Published in Mol Cell Proteomics on March 18, 2008
Cancer-associated regulation of alternative splicing. Nat Struct Mol Biol (2009) 3.35
Detection of clinically relevant exonic copy-number changes by array CGH. Hum Mutat (2010) 2.93
Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB. Nat Struct Mol Biol (2010) 2.19
Effect of polymorphisms within probe-target sequences on olignonucleotide microarray experiments. Nucleic Acids Res (2008) 1.80
Gene expression and isoform variation analysis using Affymetrix Exon Arrays. BMC Genomics (2008) 1.76
RNA sequencing of cancer reveals novel splicing alterations. Sci Rep (2013) 1.57
Nonsense-mediated RNA decay regulation by cellular stress: implications for tumorigenesis. Mol Cancer Res (2010) 1.44
Alternative splicing and tumor progression. Curr Genomics (2008) 1.43
Identification of novel alternative splice isoforms of circulating proteins in a mouse model of human pancreatic cancer. Cancer Res (2009) 1.40
Dysregulation of the transcription factors SOX4, CBFB and SMARCC1 correlates with outcome of colorectal cancer. Br J Cancer (2009) 1.40
Alternative splicing and biological heterogeneity in prostate cancer. Nat Rev Urol (2009) 1.33
Repression of KIAA1199 attenuates Wnt-signalling and decreases the proliferation of colon cancer cells. Br J Cancer (2011) 1.32
Comprehensive analysis of transcriptome variation uncovers known and novel driver events in T-cell acute lymphoblastic leukemia. PLoS Genet (2013) 1.29
Colorectal Neoplasia Differentially Expressed (CRNDE), a Novel Gene with Elevated Expression in Colorectal Adenomas and Adenocarcinomas. Genes Cancer (2011) 1.28
Alternative splicing of SLC39A14 in colorectal cancer is regulated by the Wnt pathway. Mol Cell Proteomics (2010) 1.22
The miR-143/-145 cluster regulates plasminogen activator inhibitor-1 in bladder cancer. Br J Cancer (2011) 1.16
Functional implications of structural predictions for alternative splice proteins expressed in Her2/neu-induced breast cancers. J Proteome Res (2011) 1.16
Melanoma spheroids grown under neural crest cell conditions are highly plastic migratory/invasive tumor cells endowed with immunomodulator function. PLoS One (2011) 1.07
Splicing programs and cancer. J Nucleic Acids (2011) 1.06
Detection of recurrent alternative splicing switches in tumor samples reveals novel signatures of cancer. Nucleic Acids Res (2015) 1.06
Identification of recurrent regulated alternative splicing events across human solid tumors. Nucleic Acids Res (2015) 1.03
Exon array analysis using re-defined probe sets results in reliable identification of alternatively spliced genes in non-small cell lung cancer. BMC Genomics (2010) 1.01
Aberrant RNA splicing in cancer; expression changes and driver mutations of splicing factor genes. Oncogene (2015) 1.00
Genome-wide analysis of immune activation in human T and B cells reveals distinct classes of alternatively spliced genes. PLoS One (2009) 0.97
The dietary isothiocyanate sulforaphane modulates gene expression and alternative gene splicing in a PTEN null preclinical murine model of prostate cancer. Mol Cancer (2010) 0.97
Specific variants in the MLH1 gene region may drive DNA methylation, loss of protein expression, and MSI-H colorectal cancer. PLoS One (2010) 0.95
A genome-wide aberrant RNA splicing in patients with acute myeloid leukemia identifies novel potential disease markers and therapeutic targets. Clin Cancer Res (2013) 0.95
Tumor-specific usage of alternative transcription start sites in colorectal cancer identified by genome-wide exon array analysis. BMC Genomics (2011) 0.94
Different effects of the probe summarization algorithms PLIER and RMA on high-level analysis of Affymetrix exon arrays. BMC Bioinformatics (2010) 0.94
Development of a multiplex quantitative PCR signature to predict progression in non-muscle-invasive bladder cancer. Cancer Res (2009) 0.93
Transcriptome profiling of a multiple recurrent muscle-invasive urothelial carcinoma of the bladder by deep sequencing. PLoS One (2014) 0.93
Tumor-specific expression and alternative splicing of the COL6A3 gene in pancreatic cancer. Surgery (2011) 0.92
Review: Alternative Splicing (AS) of Genes As An Approach for Generating Protein Complexity. Curr Genomics (2013) 0.91
Exon array analysis reveals neuroblastoma tumors have distinct alternative splicing patterns according to stage and MYCN amplification status. BMC Med Genomics (2011) 0.91
Analysis of molecular intra-patient variation and delineation of a prognostic 12-gene signature in non-muscle invasive bladder cancer; technology transfer from microarrays to PCR. Br J Cancer (2012) 0.91
Development of a novel splice array platform and its application in the identification of alternative splice variants in lung cancer. BMC Genomics (2010) 0.91
