Published in Proc Natl Acad Sci U S A on February 11, 2005
The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res (2007) 23.13
Determination of tag density required for digital transcriptome analysis: application to an androgen-sensitive prostate cancer model. Proc Natl Acad Sci U S A (2008) 11.86
EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol (2006) 7.06
An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells. Nat Struct Mol Biol (2009) 6.37
Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. RNA (2008) 6.29
A post-transcriptional regulatory switch in polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons. Genes Dev (2007) 5.83
Discovery of tissue-specific exons using comprehensive human exon microarrays. Genome Biol (2007) 5.53
RNA processing and its regulation: global insights into biological networks. Nat Rev Genet (2010) 5.34
Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay. Genes Dev (2007) 4.75
Unusual intron conservation near tissue-regulated exons found by splicing microarrays. PLoS Comput Biol (2006) 4.63
Evolutionary dynamics of gene and isoform regulation in Mammalian tissues. Science (2012) 4.52
Genomewide comparative analysis of alternative splicing in plants. Proc Natl Acad Sci U S A (2006) 4.51
Alternative splicing and evolution: diversification, exon definition and function. Nat Rev Genet (2010) 4.30
Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2. Genes Dev (2008) 4.24
Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines. Nat Genet (2008) 3.78
A postnatal switch of CELF and MBNL proteins reprograms alternative splicing in the developing heart. Proc Natl Acad Sci U S A (2008) 3.33
Functional consequences of developmentally regulated alternative splicing. Nat Rev Genet (2011) 3.27
Transcription-mediated gene fusion in the human genome. Genome Res (2005) 3.19
Noisy splicing drives mRNA isoform diversity in human cells. PLoS Genet (2010) 3.19
Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression. Genes Dev (2006) 3.18
Phylogenetic reconstruction of orthology, paralogy, and conserved synteny for dog and human. PLoS Comput Biol (2006) 3.07
Transcriptional signature and memory retention of human-induced pluripotent stem cells. PLoS One (2009) 3.07
Alternative splicing events identified in human embryonic stem cells and neural progenitors. PLoS Comput Biol (2007) 2.71
Protein modularity of alternatively spliced exons is associated with tissue-specific regulation of alternative splicing. PLoS Genet (2005) 2.63
Discovery and analysis of evolutionarily conserved intronic splicing regulatory elements. PLoS Genet (2007) 2.60
Widespread mRNA polyadenylation events in introns indicate dynamic interplay between polyadenylation and splicing. Genome Res (2007) 2.55
FIRMA: a method for detection of alternative splicing from exon array data. Bioinformatics (2008) 2.49
An ESRP-regulated splicing programme is abrogated during the epithelial-mesenchymal transition. EMBO J (2010) 2.42
Regulation of multiple core spliceosomal proteins by alternative splicing-coupled nonsense-mediated mRNA decay. Mol Cell Biol (2008) 2.25
Characterization and predictive discovery of evolutionarily conserved mammalian alternative promoters. Genome Res (2007) 2.12
Coupling mRNA processing with transcription in time and space. Nat Rev Genet (2014) 2.09
Global analysis of alternative splicing differences between humans and chimpanzees. Genes Dev (2007) 2.00
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HOLLYWOOD: a comparative relational database of alternative splicing. Nucleic Acids Res (2006) 1.66
Intronic alternative splicing regulators identified by comparative genomics in nematodes. PLoS Comput Biol (2006) 1.59
A comprehensive computational characterization of conserved mammalian intronic sequences reveals conserved motifs associated with constitutive and alternative splicing. Genome Res (2007) 1.58
PSD-95 is post-transcriptionally repressed during early neural development by PTBP1 and PTBP2. Nat Neurosci (2012) 1.58
The epithelial splicing factors ESRP1 and ESRP2 positively and negatively regulate diverse types of alternative splicing events. RNA Biol (2009) 1.57
Intragenic motifs regulate the transcriptional complexity of Pkhd1/PKHD1. J Mol Med (Berl) (2014) 1.56
Identification of nuclear and cytoplasmic mRNA targets for the shuttling protein SF2/ASF. PLoS One (2008) 1.51
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Global regulation of alternative splicing during myogenic differentiation. Nucleic Acids Res (2010) 1.39
Intronic splicing enhancers, cognate splicing factors and context-dependent regulation rules. Nat Struct Mol Biol (2012) 1.36
Plant SET domain-containing proteins: structure, function and regulation. Biochim Biophys Acta (2007) 1.36
