Multiple haplotype-resolved genomes reveal population patterns of gene and protein diplotypes

[1]  John N. Hutchinson,et al.  Widespread Monoallelic Expression on Human Autosomes , 2007, Science.

[2]  P. Bork,et al.  A method and server for predicting damaging missense mutations , 2010, Nature Methods.

[3]  S. Henikoff,et al.  Predicting deleterious amino acid substitutions. , 2001, Genome research.

[4]  Yoshio Sato,et al.  Current State and Future Directions , 2009 .

[5]  Alison M. Dunning,et al.  Rat Mcs5a is a compound quantitative trait locus with orthologous human loci that associate with breast cancer risk , 2007, Proceedings of the National Academy of Sciences.

[6]  V. Bansal,et al.  The importance of phase information for human genomics , 2011, Nature Reviews Genetics.

[7]  J. Knight,et al.  Allele-specific gene expression uncovered. , 2004, Trends in genetics : TIG.

[8]  Francisco M. De La Vega,et al.  Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. , 2009, Genome research.

[9]  Mostafa Ronaghi,et al.  Whole-genome haplotyping by dilution, amplification, and sequencing , 2013, Proceedings of the National Academy of Sciences.

[10]  Timothy B. Stockwell,et al.  The Diploid Genome Sequence of an Individual Human , 2007, PLoS biology.

[11]  Michael Krawczak,et al.  PopGen – Bevölkerungsbasierte Rekrutierung von Patienten und Kontrollen für die Untersuchung komplexer Genotyp-Phänotyp-Beziehungen (PopGen – Population-based Recruitment of Patients and Controls for the Analysis of Complex Genotype-phenotype Relationships) , 2007, it Inf. Technol..

[12]  Erhard Rahm,et al.  FUNC: a package for detecting significant associations between gene sets and ontological annotations , 2007, BMC Bioinformatics.

[13]  Katja Nowick,et al.  A comprehensively molecular haplotype-resolved genome of a European individual. , 2011, Genome research.

[14]  R S Judson,et al.  Complex promoter and coding region beta 2-adrenergic receptor haplotypes alter receptor expression and predict in vivo responsiveness. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[15]  A. Chess,et al.  Mechanisms and consequences of widespread random monoallelic expression , 2012, Nature Reviews Genetics.

[16]  K K Kidd,et al.  Sequence variability and candidate gene analysis in complex disease: association of mu opioid receptor gene variation with substance dependence. , 2000, Human molecular genetics.

[17]  P. Baldi,et al.  The architecture of pre-mRNAs affects mechanisms of splice-site pairing. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[18]  Matthew D. Young,et al.  Gene ontology analysis for RNA-seq: accounting for selection bias , 2010, Genome Biology.

[19]  M. Gerstein,et al.  What is a gene, post-ENCODE? History and updated definition. , 2007, Genome research.

[20]  C. H. WADDINGTON,et al.  Advances in Genetics , 1947, Nature.

[21]  K. Robasky,et al.  On the design of clone-based haplotyping , 2013, Genome Biology.

[22]  T. Tatusova,et al.  NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2006, Nucleic Acids Research.

[23]  Joaquín Goñi,et al.  Allele-Specific Gene Expression Is Widespread Across the Genome and Biological Processes , 2009, PloS one.

[24]  Nicole Rusk.  Causal mutations in a haploid landscape , 2011, Nature Methods.

[25]  B. Browning,et al.  Haplotype phasing: existing methods and new developments , 2011, Nature Reviews Genetics.

[26]  J. Shendure,et al.  Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data , 2011, Nature Reviews Genetics.

[27]  Jessica C. Ebert,et al.  Accurate whole genome sequencing and haplotyping from10-20 human cells , 2012, Nature.

[28]  Armin R. Mikler,et al.  Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, BCB 2010, Niagara Falls, NY, USA, August 2-4, 2010 , 2010, BCB.

[29]  Kenny Q. Ye,et al.  An integrated map of genetic variation from 1,092 human genomes , 2012, Nature.

[30]  D. Altshuler,et al.  A map of human genome variation from population-scale sequencing , 2010, Nature.

[31]  C.-ting Wu,et al.  Homology effects: the difference between 1 and 2. , 2002, Advances in genetics.

[32]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[33]  Bradley P. Coe,et al.  Genome structural variation discovery and genotyping , 2011, Nature Reviews Genetics.

[34]  A. Kornberg.  The Chemical Basis of Heredity , 1961 .

[35]  Cathy H. Wu,et al.  The Human Proteome Project: Current State and Future Direction , 2011, Molecular & Cellular Proteomics.

[36]  M. Hoehe,et al.  Haplotypes and the systematic analysis of genetic variation in genes and genomes. , 2003, Pharmacogenomics.

[37]  Tatiana Tatusova,et al.  NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2004, Nucleic Acids Res..

[38]  Paul Scheet,et al.  A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. , 2006, American journal of human genetics.

[39]  Ralf Herwig,et al.  The ConsensusPathDB interaction database: 2013 update , 2012, Nucleic Acids Res..

[40]  K. Verstrepen,et al.  Fosmid-based whole genome haplotyping of a HapMap trio child: evaluation of Single Individual Haplotyping techniques , 2011, Nucleic acids research.

[41]  L. Donehower,et al.  Allelic phasing of a mouse chromosome 11 deficiency influences p53 tumorigenicity , 2003, Oncogene.

[42]  J. Stephens,et al.  Haplotype Variation and Linkage Disequilibrium in 313 Human Genes , 2001, Science.

[43]  Virginia Savova,et al.  Chromatin signature of widespread monoallelic expression , 2013, eLife.

[44]  Ralf Herwig,et al.  ConsensusPathDB: toward a more complete picture of cell biology , 2010, Nucleic Acids Res..

[45]  V. Bansal,et al.  The next phase in human genetics , 2011, Nature Biotechnology.

[46]  Hans Lehrach,et al.  Clone-based systematic haplotyping (CSH): a procedure for physical haplotyping of whole genomes. , 2003, Genome research.