Published in Bioinformatics on March 01, 2013
Evaluation of de novo transcriptome assemblies from RNA-Seq data. Genome Biol (2014) 1.46
Extensive differences in gene expression between symbiotic and aposymbiotic cnidarians. G3 (Bethesda) (2014) 1.09
Discovering and understanding oncogenic gene fusions through data intensive computational approaches. Nucleic Acids Res (2016) 0.85
Transcriptomic analysis of Petunia hybrida in response to salt stress using high throughput RNA sequencing. PLoS One (2014) 0.85
YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut. F1000Res (2015) 0.78
YeATSAM analysis of the walnut and chickpea transcriptome reveals key genes undetected by current annotation tools. F1000Res (2016) 0.75
Neofunctionalization of zona pellucida proteins enhances freeze-prevention in the eggs of Antarctic notothenioids. Nat Commun (2016) 0.75
Heuristic pairwise alignment of de Bruijn graphs to facilitate simultaneous transcript discovery in related organisms from RNA-Seq data. BMC Genomics (2015) 0.75
The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. Proc Natl Acad Sci U S A (2006) 4.18
Evaluation of genomic island predictors using a comparative genomics approach. BMC Bioinformatics (2008) 2.62
Detecting genomic islands using bioinformatics approaches. Nat Rev Microbiol (2010) 2.22
Contralateral recurrence of primary spontaneous pneumothorax. Chest (2007) 1.82
Transcriptional signature of flavopiridol-induced tumor cell death. Mol Cancer Ther (2004) 1.80
Identification of a novel biomarker, SEMA5A, for non-small cell lung carcinoma in nonsmoking women. Cancer Epidemiol Biomarkers Prev (2010) 1.74
POINT: a database for the prediction of protein-protein interactions based on the orthologous interactome. Bioinformatics (2004) 1.58
A stochastic differential equation model for quantifying transcriptional regulatory network in Saccharomyces cerevisiae. Bioinformatics (2005) 1.56
miRSystem: an integrated system for characterizing enriched functions and pathways of microRNA targets. PLoS One (2012) 1.54
The association of virulence factors with genomic islands. PLoS One (2009) 1.47
PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database. Bioinformatics (2008) 1.47
Recruitment of CRABS CLAW to promote nectary development within the eudicot clade. Development (2005) 1.40
Gene expression after treatment with hydrogen peroxide, menadione, or t-butyl hydroperoxide in breast cancer cells. Cancer Res (2002) 1.32
Hypoxia upregulates hypoxia inducible factor (HIF)-3alpha expression in lung epithelial cells: characterization and comparison with HIF-1alpha. Cell Res (2006) 1.22
Integrated analyses of copy number variations and gene expression in lung adenocarcinoma. PLoS One (2011) 1.19
Dissection of the Kaposi's sarcoma-associated herpesvirus gene expression program by using the viral DNA replication inhibitor cidofovir. J Virol (2004) 1.19
Genetic and molecular analysis of GogB, a phage-encoded type III-secreted substrate in Salmonella enterica serovar typhimurium with autonomous expression from its associated phage. J Mol Biol (2005) 1.18
Improving disulfide connectivity prediction with sequential distance between oxidized cysteines. Bioinformatics (2005) 1.15
Molecular changes occurring during acquisition of abscission competence following auxin depletion in Mirabilis jalapa. Plant Physiol (2006) 1.13
Functional characterization of a catabolic plasmid from polychlorinated- biphenyl-degrading Rhodococcus sp. strain RHA1. J Bacteriol (2004) 1.12
Ortholog-based protein-protein interaction prediction and its application to inter-species interactions. BMC Bioinformatics (2008) 1.12
Cysteine separations profiles on protein sequences infer disulfide connectivity. Bioinformatics (2004) 1.09
Comparative genomics of Rickettsia prowazekii Madrid E and Breinl strains. J Bacteriol (2004) 1.08
Immunomodulatory Activity of Lactococcus lactis A17 from Taiwan Fermented Cabbage in OVA-Sensitized BALB/c Mice. Evid Based Complement Alternat Med (2013) 1.07
