Published in Nucleic Acids Res on November 25, 1994
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res (1997) 142.55
Infernal 1.0: inference of RNA alignments. Bioinformatics (2009) 12.98
A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure. BMC Bioinformatics (2002) 10.84
Query-dependent banding (QDB) for faster RNA similarity searches. PLoS Comput Biol (2007) 6.34
RSEARCH: finding homologs of single structured RNA sequences. BMC Bioinformatics (2003) 4.14
Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction. BMC Bioinformatics (2004) 3.60
Accelerated probabilistic inference of RNA structure evolution. BMC Bioinformatics (2005) 2.16
Discovering common stem-loop motifs in unaligned RNA sequences. Nucleic Acids Res (2001) 2.12
Evolutionary models for insertions and deletions in a probabilistic modeling framework. BMC Bioinformatics (2005) 1.90
Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes. Proc Natl Acad Sci U S A (2008) 1.51
Artificial grammar learning meets formal language theory: an overview. Philos Trans R Soc Lond B Biol Sci (2012) 1.37
De novo prediction of structured RNAs from genomic sequences. Trends Biotechnol (2009) 1.31
XRate: a fast prototyping, training and annotation tool for phylo-grammars. BMC Bioinformatics (2006) 1.29
A method for aligning RNA secondary structures and its application to RNA motif detection. BMC Bioinformatics (2005) 1.25
Local RNA structure alignment with incomplete sequence. Bioinformatics (2009) 1.24
Hidden Markov Models and their Applications in Biological Sequence Analysis. Curr Genomics (2009) 1.22
MODENA: a multi-objective RNA inverse folding. Adv Appl Bioinform Chem (2010) 1.13
RNIE: genome-wide prediction of bacterial intrinsic terminators. Nucleic Acids Res (2011) 1.09
Computational analysis of conserved RNA secondary structure in transcriptomes and genomes. Annu Rev Biophys (2014) 1.08
Computational methods in noncoding RNA research. J Math Biol (2007) 1.08
Semiautomated improvement of RNA alignments. RNA (2007) 1.02
SeLOX--a locus of recombination site search tool for the detection and directed evolution of site-specific recombination systems. Nucleic Acids Res (2010) 1.02
Finding the target sites of RNA-binding proteins. Wiley Interdiscip Rev RNA (2013) 0.99
From structure prediction to genomic screens for novel non-coding RNAs. PLoS Comput Biol (2011) 0.99
Correlation of RNA secondary structure statistics with thermodynamic stability and applications to folding. J Mol Biol (2009) 0.91
Genome-wide searching with base-pairing kernel functions for noncoding RNAs: computational and expression analysis of snoRNA families in Caenorhabditis elegans. Nucleic Acids Res (2009) 0.89
A composite method based on formal grammar and DNA structural features in detecting human polymerase II promoter region. PLoS One (2013) 0.88
Evolving stochastic context--free grammars for RNA secondary structure prediction. BMC Bioinformatics (2012) 0.88
Reducing the worst case running times of a family of RNA and CFG problems, using Valiant's approach. Algorithms Mol Biol (2011) 0.87
Modeling RNA tertiary structure motifs by graph-grammars. Nucleic Acids Res (2007) 0.86
Data Compression Concepts and Algorithms and their Applications to Bioinformatics. Entropy (Basel) (2010) 0.86
Functional characterization of spliceosomal introns and identification of U2, U4, and U5 snRNAs in the deep-branching eukaryote Entamoeba histolytica. Eukaryot Cell (2007) 0.86
Rapid ab initio prediction of RNA pseudoknots via graph tree decomposition. J Math Biol (2007) 0.85
Annotating RNA motifs in sequences and alignments. Nucleic Acids Res (2014) 0.83
Incorporating phylogenetic-based covarying mutations into RNAalifold for RNA consensus structure prediction. BMC Bioinformatics (2013) 0.83
Directed acyclic graph kernels for structural RNA analysis. BMC Bioinformatics (2008) 0.83
Identifying novel sequence variants of RNA 3D motifs. Nucleic Acids Res (2015) 0.82
Conservation and losses of non-coding RNAs in avian genomes. PLoS One (2015) 0.82
The four ingredients of single-sequence RNA secondary structure prediction. A unifying perspective. RNA Biol (2013) 0.81
A formal language-based approach in biology. Comp Funct Genomics (2004) 0.81
