PubRank

Zhongming Zhao

Author PubWeight™ 133.89‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 TSGene: a web resource for tumor suppressor genes. Nucleic Acids Res 2012 2.90
2 BRAF(L597) mutations in melanoma are associated with sensitivity to MEK inhibitors. Cancer Discov 2012 2.48
3 dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks. Bioinformatics 2010 2.23
4 Hdac3 is essential for the maintenance of chromatin structure and genome stability. Cancer Cell 2010 2.20
5 Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives. BMC Bioinformatics 2013 2.07
6 Common variants conferring risk of schizophrenia: a pathway analysis of GWAS data. Schizophr Res 2010 1.79
7 No-boundary thinking in bioinformatics research. BioData Min 2013 1.76
8 Gene set analysis of genome-wide association studies: methodological issues and perspectives. Genomics 2011 1.76
9 Schizophrenia gene networks and pathways and their applications for novel candidate gene selection. PLoS One 2010 1.67
10 Mutations in GDF6 are associated with vertebral segmentation defects in Klippel-Feil syndrome. Hum Mutat 2008 1.62
11 Construction of a chloroplast protein interaction network and functional mining of photosynthetic proteins in Arabidopsis thaliana. Cell Res 2008 1.58
12 Uncovering MicroRNA and Transcription Factor Mediated Regulatory Networks in Glioblastoma. PLoS Comput Biol 2012 1.54
13 A multi-dimensional evidence-based candidate gene prioritization approach for complex diseases-schizophrenia as a case. Bioinformatics 2009 1.50
14 Epithelial cell organization suppresses Myc function by attenuating Myc expression. Cancer Res 2011 1.44
15 Large-scale prediction of adverse drug reactions using chemical, biological, and phenotypic properties of drugs. J Am Med Inform Assoc 2012 1.43
16 A novel microRNA and transcription factor mediated regulatory network in schizophrenia. BMC Syst Biol 2010 1.40
17 VirusFinder: software for efficient and accurate detection of viruses and their integration sites in host genomes through next generation sequencing data. PLoS One 2013 1.35
18 Candidate genes for schizophrenia: a survey of association studies and gene ranking. Am J Med Genet B Neuropsychiatr Genet 2008 1.31
19 CpG island density and its correlations with genomic features in mammalian genomes. Genome Biol 2008 1.30
20 IL-15 regulates homeostasis and terminal maturation of NKT cells. J Immunol 2011 1.29
21 Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives. Brief Bioinform 2012 1.23
22 A comparative study of cancer proteins in the human protein-protein interaction network. BMC Genomics 2010 1.23
23 Network-assisted investigation of combined causal signals from genome-wide association studies in schizophrenia. PLoS Comput Biol 2012 1.23
24 Features and trend of loss of promoter-associated CpG islands in the human and mouse genomes. Mol Biol Evol 2007 1.23
25 Targeted next-generation sequencing of DNA regions proximal to a conserved GXGXXG signaling motif enables systematic discovery of tyrosine kinase fusions in cancer. Nucleic Acids Res 2010 1.17
26 A bias-reducing pathway enrichment analysis of genome-wide association data confirmed association of the MHC region with schizophrenia. J Med Genet 2011 1.15
27 Rare variants in RTEL1 are associated with familial interstitial pneumonia. Am J Respir Crit Care Med 2015 1.15
28 A comprehensive network and pathway analysis of candidate genes in major depressive disorder. BMC Syst Biol 2011 1.13
29 Interdisciplinary dialogue for education, collaboration, and innovation: intelligent Biology and Medicine in and beyond 2013. BMC Genomics 2013 1.11
30 New genomic structure for prostate cancer specific gene PCA3 within BMCC1: implications for prostate cancer detection and progression. PLoS One 2009 1.11
31 Mutational spectrum in the recent human genome inferred by single nucleotide polymorphisms. Genomics 2006 1.09
32 Conservation and divergence of DNA methylation in eukaryotes: new insights from single base-resolution DNA methylomes. Epigenetics 2011 1.08
33 L-arginine supplementation improves responses to injury and inflammation in dextran sulfate sodium colitis. PLoS One 2012 1.08
34 The current Salmonella-host interactome. Proteomics Clin Appl 2011 1.08
35 Pathway-based analysis of GWAS datasets: effective but caution required. Int J Neuropsychopharmacol 2010 1.08
36 GenRev: exploring functional relevance of genes in molecular networks. Genomics 2011 1.07