Combination of microarray profiling and protein-protein interaction databases delineates the minimal discriminators as a metastasis network for esophageal squamous cell carcinoma. Int J Oncol (2009) 1.07
An evolutionary algorithm for large traveling salesman problems. IEEE Trans Syst Man Cybern B Cybern (2004) 1.06
MicrobeDB: a locally maintainable database of microbial genomic sequences. Bioinformatics (2012) 1.05
Elevated sphingosine-1-phosphate promotes sickling and sickle cell disease progression. J Clin Invest (2014) 1.03
A gene expression profile for vascular invasion can predict the recurrence after resection of hepatocellular carcinoma: a microarray approach. Ann Surg Oncol (2006) 1.01
Molecular characteristics and metastasis predictor genes of triple-negative breast cancer: a clinical study of triple-negative breast carcinomas. PLoS One (2012) 1.01
The role of 'passive chemotherapy' plus health education for schistosomiasis control in China during maintenance and consolidation phase. Acta Trop (2005) 1.01
Early-onset aging and defective DNA damage response in Cdc14b-deficient mice. Mol Cell Biol (2011) 1.00
Construction and analysis of the protein-protein interaction networks for schizophrenia, bipolar disorder, and major depression. BMC Bioinformatics (2011) 0.98
Brazilein protects the brain against focal cerebral ischemia reperfusion injury correlating to inflammatory response suppression. Eur J Pharmacol (2006) 0.97
VNTRDB: a bacterial variable number tandem repeat locus database. Nucleic Acids Res (2006) 0.97
Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma genes Online). BMC Bioinformatics (2007) 0.97
A probe-density-based analysis method for array CGH data: simulation, normalization and centralization. Bioinformatics (2008) 0.93
De novo transcriptome sequencing of axolotl blastema for identification of differentially expressed genes during limb regeneration. BMC Genomics (2013) 0.93
From midbody protein-protein interaction network construction to novel regulators in cytokinesis. J Proteome Res (2009) 0.92
Reconstruction of human protein interolog network using evolutionary conserved network. BMC Bioinformatics (2007) 0.92
Denture mis-swallowing in the sliding esophageal hiatal hernia mimics esophageal perforation. J Formos Med Assoc (2008) 0.92
Gene expression-based chemical genomics identifies potential therapeutic drugs in hepatocellular carcinoma. PLoS One (2011) 0.92
Methylation of the SPARC gene promoter and its clinical implication in pancreatic cancer. J Exp Clin Cancer Res (2010) 0.92
Estimates of relative risks for cancers in a population after prolonged low-dose-rate radiation exposure: a follow-up assessment from 1983 to 2005. Radiat Res (2008) 0.92
Age-associated decrease of oxidative repair enzymes, human 8-oxoguanine DNA glycosylases (hOgg1), in human aging. J Radiat Res (2003) 0.92
POINeT: protein interactome with sub-network analysis and hub prioritization. BMC Bioinformatics (2009) 0.92
The impact of smoking in primary spontaneous pneumothorax. J Thorac Cardiovasc Surg (2009) 0.91
CEA promoter-regulated oncolytic adenovirus-mediated Hsp70 expression in immune gene therapy for pancreatic cancer. Cancer Lett (2012) 0.91
Human Microbiome Project--paving the way to a better understanding of ourselves and our microbes. Drug Discov Today (2009) 0.91
Distinct signaling pathways after higher or lower doses of radiation in three closely related human lymphoblast cell lines. Int J Radiat Oncol Biol Phys (2010) 0.91
Integrated minimum-set primers and unique probe design algorithms for differential detection on symptom-related pathogens. Bioinformatics (2005) 0.91
A knock-in Npm1 mutation in mice results in myeloproliferation and implies a perturbation in hematopoietic microenvironment. PLoS One (2012) 0.90
MicroRNA-449a enhances radiosensitivity in CL1-0 lung adenocarcinoma cells. PLoS One (2013) 0.90
11β-hydroxysteroid dehydrogenase types 1 and 2 in postnatal development of rat testis: gene expression, localization and regulation by luteinizing hormone and androgens. Asian J Androl (2014) 0.89
Deletion of the Igf1 gene: suppressive effects on adult Leydig cell development. J Androl (2010) 0.89