Autoregulation of Fox protein expression to produce dominant negative splicing factors. RNA (2009) 1.34
Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs. Nucleic Acids Res (2006) 1.34
Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles. Nucleic Acids Res (2005) 1.34
Diversification of stem cell molecular repertoire by alternative splicing. Proc Natl Acad Sci U S A (2005) 1.27
The "alternative" choice of constitutive exons throughout evolution. PLoS Genet (2007) 1.27
A global view of cancer-specific transcript variants by subtractive transcriptome-wide analysis. PLoS One (2009) 1.23
Evolution of Nova-dependent splicing regulation in the brain. PLoS Genet (2007) 1.23
Genomic splice-site analysis reveals frequent alternative splicing close to the dominant splice site. RNA (2006) 1.22
Positive selection acting on splicing motifs reflects compensatory evolution. Genome Res (2008) 1.18
Identification of evolutionarily conserved exons as regulated targets for the splicing activator tra2β in development. PLoS Genet (2011) 1.17
Distinct patterns of expression and evolution of intronless and intron-containing mammalian genes. Mol Biol Evol (2010) 1.11
Dual-specificity splice sites function alternatively as 5' and 3' splice sites. Proc Natl Acad Sci U S A (2007) 1.10
Changes in exon-intron structure during vertebrate evolution affect the splicing pattern of exons. Genome Res (2011) 1.10
Chromatin and epigenetic regulation of pre-mRNA processing. Hum Mol Genet (2012) 1.10
Phylogenetically widespread alternative splicing at unusual GYNGYN donors. Genome Biol (2006) 1.09
Predicting functional alternative splicing by measuring RNA selection pressure from multigenome alignments. PLoS Comput Biol (2009) 1.06
Transcriptome analysis reveals strain-specific and conserved stemness genes in Schmidtea mediterranea. PLoS One (2012) 1.04
Age-dependent gain of alternative splice forms and biased duplication explain the relation between splicing and duplication. Genome Res (2010) 1.03
Fast rate of evolution in alternatively spliced coding regions of mammalian genes. BMC Genomics (2006) 1.03
Organization and post-transcriptional processing of focal adhesion kinase gene. BMC Genomics (2006) 1.03
Deciphering the plant splicing code: experimental and computational approaches for predicting alternative splicing and splicing regulatory elements. Front Plant Sci (2012) 1.02
Identify alternative splicing events based on position-specific evolutionary conservation. PLoS One (2008) 1.02
The animal in the genome: comparative genomics and evolution. Philos Trans R Soc Lond B Biol Sci (2008) 1.02
Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat. BMC Bioinformatics (2006) 1.02
Differing patterns of selection in alternative and constitutive splice sites. Genome Res (2007) 1.02
Species-specific differences in the expression of the HNF1A, HNF1B and HNF4A genes. PLoS One (2009) 1.02
Regulation of the mutually exclusive exons 8a and 8 in the CaV1.2 calcium channel transcript by polypyrimidine tract-binding protein. J Biol Chem (2011) 1.01
Violating the splicing rules: TG dinucleotides function as alternative 3' splice sites in U2-dependent introns. Genome Biol (2007) 1.01
Structural implication of splicing stochastics. Nucleic Acids Res (2009) 1.01
Next-generation SELEX identifies sequence and structural determinants of splicing factor binding in human pre-mRNA sequence. RNA (2009) 0.99
RNA-Seq analysis reveals new gene models and alternative splicing in the fungal pathogen Fusarium graminearum. BMC Genomics (2013) 0.99
Non-EST based prediction of exon skipping and intron retention events using Pfam information. Nucleic Acids Res (2005) 0.97
Limitations of animal models of Parkinson's disease. Parkinsons Dis (2010) 0.96
Assessing the fraction of short-distance tandem splice sites under purifying selection. RNA (2008) 0.95
Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events. PLoS Comput Biol (2008) 0.94
Characterization of sequences and mechanisms through which ISE/ISS-3 regulates FGFR2 splicing. Nucleic Acids Res (2006) 0.93
Computational analysis of splicing errors and mutations in human transcripts. BMC Genomics (2008) 0.93
The adaptive significance of unproductive alternative splicing in primates. RNA (2010) 0.93
Differentiated evolutionary rates in alternative exons and the implications for splicing regulation. BMC Evol Biol (2006) 0.93
Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human. Nucleic Acids Res (2007) 0.93
Lineage-specific splicing of a brain-enriched alternative exon promotes glioblastoma progression. J Clin Invest (2014) 0.93
RNA splicing factors as oncoproteins and tumour suppressors. Nat Rev Cancer (2016) 0.92