37 The influence of neighboring-nucleotide composition on single nucleotide polymorphisms (SNPs) in the mouse genome and its comparison with human SNPs. Genomics 2004 1.07
38 Deciphering the unique microRNA signature in human esophageal adenocarcinoma. PLoS One 2013 1.05
39 NGS catalog: A database of next generation sequencing studies in humans. Hum Mutat 2012 1.05
40 Discovering disease-specific biomarker genes for cancer diagnosis and prognosis. Technol Cancer Res Treat 2010 1.04
41 ERGR: An ethanol-related gene resource. Nucleic Acids Res 2008 1.04
42 Next-generation sequencing of paired tyrosine kinase inhibitor-sensitive and -resistant EGFR mutant lung cancer cell lines identifies spectrum of DNA changes associated with drug resistance. Genome Res 2013 1.03
43 Integrative network analysis identifies key genes and pathways in the progression of hepatitis C virus induced hepatocellular carcinoma. BMC Med Genomics 2011 1.02
44 Functional complementation between transcriptional methylation regulation and post-transcriptional microRNA regulation in the human genome. BMC Genomics 2011 1.02
45 DCGL v2.0: an R package for unveiling differential regulation from differential co-expression. PLoS One 2013 1.02
46 Beyond histology: translating tumor genotypes into clinically effective targeted therapies. Clin Cancer Res 2014 1.01
47 An efficient hierarchical generalized linear mixed model for pathway analysis of genome-wide association studies. Bioinformatics 2011 1.01
48 Phylogenetic profiles for the prediction of protein-protein interactions: how to select reference organisms? Biochem Biophys Res Commun 2006 1.01
49 Advances in systems biology: computational algorithms and applications. BMC Syst Biol 2012 1.00
50 Synergetic regulatory networks mediated by oncogene-driven microRNAs and transcription factors in serous ovarian cancer. Mol Biosyst 2013 0.99
51 A weighted and integrated drug-target interactome: drug repurposing for schizophrenia as a use case. BMC Syst Biol 2015 0.99
52 CpG islands or CpG clusters: how to identify functional GC-rich regions in a genome? BMC Bioinformatics 2009 0.98
53 Adenoma formation following limited ablation of p120-catenin in the mouse intestine. PLoS One 2011 0.98
54 RNA-Seq analysis implicates dysregulation of the immune system in schizophrenia. BMC Genomics 2012 0.97
55 Directionality of point mutation and 5-methylcytosine deamination rates in the chimpanzee genome. BMC Genomics 2006 0.97
56 Comparative analysis of CpG islands in four fish genomes. Comp Funct Genomics 2008 0.97
57 Methylation-dependent transition rates are dependent on local sequence lengths and genomic regions. Mol Biol Evol 2006 0.97
58 Consensus rules in variant detection from next-generation sequencing data. PLoS One 2012 0.96
59 Dynamic protein interaction modules in human hepatocellular carcinoma progression. BMC Syst Biol 2013 0.96
60 Distinct and competitive regulatory patterns of tumor suppressor genes and oncogenes in ovarian cancer. PLoS One 2012 0.96
61 The dystrobrevin binding protein 1 (DTNBP1) gene is associated with schizophrenia in the Irish Case Control Study of Schizophrenia (ICCSS) sample. Schizophr Res 2009 0.95
62 Investigating the relationship of DNA methylation with mutation rate and allele frequency in the human genome. BMC Genomics 2012 0.95
63 Gastric adenocarcinoma has a unique microRNA signature not present in esophageal adenocarcinoma. Cancer 2013 0.95
64 InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes. BMC Bioinformatics 2007 0.95
65 Integrative pathway analysis of genome-wide association studies and gene expression data in prostate cancer. BMC Syst Biol 2012 0.95
66 Network.assisted analysis to prioritize GWAS results: principles, methods and perspectives. Hum Genet 2014 0.94
67 Enriched pathways for major depressive disorder identified from a genome-wide association study. Int J Neuropsychopharmacol 2012 0.93
68 Prioritization and evaluation of depression candidate genes by combining multidimensional data resources. PLoS One 2011 0.93
69 CNVannotator: a comprehensive annotation server for copy number variation in the human genome. PLoS One 2013 0.93
70 Application of systems biology approach identifies and validates GRB2 as a risk gene for schizophrenia in the Irish Case Control Study of Schizophrenia (ICCSS) sample. Schizophr Res 2010 0.92
71 Prioritization of epilepsy associated candidate genes by convergent analysis. PLoS One 2011 0.92
