(Q33497902)

27 July 2017

title

Evolutionary triplet models of structured RNA (English)

1 reference

27 July 2017

1

0 references

Ian Holmes

series ordinal

2

0 references

publication date

28 August 2009

1 reference

PLOS Computational Biology

27 July 2017

published in

1 reference

27 July 2017

volume

5

1 reference

27 July 2017

issue

8

1 reference

27 July 2017

page(s)

e1000483

1 reference

Creative Commons Attribution 4.0 International

27 July 2017

copyright license

start time

28 August 2009

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Genome-wide nucleotide-level mammalian ancestor reconstruction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Probabilistic phylogenetic inference with insertions and deletions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Ribosomal RNAs are tolerant toward genetic insertions: evolutionary origin of the expansion segments

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

The origin and evolution of the ribosome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Crystal structure of an ancient protein: evolution by conformational epistasis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

SimulFold: simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

HMMoC--a compiler for hidden Markov models

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Query-dependent banding (QDB) for faster RNA similarity searches

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

The extant core bacterial proteome is an archive of the origin of life

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Sequencing and analysis of Neanderthal genomic DNA

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

An enhanced RNA alignment benchmark for sequence alignment programs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Reconstructing contiguous regions of an ancestral genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Rooting the tree of life by transition analyses

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Identification and classification of conserved RNA secondary structures in the human genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Introns and the origin of nucleus-cytosol compartmentalization

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: a hypothesis for the origin of cellular domain

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Translation initiation: structures, mechanisms and evolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Thermosynthesis as energy source for the RNA World: a model for the bioenergetics of the origin of life

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Joint Bayesian Estimation of Alignment and Phylogeny

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Resurrecting ancestral alcohol dehydrogenases from yeast

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

A benchmark of multiple sequence alignment programs upon structural RNAs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Accelerated probabilistic inference of RNA structure evolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Reconstructing large regions of an ancestral mammalian genome in silico

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

A probabilistic model for the evolution of RNA structure

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Group II introns: structure and catalytic versatility of large natural ribozymes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Pfold: RNA secondary structure prediction using stochastic context-free grammars

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Rfam: an RNA family database

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Recreating a functional ancestral archosaur visual pigment

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

An expectation maximization algorithm for training hidden substitution models.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Multiple sequence alignment using partial order graphs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Complementary advantageous substitutions in the evolution of an antiviral RNase of higher primates

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Analysis of the structure of human telomerase RNA in vivo

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Noncoding RNA gene detection using comparative sequence analysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Non–coding RNA genes and the modern RNA world

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Evolutionary HMMs: a Bayesian approach to multiple alignment

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Mutations as missing data: inferences on the ages and distributions of nonsynonymous and synonymous mutations.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Conserved features of Y RNAs: a comparison of experimentally derived secondary structures

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

A comprehensive comparison of multiple sequence alignment programs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

A computational screen for methylation guide snoRNAs in yeast

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

A dynamic programming algorithm for RNA structure prediction including pseudoknots

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Dynamic programming alignment accuracy

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Compilation of tRNA sequences and sequences of tRNA genes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Molecular reconstruction of Sleeping Beauty, a Tc1-like transposon from fish, and its transposition in human cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Collection of small subunit (16S- and 16S-like) ribosomal RNA structures

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Molecular resurrection of an extinct ancestral promoter for mouse L1.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

RNA sequence analysis using covariance models

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Stochastic context-free grammars for tRNA modeling

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Evolutionary trees from DNA sequences: A maximum likelihood approach

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

A General Model for the Genetic Analysis of Pedigree Data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

The origin of the genetic code

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Evolution of the secondary structures and compensatory mutations of the ribosomal RNAs of Drosophila melanogaster.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Ancestral lysozymes reconstructed, neutrality tested, and thermostability linked to hydrocarbon packing.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

The ribonuclease from an extinct bovid ruminant

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

'Compensatory slippage' in the evolution of ribosomal RNA genes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

An evolutionary model for maximum likelihood alignment of DNA sequences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Motif prediction in ribosomal RNAs Lessons and prospects for automated motif prediction in homologous RNA molecules

21 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000483

RSEARCH: finding homologs of single structured RNA sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000483

Specific alignment of structured RNA: stochastic grammars and sequence annealing

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000483

Phylocomposer and phylodirector: analysis and visualization of transducer indel models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000483

Multiple alignment by sequence annealing.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000483

A "Long Indel" model for evolutionary sequence alignment.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000483

Chemical Paleogenetics. Molecular "Restoration Studies" of Extinct Forms of Life

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000483

Identification of essential amino acid changes in paired domain evolution using a novel combination of evolutionary analysis and in vitro and in vivo studies.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000483

Reconstruction of ancestral genomic sequences using likelihood

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000483

A model for the origin of protein synthesis as coreplicational scanning of nascent RNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000483

Branch and bound algorithms to determine minimal evolutionary trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000483

Statistical alignment: computational properties, homology testing and goodness-of-fit.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000483

An efficient algorithm for statistical multiple alignment on arbitrary phylogenetic trees.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000483

Combining statistical alignment and phylogenetic footprinting to detect regulatory elements.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000483

Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000483

Exact and heuristic algorithms for the Indel Maximum Likelihood Problem.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000483

Pair hidden Markov models on tree structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000483

Pairwise RNA structure comparison with stochastic context-free grammars.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

An algorithm for statistical alignment of sequences related by a binary tree.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2725318

Transducers: an emerging probabilistic framework for modeling indels on trees

31 October 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000483

Using guide trees to construct multiple-sequence evolutionary HMMs

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000483

Estimating the pattern of nucleotide substitution

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19714212

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Sequence alignments and pair hidden Markov models using evolutionary history

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19714212

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Database on the structure of large ribosomal subunit RNA

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19714212

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.1000483

1 reference

journals/ploscb/BradleyH09

27 July 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

27 July 2017

1 reference