The birth of a human-specific neural gene by incomplete duplication and gene fusion

[1]  C. Baker,et al.  The evolution and population diversity of human-specific segmental duplications , 2017, Nature Ecology &Evolution.

[2]  Evan E Eichler,et al.  Human adaptation and evolution by segmental duplication. , 2016, Current opinion in genetics & development.

[3]  Lior Pachter,et al.  Near-optimal probabilistic RNA-seq quantification , 2016, Nature Biotechnology.

[4]  H. Mefford,et al.  Clinical phenotype of the recurrent 1q21.1 copy-number variant , 2015, Genetics in Medicine.

[5]  Gabor T. Marth,et al.  An integrated map of structural variation in 2,504 human genomes , 2015, Nature.

[6]  Bradley P. Coe,et al.  Global diversity, population stratification, and selection of human copy-number variation , 2015, Science.

[7]  Janet Kelso,et al.  Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion , 2015, Science.

[8]  Alessandro Vullo,et al.  Ensembl 2015 , 2014, Nucleic Acids Res..

[9]  Heng Li,et al.  Genome sequence of a 45,000-year-old modern human from western Siberia , 2014, Nature.

[10]  Kali T. Witherspoon,et al.  Recurrent de novo mutations implicate novel genes underlying simplex autism risk , 2014, Nature Communications.

[11]  Peter H. Sudmant,et al.  Palindromic GOLGA8 core duplicons promote chromosome 15q13.3 microdeletion and evolutionary instability , 2014, Nature Genetics.

[12]  Akash Kumar,et al.  MIPgen: optimized modeling and design of molecular inversion probes for targeted resequencing , 2014, Bioinform..

[13]  Kali T. Witherspoon,et al.  Refining analyses of copy number variation identifies specific genes associated with developmental delay , 2014, Nature Genetics.

[14]  Faraz Hach,et al.  mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications , 2014, Nucleic Acids Res..

[15]  Mark J. P. Chaisson,et al.  Reconstructing complex regions of genomes using long-read sequencing technology , 2014, Genome research.

[16]  Bonnie Berger,et al.  Ancient human genomes suggest three ancestral populations for present-day Europeans , 2013, Nature.

[17]  T. Graves,et al.  Finished sequence and assembly of the DUF1220-rich 1q21 region using a haploid human genome , 2014, BMC Genomics.

[18]  Koichiro Tamura,et al.  MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. , 2013, Molecular biology and evolution.

[19]  M. Long,et al.  New genes as drivers of phenotypic evolution , 2013, Nature Reviews Genetics.

[20]  M. Long,et al.  New genes as drivers of phenotypic evolution , 2013, Nature Reviews Genetics.

[21]  Carl Baker,et al.  Evolution and diversity of copy number variation in the great ape lineage , 2013, Genome research.

[22]  Alex P. Reynolds,et al.  Genome-scale mapping of DNase I hypersensitivity. , 2013, Current protocols in molecular biology.

[23]  Arcadi Navarro,et al.  Great ape genetic diversity and population history , 2013, Nature.

[24]  Jay Shendure,et al.  Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation , 2013, Genome research.

[25]  Ellen T. Gelfand,et al.  The Genotype-Tissue Expression (GTEx) project , 2013, Nature Genetics.

[26]  L. Maquat,et al.  Rules that govern UPF1 binding to mRNA 3′ UTRs , 2013, Proceedings of the National Academy of Sciences.

[27]  Bradley P. Coe,et al.  Refinement and discovery of new hotspots of copy-number variation associated with autism spectrum disorder. , 2013, American journal of human genetics.

[28]  Philip L. F. Johnson,et al.  The complete genome sequence of a Neanderthal from the Altai Mountains , 2013 .

[29]  Bradley P. Coe,et al.  Multiplex Targeted Sequencing Identifies Recurrently Mutated Genes in Autism Spectrum Disorders , 2012, Science.

[30]  J. Sikela,et al.  Evolution of genetic and genomic features unique to the human lineage , 2012, Nature Reviews Genetics.

[31]  Adrian W. Briggs,et al.  A High-Coverage Genome Sequence from an Archaic Denisovan Individual , 2012, Science.

[32]  M. Hurles,et al.  Recessive HYDIN mutations cause primary ciliary dyskinesia without randomization of left-right body asymmetry. , 2012, American journal of human genetics.

[33]  Nathan C. Sheffield,et al.  The accessible chromatin landscape of the human genome , 2012, Nature.

[34]  Bronwen L. Aken,et al.  GENCODE: The reference human genome annotation for The ENCODE Project , 2012, Genome research.

[35]  Peter H. Sudmant,et al.  Evolution of Human-Specific Neural SRGAP2 Genes by Incomplete Segmental Duplication , 2012, Cell.

[36]  Anirvan Ghosh,et al.  Inhibition of SRGAP2 Function by Its Human-Specific Paralogs Induces Neoteny during Spine Maturation , 2012, Cell.

[37]  Philip L. F. Johnson,et al.  Genetic history of an archaic hominin group from Denisova Cave in Siberia , 2010, Nature.

