Published in BMC Bioinformatics on December 16, 2014
Novel personalized pathway-based metabolomics models reveal key metabolic pathways for breast cancer diagnosis. Genome Med (2016) 0.91
Empirical comparison of structure-based pathway methods. Brief Bioinform (2015) 0.78
Advances in translational bioinformatics facilitate revealing the landscape of complex disease mechanisms. BMC Bioinformatics (2014) 0.76
Analysis of distribution of DNA methylation in kidney-renal-clear-cell-carcinoma specific genes using entropy. Genom Data (2016) 0.75
Gene expression-based biomarkers for discriminating early and late stage of clear cell renal cancer. Sci Rep (2017) 0.75
Variants of SCARB1 and VDR Involved in Complex Genetic Interactions May Be Implicated in the Genetic Susceptibility to Clear Cell Renal Cell Carcinoma. Biomed Res Int (2015) 0.75
Transcriptome analysis reveals manifold mechanisms of cyst development in ADPKD. Hum Genomics (2016) 0.75
Renal Carcinogenesis, Tumor Heterogeneity, and Reactive Oxygen Species: Tactics Evolved. Antioxid Redox Signal (2016) 0.75
Genetic architecture of renal cell carcinoma: Do we have to know? World J Urol (2015) 0.75
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res (2000) 117.00
Cancer statistics, 2013. CA Cancer J Clin (2013) 84.72
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics (2009) 67.17
Moderated statistical tests for assessing differences in tag abundance. Bioinformatics (2007) 22.87
Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature (2013) 13.60
Using GOstats to test gene lists for GO term association. Bioinformatics (2006) 12.58
Molecular Stratification of Clear Cell Renal Cell Carcinoma by Consensus Clustering Reveals Distinct Subtypes and Survival Patterns. Genes Cancer (2010) 3.78
The genetic basis of cancer of the kidney. J Urol (2003) 3.45
Surveillance after radical or partial nephrectomy for localized renal cell carcinoma and management of recurrent disease. Urol Clin North Am (2003) 3.44
Increased nuclear factor-kappa B activation is related to the tumor development of renal cell carcinoma. Carcinogenesis (2003) 1.37
Constitutive activation of nuclear factor-kappaB prevents TRAIL-induced apoptosis in renal cancer cells. Oncogene (2001) 1.30
Down-regulation of HLA class I antigen is an independent prognostic factor for clear cell renal cell carcinoma. J Urol (2007) 1.17
Risk for renal cell carcinoma in chronic hepatitis C infection. Cancer Epidemiol Biomarkers Prev (2010) 1.17
Histone demethylase RBP2 promotes lung tumorigenesis and cancer metastasis. Cancer Res (2013) 1.14
Histone demethylase RBP2 is critical for breast cancer progression and metastasis. Cell Rep (2014) 1.04
Ubiquitin-conjugating enzyme Ubc13 controls breast cancer metastasis through a TAK1-p38 MAP kinase cascade. Proc Natl Acad Sci U S A (2014) 0.96
Risk of kidney cancer and chronic kidney disease in relation to hepatitis C virus infection: a nationwide register-based cohort study in Sweden. Eur J Cancer Prev (2011) 0.89
Renal cell carcinoma and hepatitis C virus infection: is there any cause-outcome relationship? J Cancer Res Ther (2011) 0.88
Principles of nephrectomy for malignant disease. BJU Int (2002) 0.85
Tumor necrosis factor α-induced proteins: natural brakes on inflammation. Arthritis Rheum (2012) 0.81
Expression profiling based graph-clustering approach to determine renal carcinoma related pathway in response to kidney cancer. Eur Rev Med Pharmacol Sci (2012) 0.81
The complete genome of an individual by massively parallel DNA sequencing. Nature (2008) 52.81
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol (2006) 30.90
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature (2012) 18.23
Genome sequence of the palaeopolyploid soybean. Nature (2010) 17.82
Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21
Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms. Am J Hum Genet (2001) 10.48
An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat Biotechnol (2002) 10.23
Partition-ligation-expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms. Am J Hum Genet (2002) 10.12
The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science (2009) 8.23
A catalog of reference genomes from the human microbiome. Science (2010) 8.10
Methylation of histone H3 Lys 4 in coding regions of active genes. Proc Natl Acad Sci U S A (2002) 7.67
Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science (2009) 7.64
Model-based analysis of two-color arrays (MA2C). Genome Biol (2007) 7.28
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol (2010) 7.08
