(Q34007303)

30 July 2017

title

The draft assembly of the radically organized Stylonychia lemnae macronuclear genome (English)

1 reference

30 July 2017

Mariusz Nowacki

7

0 references

Jan Postberg

object named as

Jan Postberg

3

0 references

Estienne C. Swart

8

object named as

Estienne C Swart

1 reference

30 July 2017

Samuel H Aeschlimann

1

1 reference

30 July 2017

Franziska Jönsson

2

1 reference

30 July 2017

Nicholas A Stover

4

1 reference

30 July 2017

Robert L Petera

5

1 reference

30 July 2017

Hans-Joachim Lipps

6

1 reference

30 July 2017

publication date

20 June 2014

1 reference

Genome Biology and Evolution

30 July 2017

published in

1 reference

30 July 2017

volume

6

1 reference

30 July 2017

issue

7

1 reference

30 July 2017

page(s)

1707-1723

1 reference

describes a project that uses

30 July 2017

MIRA

object named as

Mira

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

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A domesticated PiggyBac transposase interacts with heterochromatin and catalyzes reproducible DNA elimination in Tetrahymena

5 July 2018

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LIA5 is required for nuclear reorganization and programmed DNA rearrangements occurring during tetrahymena macronuclear differentiation

5 July 2018

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Infernal 1.1: 100-fold faster RNA homology searches

5 July 2018

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Impaired replication elongation in Tetrahymena mutants deficient in histone H3 Lys 27 monomethylation

5 July 2018

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GAGE-B: an evaluation of genome assemblers for bacterial organisms

5 July 2018

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Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

5 July 2018

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A permissive chromatin structure is adopted prior to site-specific DNA demethylation of developmentally expressed genes involved in macronuclear differentiation

5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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5 July 2018

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Characterization and taxonomic validity of the ciliate Oxytricha trifallax (Class Spirotrichea) based on multiple gene sequences: limitations in identifying genera solely by morphology

5 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

The Oxytricha trifallax mitochondrial genome

5 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

The Pfam protein families database

5 July 2018

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Transgenerational epigenetic instability is a source of novel methylation variants

5 July 2018

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The Pot1a-associated proteins Tpt1 and Pat1 coordinate telomere protection and length regulation in Tetrahymena.

5 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

Exploiting Oxytricha trifallax nanochromosomes to screen for non-coding RNA genes

5 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

SHRiMP2: sensitive yet practical SHort Read Mapping

5 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

Adaptive seeds tame genomic sequence comparison

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

RNA-mediated epigenetic regulation of DNA copy number

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

RNA-dependent control of gene amplification

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

The evolutionary history of histone H3 suggests a deep eukaryotic root of chromatin modifying mechanisms

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

A domesticated piggyBac transposase plays key roles in heterochromatin dynamics and DNA cleavage during programmed DNA deletion in Tetrahymena thermophila

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

Parameters for accurate genome alignment

5 July 2018

1 reference

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5 July 2018

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BLAST+: architecture and applications

5 July 2018

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Transgenerational Epigenetic Inheritance: Prevalence, Mechanisms, and Implications for the Study of Heredity and Evolution

5 July 2018

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G-quadruplex structures: in vivo evidence and function

5 July 2018

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SHRiMP: accurate mapping of short color-space reads

5 July 2018

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Fast and accurate short read alignment with Burrows-Wheeler transform

5 July 2018

1 reference

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Estimating maximum likelihood phylogenies with PhyML.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

A functional role for transposases in a large eukaryotic genome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

Infernal 1.0: inference of RNA alignments

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

ABySS: a parallel assembler for short read sequence data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

Spatial and temporal plasticity of chromatin during programmed DNA-reorganization in Stylonychia macronuclear development.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

High-throughput functional annotation and data mining with the Blast2GO suite

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

Velvet: algorithms for de novo short read assembly using de Bruijn graphs

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

Quickly evolving histones, nucleosome stability and chromatin folding: all about histone H2A.Bbd

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

Phylogeny of the Stichotrichia (Ciliophora; Spirotrichea) reconstructed with nuclear small subunit rRNA gene sequences: discrepancies and accordances with morphological data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

Extreme genomic variation in a natural population

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

TPP1 is a homologue of ciliate TEBP-beta and interacts with POT1 to recruit telomerase

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

Tetrahymena POT1a regulates telomere length and prevents activation of a cell cycle checkpoint

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

AUGUSTUS: ab initio prediction of alternative transcripts

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

Tetrahymena Genome Database (TGD): a new genomic resource for Tetrahymena thermophila research.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

A microarray analysis of developmentally regulated genes during macronuclear differentiation in the stichotrichous ciliate Stylonychia lemnae

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

InterProScan: protein domains identifier

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

Macronuclear duplication in the ciliated protozoan Euplotes.