Evolutionary conservation and expression of human RNA-binding proteins and their role in human genetic disease. Adv Exp Med Biol (2014) 0.92
Affy exon tissues: exon levels in normal tissues in human, mouse and rat. Bioinformatics (2009) 0.90
Evolution of alternative splicing regulation: changes in predicted exonic splicing regulators are not associated with changes in alternative splicing levels in primates. PLoS One (2009) 0.90
RRP1B is a metastasis modifier that regulates the expression of alternative mRNA isoforms through interactions with SRSF1. Oncogene (2013) 0.88
Ab initio identification of functionally interacting pairs of cis-regulatory elements. Genome Res (2008) 0.88
Comparative analysis of sequence features involved in the recognition of tandem splice sites. BMC Genomics (2008) 0.88
Assessing the number of ancestral alternatively spliced exons in the human genome. BMC Genomics (2006) 0.87
HRP-2, the Caenorhabditis elegans homolog of mammalian heterogeneous nuclear ribonucleoproteins Q and R, is an alternative splicing factor that binds to UCUAUC splicing regulatory elements. J Biol Chem (2009) 0.87
Molecular evidence for natural killer-like cells in equine endometrial cups. Placenta (2012) 0.87
Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts. Genome Biol (2006) 0.85
How does Tra2β protein regulate tissue-specific RNA splicing? Biochem Soc Trans (2012) 0.85
Width of gene expression profile drives alternative splicing. PLoS One (2008) 0.85
Prediction of mammalian microRNA targets. Cell (2003) 53.70
Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci U S A (2002) 25.47
Mechanisms of alternative pre-messenger RNA splicing. Annu Rev Biochem (2003) 21.11
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Predictive identification of exonic splicing enhancers in human genes. Science (2002) 16.86
Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science (2003) 16.80
Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science (2000) 10.14
Pre-mRNA splicing and human disease. Genes Dev (2003) 9.13
Systematic identification and analysis of exonic splicing silencers. Cell (2004) 8.50
Alternative pre-mRNA splicing and proteome expansion in metazoans. Nature (2002) 7.60
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Identification of functional exonic splicing enhancer motifs recognized by individual SR proteins. Genes Dev (1998) 5.79
Protein diversity from alternative splicing: a challenge for bioinformatics and post-genome biology. Cell (2000) 5.16
A new A4 amyloid mRNA contains a domain homologous to serine proteinase inhibitors. Nature (1988) 5.11
Intronic sequences flanking alternatively spliced exons are conserved between human and mouse. Genome Res (2003) 5.01
Alternative splicing: multiple control mechanisms and involvement in human disease. Trends Genet (2002) 4.97
Finding signals that regulate alternative splicing in the post-genomic era. Genome Biol (2002) 4.73
Transcriptome and genome conservation of alternative splicing events in humans and mice. Pac Symp Biocomput (2004) 4.25
Autoregulation of polypyrimidine tract binding protein by alternative splicing leading to nonsense-mediated decay. Mol Cell (2004) 4.13
Increase of functional diversity by alternative splicing. Trends Genet (2003) 2.59
Allele-specific transcript isoforms in human. FEBS Lett (2004) 2.38
Conservation of human alternative splice events in mouse. Nucleic Acids Res (2003) 2.35
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A non-EST-based method for exon-skipping prediction. Genome Res (2004) 2.15
A computational and experimental approach toward a priori identification of alternatively spliced exons. RNA (2004) 1.79
A test of translational selection at 'silent' sites in the human genome: base composition comparisons in alternatively spliced genes. Gene (2000) 1.75
Accurate identification of alternatively spliced exons using support vector machine. Bioinformatics (2004) 1.66
Alternative pre-mRNA splicing and neuronal function. Prog Mol Subcell Biol (2003) 1.62
Influence of intron length on alternative splicing of CD44. Mol Cell Biol (1998) 1.30
Widespread production of novel soluble protein isoforms by alternative splicing removal of transmembrane anchoring domains. FEBS Lett (2003) 1.29
A database designed to computationally aid an experimental approach to alternative splicing. Pac Symp Biocomput (2004) 1.20
Identification and differential expression of a novel alternative splice isoform of the beta A4 amyloid precursor protein (APP) mRNA in leukocytes and brain microglial cells. J Biol Chem (1992) 1.18
Cell-specific RNA-binding proteins in human disease. Trends Cardiovasc Med (2003) 1.08
