation based on LC-MS/MS proteome data and its application to the analysis of signal transduction. BMC Bioinformatics 2007 0.88
72 Loss of function mutations in RPL27 and RPS27 identified by whole-exome sequencing in Diamond-Blackfan anaemia. Br J Haematol 2014 0.88
73 Comparing Pearson, Spearman and Hoeffding's D measure for gene expression association analysis. J Bioinform Comput Biol 2009 0.88
74 Analysis of PPARalpha-dependent and PPARalpha-independent transcript regulation following fenofibrate treatment of human endothelial cells. Angiogenesis 2009 0.88
75 Cell cycle gene networks are associated with melanoma prognosis. PLoS One 2012 0.88
76 Estimating genome-wide gene networks using nonparametric Bayesian network models on massively parallel computers. IEEE/ACM Trans Comput Biol Bioinform 2011 0.88
77 Fast grid layout algorithm for biological networks with sweep calculation. Bioinformatics 2008 0.88
78 DA 1.0: parameter estimation of biological pathways using data assimilation approach. Bioinformatics 2010 0.88
79 Computational strategy for discovering druggable gene networks from genome-wide RNA expression profiles. Pac Symp Biocomput 2006 0.88
80 A novel network profiling analysis reveals system changes in epithelial-mesenchymal transition. PLoS One 2011 0.88
81 N-cadherin expression is a potential survival mechanism of gefitinib-resistant lung cancer cells. Am J Cancer Res 2011 0.88
82 Genomic data assimilation for estimating hybrid functional Petri net from time-course gene expression data. Genome Inform 2006 0.88
83 Contribution of comparative fish studies to general endocrinology: structure and function of some osmoregulatory hormones. J Exp Zool A Comp Exp Biol 2006 0.87
84 Clonal leukemic evolution in myelodysplastic syndromes with TET2 and IDH1/2 mutations. Haematologica 2013 0.87
85 Identifying drug active pathways from gene networks estimated by gene expression data. Genome Inform 2005 0.86
86 Targeting BIG3-PHB2 interaction to overcome tamoxifen resistance in breast cancer cells. Nat Commun 2013 0.86
87 A microarray analysis of gnotobiotic mice indicating that microbial exposure during the neonatal period plays an essential role in immune system development. BMC Genomics 2012 0.86
88 Bayesian network and nonparametric heteroscedastic regression for nonlinear modeling of genetic network. Proc IEEE Comput Soc Bioinform Conf 2002 0.86
89 Modeling nonlinear gene regulatory networks from time series gene expression data. J Bioinform Comput Biol 2008 0.86
90 Exploring temporal transcription regulation structure of Aspergillus fumigatus in heat shock by state space model. BMC Genomics 2009 0.85
91 Weighted lasso in graphical Gaussian modeling for large gene network estimation based on microarray data. Genome Inform 2007 0.85
92 Conversion from BioPAX to CSO for system dynamics and visualization of biological pathway. Genome Inform 2007 0.85
93 Transcriptional profiling of hematopoietic stem cells by high-throughput sequencing. Int J Hematol 2008 0.85
94 Structural modeling and analysis of signaling pathways based on Petri nets. J Bioinform Comput Biol 2006 0.85
95 Multivariate gene expression analysis reveals functional connectivity changes between normal/tumoral prostates. BMC Syst Biol 2008 0.85
96 ArrayCluster: an analytic tool for clustering, data visualization and module finder on gene expression profiles. Bioinformatics 2006 0.84
97 BFL: a node and edge betweenness based fast layout algorithm for large scale networks. BMC Bioinformatics 2009 0.84
98 Enhancement of collective immunity in Tokyo metropolitan area by selective vaccination against an emerging influenza pandemic. PLoS One 2013 0.84
99 A novel meta-analysis approach of cancer transcriptomes reveals prevailing transcriptional networks in cancer cells. Genome Inform 2010 0.83