Disulfide connectivity prediction with 70% accuracy using two-level models. Proteins (2006) 0.88
Detecting well-being via computerized content analysis of brief diary entries. Psychol Assess (2013) 0.87
Prognostic prediction of the immunohistochemical expression of p53 and p16 in resected non-small cell lung cancer. Eur J Cardiothorac Surg (2003) 0.87
GEM: a Gaussian Evolutionary Method for predicting protein side-chain conformations. Protein Sci (2002) 0.87
Spontaneous regression of a mediastinal thymoma. J Thorac Cardiovasc Surg (2008) 0.87
Quantitative assessment of mitochondrial DNA copies from whole genome sequencing. BMC Genomics (2012) 0.86
Patients with Acinetobacter baumannii bloodstream infections are colonized in the gastrointestinal tract with identical strains. Am J Infect Control (2010) 0.86
Effect of Epstein-Barr virus infection on global gene expression in nasopharyngeal carcinoma. Funct Integr Genomics (2006) 0.86
Increased Human Wildtype Tau Attenuates Axonal Transport Deficits Caused by Loss of APP in Mouse Models. Magn Reson Insights (2010) 0.86
Putting their best foot forward: emotional disclosure on Facebook. Cyberpsychol Behav Soc Netw (2012) 0.86
Identification of prognostic genes for recurrent risk prediction in triple negative breast cancer patients in Taiwan. PLoS One (2011) 0.85
Radiation-induced changes in gene-expression profiles for the SCC VII tumor cells grown in vitro and in vivo. Antioxid Redox Signal (2006) 0.85
Analysis of protein-protein interactions in cross-talk pathways reveals CRKL protein as a novel prognostic marker in hepatocellular carcinoma. Mol Cell Proteomics (2013) 0.84
Diaphragmatic bleb complicated hydrothorax in peritoneal dialysis. Intern Med (2009) 0.84
Autoantibody recognition of an N-terminal epitope of hnRNP L marks the risk for developing HBV-related hepatocellular carcinoma. J Proteomics (2013) 0.84
Metabolomic characterization of laborers exposed to welding fumes. Chem Res Toxicol (2012) 0.84
SNP rs10248565 in HDAC9 as a novel genomic aberration biomarker of lung adenocarcinoma in non-smoking women. J Biomed Sci (2014) 0.84
Rapid mechanisms of glucocorticoid signaling in the Leydig cell. Steroids (2007) 0.83
Cliques in mitotic spindle network bring kinetochore-associated complexes to form dependence pathway. Proteomics (2009) 0.83
Transcription of Tnfaip3 is regulated by NF-κB and p38 via C/EBPβ in activated macrophages. PLoS One (2013) 0.83
DBCAT: database of CpG islands and analytical tools for identifying comprehensive methylation profiles in cancer cells. J Comput Biol (2011) 0.83
Virus-induced gene silencing in ornamental plants. Methods Mol Biol (2011) 0.82
Curcumin as a potent and selective inhibitor of 11β-hydroxysteroid dehydrogenase 1: improving lipid profiles in high-fat-diet-treated rats. PLoS One (2013) 0.82
Phytoplasma-induced floral abnormalities in Catharanthus roseus are associated with phytoplasma accumulation and transcript repression of floral organ identity genes. Mol Plant Microbe Interact (2011) 0.82
Bioinformatics approaches for disulfide connectivity prediction. Curr Protein Pept Sci (2007) 0.82
A model-based circular binary segmentation algorithm for the analysis of array CGH data. BMC Res Notes (2011) 0.82
Interaction of small RNA-8105 and the intron of IbMYB1 RNA regulates IbMYB1 family genes through secondary siRNAs and DNA methylation after wounding. Plant J (2013) 0.82
Three-dimensional parallel recording with a Debye diffraction-limited and aberration-free volumetric multifocal array. Opt Lett (2014) 0.82
Duodenal ulcer-related antigens from Helicobacter pylori: immunoproteome and protein microarray approaches. Mol Cell Proteomics (2007) 0.81
Down-regulation of NDRG1 promotes migration of cancer cells during reoxygenation. PLoS One (2011) 0.81
Analysis of schizophrenia and hepatocellular carcinoma genetic network with corresponding modularity and pathways: novel insights to the immune system. BMC Genomics (2013) 0.81
Inferring a transcriptional regulatory network of the cytokinesis-related genes by network component analysis. BMC Syst Biol (2009) 0.81