Unravelling the genomic features, phylogeny and genetic basis of tooth ontogenesis in Characiformes through analysis of four genomes

Fibronectin-loaded Collagen/Gelatin Hydrogel Is a Potent Signaling Biomaterial for Dental Pulp Regeneration

(2021) Maria Luísa Leite et al.   JOURNAL OF ENDODONTICS

Chromosome Fusion Affects Genetic Diversity and Evolutionary Turnover of Functional Loci but Consistently Depends on Chromosome Size

(2021) Francesco Cicconardi et al.   MOLECULAR BIOLOGY AND EVOLUTION

TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads

(2020) Mengyang Xu et al.   GigaScience

Initial data release and announcement of the 10,000 Fish Genomes Project (Fish10K)

(2020) Guangyi Fan et al.   GigaScience

MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization

(2019) Guanliang Meng et al.   NUCLEIC ACIDS RESEARCH

Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly

(2019) Ou Wang et al.   GENOME RESEARCH

Chromosomal‐level assembly of Takifugu obscurus (Abe, 1949) genome using third‐generation DNA sequencing and Hi‐C analysis

(2019) Seunghyun Kang et al.   Molecular Ecology Resources

Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data

(2018) Lily C. Hughes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A draft genome of the striped catfish, Pangasianodon hypophthalmus, for comparative analysis of genes relevant to development and a resource for aquaculture improvement

(2018) Oanh T. P. Kim et al.   BMC GENOMICS

Phylogenomic incongruence, hypothesis testing, and taxonomic sampling: The monophyly of characiform fishes

(2018) Ricardo Betancur‐R. et al.   EVOLUTION

SCPP Genes and Their Relatives in Gar: Rapid Expansion of Mineralization Genes in Osteichthyans

(2017) Kazuhiko Kawasaki et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Phylogenomic Systematics of Ostariophysan Fishes: Ultraconserved Elements Support the Surprising Non-Monophyly of Characiformes

(2017) Prosanta Chakrabarty et al.   SYSTEMATIC BIOLOGY

SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data

(2017) Yuxin Chen et al.   GigaScience

First Chromosomal Analysis in Hepsetidae (Actinopterygii, Characiformes): Insights into Relationship between African and Neotropical Fish Groups

(2017) Pedro C. Carvalho et al.   Frontiers in Genetics

Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life

(2017) Dahiana Arcila et al.   Nature Ecology & Evolution

Mutation of KREMEN1, a modulator of Wnt signaling, is responsible for ectodermal dysplasia including oligodontia in Palestinian families

(2016) Yasmin A Issa et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

Fish Karyome version 2.1: a chromosome database of fishes and other aquatic organisms

(2016) Naresh Sahebrao Nagpure et al.   Database-The Journal of Biological Databases and Curation

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

DSPP Is Essential for Normal Development of the Dental-Craniofacial Complex

(2015) Y. Chen et al.   JOURNAL OF DENTAL RESEARCH

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Convergent Evolution within an Adaptive Radiation of Cichlid Fishes

(2012) Moritz Muschick et al.   CURRENT BIOLOGY

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Resolution of ray-finned fish phylogeny and timing of diversification

(2012) T. J. Near et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) Ruibang Luo et al.   GigaScience

Phylogenetic relationships within the speciose family Characidae (Teleostei: Ostariophysi: Characiformes) based on multilocus analysis and extensive ingroup sampling

(2011) Claudio Oliveira et al.   BMC EVOLUTIONARY BIOLOGY

The SCPP Gene Family and the Complexity of Hard Tissues in Vertebrates

(2011) Kazuhiko Kawasaki   CELLS TISSUES ORGANS

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Weighted parsimony phylogeny of the family Characidae (Teleostei: Characiformes)

(2009) J. Marcos Mirande   CLADISTICS

The SCPP gene repertoire in bony vertebrates and graded differences in mineralized tissues

(2009) Kazuhiko Kawasaki   DEVELOPMENT GENES AND EVOLUTION

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

InterPro: the integrative protein signature database

(2008) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

Fusion and Fission of Genes Define a Metric between Fungal Genomes

(2008) Pascal Durrens et al.   PLoS Computational Biology