100 The GC and window-averaged DNA curvature profile of secondary metabolite gene cluster in Aspergillus fumigatus genome. Appl Microbiol Biotechnol 2008 0.83
101 A strategy to select suitable physicochemical attributes of amino acids for protein fold recognition. BMC Bioinformatics 2013 0.83
102 Boundary formation by notch signaling in Drosophila multicellular systems: experimental observations and gene network modeling by Genomic Object Net. Pac Symp Biocomput 2003 0.83
103 Sign: large-scale gene network estimation environment for high performance computing. Genome Inform 2011 0.83
104 Predicting differences in gene regulatory systems by state space models. Genome Inform 2008 0.82
105 CSO validator: improving manual curation workflow for biological pathways. Bioinformatics 2011 0.82
106 ExonMiner: Web service for analysis of GeneChip Exon array data. BMC Bioinformatics 2008 0.82
107 Extension and verification of the SEIR model on the 2009 influenza A (H1N1) pandemic in Japan. Math Biosci 2013 0.82
108 A new regulatory interaction suggested by simulations for circadian genetic control mechanism in mammals. J Bioinform Comput Biol 2006 0.82
109 Bayesian learning of biological pathways on genomic data assimilation. Bioinformatics 2008 0.82
110 Use of gene networks from full genome microarray libraries to identify functionally relevant drug-affected genes and gene regulation cascades. DNA Res 2003 0.82
111 Rule-based reasoning for system dynamics in cell systems. Genome Inform 2008 0.81
112 The impact of measurement errors in the identification of regulatory networks. BMC Bioinformatics 2009 0.81
113 Twist2 functions as a tumor suppressor in murine osteosarcoma cells. Cancer Sci 2013 0.81
114 Systematic reconstruction of TRANSPATH data into cell system markup language. BMC Syst Biol 2008 0.80
115 Cell illustrator 4.0: a computational platform for systems biology. Stud Health Technol Inform 2011 0.80
116 A novel strategy to search conserved transcription factor binding sites among coexpressing genes in human. Genome Inform 2008 0.80
117 Loss of CDCP1 expression promotes invasiveness and poor prognosis in esophageal squamous cell carcinoma. Ann Surg Oncol 2014 0.80
118 PRD: A protein-RNA interaction database. Bioinformation 2012 0.80
119 Use of gene networks for identifying and validating drug targets. J Bioinform Comput Biol 2003 0.80
120 Computational gene network analysis reveals TNF-induced angiogenesis. BMC Syst Biol 2012 0.80
121 Orengedokuto and berberine improve indomethacin-induced small intestinal injury via adenosine. J Gastroenterol 2009 0.80
122 Characterization of T-cell Receptor Repertoire in Inflamed Tissues of Patients with Crohn's Disease Through Deep Sequencing. Inflamm Bowel Dis 2016 0.80
123 Sparse overlapping group lasso for integrative multi-omics analysis. J Comput Biol 2015 0.79
124 Statistical model-based testing to evaluate the recurrence of genomic aberrations. Bioinformatics 2012 0.79
125 Simulation-based validation of the p53 transcriptional activity with hybrid functional petri net. In Silico Biol 2006 0.79
126 A string pattern regression algorithm and its application to pattern discovery in long introns. Genome Inform 2002 0.79
127 Identifying regulational alterations in gene regulatory networks by state space representation of vector autoregressive models and variational annealing. BMC Genomics 2012 0.79
128 XiP: a computational environment to create, extend and share workflows. Bioinformatics 2012 0.79
129 Utilizing evolutionary information and gene expression data for estimating gene networks with bayesian network models. J Bioinform Comput Biol 2005 0.79
130 Unraveling dynamic activities of autocrine pathways that control drug-response transcriptome networks. Pac Symp Biocomput 2009 0.79
131 Association of a single-nucleotide polymorphism in the immunoglobulin mu-binding protein 2 gene with immunoglobulin A nephropathy. J Hum Genet 2004 0.79