Random generation of RNA secondary structures according to native distributions. Algorithms Mol Biol (2011) 0.81
A stochastic context free grammar based framework for analysis of protein sequences. BMC Bioinformatics (2009) 0.80
RNAG: a new Gibbs sampler for predicting RNA secondary structure for unaligned sequences. Bioinformatics (2011) 0.79
PSSMTS: position specific scoring matrices on tree structures. J Math Biol (2007) 0.79
A grammar inference approach for predicting kinase specific phosphorylation sites. PLoS One (2015) 0.78
Evolutionary triplet models of structured RNA. PLoS Comput Biol (2009) 0.77
Probabilistic grammatical model for helix-helix contact site classification. Algorithms Mol Biol (2013) 0.77
Asymptotic distribution of motifs in a stochastic context-free grammar model of RNA folding. J Math Biol (2014) 0.76
Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families. Curr Protoc Bioinformatics (2016) 0.75
Hidden Markov models in computational biology. Applications to protein modeling. J Mol Biol (1994) 31.57
Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids. Microbiol Rev (1983) 23.08
On finding all suboptimal foldings of an RNA molecule. Science (1989) 20.36
A computer program to search for tRNA genes. Nucleic Acids Res (1980) 17.12
RNA sequence analysis using covariance models. Nucleic Acids Res (1994) 14.60
Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J Mol Biol (1990) 10.85
5S RNA secondary structure. Nature (1975) 10.58
Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res (1993) 9.16
Identifying potential tRNA genes in genomic DNA sequences. J Mol Biol (1991) 8.65
Spliceosomal snRNAs. Annu Rev Genet (1988) 8.09
Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods. Nucleic Acids Res (1992) 7.51
Comparative and functional anatomy of group II catalytic introns--a review. Gene (1989) 7.46
Pattern searching/alignment with RNA primary and secondary structures: an effective descriptor for tRNA. Comput Appl Biosci (1990) 6.67
RNA structure prediction. Annu Rev Biophys Biophys Chem (1988) 5.75
A hidden Markov model that finds genes in E. coli DNA. Nucleic Acids Res (1994) 5.50
A program for the identification of tRNA-like structures in DNA sequence data. Nucleic Acids Res (1986) 4.95
Matching relational patterns in nucleic acid sequences. Comput Appl Biosci (1987) 4.87
Inferring consensus structure from nucleic acid sequences. Comput Appl Biosci (1991) 2.99
Phylogenetic analysis and evolution of RNase P RNA in proteobacteria. J Bacteriol (1991) 2.71
Phylogenetic comparative analysis of RNA secondary structure. Methods Enzymol (1989) 2.18
Structure and function of signal recognition particle RNA. Prog Nucleic Acid Res Mol Biol (1989) 1.87
Phylogenetic and genetic evidence for base-triples in the catalytic domain of group I introns. Nature (1990) 1.74
Comparative structural analysis of nuclear RNase P RNAs from yeast. J Biol Chem (1993) 1.71
Turn prediction in proteins using a pattern-matching approach. Biochemistry (1986) 1.65
Computer analysis of nucleic acid sequences. Methods Enzymol (1988) 1.63
Rapid searches for complex patterns in biological molecules. Nucleic Acids Res (1984) 1.57
Structure detection through automated covariance search. Comput Appl Biosci (1990) 1.39
Prediction of common folding structures of homologous RNAs. Nucleic Acids Res (1993) 1.27
Scrutineer: a computer program that flexibly seeks and describes motifs and profiles in protein sequence databases. Comput Appl Biosci (1990) 1.25
Artificial neural networks for pattern recognition in biochemical sequences. Annu Rev Biophys Biomol Struct (1993) 1.08
Predicting common foldings of homologous RNAs. J Biomol Struct Dyn (1991) 1.07
Initial sequencing and analysis of the human genome. Nature (2001) 212.86
The UCSC Genome Browser Database. Nucleic Acids Res (2003) 32.84
Hidden Markov models in computational biology. Applications to protein modeling. J Mol Biol (1994) 31.57
The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res (2007) 23.13
Hidden Markov models for detecting remote protein homologies. Bioinformatics (1998) 21.29
Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology. Comput Appl Biosci (1996) 19.74
Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc Natl Acad Sci U S A (2000) 19.39
Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol (2001) 15.97
Support vector machine classification and validation of cancer tissue samples using microarray expression data. Bioinformatics (2000) 13.33
Comparative analyses of multi-species sequences from targeted genomic regions. Nature (2003) 13.31
The UCSC genome browser database: update 2007. Nucleic Acids Res (2006) 13.04
A physical map of the human genome. Nature (2001) 12.39
Improved splice site detection in Genie. J Comput Biol (1997) 11.57
A generalized hidden Markov model for the recognition of human genes in DNA. Proc Int Conf Intell Syst Mol Biol (1996) 11.45
Cofactor dynamics and sufficiency in estrogen receptor-regulated transcription. Cell (2000) 11.10
The UCSC Genome Browser Database: update 2006. Nucleic Acids Res (2006) 11.05
Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature (2001) 10.96
Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res (1998) 10.74
Using Dirichlet mixture priors to derive hidden Markov models for protein families. Proc Int Conf Intell Syst Mol Biol (1993) 10.73
The UCSC Genome Browser Database: update 2009. Nucleic Acids Res (2008) 10.31
Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J Mol Biol (1998) 9.09
Assembly of the working draft of the human genome with GigAssembler. Genome Res (2001) 8.23
Objective structured assessment of technical skill (OSATS) for surgical residents. Br J Surg (1997) 7.54
Genie--gene finding in Drosophila melanogaster. Genome Res (2000) 7.47
Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel. Nat Biotechnol (2001) 6.07
Integrating database homology in a probabilistic gene structure model. Pac Symp Biocomput (1997) 5.96
Stat5a and Stat5b proteins have essential and nonessential, or redundant, roles in cytokine responses. Cell (1998) 5.92
A hidden Markov model that finds genes in E. coli DNA. Nucleic Acids Res (1994) 5.50
HTLV-III-neutralizing antibodies in patients with AIDS and AIDS-related complex. Nature (1985) 5.10
Opacity genes in Neisseria gonorrhoeae: control of phase and antigenic variation. Cell (1986) 4.89
A controlled trial comparing continued zidovudine with didanosine in human immunodeficiency virus infection. The NIAID AIDS Clinical Trials Group. N Engl J Med (1992) 4.71
RNA modeling using Gibbs sampling and stochastic context free grammars. Proc Int Conf Intell Syst Mol Biol (1994) 4.32
Transcriptome and genome conservation of alternative splicing events in humans and mice. Pac Symp Biocomput (2004) 4.25
A Social Study of Hospital Treatment. Br Med J (1945) 4.24
Estrogen receptor-associated proteins: possible mediators of hormone-induced transcription. Science (1994) 4.22
Subset of individuals with autism spectrum disorders and extreme macrocephaly associated with germline PTEN tumour suppressor gene mutations. J Med Genet (2005) 4.14
Polarity-specific activities of retinoic acid receptors determined by a co-repressor. Nature (1995) 3.90
The association of school environments with youth physical activity. Am J Public Health (2001) 3.88
Bronchoscopic lung-volume reduction with Exhale airway stents for emphysema (EASE trial): randomised, sham-controlled, multicentre trial. Lancet (2011) 3.70
Genome-wide bioinformatic and molecular analysis of introns in Saccharomyces cerevisiae. RNA (1999) 3.40
The cytotoxic T lymphocyte response to multiple hepatitis B virus polymerase epitopes during and after acute viral hepatitis. J Exp Med (1995) 3.34
lac repressor can regulate expression from a hybrid SV40 early promoter containing a lac operator in animal cells. Cell (1987) 3.33
Differential activation of peroxisome proliferator-activated receptors by eicosanoids. J Biol Chem (1995) 3.13
The premature ageing syndrome protein, WRN, is a 3'-->5' exonuclease. Nat Genet (1998) 3.12
Cost comparison: a desflurane- versus a propofol-based general anesthetic technique. Anesth Analg (1994) 3.09
Structural analysis of the interaction between the human immunodeficiency virus Rev protein and the Rev response element. Proc Natl Acad Sci U S A (1991) 3.06