In NF1, CFTR, PER3, CARS and SYT7, alternatively included exons show higher conservation of surrounding intron sequences than constitutive exons. Eur J Hum Genet (2004) 1.06
RNA editing of a human glutamate receptor subunit. Brain Res Mol Brain Res (1994) 0.88
Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell (2005) 96.87
Prediction of mammalian microRNA targets. Cell (2003) 53.70
Alternative isoform regulation in human tissue transcriptomes. Nature (2008) 52.76
Most mammalian mRNAs are conserved targets of microRNAs. Genome Res (2008) 37.16
The widespread impact of mammalian MicroRNAs on mRNA repression and evolution. Science (2005) 20.51
A uniform system for microRNA annotation. RNA (2003) 20.28
Prediction of plant microRNA targets. Cell (2002) 19.20
The microRNAs of Caenorhabditis elegans. Genes Dev (2003) 17.70
Vertebrate microRNA genes. Science (2003) 17.42
Predictive identification of exonic splicing enhancers in human genes. Science (2002) 16.86
Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature (2002) 15.36
c-Myc regulates transcriptional pause release. Cell (2010) 11.64
Proliferating cells express mRNAs with shortened 3' untranslated regions and fewer microRNA target sites. Science (2008) 11.33
Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat Methods (2010) 10.13
Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J Comput Biol (2004) 9.00
Systematic identification and analysis of exonic splicing silencers. Cell (2004) 8.50
Transcriptional amplification in tumor cells with elevated c-Myc. Cell (2012) 8.24
An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput Biol (2009) 7.47
Determinants of targeting by endogenous and exogenous microRNAs and siRNAs. RNA (2007) 6.44
Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. RNA (2008) 6.29
Variation in alternative splicing across human tissues. Genome Biol (2004) 5.70
Dynamic regulation of miRNA expression in ordered stages of cellular development. Genes Dev (2007) 4.79
Fast readout of object identity from macaque inferior temporal cortex. Science (2005) 4.54
Evolutionary dynamics of gene and isoform regulation in Mammalian tissues. Science (2012) 4.52
Robust object recognition with cortex-like mechanisms. IEEE Trans Pattern Anal Mach Intell (2007) 4.16
General and specific functions of exonic splicing silencers in splicing control. Mol Cell (2006) 3.76
Biased chromatin signatures around polyadenylation sites and exons. Mol Cell (2009) 3.74
RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons. Nucleic Acids Res (2004) 3.70
Revisiting global gene expression analysis. Cell (2012) 3.63
A feedforward architecture accounts for rapid categorization. Proc Natl Acad Sci U S A (2007) 3.43
Braveheart, a long noncoding RNA required for cardiovascular lineage commitment. Cell (2013) 3.35
Variation in sequence and organization of splicing regulatory elements in vertebrate genes. Proc Natl Acad Sci U S A (2004) 3.34
A postnatal switch of CELF and MBNL proteins reprograms alternative splicing in the developing heart. Proc Natl Acad Sci U S A (2008) 3.33
Transcriptome-wide regulation of pre-mRNA splicing and mRNA localization by muscleblind proteins. Cell (2012) 3.20
A comparison of primate prefrontal and inferior temporal cortices during visual categorization. J Neurosci (2003) 3.00
An EMT-driven alternative splicing program occurs in human breast cancer and modulates cellular phenotype. PLoS Genet (2011) 2.99
Widespread selection for local RNA secondary structure in coding regions of bacterial genes. Genome Res (2003) 2.81
Single nucleotide polymorphism-based validation of exonic splicing enhancers. PLoS Biol (2004) 2.77
Neural mechanisms for the recognition of biological movements. Nat Rev Neurosci (2003) 2.70
Promoter directionality is controlled by U1 snRNP and polyadenylation signals. Nature (2013) 2.63
Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument. Nat Biotechnol (2011) 2.60
Identification of let-7-regulated oncofetal genes. Cancer Res (2008) 2.56
Object selectivity of local field potentials and spikes in the macaque inferior temporal cortex. Neuron (2006) 2.55
MBNL proteins repress ES-cell-specific alternative splicing and reprogramming. Nature (2013) 2.49
A combinatorial code for splicing silencing: UAGG and GGGG motifs. PLoS Biol (2005) 2.48
Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification. RNA (2004) 2.17
Dynamic population coding of category information in inferior temporal and prefrontal cortex. J Neurophysiol (2008) 2.14
Splice site strength-dependent activity and genetic buffering by poly-G runs. Nat Struct Mol Biol (2009) 1.99
SR proteins collaborate with 7SK and promoter-associated nascent RNA to release paused polymerase. Cell (2013) 1.97
Neural mechanisms of object recognition. Curr Opin Neurobiol (2002) 1.90