132 Somatic mosaicism for a NRAS mutation associates with disparate clinical features in RAS-associated leukoproliferative disease: a report of two cases. J Clin Immunol 2015 0.79
133 Quality control and reproducibility in DNA microarray experiments. Genome Inform 2009 0.78
134 Allelic imbalance at an 8q24 oncogenic SNP is involved in activating MYC in human colorectal cancer. Ann Surg Oncol 2014 0.78
135 Systems biology analysis of Drosophila in vivo screen data elucidates core networks for DNA damage repair in SCA1. Hum Mol Genet 2013 0.78
136 Tracing the development of acute myeloid leukemia in CBL syndrome. Blood 2014 0.78
137 Multi-omics approach for estimating metabolic networks using low-order partial correlations. J Comput Biol 2013 0.78
138 Vasohibin-1 is identified as a master-regulator of endothelial cell apoptosis using gene network analysis. BMC Genomics 2013 0.78
139 A rank-based statistical test for measuring synergistic effects between two gene sets. Bioinformatics 2011 0.78
140 Efficiently finding regulatory elements using correlation with gene expression. J Bioinform Comput Biol 2004 0.78
141 A between-class overlapping filter-based method for transcriptome data analysis. J Bioinform Comput Biol 2012 0.77
142 Gene regulatory network clustering for graph layout based on microarray gene expression data. Genome Inform 2010 0.77
143 Comparison of gene expression profiles produced by CAGE, illumina microarray and real time RT-PCR. Genome Inform 2010 0.77
144 Identification of activated transcription factors from microarray gene expression data of Kampo medicine-treated mice. Genome Inform 2007 0.77
145 Erratum: Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer. Nat Genet 2016 0.77
146 Systems biology model repository for macrophage pathway simulation. Bioinformatics 2011 0.77
147 A fast and robust statistical test based on likelihood ratio with Bartlett correction to identify Granger causality between gene sets. Bioinformatics 2010 0.77
148 An efficient data assimilation schema for restoration and extension of gene regulatory networks using time-course observation data. J Comput Biol 2014 0.77
149 An efficient biological pathway layout algorithm combining grid-layout and spring embedder for complicated cellular location information. BMC Bioinformatics 2010 0.77
150 Estimation of nonlinear gene regulatory networks via L1 regularized NVAR from time series gene expression data. Genome Inform 2008 0.77
151 Increased risk for CRC in diabetic patients with the nonrisk allele of SNPs at 8q24. Ann Surg Oncol 2012 0.76
152 MRG-binding protein contributes to colorectal cancer development. Cancer Sci 2011 0.76
153 A female patient with incomplete hemophagocytic lymphohistiocytosis caused by a heterozygous XIAP mutation associated with non-random X-chromosome inactivation skewed towards the wild-type XIAP allele. J Clin Immunol 2015 0.76
154 SiGN-SSM: open source parallel software for estimating gene networks with state space models. Bioinformatics 2011 0.76
155 Identification of a homozygous JAK3 V674A mutation caused by acquired uniparental disomy in a relapsed early T-cell precursor ALL patient. Int J Hematol 2014 0.76
156 Simulation-Based Validation of the p53 Transcriptional Activity with Hybrid Functional Petri Net. Stud Health Technol Inform 2011 0.76
157 Performance improvement in protein N-myristoyl classification by BONSAI with insignificant indexing symbol. Genome Inform 2007 0.76
158 ChopSticks: High-resolution analysis of homozygous deletions by exploiting concordant read pairs. BMC Bioinformatics 2012 0.76
159 Clonal selection in xenografted TAM recapitulates the evolutionary process of myeloid leukemia in Down syndrome. Blood 2013 0.76
160 2D-Qsar for 450 types of amino acid induction peptides with a novel substructure pair descriptor having wider scope. J Cheminform 2011 0.76