Affy exon tissues: exon levels in normal tissues in human, mouse and rat. Bioinformatics (2009) 0.90
Low ANXA10 expression is associated with disease aggressiveness in bladder cancer. Br J Cancer (2011) 0.90
RRP1B is a metastasis modifier that regulates the expression of alternative mRNA isoforms through interactions with SRSF1. Oncogene (2013) 0.88
Exon-level transcriptome profiling in murine breast cancer reveals splicing changes specific to tumors with different metastatic abilities. PLoS One (2010) 0.87
Transcriptome-wide detection of differentially expressed coding and non-coding transcripts and their clinical significance in prostate cancer. J Oncol (2012) 0.87
SplicerAV: a tool for mining microarray expression data for changes in RNA processing. BMC Bioinformatics (2010) 0.87
Leveraging transcript quantification for fast computation of alternative splicing profiles. RNA (2015) 0.87
Prognostic significance of aberrantly silenced ANPEP expression in prostate cancer. Br J Cancer (2013) 0.85
Alternative splicing in oncogenic kinases: from physiological functions to cancer. J Nucleic Acids (2011) 0.83
A network-based analysis of colon cancer splicing changes reveals a tumorigenesis-favoring regulatory pathway emanating from ELK1. Genome Res (2016) 0.82
Identification and validation of potential new biomarkers for prostate cancer diagnosis and prognosis using 2D-DIGE and MS. Biomed Res Int (2015) 0.82
The role of mRNA splicing in prostate cancer. Asian J Androl (2014) 0.82
Overexpression of collagen VI α3 in gastric cancer. Oncol Lett (2014) 0.81
Alternative splicing of VEGFA, APP and NUMB genes in colorectal cancer. World J Gastroenterol (2015) 0.81
Differentially expressed alternatively spliced genes in malignant pleural mesothelioma identified using massively parallel transcriptome sequencing. BMC Med Genet (2009) 0.81
Up-regulated expression of l-caldesmon associated with malignancy of colorectal cancer. BMC Cancer (2012) 0.80
MUFFINN: cancer gene discovery via network analysis of somatic mutation data. Genome Biol (2016) 0.80
Alternative splicing in bone following mechanical loading. Bone (2010) 0.80
ToP: a trend-of-disease-progression procedure works well for identifying cancer genes from multi-state cohort gene expression data for human colorectal cancer. PLoS One (2013) 0.79
Placenta-specific novel splice variants of Rho GDP dissociation inhibitor β are highly expressed in cancerous cells. BMC Res Notes (2012) 0.79
Serum response factor: positive and negative regulation of an epithelial gene expression network in the destrin mutant cornea. Physiol Genomics (2014) 0.78
Characterization of alternative spliceoforms and the RNA splicing machinery in pancreatic cancer. Pancreas (2011) 0.78
Identification of tumor-associated cassette exons in human cancer through EST-based computational prediction and experimental validation. Mol Cancer (2010) 0.78
The Associations between RNA Splicing Complex Gene SF3A1 Polymorphisms and Colorectal Cancer Risk in a Chinese Population. PLoS One (2015) 0.77
MYCN controls an alternative RNA splicing program in high-risk metastatic neuroblastoma. Cancer Lett (2015) 0.77
Alternative Splicing in Adhesion- and Motility-Related Genes in Breast Cancer. Int J Mol Sci (2016) 0.77
The cancer exome generated by alternative mRNA splicing dilutes predicted HLA class I epitope density. PLoS One (2012) 0.77
iGEMS: an integrated model for identification of alternative exon usage events. Nucleic Acids Res (2016) 0.77
Overexpression of caldesmon is associated with tumor progression in patients with primary non-muscle-invasive bladder cancer. Oncotarget (2015) 0.76
Calcium affinity of human α-actinin 1. PeerJ (2015) 0.76
Evaluation of copy number variation and gene expression in neurofibromatosis type-1-associated malignant peripheral nerve sheath tumours. Hum Genomics (2015) 0.76
Splice variants of zinc finger protein 695 mRNA associated to ovarian cancer. J Ovarian Res (2013) 0.76
Identification of aldolase A as a potential diagnostic biomarker for colorectal cancer based on proteomic analysis using formalin-fixed paraffin-embedded tissue. Tumour Biol (2016) 0.75
Algorithms for differential splicing detection using exon arrays: a comparative assessment. BMC Genomics (2015) 0.75
Differential expression of alternatively spliced transcripts related to energy metabolism in colorectal cancer. BMC Genomics (2016) 0.75
The role of splicing factors in deregulation of alternative splicing during oncogenesis and tumor progression. Mol Cell Oncol (2014) 0.75
hnRNP I regulates neonatal immune adaptation and prevents colitis and colorectal cancer. PLoS Genet (2017) 0.75
Splicing imbalances in basal-like breast cancer underpin perturbation of cell surface and oncogenic pathways and are associated with patients' survival. Sci Rep (2017) 0.75
