(Q28604088)

Natascha May Thevasagayam

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Yu Huang

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He Zhang

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Vydianathan Ravi

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Marsel Kabilov

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László Orbán

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Jun Wang

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Yang Huanming

Huanming Yang

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Linsheng Song

Linsheng Song

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Stephen J. O'Brien

Stephen J O'Brien

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Zijun Xiong

Zijun Xiong

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Xueyan Shen

Xueyan Shen

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author name string

Chao Bian

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Yinchang Hu

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Inna S Kuznetsova

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Xidong Mu

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Ying Sun

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Xinxin You

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Jia Li

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Xiaofeng Li

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Ying Qiu

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Boon-Hui Tay

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Aleksey S Komissarov

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Vladimir Trifonov

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Alexey Tupikin

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Jianren Luo

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Yi Liu

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Hongmei Song

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Chao Liu

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Xuejie Wang

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Dangen Gu

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Yexin Yang

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Wujiao Li

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Gianluca Polgar

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Guangyi Fan

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Peng Zeng

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Zhujing Tang

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Chao Peng

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Zhiqiang Ruan

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Hui Yu

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Jieming Chen

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Mingjun Fan

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Min Wang

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Xiaomeng Zhao

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Guojun Hu

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Jian Wang

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Xun Xu

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Gangchun Xu

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Pao Xu

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Junmin Xu

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Qiong Shi

Creative Commons Attribution 4.0 International

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language of work or name

English

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publication date

19 April 2016

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24501

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start time

1 April 2016

1 reference

April 2022 Public Data File from Crossref

copyrighted

0 references

describes a project that uses

edgeR

edgeR

1 reference

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

cites work

Evolution of the fish heart by sub/neofunctionalization of an elastin gene.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Whole Genome Sequencing of the Asian Arowana (Scleropages formosus) Provides Insights into the Evolution of Ray-Finned Fishes

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Enigmatic orthology relationships between Hox clusters of the African butterfly fish and other teleosts following ancient whole-genome duplication

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs)

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

The tree of life and a new classification of bony fishes

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Resolution of ray-finned fish phylogeny and timing of diversification

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Primitive duplicate Hox clusters in the European eel's genome

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Full-length transcriptome assembly from RNA-Seq data without a reference genome

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Divergence time of the two regional medaka populations in Japan as a new time scale for comparative genomics of vertebrates

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

The Sequence Alignment/Map format and SAMtools

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

SOAP2: an improved ultrafast tool for short read alignment

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

TopHat: discovering splice junctions with RNA-Seq

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Assessing the gene space in draft genomes

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

A new look at the evolution of avian sex chromosomes

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

The medaka draft genome and insights into vertebrate genome evolution

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Inparanoid: a comprehensive database of eukaryotic orthologs

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

17 March 2017

GeneWise and Genomewise

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

MrBayes 3: Bayesian phylogenetic inference under mixed models

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

BLAT—The BLAST-Like Alignment Tool

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

A new mathematical model for relative quantification in real-time RT-PCR

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Gene ontology: tool for the unification of biology

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

KEGG: kyoto encyclopedia of genes and genomes

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Tandem repeats finder: a program to analyze DNA sequences

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

PAML: a program package for phylogenetic analysis by maximum likelihood

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Prediction of complete gene structures in human genomic DNA

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Circos: an information aesthetic for comparative genomics

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide 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=4835728

Repbase Update, a database of eukaryotic repetitive elements

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

CONSEL: for assessing the confidence of phylogenetic tree selection

7 April 2017

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

7 April 2017

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

28 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000.

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

The zebrafish reference genome sequence and its relationship to the human genome

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Differential analysis of gene regulation at transcript resolution with RNA-seq

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Automatic clustering of orthologs and in-paralogs from pairwise species comparisons

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

De novo identification of repeat families in large genomes

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Neofunctionalization of Androgen Receptor by Gain-of-Function Mutations in Teleost Fish Lineage.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Turnover of Sex Chromosomes in Celebensis Group Medaka Fishes.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

The evolution of cichlid fish egg-spots is linked with a cis-regulatory change

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

The first transcriptome and genetic linkage map for Asian arowana.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

The sexually dimorphic on the Y-chromosome gene (sdY) is a conserved male-specific Y-chromosome sequence in many salmonids.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Expansion of microsatellites on evolutionary young Y chromosome.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

The key role of repeated DNAs in sex chromosome evolution in two fish species with ZW sex chromosome system

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

i-ADHoRe 3.0--fast and sensitive detection of genomic homology in extremely large data sets

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Small but mighty: the evolutionary dynamics of W and Y sex chromosomes.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

SyMAP v3.4: a turnkey synteny system with application to plant genomes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Using RepeatMasker to identify repetitive elements in genomic sequences

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Adaptive sequence evolution in a color gene involved in the formation of the characteristic egg-dummies of male haplochromine cichlid fishes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

AUGUSTUS: ab initio prediction of alternative transcripts

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Developmental roles of pufferfish Hox clusters and genome evolution in ray-fin fish

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Hox cluster duplications and the opportunity for evolutionary novelties

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Hox genes and chordate evolution.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

The origin and function of the mammalian Y chromosome and Y-borne genes--an evolving understanding.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Creating a honey bee consensus gene set

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

A mitogenomic perspective on the basal teleostean phylogeny: resolving higher-level relationships with longer DNA sequences

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

A 28S rRNA-based phylogeny of the gnathostomes: first steps in the analysis of conflict and congruence with morphologically based cladograms

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes

3 June 2018

1 reference

Selecting Question-Specific Genes to Reduce Incongruence in Phylogenomics: A Case Study of Jawed Vertebrate Backbone Phylogeny

21 January 2018

1 reference

Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of the "ancient fish".

21 January 2018

1 reference

The sister-group of Teleostei: consensus and disagreements

21 January 2018

1 reference

Reciprocal gene loss between Tetraodon and zebrafish after whole genome duplication in their ancestor

21 January 2018

1 reference

Rearrangement rate following the whole-genome duplication in teleosts.

21 January 2018

1 reference

Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle

21 January 2018

1 reference

A primitive Y chromosome in papaya marks incipient sex chromosome evolution

21 January 2018

1 reference

Mitogenomic evidence for the monophyly of elopomorph fishes (Teleostei) and the evolutionary origin of the leptocephalus larva

21 January 2018

1 reference

High‐Resolution Cell Cycle and DNA Ploidy Analysis in Tissue Samples

21 January 2018

1 reference

Cutadapt removes adapter sequences from high-throughput sequencing reads

21 January 2018

1 reference

The ontogenetic development of egg-spots in the haplochromine cichlid fish Astatotilapia burtoni

21 January 2018

1 reference

Hoxb-5 is expressed in gill arch 5 during pharyngeal arch development of flounder Paralichthys olivaceus embryos.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4835728

Conserved 5S and variable 45S rDNA chromosomal localisation revealed by FISH in Astyanax scabripinnis (Pisces, Characidae)

27 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27089831

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/SREP24501

1 reference

Dimensions Publication ID

1043622728

0 references

1 reference

1 reference

PubMed publication ID

27089831

1 reference