First complete genome sequence in Arborophila and comparative genomics reveals the evolutionary adaptation of Hainan Partridge (Arborophila ardens)

[1]  Mosè Manni,et al.  BUSCO: Assessing Genome Assembly and Annotation Completeness. , 2019, Methods in molecular biology.

[2]  R. Nho,et al.  FoxM1-dependent RAD51 and BRCA2 signaling protects idiopathic pulmonary fibrosis fibroblasts from radiation-induced cell death , 2018, Cell Death & Disease.

[3]  Timothy B Sackton,et al.  Assembly and RNA‐free annotation of highly heterozygous genomes: The case of the thick‐billed murre (Uria lomvia) , 2018, Molecular ecology resources.

[4]  Canchao Yang,et al.  Breeding biology and novel reproductive behaviour in the Hainan Partridge (Arborophila ardens) , 2017, Avian Research.

[5]  Z. Lou,et al.  A phosphorylation–deubiquitination cascade regulates the BRCA2–RAD51 axis in homologous recombination , 2016, Genes & development.

[6]  Kun-Liang Guan,et al.  Mechanisms of Hippo pathway regulation , 2016, Genes & development.

[7]  H. Tsuda,et al.  Overexpression of denticleless E3 ubiquitin protein ligase homolog (DTL) is related to poor outcome in gastric carcinoma , 2015, Oncotarget.

[8]  Yang Liu,et al.  Revival of the genus Tropicoperdix Blyth 1859 (Phasianidae, Aves) using multilocus sequence data , 2015 .

[9]  Evgeny M. Zdobnov,et al.  BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..

[10]  Takamitsu A Kato,et al.  Caspase-3 promotes genetic instability and carcinogenesis. , 2015, Molecular cell.

[11]  Yang Liu,et al.  Was the exposed continental shelf a long-distance colonization route in the ice age? The Southeast Asia origin of Hainan and Taiwan partridges. , 2015, Molecular phylogenetics and evolution.

[12]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[13]  Jun Wang,et al.  Genome sequence of ground tit Pseudopodoces humilis and its adaptation to high altitude , 2013, Genome Biology.

[14]  Jian Wang,et al.  SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler , 2012, GigaScience.

[15]  Xinping Ye,et al.  Coupling Genetic and Species Distribution Models to Examine the Response of the Hainan Partridge (Arborophila ardens) to Late Quaternary Climate , 2012, PloS one.

[16]  Yan Cai,et al.  Extreme levels of hunting of birds in a remote village of Hainan Island, China , 2011, Bird Conservation International.

[17]  R. Durbin,et al.  Inference of human population history from individual whole-genome sequences. , 2011, Nature.

[18]  R. Durbin,et al.  Inference of Human Population History From Whole Genome Sequence of A Single Individual , 2011, Nature.

[19]  B. Stokke,et al.  Female Crowing and Differential Responses to Simulated Conspecific Intrusion in Male and Female Hainan Partridge (Arborophila ardens) , 2011, Zoological science.

[20]  M. Frith,et al.  Adaptive seeds tame genomic sequence comparison. , 2011, Genome research.

[21]  Walter Pirovano,et al.  BIOINFORMATICS APPLICATIONS , 2022 .

[22]  Yulong Yin,et al.  Integrating miRNA and mRNA expression profiles in response to heat stress-induced injury in rat small intestine , 2011, Functional & Integrative Genomics.

[23]  Kang Ning,et al.  The utility of mass spectrometry-based proteomic data for validation of novel alternative splice forms reconstructed from RNA-Seq data: a preliminary assessment , 2010, BMC Bioinformatics.

[24]  Ari Löytynoja,et al.  webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser , 2010, BMC Bioinformatics.

[25]  S. Berquist,et al.  Phylogeography and population genetic structure of the great leaf-nosed bat (Hipposideros armiger) in China. , 2010, The Journal of heredity.

[26]  Xinhai Li,et al.  Climate change induced range shifts of Galliformes in China. , 2010, Integrative zoology.