[Identification and validation of clinically relevant molecular alterations in prostate cancer]. Pathologe (2009) 0.75
Verification and characterization of an alternative low density lipoprotein receptor-related protein 1 splice variant. PLoS One (2017) 0.75
Improved prediction of signal peptides: SignalP 3.0. J Mol Biol (2004) 48.40
A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63
SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods (2011) 33.90
Enterotypes of the human gut microbiome. Nature (2011) 24.36
Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc (2007) 19.50
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. Nat Genet (2010) 17.38
Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nat Rev Genet (2002) 16.29
Functional impact of global rare copy number variation in autism spectrum disorders. Nature (2010) 14.66
Rare variants create synthetic genome-wide associations. PLoS Biol (2010) 14.43
Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis. Nature (2011) 13.23
ESEfinder: A web resource to identify exonic splicing enhancers. Nucleic Acids Res (2003) 12.81
Genotype, haplotype and copy-number variation in worldwide human populations. Nature (2008) 12.40
Oncogene-induced senescence is part of the tumorigenesis barrier imposed by DNA damage checkpoints. Nature (2006) 11.76
A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotechnol (2007) 9.90
Autism genome-wide copy number variation reveals ubiquitin and neuronal genes. Nature (2009) 9.47
Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci Signal (2010) 8.61
Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing. Nat Biotechnol (2013) 7.97
Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics (2004) 7.76
Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature (2010) 7.51
A new non-linear normalization method for reducing variability in DNA microarray experiments. Genome Biol (2002) 7.12
Richness of human gut microbiome correlates with metabolic markers. Nature (2013) 6.93
Prediction of lipoprotein signal peptides in Gram-negative bacteria. Protein Sci (2003) 6.85
The microRNA spectrum in 12 body fluids. Clin Chem (2010) 6.82
The gene encoding the splicing factor SF2/ASF is a proto-oncogene. Nat Struct Mol Biol (2007) 6.16
Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites. Glycobiology (2004) 6.13
Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Sci (2003) 5.94
Disruption of an SF2/ASF-dependent exonic splicing enhancer in SMN2 causes spinal muscular atrophy in the absence of SMN1. Nat Genet (2002) 5.80
Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA (2012) 5.16
Analysis and prediction of leucine-rich nuclear export signals. Protein Eng Des Sel (2004) 5.15
Dynamic complex formation during the yeast cell cycle. Science (2005) 5.11
Multiple colorectal adenomas, classic adenomatous polyposis, and germ-line mutations in MYH. N Engl J Med (2003) 4.88
An Aboriginal Australian genome reveals separate human dispersals into Asia. Science (2011) 4.84
An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers. Hum Mol Genet (2006) 4.56
Feature-based prediction of non-classical and leaderless protein secretion. Protein Eng Des Sel (2004) 4.54
Mining electronic health records: towards better research applications and clinical care. Nat Rev Genet (2012) 4.42
Copy number variants in schizophrenia: confirmation of five previous findings and new evidence for 3q29 microdeletions and VIPR2 duplications. Am J Psychiatry (2011) 4.29
Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2. Genes Dev (2008) 4.24
Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms. Nucleic Acids Res (2008) 4.22
Diagnostic and prognostic microRNAs in stage II colon cancer. Cancer Res (2008) 4.20
Variants of DENND1B associated with asthma in children. N Engl J Med (2009) 4.18
Copy number variation at 1q21.1 associated with neuroblastoma. Nature (2009) 4.10
Peripheral SMN restoration is essential for long-term rescue of a severe spinal muscular atrophy mouse model. Nature (2011) 4.04
The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A (2007) 3.93
Identifying distinct classes of bladder carcinoma using microarrays. Nat Genet (2002) 3.82
Common variants at five new loci associated with early-onset inflammatory bowel disease. Nat Genet (2009) 3.82
Linear motif atlas for phosphorylation-dependent signaling. Sci Signal (2008) 3.77
Gene expression in the urinary bladder: a common carcinoma in situ gene expression signature exists disregarding histopathological classification. Cancer Res (2004) 3.76
Correction of disease-associated exon skipping by synthetic exon-specific activators. Nat Struct Biol (2003) 3.75
Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach. Bioinformatics (2004) 3.72
