(Q22065753)

4

Min

Pan

1 reference

7 February 2023

Paul Shannon

7

Paul

Shannon

1 reference

7 February 2023

Yulun Chiu

8

Yulun

Chiu

1 reference

7 February 2023

Rueyhung Sting Weng

9

Rueyhung Sting

Weng

1 reference

7 February 2023

Rueichi Richie Gan

10

Rueichi Richie

Gan

1 reference

7 February 2023

Pingliang Hung

11

Pingliang

Hung

1 reference

7 February 2023

Shailesh V Date

12

Shailesh V

describes a project that uses

Date

1 reference

7 February 2023

language of work or name

English

0 references

publication date

November 2004

0 references

published in

Genome Research

0 references

volume

14

0 references

page(s)

2221-34

0 references

issue

11

0 references

Cytoscape

1 reference

Europe PubMed Central

9 June 2022

https://europepmc.org/search?query=(METHODS:'Cytoscape')

inferred from PubMed Central ID database lookup

cites work

Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1

1 reference

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Low-pass sequencing for microbial comparative genomics

19 March 2017

1 reference

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Cytoscape: a software environment for integrated models of biomolecular interaction networks

19 March 2017

1 reference

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Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ

19 March 2017

1 reference

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Genome sequence of Halobacterium species NRC-1

19 March 2017

1 reference

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The use of gene clusters to infer functional coupling

19 March 2017

1 reference

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Analyzing genomes with cumulative skew diagrams

19 March 2017

1 reference

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

19 March 2017

1 reference

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

19 March 2017

1 reference

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Crystal structure of the bromide-bound D85S mutant of bacteriorhodopsin: principles of ion pumping

19 March 2017

1 reference

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Crystal structure of the D85S mutant of bacteriorhodopsin: model of an O-like photocycle intermediate

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Crystal Structure of Sensory Rhodopsin II at 2.4 Angstroms: Insights into Color Tuning and Transducer Interaction

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

The Pfam protein families database.

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Improved microbial gene identification with GLIMMER

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Consed: a graphical tool for sequence finishing

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Base-calling of automated sequencer traces using phred. II. Error probabilities

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Base-calling of automated sequencer traces using phred. I. Accuracy assessment

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Selfish operons: the evolutionary impact of gene clustering in prokaryotes and eukaryotes

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Detecting protein function and protein-protein interactions from genome sequences

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

A hidden Markov model for predicting transmembrane helices in protein sequences

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

PAS domains: internal sensors of oxygen, redox potential, and light

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Automated prediction of CASP-5 structures using the Robetta server.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

An Archaeal Chromosomal Autonomously Replicating Sequence Element from an Extreme Halophile,Halobacteriumsp. Strain NRC-1

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Repair of UV damage in Halobacterium salinarum

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Cyanobacterial circadian clockwork: roles of KaiA, KaiB and the kaiBC promoter in regulating KaiC

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Archaeal DNA replication: spotlight on a rapidly moving field

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Purification, characterization, and genetic analysis of Cu-containing dissimilatory nitrite reductase from a denitrifying halophilic archaeon, Haloarcula marismortui

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Homologous recombination as a mechanism for genome rearrangements: environmental and genetic effects

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Bacterial cryptochrome and photolyase: characterization of two photolyase-like genes of Synechocystis sp. PCC6803

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Chromosome replication, nucleoid segregation and cell division in archaea

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

12 September 2017

Transcription in Archaea

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Cryptochromes: blue light receptors for plants and animals

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Snapshot of a large dynamic replicon in a halophilic archaeon: megaplasmid or minichromosome?

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Archaea and the cell cycle

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Transcription analysis of two disparate rRNA operons in the halophilic archaeon Haloarcula marismortui

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

The GAF domain: an evolutionary link between diverse phototransducing proteins.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Fermentative arginine degradation in Halobacterium salinarium (formerly Halobacterium halobium): genes, gene products, and transcripts of the arcRACB gene cluster

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

The primary structure of halocyanin, an archaeal blue copper protein, predicts a lipid anchor for membrane fixation.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

An expert system for processing sequence homology data.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Light guides. Directional energy transfer in a photosynthetic antenna

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Metabolic regulation including anaerobic metabolism in Paracoccus denitrificans

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Ureases of extreme halophiles of the genus Haloarcula with a unique structure of gene cluster

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Sequence heterogeneity between the two genes encoding 16S rRNA from the halophilic archaebacterium Haloarcula marismortui

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Systems approaches applied to the study of Saccharomyces cerevisiae and Halobacterium sp.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Predicting functional linkages from gene fusions with confidence.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Multiple replication origins of the archaeon Halobacterium species NRC-1.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

A powerful non-homology method for the prediction of operons in prokaryotes.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Sequence and electron paramagnetic resonance analyses of nitrate reductase NarGH from a denitrifying halophilic euryarchaeote Haloarcula marismortui

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

GRIMM: genome rearrangements web server

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Purification and characterization of dissimilatory nitrate reductase from a denitrifying halophilic archaeon, Haloarcula marismortui

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Expression and heat-responsive regulation of a TFIIB homologue from the archaeon Haloferax volcanii.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=525680

Is gene expression in Halobacterium NRC-1 regulated by multiple TBP and TFB transcription factors?

29 November 2018

1 reference

12 December 2020

Detailed physical map and set of overlapping clones covering the genome of the archaebacterium Haloferax volcanii DS2

1 reference

12 December 2020

Striking sequence similarity over almost 100 kilobases of human and mouse T–cell receptor DNA

1 reference

12 December 2020

De Novo Prediction of Three-dimensional Structures for Major Protein Families

1 reference

12 December 2020

Identifiers

DOI

10.1101/GR.2700304

1 reference

release_45ev7km4w5etznoytsm3ryb5ci

626464

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/45ev7km4w5etznoytsm3ryb5ci

24 November 2022

mapped directly with Wikidata item

626464

1 reference

1 reference

1 reference