[27]  R. Murphy,et al.  A mitogenomic perspective on the ancient, rapid radiation in the Galliformes with an emphasis on the Phasianidae , 2010, BMC Evolutionary Biology.

[28]  Albert J. Vilella,et al.  The genome of a songbird , 2010, Nature.

[29]  F. Chan,et al.  Identification of retinoic acid-regulated nuclear matrix-associated protein as a novel regulator of gastric cancer , 2009, British Journal of Cancer.

[30]  Robert D. Finn,et al.  InterPro: the integrative protein signature database , 2008, Nucleic Acids Res..

[31]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[32]  Jonathan E. Allen,et al.  Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments , 2007, Genome Biology.

[33]  Ziheng Yang.  PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.

[34]  Keith Bradnam,et al.  CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes , 2007, Bioinform..

[35]  Yuki Moriya,et al.  KAAS: an automatic genome annotation and pathway reconstruction server , 2007, Nucleic Acids Res..

[36]  T. Hedderson,et al.  Phylogenetics, biogeography and classification of, and character evolution in, gamebirds (Aves: Galliformes): effects of character exclusion, data partitioning and missing data , 2006, Cladistics : the international journal of the Willi Hennig Society.

[37]  Hongkun Zheng,et al.  Detecting lineage-specific adaptive evolution of brain-expressed genes in human using rhesus macaque as outgroup. , 2006, Genomics.

[38]  Hui Zhang,et al.  L2DTL/CDT2 and PCNA Interact with p53 and Regulate p53 Polyubiquitination and Protein Stability through MDM2 and CUL4A/DDB1 Complexes , 2006, Cell cycle.

[39]  Burkhard Morgenstern,et al.  AUGUSTUS: ab initio prediction of alternative transcripts , 2006, Nucleic Acids Res..

[40]  I. Cousineau,et al.  BRCA2 regulates homologous recombination in response to DNA damage: implications for genome stability and carcinogenesis. , 2005, Cancer research.

[41]  Sébastien Carrère,et al.  The ProDom database of protein domain families: more emphasis on 3D , 2004, Nucleic Acids Res..

[42]  R. Durbin,et al.  GeneWise and Genomewise. , 2004, Genome research.

[43]  G. Hewitt.  Genetic consequences of climatic oscillations in the Quaternary. , 2004, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[44]  Peer Bork,et al.  SMART 4.0: towards genomic data integration , 2004, Nucleic Acids Res..

[45]  Robert S. Ledley,et al.  PIRSF: family classification system at the Protein Information Resource , 2004, Nucleic Acids Res..

[46]  C. Stoeckert,et al.  OrthoMCL: identification of ortholog groups for eukaryotic genomes. , 2003, Genome research.

[47]  Z. Zheng.  The current status and a conservation strategy for species of Galliformes in China , 2003, Biodiversity Science.

[48]  Maria Jesus Martin,et al.  The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 , 2003, Nucleic Acids Res..

[49]  Anushya Muruganujan,et al.  PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification , 2003, Nucleic Acids Res..

[50]  Ziheng Yang,et al.  Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci. , 2002, Genetics.

[51]  Amos Bairoch,et al.  PROSITE: A Documented Database Using Patterns and Profiles as Motif Descriptors , 2002, Briefings Bioinform..

[52]  Cyrus Chothia,et al.  SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments , 2002, Nucleic Acids Res..

[53]  Terri K. Attwood,et al.  PRINTS-S: the database formerly known as PRINTS , 2000, Nucleic Acids Res..

[54]  Gao Yu-ren.  Conservation status of endemic Galliformes on Hainan Island, China , 1998, Bird Conservation International.

[55]  David Posada,et al.  MODELTEST: testing the model of DNA substitution , 1998, Bioinform..

[56]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[57]  S. Karlin,et al.  Prediction of complete gene structures in human genomic DNA. , 1997, Journal of molecular biology.