RNA therapeutics: beyond RNA interference and antisense oligonucleotides. Nat Rev Drug Discov (2012) 3.70
Reverse engineering cellular networks. Nat Protoc (2006) 3.67
p53-Responsive micrornas 192 and 215 are capable of inducing cell cycle arrest. Cancer Res (2008) 3.58
A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes. Proc Natl Acad Sci U S A (2008) 3.57
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature (2013) 3.45
Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency. Am J Hum Genet (2011) 3.43
A genome-wide scan for common alleles affecting risk for autism. Hum Mol Genet (2010) 3.42
Genome-wide analyses of exonic copy number variants in a family-based study point to novel autism susceptibility genes. PLoS Genet (2009) 3.42
Clustering patterns of cytotoxic T-lymphocyte epitopes in human immunodeficiency virus type 1 (HIV-1) proteins reveal imprints of immune evasion on HIV-1 global variation. J Virol (2002) 3.38
Comprehensive splice-site analysis using comparative genomics. Nucleic Acids Res (2006) 3.30
Co-evolution of transcriptional and post-translational cell-cycle regulation. Nature (2006) 3.28
Ethics and scientific publication. Adv Physiol Educ (2005) 3.26
Antisense masking of an hnRNP A1/A2 intronic splicing silencer corrects SMN2 splicing in transgenic mice. Am J Hum Genet (2008) 3.24
Non-classical protein secretion in bacteria. BMC Microbiol (2005) 3.17
The alternative splicing repressors hnRNP A1/A2 and PTB influence pyruvate kinase isoform expression and cell metabolism. Proc Natl Acad Sci U S A (2010) 3.08
Metastasis-Associated Gene Expression Changes Predict Poor Outcomes in Patients with Dukes Stage B and C Colorectal Cancer. Clin Cancer Res (2009) 3.08
Seven prostate cancer susceptibility loci identified by a multi-stage genome-wide association study. Nat Genet (2011) 3.07
The landscape of recombination in African Americans. Nature (2011) 3.06
Prediction of proprotein convertase cleavage sites. Protein Eng Des Sel (2004) 3.05
SR proteins function in coupling RNAP II transcription to pre-mRNA splicing. Mol Cell (2007) 3.04
Prediction of twin-arginine signal peptides. BMC Bioinformatics (2005) 3.03
Antisense correction of SMN2 splicing in the CNS rescues necrosis in a type III SMA mouse model. Genes Dev (2010) 3.02
From disease association to risk assessment: an optimistic view from genome-wide association studies on type 1 diabetes. PLoS Genet (2009) 2.99
A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas. Mol Syst Biol (2008) 2.99
Validation of candidate causal genes for obesity that affect shared metabolic pathways and networks. Nat Genet (2009) 2.97
A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers. Mol Syst Biol (2010) 2.92
Molecular staging for survival prediction of colorectal cancer patients. J Clin Oncol (2005) 2.88
Comparison of computational methods for the identification of cell cycle-regulated genes. Bioinformatics (2004) 2.83
Detection of microRNAs in frozen tissue sections by fluorescence in situ hybridization using locked nucleic acid probes and tyramide signal amplification. Nat Protoc (2007) 2.80
Genomic profiling of microRNAs in bladder cancer: miR-129 is associated with poor outcome and promotes cell death in vitro. Cancer Res (2009) 2.80
Safety and efficacy of warfarin plus aspirin combination therapy for giant coronary artery aneurysm secondary to Kawasaki disease: a meta-analysis. Cardiology (2014) 2.64
Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks. Bioinformatics (2007) 2.63
Interleukin-17 signaling in inflammatory, Kupffer cells, and hepatic stellate cells exacerbates liver fibrosis in mice. Gastroenterology (2012) 2.58
Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology. EMBO J (2013) 2.58
Intrinsic markers of tumour hypoxia and angiogenesis in localised prostate cancer and outcome of radical treatment: a retrospective analysis of two randomised radiotherapy trials and one surgical cohort study. Lancet Oncol (2008) 2.56
Denoising array-based comparative genomic hybridization data using wavelets. Biostatistics (2005) 2.56
Antisense oligonucleotides delivered to the mouse CNS ameliorate symptoms of severe spinal muscular atrophy. Sci Transl Med (2011) 2.56
Extracellular microRNA: a new source of biomarkers. Mutat Res (2011) 2.55
Metagenomic species profiling using universal phylogenetic marker genes. Nat Methods (2013) 2.51
Coordinated epigenetic repression of the miR-200 family and miR-205 in invasive bladder cancer. Int J Cancer (2011) 2.49
Disease phenotype of a ferret CFTR-knockout model of cystic fibrosis. J Clin Invest (2010) 2.45
A genome-wide association study identifies a locus for nonsyndromic cleft lip with or without cleft palate on 8q24. J Pediatr (2009) 2.44