[38]  Peter H. Sudmant,et al.  Diversity of Human Copy Number Variation and Multicopy Genes , 2010, Science.

[39]  Faraz Hach,et al.  mrsFAST: a cache-oblivious algorithm for short-read mapping , 2010, Nature Methods.

[40]  David C. Schwartz,et al.  A large, complex structural polymorphism at 16p12.1 underlies microdeletion disease risk , 2010, Nature Genetics.

[41]  Jin Jun,et al.  Duplication Mechanism and Disruptions in Flanking Regions Determine the Fate of Mammalian Gene Duplicates , 2009, J. Comput. Biol..

[42]  Arcadi Navarro,et al.  A burst of segmental duplications in the genome of the African great ape ancestor , 2009, Nature.

[43]  P. Stankiewicz,et al.  Recurrent reciprocal 1q21.1 deletions and duplications associated with microcephaly or macrocephaly and developmental and behavioral abnormalities , 2008, Nature Genetics.

[44]  C. Baker,et al.  Recurrent rearrangements of chromosome 1q21.1 and variable pediatric phenotypes. , 2008, The New England journal of medicine.

[45]  M. Sanderson,et al.  Mutations in Hydin impair ciliary motility in mice , 2008, The Journal of cell biology.

[46]  E. Eichler,et al.  Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution , 2007, Nature Genetics.

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

[48]  G. Witman,et al.  Chlamydomonas reinhardtii hydin is a central pair protein required for flagellar motility , 2007, The Journal of cell biology.

[49]  K. Gull,et al.  The hydrocephalus inducing gene product, Hydin, positions axonemal central pair microtubules , 2007, BMC Biology.

[50]  A. Sehara-Fujisawa,et al.  Bmc Biology the Vertebrate Phylotypic Stage and an Early Bilaterian-related Stage in Mouse Embryogenesis Defined by Genomic Information , 2007 .

[51]  J. Weber,et al.  A 360-kb interchromosomal duplication of the human HYDIN locus. , 2006, Genomics.

[52]  Gerald J Wyckoff,et al.  Human Lineage–Specific Amplification, Selection, and Neuronal Expression of DUF1220 Domains , 2006, Science.

[53]  E. Eichler,et al.  Primate segmental duplications: crucibles of evolution, diversity and disease , 2006, Nature Reviews Genetics.

[54]  F. Speleman,et al.  A novel gene family NBPF: intricate structure generated by gene duplications during primate evolution. , 2005, Molecular biology and evolution.

[55]  E. Eichler,et al.  Segmental duplications and copy-number variation in the human genome. , 2005, American journal of human genetics.

[56]  M. Kimura.  A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences , 1980, Journal of Molecular Evolution.

[57]  P. Stankiewicz,et al.  Serial segmental duplications during primate evolution result in complex human genome architecture. , 2004, Genome research.

[58]  J. Sikela,et al.  Lineage-Specific Gene Duplication and Loss in Human and Great Ape Evolution , 2004, PLoS biology.

[59]  N. Nomura,et al.  Complete sequencing and characterization of 21,243 full-length human cDNAs , 2004, Nature Genetics.

[60]  Joseph P. Bielawski,et al.  Maximum likelihood methods for detecting adaptive evolution after gene duplication , 2004, Journal of Structural and Functional Genomics.

[61]  M. Robinson,et al.  Congenital hydrocephalus in hy3 mice is caused by a frameshift mutation in Hydin, a large novel gene. , 2003, Human molecular genetics.

[62]  G. Glazko,et al.  Estimation of divergence times for major lineages of primate species. , 2003, Molecular biology and evolution.

[63]  Ziheng Yang,et al.  Maximum likelihood methods for detecting adaptive evolution after gene duplication. Gene and Genome Duplications and the Origin of Novel Gene Functions , 2003 .

[64]  M. Adams,et al.  Recent Segmental Duplications in the Human Genome , 2002, Science.

[65]  Tom H. Pringle,et al.  The human genome browser at UCSC. , 2002, Genome research.

[66]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[67]  M. Lynch,et al.  The evolutionary fate and consequences of duplicate genes. , 2000, Science.

[68]  J. Lupski.  Genomic disorders: structural features of the genome can lead to DNA rearrangements and human disease traits. , 1998, Trends in genetics : TIG.

[69]  J. D. Parsons,et al.  Miropeats: graphical DNA sequence comparisons , 1995, Comput. Appl. Biosci..

[70]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[71]  M. Kozak.  Structural features in eukaryotic mRNAs that modulate the initiation of translation. , 1991, The Journal of biological chemistry.

[72]  M. Kozak.  The scanning model for translation: an update , 1989, The Journal of cell biology.

[73]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[74]  M. Nei,et al.  Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. , 1986, Molecular biology and evolution.

[75]  J. Felsenstein.  CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP , 1985, Evolution; international journal of organic evolution.

[76]  Dr. Susumu Ohno.  Evolution by Gene Duplication , 1970, Springer Berlin Heidelberg.