72 Contrast features of CpG islands in the promoter and other regions in the dog genome. Genomics 2009 0.92
73 Role of insulin-like growth factor-1 signaling pathway in cisplatin-resistant lung cancer cells. Int J Radiat Oncol Biol Phys 2011 0.92
74 Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes. Brief Bioinform 2015 0.91
75 Education, collaboration, and innovation: intelligent biology and medicine in the era of big data. BMC Genomics 2015 0.90
76 DTome: a web-based tool for drug-target interactome construction. BMC Bioinformatics 2012 0.89
77 Connectivity map analysis of nonsense-mediated decay-positive BMPR2-related hereditary pulmonary arterial hypertension provides insights into disease penetrance. Am J Respir Cell Mol Biol 2012 0.88
78 Features of methylation and gene expression in the promoter-associated CpG islands using human methylome data. Comp Funct Genomics 2012 0.87
79 Apoptotic engulfment pathway and schizophrenia. PLoS One 2009 0.86
80 Ranking gene-drug relationships in biomedical literature using Latent Dirichlet Allocation. Pac Symp Biocomput 2012 0.86
81 Intravenous glial growth factor 2 (GGF2) isoform of neuregulin-1β improves left ventricular function, gene and protein expression in rats after myocardial infarction. PLoS One 2013 0.86
82 Do cancer proteins really interact strongly in the human protein-protein interaction network? Comput Biol Chem 2011 0.85
83 Assessing gene length biases in gene set analysis of Genome-Wide Association Studies. Int J Comput Biol Drug Des 2011 0.85
84 Protein-protein interaction and pathway analyses of top schizophrenia genes reveal schizophrenia susceptibility genes converge on common molecular networks and enrichment of nucleosome (chromatin) assembly genes in schizophrenia susceptibility loci. Schizophr Bull 2013 0.85
85 Searching joint association signals in CATIE schizophrenia genome-wide association studies through a refined integrative network approach. BMC Genomics 2012 0.85
86 MSEA: detection and quantification of mutation hotspots through mutation set enrichment analysis. Genome Biol 2014 0.85
87 Functional features, biological pathways, and protein interaction networks of addiction-related genes. Chem Biodivers 2010 0.84
88 An evidence-based knowledgebase of pulmonary arterial hypertension to identify genes and pathways relevant to pathogenesis. Mol Biosyst 2014 0.84
89 SNPNB: analyzing neighboring-nucleotide biases on single nucleotide polymorphisms (SNPs). Bioinformatics 2005 0.84
90 Adaptive evolution of MRGX2, a human sensory neuron specific gene involved in nociception. Gene 2005 0.83
91 Discovery and characterization of long intergenic non-coding RNAs (lincRNA) module biomarkers in prostate cancer: an integrative analysis of RNA-Seq data. BMC Genomics 2015 0.83
92 Histone H2B ubiquitylation and H3 lysine 4 methylation prevent ectopic silencing of euchromatic loci important for the cellular response to heat. Mol Biol Cell 2011 0.83
93 Prioritization and association analysis of murine-derived candidate genes in anxiety-spectrum disorders. Biol Psychiatry 2011 0.83
94 Heterogeneous DNA methylation contributes to tumorigenesis through inducing the loss of coexpression connectivity in colorectal cancer. Genes Chromosomes Cancer 2014 0.83
95 Genetic variation in VEGF family genes and breast cancer risk: a report from the Shanghai Breast Cancer Genetics Study. Cancer Epidemiol Biomarkers Prev 2010 0.82
96 MicroRNA-31 initiates lung tumorigenesis and promotes mutant KRAS-driven lung cancer. J Clin Invest 2015 0.81
97 Network-assisted Causal Gene Detection in Genome-wide Association Studies: An Improved Module Search Algorithm. IEEE Int Workshop Genomic Signal Process Stat 2011 0.81
98 Exploring schizophrenia drug-gene interactions through molecular network and pathway modeling. AMIA Annu Symp Proc 2011 0.80
99 Network-assisted investigation of antipsychotic drugs and their targets. Chem Biodivers 2012 0.80
100 Multi-dimensional prioritization of dental caries candidate genes and its enriched dense network modules. PLoS One 2013 0.80
101 A systematic gene-based screen of chr4q22-q32 identifies association of a novel susceptibility gene, DKK2, with the quantitative trait of alcohol dependence symptom counts. Hum Mol Genet 2010 0.80
102 Two non-synonymous markers in PTPN21, identified by genome-wide association study data-mining and replication, are associated with schizophrenia. Schizophr Res 2011 0.80