5 July 2018

1 reference

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Rfam: an RNA family database

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

The generic genome browser: a building block for a model organism system database

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

Regulation of transcription by H1 phosphorylation in Tetrahymena is position independent and requires clustered sites

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

BLAT—The BLAST-Like Alignment Tool

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

Clustering of highly homologous sequences to reduce the size of large protein databases

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

Genome gymnastics: unique modes of DNA evolution and processing in ciliates

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

CAP3: A DNA sequence assembly program

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

Several highly divergent histone H3 genes are present in the hypotrichous ciliate Stylonychia lemnae

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence

5 July 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

5 July 2018

https://api.crossref.org/works/10.1093%2FGBE%2FEVU139

Linker histone H1 regulates specific gene expression but not global transcription in vivo

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

Cloning and analysis of the macronuclear gene for histone H1 from Euplotes eurystomus

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

Four distinct and unusual linker proteins in a mitotically dividing nucleus are derived from a 71-kilodalton polyprotein, lack p34cdc2 sites, and contain protein kinase A sites

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

The DNA of ciliated protozoa

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

The terminal organization of macronuclear DNA in Oxytricha fallax

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

Higher order DNA structure in macronuclear chromatin of the hypotrichous ciliate Oxytricha nova

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

Physical structure of gene-sized chromatin from the protozoan Oxytricha

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

All gene-sized DNA molecules in four species of hypotrichs have the same terminal sequence and an unusual 3' terminus

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

Proteolytic processing of h1-like histones in chromatin: a physiologically and developmentally regulated event in Tetrahymena micronuclei

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

Synthesis and decomposition of nucleic acids during macronuclear development in Stylonychia mytilus (Protozoa, Ciliata)

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

Histone F1 of Tetrahymena macronuclei: unique electrophoretic properties and phosphorylation of F1 in an amitotic nucleus

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

An intervening sequence in an unusual histone H1 gene of Tetrahymena thermophila

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

Multiple sequence versions of the Oxytricha fallax 81-MAC alternate processing family

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

Mobile elements bounded by C4A4 telomeric repeats in Oxytricha fallax

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

The two macronuclear histone H4 genes of the hypotrichous ciliate Stylonychia lemnae

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

Overamplification of macronuclear linear DNA molecules during prolonged vegetative growth of Oxytricha nova

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

Absence of histone F1 in a mitotically dividing, genetically inactive nucleus

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

Histones and other basic nuclear proteins in genetically active and genetically inactive nuclei of the ciliate, Oxytricha sp

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

Free genes for rRNAs in the macronuclear genome of the ciliate Stylonychia mytilus

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4122937

PiggyMac, a domesticated piggyBac transposase involved in programmed genome rearrangements in the ciliate Paramecium tetraurelia

5 July 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVU139

Space-efficient and exact de Bruijn graph representation based on a Bloom filter

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVU139

Modeling senescence in hypotrichous ciliates.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVU139

Dramatic diversity of ciliate histone H4 genes revealed by comparisons of patterns of substitutions and paralog divergences among eukaryotes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVU139

RNA-dependent genome processing during nuclear differentiation: the model systems of stichotrichous ciliates

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVU139

Tetrahymena histone H1. Isolation and amino acid sequence lacking the central hydrophobic domain conserved in other H1 histones

21 January 2018

1 reference

12 December 2020

The development of the macronucleus in the ciliated protozoan Stylonychia mytilus

1 reference

12 December 2020

Phosphorylation of linker histone H1 regulates gene expression in vivo by creating a charge patch

1 reference

12 December 2020

The organization of macronuclear rDNA molecules of four hypotrichous ciliated protozoans

1 reference

12 December 2020

Copy number variations of 11 macronuclear chromosomes and their gene expression in Oxytricha trifallax

1 reference

12 December 2020

DNase I hypersensitivity of the terminal inverted repeat DNA sequences in the macronucleus of the ciliate Stylonychia mytilus

1 reference

12 December 2020

Inverted terminal repeat sequence in the macronuclear DNA of Stylonychia pustulata

1 reference

12 December 2020

Phosphorylation of linker histone H1 regulates gene expression in vivo by mimicking H1 removal

1 reference

12 December 2020

Isolation and mapping of the rRNA genes in the macronucleus of Oxytricha fallax

1 reference

12 December 2020

Morphology and development of the macronuclei of the ciliates Stylonychia mytilus and Euplotes aediculatus

1 reference

12 December 2020

Arrangement of coding and non-coding sequences in the DNA molecules coding for rRNAs in Oxytricha sp. DNA of ciliated protozoa. VII

1 reference

12 December 2020

Synthesis of pre-rRNA and mRNA is directed to a chromatin-poor compartment in the macronucleus of the spirotrichous ciliate Stylonychia lemnae

1 reference

12 December 2020

Genome architecture drives protein evolution in ciliates

1 reference

12 December 2020

An H1-like protein from the macronucleus of Euplotes eurystomus

1 reference

12 December 2020

Telomere proteins: specific recognition and protection of the natural termini of Oxytricha macronuclear DNA

1 reference

12 December 2020

[Draft macronuclear genome of a ciliate Euplotes crassus]

1 reference

12 December 2020

Identifiers

DOI

10.1093/GBE/EVU139

1 reference

30 July 2017

1 reference

30 July 2017

1 reference