161 Does Twitter trigger bursts in signature collections? PLoS One 2013 0.75
162 A restricted level of PQBP1 is needed for the best longevity of Drosophila. Neurobiol Aging 2012 0.75
163 Gene set-based module discovery decodes cis-regulatory codes governing diverse gene expression across human multiple tissues. PLoS One 2010 0.75
164 Functional clustering of time series gene expression data by Granger causality. BMC Syst Biol 2012 0.75
165 Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram. BMC Syst Biol 2010 0.75
166 Human papillomavirus vaccine coverage. Lancet 2010 0.75
167 IRView: a database and viewer for protein interacting regions. Bioinformatics 2012 0.75
168 Biopathways representation and simulation on hybrid functional petri net. Stud Health Technol Inform 2011 0.75
169 Aggressive transformation of anaplastic large cell lymphoma with increased number of ALK-translocated chromosomes. Int J Hematol 2014 0.75
170 On determining firing delay time of transitions for petri net based signaling pathways by introducing stochastic decision rules. Stud Health Technol Inform 2011 0.75
171 [Dynamic pathway modeling language: CSML]. Tanpakushitsu Kakusan Koso 2005 0.75
172 The systems approach to the prespore-specific activation of sigma factor SigF in Bacillus subtilis. Biosystems 2010 0.75
173 Inferring contagion in regulatory networks. IEEE/ACM Trans Comput Biol Bioinform 2011 0.75
174 Prediction of debacle points for robustness of biological pathways by using recurrent neural networks. Genome Inform 2005 0.75
175 [Digitalizaing pathways]. Tanpakushitsu Kakusan Koso 2002 0.75
176 Finding optimal gene networks using biological constraints. Genome Inform 2003 0.75
177 Constructing biological pathway models with hybrid functional petri nets. Stud Health Technol Inform 2011 0.75
178 Identifying gene pathways associated with cancer characteristics via sparse statistical methods. IEEE/ACM Trans Comput Biol Bioinform 2012 0.75
179 On determining firing delay time of transitions for Petri net based signaling pathways by introducing stochastic decision rules. In Silico Biol 2010 0.75
180 A novel adaptive penalized logistic regression for uncovering biomarker associated with anti-cancer drug sensitivity. IEEE/ACM Trans Comput Biol Bioinform 2016 0.75
181 Clustering samples characterized by time course gene expression profiles using the mixture of state space models. Genome Inform 2007 0.75
182 Correction: Integrated Multiregional Analysis Proposing a New Model of Colorectal Cancer Evolution. PLoS Genet 2017 0.75
183 Model-free unsupervised gene set screening based on information enrichment in expression profiles. Bioinformatics 2010 0.75
184 A combined pathway to simulate CDK-dependent phosphorylation and ARF-dependent stabilization for p53 transcriptional activity. Genome Inform 2006 0.75
185 An O(N2) algorithm for discovering optimal Boolean pattern pairs. IEEE/ACM Trans Comput Biol Bioinform 2006 0.75
186 High performance hybrid functional Petri net simulations of biological pathway models on CUDA. IEEE/ACM Trans Comput Biol Bioinform 2011 0.75
187 Simulation analysis for the effect of light-dark cycle on the entrainment in circadian rhythm. Genome Inform 2008 0.75
188 Analysis of gene networks for drug target discovery and validation. Methods Mol Biol 2007 0.75
189 Collocation-based sparse estimation for constructing dynamic gene networks. Genome Inform 2010 0.75
190 OVarCall: Bayesian Mutation Calling Method Utilizing Overlapping Paired-End Reads. IEEE Trans Nanobioscience 2017 0.75
191 Introduction--the First IEEE Conference on Healthcare Informatics, Imaging, and Systems Biology HISB'11. J Bioinform Comput Biol 2011 0.75
192 A tutorial to identify nonlinear associations in gene expression time series data. Methods Mol Biol 2014 0.75