103 Identifying genes progressively silenced in preneoplastic and neoplastic liver tissues. Int J Comput Biol Drug Des 2010 0.79
104 Investigating association of four gene regions (GABRB3, MAOB, PAH, and SLC6A4) with five symptoms in schizophrenia. Psychiatry Res 2012 0.79
105 Methylation of promoters of microRNAs and their host genes in myelodysplastic syndromes. Leuk Lymphoma 2013 0.79
106 Genetic overlap of schizophrenia and bipolar disorder in a high-density linkage survey in the Portuguese Island population. Am J Med Genet B Neuropsychiatr Genet 2012 0.79
107 Exploring drug-target interaction networks of illicit drugs. BMC Genomics 2013 0.79
108 Characterization of schizophrenia adverse drug interactions through a network approach and drug classification. Biomed Res Int 2013 0.79
109 Integrative analysis of common neurodegenerative diseases using gene association, interaction networks and mRNA expression data. AMIA Jt Summits Transl Sci Proc 2012 0.79
110 A rapid association test procedure robust under different genetic models accounting for population stratification. Hum Hered 2013 0.78
111 Meta-analyses of genome-wide linkage scans of anxiety-related phenotypes. Eur J Hum Genet 2012 0.78
112 Network analysis of EtOH-related candidate genes. Chem Biodivers 2010 0.78
113 Advances in intelligent biology and medicine. Int J Comput Biol Drug Des 2013 0.78
114 Gene- and evidence-based candidate gene selection for schizophrenia and gene feature analysis. Artif Intell Med 2009 0.78
115 Construction of phylogenetic profiles based on the genetic distance of hundreds of genomes. Biochem Biophys Res Commun 2007 0.78
116 Association signals unveiled by a comprehensive gene set enrichment analysis of dental caries genome-wide association studies. PLoS One 2013 0.78
117 Systematic dissection of dysregulated transcription factor-miRNA feed-forward loops across tumor types. Brief Bioinform 2015 0.77
118 Personalized pathway enrichment map of putative cancer genes from next generation sequencing data. PLoS One 2012 0.77
119 Next-generation sequencing. J Biomed Biotechnol 2011 0.77
120 Association of FAS, a TNF-α receptor gene, with treatment resistant schizophrenia. Schizophr Res 2011 0.77
121 Comprehensive gene-based association study of a chromosome 20 linked region implicates novel risk loci for depressive symptoms in psychotic illness. PLoS One 2011 0.77
122 Gene regulation in glioblastoma: a combinatorial analysis of microRNAs and transcription factors. Int J Comput Biol Drug Des 2011 0.77
123 Systems biology: molecular networks and disease. Chem Biodivers 2012 0.76
124 Impacts of somatic mutations on gene expression: an association perspective. Brief Bioinform 2017 0.76
125 Association study of 83 candidate genes for bipolar disorder in chromosome 6q selected using an evidence-based prioritization algorithm. Am J Med Genet B Neuropsychiatr Genet 2013 0.76
126 DNA methylation profiling distinguishes three clusters of breast cancer cell lines. Chem Biodivers 2012 0.76
127 Systems biology approaches in biological and biomedical research: opportunities and challenges. Int J Comput Biol Drug Des 2012 0.76
128 Linking biochemical pathways and networks to adverse drug reactions. IEEE Trans Nanobioscience 2014 0.76
129 BioEve Search: A Novel Framework to Facilitate Interactive Literature Search. Adv Bioinformatics 2012 0.75
130 MentalSquares: a generic bipolar Support Vector Machine for psychiatric disorder classification, diagnostic analysis and neurobiological data mining. Int J Data Min Bioinform 2011 0.75
131 Oncogenes and tumor suppressor genes: comparative genomics and network perspectives. BMC Genomics 2015 0.75
132 A novel statistical method to estimate the effective SNP size in vertebrate genomes and categorized genomic regions. BMC Genomics 2006 0.75
133 Integrative data analysis in systems biology. Int J Comput Biol Drug Des 2011 0.75
134 Kinase impact assessment in the landscape of fusion genes that retain kinase domains: a pan-cancer study. Brief Bioinform 2016 0.75
135 Translational bioinformatics in mental health: open access data sources and computational biomarker discovery. Brief Bioinform 2017 0.75
136 Gene network and pathway generation and analysis. Int J Comput Biol Drug Des 2011 0.75
137 NO-BOUNDARY THINKING IN BIOINFORMATICS. Pac Symp Biocomput 2016 0.75
138 Systems biology in the microbial world and beyond. Chem Biodivers 2010 0.75