Finding the missing honey bee genes: lessons learned from a genome upgrade (Q33637535)

28 July 2017

Finding the missing honey bee genes: lessons learned from a genome upgrade (English)

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28 July 2017

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Matthias Van Vaerenbergh

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Martin Beye

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Jennifer M Tsuruda

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Daniel B Weaver

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Charles W Whitfield

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Evgeny M Zdobnov

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Lan Zhang

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Dianhui Zhu

48

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3 June 2020

Honey Bee Genome Sequencing Consortium

50

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Francisco Camara

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language of work or name

English

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publication date

30 January 2014

1 reference

28 July 2017

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3 June 2020

volume

15

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page(s)

86

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https://scigraph.springernature.com/pub.10.1186/1471-2164-15-86

3 June 2020

exact match

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21 June 2018

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21 June 2018

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21 June 2018

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21 June 2018

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21 June 2018

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21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

The complete genome of an individual by massively parallel DNA sequencing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

Transposable elements and the evolution of regulatory networks

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

A unified classification system for eukaryotic transposable elements

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

Creating a honey bee consensus gene set

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

CDD: a conserved domain database for interactive domain family 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=4028053

Insights into social insects from the genome of the honeybee Apis mellifera

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

The chemoreceptor superfamily in the honey bee, Apis mellifera: expansion of the odorant, but not gustatory, receptor family

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

Exceptionally high levels of recombination across the honey bee 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=4028053

Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

Automatic annotation of eukaryotic genes, pseudogenes and promoters

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

Quantitative comparison of caste differences in honeybee hemolymph

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

WindowMasker: window-based masker for sequenced genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

Repbase Update, a database of eukaryotic repetitive elements

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

De novo identification of repeat families in large genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

PILER: identification and classification of genomic repeats

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

GMAP: a genomic mapping and alignment program for mRNA and EST 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=4028053

Automated generation of heuristics for biological sequence comparison

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

The ProDom database of protein domain families: more emphasis on 3D

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

Finishing the euchromatic sequence of 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=4028053

Large retrotransposon derivatives: abundant, conserved but nonautonomous retroelements of barley and related genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

PIRSF: family classification system at the Protein Information Resource

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

mreps: Efficient and flexible detection of tandem repeats in 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=4028053

GeneMerge—post-genomic analysis, data mining, and hypothesis testing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

Recent horizontal transfer of mellifera subfamily mariner transposons into insect lineages representing four different orders shows that selection acts only during horizontal transfer

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

Comparative gene prediction in human and mouse

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

The TIGRFAMs database of protein families

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

BLAT—The BLAST-Like Alignment Tool

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

Annotated expressed sequence tags and cDNA microarrays for studies of brain and behavior in the honey bee.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

Terminal-repeat retrotransposons in miniature (TRIM) are involved in restructuring plant genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

InterProScan--an integration platform for the signature-recognition methods in InterPro

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

Initial sequencing and analysis of 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=4028053

The Sequence of 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=4028053

A greedy algorithm for aligning 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=4028053

Gene ontology: tool for the unification of biology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

Tandem repeats finder: a program to analyze 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=4028053

Genome sequence of the nematode C. elegans: a platform for investigating biology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

Gapped BLAST and PSI-BLAST: a new generation of protein database search 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=4028053

The precursors of the bee venom constituents apamin and MCD peptide are encoded by two genes in tandem which share the same 3'-exon

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

Basic local alignment search tool

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

Rapid and sensitive sequence comparison with FASTP and FASTA

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

The 'effective number of codons' used in a gene

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

Differential expressions of nuclear proteomes between honeybee (Apis mellifera L.) Queen and Worker Larvae: a deep insight into caste pathway decisions.

21 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2F1471-2164-15-86

Proteome profile and lentiviral transduction of cultured honey bee (Apis mellifera L.) cells

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2F1471-2164-15-86

A universal classification of eukaryotic transposable elements implemented in Repbase.

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2F1471-2164-15-86

Using N-SCAN or TWINSCAN to predict gene structures in genomic DNA sequences.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

Detection of new transposable element families in Drosophila melanogaster and Anopheles gambiae genomes

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028053

EMBOSS opens up sequence analysis. European Molecular Biology Open Software Suite

30 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24479613

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2164-15-86

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24479613%20AND%20SRC:MED&resulttype=core&format=json

Dimensions Publication ID

3 June 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24479613%20AND%20SRC:MED&resulttype=core&format=json

3 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24479613%20AND%20SRC:MED&resulttype=core&format=json