Visual categorization and the primate prefrontal cortex: neurophysiology and behavior. J Neurophysiol (2002) 1.88
Widespread regulation of translation by elongation pausing in heat shock. Mol Cell (2013) 1.85
Recognition of unknown conserved alternatively spliced exons. PLoS Comput Biol (2005) 1.77
DNA sequence evolution with neighbor-dependent mutation. J Comput Biol (2003) 1.76
Patterns of intron gain and loss in fungi. PLoS Biol (2004) 1.72
Alternative splicing of RNA triplets is often regulated and accelerates proteome evolution. PLoS Biol (2012) 1.71
Inference of splicing regulatory activities by sequence neighborhood analysis. PLoS Genet (2006) 1.71
HOLLYWOOD: a comparative relational database of alternative splicing. Nucleic Acids Res (2006) 1.66
Prefrontal cortex activity during flexible categorization. J Neurosci (2010) 1.64
Trade-off between object selectivity and tolerance in monkey inferotemporal cortex. J Neurosci (2007) 1.58
A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA. Proc Natl Acad Sci U S A (2005) 1.54
Coevolutionary networks of splicing cis-regulatory elements. Proc Natl Acad Sci U S A (2007) 1.54
A model of V4 shape selectivity and invariance. J Neurophysiol (2007) 1.53
Experience-dependent sharpening of visual shape selectivity in inferior temporal cortex. Cereb Cortex (2005) 1.51
A canonical neural circuit for cortical nonlinear operations. Neural Comput (2008) 1.43
Global regulation of alternative splicing during myogenic differentiation. Nucleic Acids Res (2010) 1.39
Global analyses of UPF1 binding and function reveal expanded scope of nonsense-mediated mRNA decay. Genome Res (2013) 1.39
A latent pro-survival function for the mir-290-295 cluster in mouse embryonic stem cells. PLoS Genet (2011) 1.31
A complex network of factors with overlapping affinities represses splicing through intronic elements. Nat Struct Mol Biol (2012) 1.26
A quantitative theory of immediate visual recognition. Prog Brain Res (2007) 1.26
Automated home-cage behavioural phenotyping of mice. Nat Commun (2010) 1.26
Hepatitis C virus infection and hepatic stellate cell activation downregulate miR-29: miR-29 overexpression reduces hepatitis C viral abundance in culture. J Infect Dis (2011) 1.20
Intracellular measurements of spatial integration and the MAX operation in complex cells of the cat primary visual cortex. J Neurophysiol (2004) 1.19
3' UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts. Genome Res (2013) 1.10
What and where: a Bayesian inference theory of attention. Vision Res (2010) 1.09
'United' we stand. Perception (2002) 1.07
Detection of broadly expressed neuronal genes in C. elegans. Dev Biol (2006) 1.03
Linking C5 deficiency to an exonic splicing enhancer mutation. J Immunol (2005) 1.03
The dynamics of invariant object recognition in the human visual system. J Neurophysiol (2013) 1.02
The cardiotonic steroid digitoxin regulates alternative splicing through depletion of the splicing factors SRSF3 and TRA2B. RNA (2012) 1.00
Universal 1/f noise, crossovers of scaling exponents, and chromosome-specific patterns of guanine-cytosine content in DNA sequences of the human genome. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 0.99
Learning and disrupting invariance in visual recognition with a temporal association rule. Front Comput Neurosci (2012) 0.97
Weak definition of IKBKAP exon 20 leads to aberrant splicing in familial dysautonomia. Hum Mutat (2007) 0.93
Genome-wide impact of a recently expanded microRNA cluster in mouse. Proc Natl Acad Sci U S A (2011) 0.92
Comparative analysis of sequence features involved in the recognition of tandem splice sites. BMC Genomics (2008) 0.88
Reduced expression of ribosomal proteins relieves microRNA-mediated repression. Mol Cell (2012) 0.88
Ab initio identification of functionally interacting pairs of cis-regulatory elements. Genome Res (2008) 0.88
Does mapping reveal correlation between gene expression and protein-protein interaction? Nat Genet (2003) 0.85
MicroRNA target finding by comparative genomics. Methods Mol Biol (2014) 0.80
Gene structure prediction using an orthologous gene of known exon-intron structure. Appl Bioinformatics (2004) 0.77
Genomic analysis of RNA localization. RNA Biol (2014) 0.76
Invariant representations for action recognition in the visual system. J Vis (2015) 0.75
An unusual 500,000 bases long oscillation of guanine and cytosine content in human chromosome 21. Comput Biol Chem (2004) 0.75
Sequence-related human proteins cluster by degree of evolutionary conservation. Phys Rev E Stat Nonlin Soft Matter Phys (2004) 0.75
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Untangling influences of hydrophobicity on protein sequences and structures. Proteins (2006) 0.75