Investigating genomic structure using changept: A Bayesian segmentation model (Q38263201)

1 September 2017

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title

Investigating genomic structure using changept: A Bayesian segmentation model (English)

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1 September 2017

Jonathan M Keith

2

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author name string

Manjula Algama

series ordinal

1

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1 September 2017

1 July 2014

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Computational and Structural Biotechnology Journal

1 September 2017

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1 September 2017

10

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1 September 2017

17

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1 September 2017

107-115

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PMCID

4204429

describes a project that uses

1 September 2017

Bayes' theorem

1 reference

18 June 2022

https://europepmc.org/article/PMC/4204429

inferred from PubMed Central ID database lookup

cites work

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Multiscale DNA partitioning: statistical evidence for segments.

6 September 2017

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Detecting the borders between coding and non-coding DNA regions in prokaryotes based on recursive segmentation and nucleotide doublets statistics

6 September 2017

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Interpreting genomic data via entropic dissection

6 September 2017

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An integrated encyclopedia of DNA elements in the human genome

6 September 2017

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Computational characterization of 3' splice variants in the GFAP isoform family

6 September 2017

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Identifying compositionally homogeneous and nonhomogeneous domains within the human genome using a novel segmentation algorithm

6 September 2017

1 reference

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6 September 2017

Sequence segmentation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

Isochore patterns and gene distributions in fish genomes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

Spatial smoothing and hot spot detection for CGH data using the fused lasso

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

A modified Bayes information criterion with applications to the analysis of comparative genomic hybridization data

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

Continuous-index hidden Markov modelling of array CGH copy number data

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

A faster circular binary segmentation algorithm for the analysis of array CGH data

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

An isochore map of human chromosomes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

BioHMM: a heterogeneous hidden Markov model for segmenting array CGH data

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

Genomic regions exhibiting positive selection identified from dense genotype data

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

A comparison study: applying segmentation to array CGH data for downstream analyses

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

Genomic islands of speciation in Anopheles gambiae

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

Sarment: Python modules for HMM analysis and partitioning of sequences

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

GC composition of the human genome: in search of isochores

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

Circular binary segmentation for the analysis of array-based DNA copy number data

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

Probabilistic methods of identifying genes in prokaryotic genomes: connections to the HMM theory

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

Identification of conserved regulatory elements by comparative genome analysis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

Initial sequencing and comparative analysis of the mouse genome

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

Evidence for large domains of similarly expressed genes in the Drosophila genome

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

Non-coding RNAs: the architects of eukaryotic complexity

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

Misunderstandings about isochores. Part 1

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

Initial sequencing and analysis of the human genome

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

GeneMark.hmm: new solutions for gene finding

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

Hidden Markov models in computational biology. Applications to protein modeling

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

Construction of phylogenetic trees

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

Mining Bacillus subtilis chromosome heterogeneities using hidden Markov models

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

A Bayesian approach to discriminate between alternative DNA sequence segmentations

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

IsoFinder: computational prediction of isochores in genome sequences

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

Segmentation of yeast DNA using hidden Markov models.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

Bayesian inference on biopolymer models.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

Promoter structure of human sonic hedgehog gene.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

Stochastic models for heterogeneous DNA sequences

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

Determination of window size for analyzing DNA sequences

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

Model selection in Bayesian segmentation of multiple DNA alignments.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

Comparative testing of DNA segmentation algorithms using benchmark simulations

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

Multiple evolutionary rate classes in animal genome evolution.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

Delineating slowly and rapidly evolving fractions of the Drosophila genome.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

Discovering isochores by least-squares optimal segmentation.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

A heuristic Bayesian method for segmenting DNA sequence alignments and detecting evidence for recombination and gene conversion.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

Segmenting eukaryotic genomes with the Generalized Gibbs Sampler.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

A Bayesian approach to DNA sequence segmentation.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

Genome segmentation using piecewise constant intensity models and reversible jump MCMC.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

Applications of recursive segmentation to the analysis of DNA sequences.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

DNA segmentation through the Bayesian approach.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

SEGMENT: identifying compositional domains in DNA sequences.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

Computation of biopolymers: a general approach to different problems.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

A Sliding Window-Based Method to Detect Selective Constraints in Protein-Coding Genes and Its Application to RNA Viruses

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204429

A novel method to calculate the G+C content of genomic DNA sequences

3 December 2018

1 reference

12 December 2020

Identification of isochore boundaries in the human genome using the technique of wavelet multiresolution analysis

1 reference

12 December 2020

Compositional heterogeneity within and among isochores in mammalian genomes. I. CsCl and sequence analyses

1 reference

12 December 2020

Compositional segmentation and long-range fractal correlations in DNA sequences

1 reference

12 December 2020

10.1016/J.CSBJ.2014.08.003

Identifiers

DOI

1 reference

1 September 2017

1 reference

1 September 2017

1 reference

PMCID

4204429