Nocturnal asthma and changes in circulating epinephrine, histamine, and cortisol. N Engl J Med (1980) 3.04
Introduction and audit of a general practice antibiotic formulary. J R Coll Gen Pract (1988) 3.00
Toxicity evaluation of replication-competent herpes simplex virus (ICP 34.5 null mutant 1716) in patients with recurrent malignant glioma. Gene Ther (2000) 2.94
Assessment of technical skills transfer from the bench training model to the human model. Am J Surg (1999) 2.90
The urethral pressure profile. Br J Urol (1969) 2.88
The share of human genomic DNA under selection estimated from human-mouse genomic alignments. Cold Spring Harb Symp Quant Biol (2003) 2.83
Optimally parsing a sequence into different classes based on multiple types of evidence. Proc Int Conf Intell Syst Mol Biol (1994) 2.73
p300 is a component of an estrogen receptor coactivator complex. Proc Natl Acad Sci U S A (1996) 2.58
The proofreading domain of Escherichia coli DNA polymerase I and other DNA and/or RNA exonuclease domains. Nucleic Acids Res (1997) 2.55
The CAG repeat within the androgen receptor gene and its relationship to prostate cancer. Proc Natl Acad Sci U S A (1997) 2.54
Vertical integration: exploration of a popular strategic concept. Health Care Manage Rev (1986) 2.50
Specific missense mutations in NEMO result in hyper-IgM syndrome with hypohydrotic ectodermal dysplasia. Nat Immunol (2001) 2.42
Cyclin D1 stimulation of estrogen receptor transcriptional activity independent of cdk4. Mol Cell Biol (1997) 2.40
Application of an algorithm for staging small-cell lung cancer can save one third of the initial evaluation costs. Arch Intern Med (1993) 2.36
A Z-DNA binding domain present in the human editing enzyme, double-stranded RNA adenosine deaminase. Proc Natl Acad Sci U S A (1997) 2.35
Angiogenesis in skeletal and cardiac muscle. Physiol Rev (1992) 2.34
Cationic bactericidal peptides. Adv Microb Physiol (1995) 2.33
Statistical modeling and analysis of the LAGLIDADG family of site-specific endonucleases and identification of an intein that encodes a site-specific endonuclease of the HNH family. Nucleic Acids Res (1997) 2.33
A discriminative framework for detecting remote protein homologies. J Comput Biol (2000) 2.30
Role of mitochondrial lactate dehydrogenase and lactate oxidation in the intracellular lactate shuttle. Proc Natl Acad Sci U S A (1999) 2.30
Induction of DNA polymerase in mouse L cells. J Mol Biol (1973) 2.28
Using the Fisher kernel method to detect remote protein homologies. Proc Int Conf Intell Syst Mol Biol (1999) 2.28
Optimizing reduced-space sequence analysis. Bioinformatics (2000) 2.21
Predicting protein structure using hidden Markov models. Proteins (1997) 2.20
AIB1 is a conduit for kinase-mediated growth factor signaling to the estrogen receptor. Mol Cell Biol (2000) 2.18
Identifying marker genes in transcription profiling data using a mixture of feature relevance experts. Physiol Genomics (2001) 2.17
Taste genes associated with dental caries. J Dent Res (2010) 2.17
Treatment of multiple-hormone-producing malignant islet-cell tumour with streptozotocin. Lancet (1968) 2.14
Modification of BRCA1-associated breast cancer risk by the polymorphic androgen-receptor CAG repeat. Am J Hum Genet (1999) 2.14
SV40 small t antigen enhances the transformation activity of limiting concentrations of SV40 large T antigen. Cell (1987) 2.13
Skeletal muscle adaptations to endurance training in 60- to 70-yr-old men and women. J Appl Physiol (1985) (1992) 2.06
What is the value added by human intervention in protein structure prediction? Proteins (2001) 1.97
ICI D1694, a quinazoline antifolate thymidylate synthase inhibitor that is a potent inhibitor of L1210 tumor cell growth in vitro and in vivo: a new agent for clinical study. Cancer Res (1991) 1.94
Detection of group C rotavirus in infants with extrahepatic biliary atresia. J Infect Dis (1996) 1.91
Hypopyon uveitis in patients with acquired immunodeficiency syndrome treated for systemic Mycobacterium avium complex infection with rifabutin. Arch Ophthalmol (1994) 1.88
Comparison of DNA ploidy, histologic, and immunohistochemical findings with clinical outcome in inflammatory myofibroblastic tumors. Mod Pathol (1999) 1.88