Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility
暂无分享,去创建一个
Fred H. Gage | Kelsi Penewit | Archana Raja | Carl Baker | Joshua M. Akey | Lucia Banci | Evan E. Eichler | Simone Ciofi-Baffoni | Francesca Antonacci | Alexandre Reymond | Chris T. Amemiya | John Huddleston | Osnat Penn | Joshua G. Schraiber | Mario Ventura | Peter H. Sudmant | C. Baker | E. Eichler | John Huddleston | M. Malig | F. Antonacci | P. Sudmant | A. Reymond | Laura Denman | A. Raja | C. Amemiya | Osnat Penn | F. Gage | M. Ventura | J. Akey | G. Giannuzzi | J. Schraiber | L. Banci | M. Marchetto | I. Narvaiza | L. Harshman | H. Stessman | X. Nuttle | G. Chiatante | Nicolette Janke | Maika Malig | Giuliana Giannuzzi | Maria C. N. Marchetto | S. Ciofi‐Baffoni | C. Benner | Xander Nuttle | Lana Harshman | Michael H. Duyzend | Iñigo Narvaiza | Chris Benner | Giorgia Chiatante | Francesca Camponeschi | Holly A.F. Stessman | Laura Denman | Nicolette Janke | W. Joyce Tang | W. J. Tang | Francesca Camponeschi | M. Duyzend | K. Penewit | Carl A. Baker | Christopher Benner | J. Huddleston | Nicolette R. Janke | Giorgia Chiatante | Maika Malig | Michael H. Duyzend
[1] Lior Pachter,et al. Near-optimal RNA-Seq quantification , 2015, ArXiv.
[2] D. Conrad,et al. Recurrent 16p11.2 microdeletions in autism. , 2007, Human molecular genetics.
[3] Tetsuo Nishikawa,et al. Assessing protein coding region integrity in cDNA sequencing projects , 1998, Bioinform..
[4] Nicholas T. Ingolia,et al. Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins , 2013, Cell.
[5] Nicholas T. Ingolia,et al. Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling , 2009, Science.
[6] Philip L. F. Johnson,et al. The complete genome sequence of a Neandertal from the Altai Mountains , 2013, Nature.
[7] Uwe Ohler,et al. Detecting actively translated open reading frames in ribosome profiling data , 2015, Nature Methods.
[8] Michael P Snyder,et al. Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans , 2015, Genome research.
[9] Peter H. Sudmant,et al. Palindromic GOLGA8 core duplicons promote chromosome 15q13.3 microdeletion and evolutionary instability , 2014, Nature Genetics.
[10] M. Daly,et al. A Potential Contributory Role for Ciliary Dysfunction in the 16p11.2 600 kb BP4-BP5 Pathology. , 2015, American journal of human genetics.
[11] P. Elliott,et al. Mirror extreme BMI phenotypes associated with gene dosage at the chromosome 16p11.2 locus , 2011, Nature.
[12] Jay Shendure,et al. Rapid and accurate large-scale genotyping of duplicated genes and discovery of novel sites of interlocus gene conversion , 2013, Nature Methods.
[13] Michael K. Johnson,et al. Human glutaredoxin 3 forms [2Fe-2S]-bridged complexes with human BolA2. , 2012, Biochemistry.
[14] Geoffrey J. Barton,et al. Jalview Version 2—a multiple sequence alignment editor and analysis workbench , 2009, Bioinform..
[15] Julie D Thompson,et al. Multiple Sequence Alignment Using ClustalW and ClustalX , 2003, Current protocols in bioinformatics.
[16] E. Eichler,et al. Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution , 2007, Nature Genetics.
[17] Thomas R. Gingeras,et al. STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..
[18] Peter H. Sudmant,et al. Diversity of Human Copy Number Variation and Multicopy Genes , 2010, Science.
[19] Gene W. Yeo,et al. Differential LINE-1 regulation in pluripotent stem cells of humans and other great apes , 2013, Nature.
[20] Andrew C. Adey,et al. Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition , 2010, Genome Biology.
[21] Scott M. Williams,et al. The Genetic Structure and History of Africans and African Americans , 2009, Science.
[22] Gonçalo R. Abecasis,et al. The variant call format and VCFtools , 2011, Bioinform..
[23] Gregory Ewing,et al. MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus , 2010, Bioinform..
[24] Eric W. Deutsch,et al. The PeptideAtlas project , 2005, Nucleic Acids Res..
[25] D. Winge,et al. Identification of FRA1 and FRA2 as Genes Involved in Regulating the Yeast Iron Regulon in Response to Decreased Mitochondrial Iron-Sulfur Cluster Synthesis* , 2008, Journal of Biological Chemistry.
[26] Evan E. Eichler,et al. Positive selection of a gene family during the emergence of humans and African apes , 2001, Nature.
[27] Peter H. Sudmant,et al. Evolution of Human-Specific Neural SRGAP2 Genes by Incomplete Segmental Duplication , 2012, Cell.
[28] C. Lillig,et al. Crucial function of vertebrate glutaredoxin 3 (PICOT) in iron homeostasis and hemoglobin maturation , 2013, Molecular biology of the cell.
[29] Jay Shendure,et al. Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation , 2013, Genome research.
[30] Ziheng Yang. PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.
[31] C. Lord,et al. The Simons Simplex Collection: A Resource for Identification of Autism Genetic Risk Factors , 2010, Neuron.
[32] Mark J. P. Chaisson,et al. Resolving the complexity of the human genome using single-molecule sequencing , 2014, Nature.
[33] Bradley P. Coe,et al. Global diversity, population stratification, and selection of human copy-number variation , 2015, Science.
