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Results 1 - 10
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18,699
Hidden Markov models in computational biology: applications to protein modeling
- JOURNAL OF MOLECULAR BIOLOGY
, 1994
"... Hidden.Markov Models (HMMs) are applied t.0 the problems of statistical modeling, database searching and multiple sequence alignment of protein families and protein domains. These methods are demonstrated the on globin family, the protein kinase catalytic domain, and the EF-hand calcium binding moti ..."
Abstract
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Cited by 655 (39 self)
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) perform better in these tests than PROSITE (a dictionary of sites and patterns in proteins). The HMM appecvs to have a slight advantage over PROFILESEARCH in terms of lower rates of false
PAML: a program package for phylogenetic analysis by maximum likelihood
- COMPUT APPL BIOSCI 13:555–556
, 1997
"... PAML, currently in version 1.2, is a package of programs for phylogenetic analyses of DNA and protein sequences using the method of maximum likelihood (ML). The programs can be used for (i) maximum likelihood estimation of evolutionary parameters such as branch lengths in a phylogenetic tree, the tr ..."
Abstract
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Cited by 1459 (17 self)
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PAML, currently in version 1.2, is a package of programs for phylogenetic analyses of DNA and protein sequences using the method of maximum likelihood (ML). The programs can be used for (i) maximum likelihood estimation of evolutionary parameters such as branch lengths in a phylogenetic tree
Paml 4: Phylogenetic analysis by maximum likelihood
- Mol. Biol. Evol
, 2007
"... PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). The programs may be used to compare and test phylogenetic trees, but their main strengths lie in the rich repertoire of evolutionary models implemented, which ..."
Abstract
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Cited by 1201 (28 self)
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can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses. Uses of the programs include estimation of synonymous and nonsynonymous rates (dN and dS) between two protein-coding DNA sequences, inference of positive Darwinian selection through
Protein homology detection by HMM-HMM comparison
- BIOINFORMATICS
, 2005
"... Motivation: Protein homology detection and sequence alignment are at the basis of protein structure prediction, function prediction, and evolution. Results: We have generalized the alignment of protein se-quences with a profile hidden Markov model (HMM) to the case of pairwise alignment of profile H ..."
Abstract
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Cited by 401 (8 self)
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Motivation: Protein homology detection and sequence alignment are at the basis of protein structure prediction, function prediction, and evolution. Results: We have generalized the alignment of protein se-quences with a profile hidden Markov model (HMM) to the case of pairwise alignment of profile
Human DNA methylomes at base resolution show widespread epigenomic differences.
- Nature,
, 2009
"... DNA cytosine methylation is a central epigenetic modification that has essential roles in cellular processes including genome regulation, development and disease. Here we present the first genome-wide, single-base-resolution maps of methylated cytosines in a mammalian genome, from both human embryo ..."
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Cited by 401 (6 self)
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embryonic stem cells and fetal fibroblasts, along with comparative analysis of messenger RNA and small RNA components of the transcriptome, several histone modifications, and sites of DNA-protein interaction for several key regulatory factors. Widespread differences were identified in the composition
Cellular motility driven by assembly and disassembly of actin filaments
- Cell
"... Motile cells extend a leading edge by assembling a branched network of actin filaments that produces physical force as the polymers grow beneath the plasma membrane. A core set of proteins including actin, Arp2/3 complex, profilin, capping protein, and ADF/cofilin can reconstitute the process in vit ..."
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Cited by 343 (5 self)
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in vitro, and mathematical models of the constituent reactions pre-dict the rate of motion. Signaling pathways converging on WASp/Scar proteins regulate the activity of Arp2/3 complex, which mediates the initiation of new filaments as branches on preexisting filaments. After a brief spurt of growth
Entrez Gene: gene-centered information at NCBI
- Nucleic Acids Res
, 2007
"... Entrez Gene (www.ncbi.nlm.nih.gov/entrez/query. fcgi?db=gene) is NCBI’s database for gene-specific information. Entrez Gene includes records from genomes that have been completely sequenced, that have an active research community to con-tribute gene-specific information or that are sched-uled for in ..."
Abstract
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Cited by 340 (12 self)
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-uled for intense sequence analysis. The content of Entrez Gene represents the result of both curation and automated integration of data from NCBI’s Reference Sequence project (RefSeq), from collabo-rating model organism databases and from other databases within NCBI. Records in Entrez Gene are assigned unique
Predicting the secondary structure of globular proteins using neural networks models
- J. Molecular Biology
, 1988
"... We present a new method for predicting the secondary structure of globular proteins based on non-linear neural network models. Network models learn from existing protein structures how to predict the secondary structure of local sequences of amino acids. The average success rate of our method on a t ..."
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Cited by 271 (2 self)
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We present a new method for predicting the secondary structure of globular proteins based on non-linear neural network models. Network models learn from existing protein structures how to predict the secondary structure of local sequences of amino acids. The average success rate of our method on a
Identification of protein coding regions by database similarity search
- Nature Genetics
, 1993
"... Correspondence should be addressed to W.G. page 1 Summary Sequence similarity between a translated nucleotide sequence and a known biological protein can provide strong evidence for the presence of a homologous coding region, and such similarities can often be identified even between distantly relat ..."
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Cited by 262 (2 self)
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Correspondence should be addressed to W.G. page 1 Summary Sequence similarity between a translated nucleotide sequence and a known biological protein can provide strong evidence for the presence of a homologous coding region, and such similarities can often be identified even between distantly
The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiation of translation
- Dev. Biol
, 1999
"... lin-4 encodes a small RNA that is complementary to sequences in the 3 � untranslated region (UTR) of lin-14 mRNA and that acts to developmentally repress the accumulation of LIN-14 protein. This repression is essential for the proper timing of numerous events of Caenorhabditis elegans larval develop ..."
Abstract
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Cited by 255 (7 self)
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lin-4 encodes a small RNA that is complementary to sequences in the 3 � untranslated region (UTR) of lin-14 mRNA and that acts to developmentally repress the accumulation of LIN-14 protein. This repression is essential for the proper timing of numerous events of Caenorhabditis elegans larval
Results 1 - 10
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18,699