The genome of the model beetle and pest Tribolium castaneum. Nature (2008) 6.50
miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res (2008) 6.30
Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project. Nat Biotechnol (2006) 5.92
ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. Bioinformatics (2010) 5.60
Breast cancer subtype approximated by estrogen receptor, progesterone receptor, and HER-2 is associated with local and distant recurrence after breast-conserving therapy. J Clin Oncol (2008) 5.28
Rat toxicogenomic study reveals analytical consistency across microarray platforms. Nat Biotechnol (2006) 5.14
Protective variant for hippocampal atrophy identified by whole exome sequencing. Ann Neurol (2015) 5.10
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol (2008) 4.78
Integrating regulatory motif discovery and genome-wide expression analysis. Proc Natl Acad Sci U S A (2003) 4.74
Toward interoperable bioscience data. Nat Genet (2012) 4.72
Bayesian inference of epistatic interactions in case-control studies. Nat Genet (2007) 4.31
The Spo0A regulon of Bacillus subtilis. Mol Microbiol (2003) 4.19
Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology. PLoS One (2012) 4.18
The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?". OMICS (2008) 4.15
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience (2013) 4.11
Long-term monitoring shows hepatitis B virus resistance to entecavir in nucleoside-naïve patients is rare through 5 years of therapy. Hepatology (2009) 4.00
Cross-platform comparability of microarray technology: intra-platform consistency and appropriate data analysis procedures are essential. BMC Bioinformatics (2005) 3.93
Enhanced computer vision with Microsoft Kinect sensor: a review. IEEE Trans Cybern (2013) 3.75
Slug antagonizes p53-mediated apoptosis of hematopoietic progenitors by repressing puma. Cell (2005) 3.73
A strategy capitalizing on synergies: the Reporting Structure for Biological Investigation (RSBI) working group. OMICS (2006) 3.51
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born. J Chem Theory Comput (2012) 3.40
Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing. Cancer Res (2007) 3.40
The program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis. PLoS Biol (2004) 3.33
Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts. Genome Res (2008) 3.33
Canadian 2003 International Consensus Algorithm For the Diagnosis, Therapy, and Management of Hereditary Angioedema. J Allergy Clin Immunol (2004) 3.30
Subtle genetic changes enhance virulence of methicillin resistant and sensitive Staphylococcus aureus. BMC Microbiol (2007) 3.25
Genomic sequence is highly predictive of local nucleosome depletion. PLoS Comput Biol (2007) 3.24
Relative biological effectiveness (RBE) values for proton beam therapy. Int J Radiat Oncol Biol Phys (2002) 3.21
Genetic basis for in vivo daptomycin resistance in enterococci. N Engl J Med (2011) 3.20
Long-term outcomes of selective bladder preservation by combined-modality therapy for invasive bladder cancer: the MGH experience. Eur Urol (2011) 3.17
Optimization of intensity-modulated radiotherapy plans based on the equivalent uniform dose. Int J Radiat Oncol Biol Phys (2002) 3.15
Graph embedding and extensions: a general framework for dimensionality reduction. IEEE Trans Pattern Anal Mach Intell (2007) 3.06
Icatibant, a new bradykinin-receptor antagonist, in hereditary angioedema. N Engl J Med (2010) 2.98
The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. J Bacteriol (2008) 2.97
The phenylpropanoid pathway and plant defence-a genomics perspective. Mol Plant Pathol (2002) 2.93
QA/QC: challenges and pitfalls facing the microarray community and regulatory agencies. Expert Rev Mol Diagn (2004) 2.73
Joint analysis of two microarray gene-expression data sets to select lung adenocarcinoma marker genes. BMC Bioinformatics (2004) 2.73
Nomogram for the prediction of having four or more involved nodes for sentinel lymph node-positive breast cancer. J Clin Oncol (2008) 2.72
The unfoldomics decade: an update on intrinsically disordered proteins. BMC Genomics (2008) 2.72
Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF. Genome Biol (2008) 2.71
Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome. Gastroenterology (2011) 2.60
The sigmaE regulon and the identification of additional sporulation genes in Bacillus subtilis. J Mol Biol (2003) 2.59
The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies. BMC Bioinformatics (2008) 2.54
Recursive SVM feature selection and sample classification for mass-spectrometry and microarray data. BMC Bioinformatics (2006) 2.53
Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation. Proc Natl Acad Sci U S A (2003) 2.52
Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners. BMC Genomics (2008) 2.50
Inferring gene regulatory networks from multiple microarray datasets. Bioinformatics (2006) 2.49
B lymphocyte stimulator overexpression in patients with systemic lupus erythematosus: longitudinal observations. Arthritis Rheum (2003) 2.47
Complete genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae. J Bacteriol (2004) 2.44
An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants. Plant J (2010) 2.41
Visualization of nitric oxide in living cells by a copper-based fluorescent probe. Nat Chem Biol (2006) 2.33
Modeling within-motif dependence for transcription factor binding site predictions. Bioinformatics (2004) 2.29
Estradiol-regulated microRNAs control estradiol response in breast cancer cells. Nucleic Acids Res (2009) 2.27
Predicting intrinsic disorder in proteins: an overview. Cell Res (2009) 2.24
The WRKY transcription factor superfamily: its origin in eukaryotes and expansion in plants. BMC Evol Biol (2005) 2.23
GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data. Bioinformatics (2012) 2.21
Local production of B lymphocyte stimulator protein and APRIL in arthritic joints of patients with inflammatory arthritis. Arthritis Rheum (2003) 2.21
De novo cis-regulatory module elicitation for eukaryotic genomes. Proc Natl Acad Sci U S A (2005) 2.20
A data-driven clustering method for time course gene expression data. Nucleic Acids Res (2006) 2.20
Patient-reported long-term outcomes after conventional and high-dose combined proton and photon radiation for early prostate cancer. JAMA (2010) 2.16
Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase. J Med Chem (2008) 2.14
Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome. Proc Natl Acad Sci U S A (2007) 2.09
Treatment of benign prostatic hyperplasia using transurethral split of the prostate with a columnar balloon catheter. J Endourol (2014) 2.08
High lipophilicity and high daily dose of oral medications are associated with significant risk for drug-induced liver injury. Hepatology (2013) 2.02
Microarray scanner calibration curves: characteristics and implications. BMC Bioinformatics (2005) 2.02
A phase I, open-label study of siltuximab, an anti-IL-6 monoclonal antibody, in patients with B-cell non-Hodgkin lymphoma, multiple myeloma, or Castleman disease. Clin Cancer Res (2013) 2.02
GeneVenn - A web application for comparing gene lists using Venn diagrams. Bioinformation (2007) 2.00
Age, breast cancer subtype approximation, and local recurrence after breast-conserving therapy. J Clin Oncol (2011) 1.99
Analysis of data errors in clinical research databases. AMIA Annu Symp Proc (2008) 1.99
Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples. BMC Bioinformatics (2008) 1.98
Tall fescue EST-SSR markers with transferability across several grass species. Theor Appl Genet (2004) 1.97
The genome of th17 cell-inducing segmented filamentous bacteria reveals extensive auxotrophy and adaptations to the intestinal environment. Cell Host Microbe (2011) 1.97
Virulence effect of Enterococcus faecalis protease genes and the quorum-sensing locus fsr in Caenorhabditis elegans and mice. Infect Immun (2002) 1.96
MicroRNA cluster 221-222 and estrogen receptor alpha interactions in breast cancer. J Natl Cancer Inst (2010) 1.94
Understanding the unique characteristics of suicide in China: national psychological autopsy study. Biomed Environ Sci (2005) 1.90
Alcohol alters DNA methylation patterns and inhibits neural stem cell differentiation. Alcohol Clin Exp Res (2011) 1.88
Proton beams to replace photon beams in radical dose treatments. Acta Oncol (2003) 1.87
Acute myeloid leukemia and myelodysplastic syndromes after radiation therapy are similar to de novo disease and differ from other therapy-related myeloid neoplasms. J Clin Oncol (2012) 1.87
Multidisciplinary care and pursuit of active surveillance in low-risk prostate cancer. J Clin Oncol (2012) 1.86
HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms. Bioinformatics (2004) 1.86
Bos taurus genome assembly. BMC Genomics (2009) 1.83
A free program for calculating EUD-based NTCP and TCP in external beam radiotherapy. Phys Med (2007) 1.81
Clustering gene expression data using a graph-theoretic approach: an application of minimum spanning trees. Bioinformatics (2002) 1.81
Microarray analysis of chitin elicitation in Arabidopsis thaliana. Mol Plant Pathol (2002) 1.80