[34] B. Trask,et al. Segmental duplications: organization and impact within the current human genome project assembly. , 2001, Genome research.
[35] Jonathan Scott Friedlaender,et al. Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals , 2016, Science.
[36] S. Bergmann,et al. The evolution of gene expression levels in mammalian organs , 2011, Nature.
[37] Rob Patro,et al. Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms , 2013, Nature Biotechnology.
[38] J. Shendure,et al. Resolving genomic disorder–associated breakpoints within segmental DNA duplications using massively parallel sequencing , 2014, Nature Protocols.
[39] J. Thomson,et al. Embryonic stem cell lines derived from human blastocysts. , 1998, Science.
[40] Desmond G. Higgins,et al. GWIPS-viz: development of a ribo-seq genome browser , 2013, Nucleic Acids Res..
[41] C. Kai,et al. CAGE: cap analysis of gene expression , 2006, Nature Methods.
[42] Anders Gorm Pedersen,et al. Neural Network Prediction of Translation Initiation Sites in Eukaryotes: Perspectives for EST and Genome Analysis , 1997, ISMB.
[43] Steven Scherer,et al. Recurrent duplication-driven transposition of DNA during hominoid evolution , 2006, Proceedings of the National Academy of Sciences.
[44] Fabian Sievers,et al. Clustal Omega , 2014, Current protocols in bioinformatics.
[45] Arcadi Navarro,et al. Great ape genetic diversity and population history , 2013, Nature.
[46] W. Pearson,et al. Current Protocols in Bioinformatics , 2002 .
[47] Heng Li,et al. Genome sequence of a 45,000-year-old modern human from western Siberia , 2014, Nature.
[48] J. D. Parsons,et al. Miropeats: graphical DNA sequence comparisons , 1995, Comput. Appl. Biosci..
[49] Chad A. Cowan,et al. Derivation of embryonic stem-cell lines from human blastocysts. , 2004, The New England journal of medicine.
[50] M. Nei,et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. , 2011, Molecular biology and evolution.
[51] L. Banci,et al. Elucidating the Molecular Function of Human BOLA2 in GRX3-Dependent Anamorsin Maturation Pathway. , 2015, Journal of the American Chemical Society.
[52] Judith D. Cohn,et al. The sequence and analysis of duplication-rich human chromosome 16 , 2004, Nature.
[53] B. Berger,et al. Ancient human genomes suggest three ancestral populations for present-day Europeans , 2013, Nature.
[54] Pedro G. Ferreira,et al. Transcriptome and genome sequencing uncovers functional variation in humans , 2013, Nature.
[55] Joshua M. Korn,et al. Mapping and sequencing of structural variation from eight human genomes , 2008, Nature.
[56] E. Eichler,et al. DupMasker: a tool for annotating primate segmental duplications. , 2008, Genome research.
[57] Gabor T. Marth,et al. A global reference for human genetic variation , 2015, Nature.
[58] M. King,et al. Evolution at two levels in humans and chimpanzees. , 1975, Science.
[59] Andres Metspalu,et al. A common 16p11.2 inversion underlies the joint susceptibility to asthma and obesity. , 2014, American journal of human genetics.
[60] Pardis C Sabeti,et al. Genetic signatures of strong recent positive selection at the lactase gene. , 2004, American journal of human genetics.
[61] B. Blencowe,et al. Smg1 is required for embryogenesis and regulates diverse genes via alternative splicing coupled to nonsense-mediated mRNA decay , 2010, Proceedings of the National Academy of Sciences.
[62] Adrian W. Briggs,et al. A High-Coverage Genome Sequence from an Archaic Denisovan Individual , 2012, Science.
[63] Joshua M. Korn,et al. Association between microdeletion and microduplication at 16p11.2 and autism , 2008 .
[64] M. Slatkin,et al. The Projection of a Test Genome onto a Reference Population and Applications to Humans and Archaic Hominins , 2014, Genetics.
[65] Koichiro Tamura,et al. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. , 2013, Molecular biology and evolution.
[66] Mark J. P. Chaisson,et al. Reconstructing complex regions of genomes using long-read sequencing technology , 2014, Genome research.
[67] Joshua M. Korn,et al. Association between microdeletion and microduplication at 16p11.2 and autism. , 2008, The New England journal of medicine.
[68] C. Outten,et al. Monothiol CGFS glutaredoxins and BolA-like proteins: [2Fe-2S] binding partners in iron homeostasis. , 2012, Biochemistry.
[69] Richard R. Hudson,et al. Generating samples under a Wright-Fisher neutral model of genetic variation , 2002, Bioinform..
[70] Evan E. Eichler,et al. A hot spot of genetic instability in autism. , 2008, The New England journal of medicine.
[71] Allison G. Dempsey,et al. A 600 kb deletion syndrome at 16p11.2 leads to energy imbalance and neuropsychiatric disorders , 2012, Journal of Medical Genetics.
[72] Fred H. Gage,et al. A Model for Neural Development and Treatment of Rett Syndrome Using Human Induced Pluripotent Stem Cells , 2010, Cell.
[73] Kenny Q. Ye,et al. An integrated map of genetic variation from 1,092 human genomes , 2012, Nature.
[74] The Simons,et al. Simons Variation in Individuals Project (Simons VIP): A Genetics-First Approach to Studying Autism Spectrum and Related Neurodevelopmental Disorders , 2012, Neuron.
[75] Jun S. Liu,et al. The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans , 2015, Science.
[76] Eric S. Lander,et al. Genetic evidence for complex speciation of humans and chimpanzees , 2006, Nature.
[77] Aaron A. Klammer,et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data , 2013, Nature Methods.