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  • 1
    Publication Date: 2014-11-11
    Description: The human genome is arguably the most complete mammalian reference assembly, yet more than 160 euchromatic gaps remain and aspects of its structural variation remain poorly understood ten years after its completion. To identify missing sequence and genetic variation, here we sequence and analyse a haploid human genome (CHM1) using single-molecule, real-time DNA sequencing. We close or extend 55% of the remaining interstitial gaps in the human GRCh37 reference genome--78% of which carried long runs of degenerate short tandem repeats, often several kilobases in length, embedded within (G+C)-rich genomic regions. We resolve the complete sequence of 26,079 euchromatic structural variants at the base-pair level, including inversions, complex insertions and long tracts of tandem repeats. Most have not been previously reported, with the greatest increases in sensitivity occurring for events less than 5 kilobases in size. Compared to the human reference, we find a significant insertional bias (3:1) in regions corresponding to complex insertions and long short tandem repeats. Our results suggest a greater complexity of the human genome in the form of variation of longer and more complex repetitive DNA that can now be largely resolved with the application of this longer-read sequencing technology.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4317254/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4317254/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chaisson, Mark J P -- Huddleston, John -- Dennis, Megan Y -- Sudmant, Peter H -- Malig, Maika -- Hormozdiari, Fereydoun -- Antonacci, Francesca -- Surti, Urvashi -- Sandstrom, Richard -- Boitano, Matthew -- Landolin, Jane M -- Stamatoyannopoulos, John A -- Hunkapiller, Michael W -- Korlach, Jonas -- Eichler, Evan E -- HG002385/HG/NHGRI NIH HHS/ -- HG007497/HG/NHGRI NIH HHS/ -- K99 NS083627/NS/NINDS NIH HHS/ -- K99NS083627/NS/NINDS NIH HHS/ -- R01 HG002385/HG/NHGRI NIH HHS/ -- U41 HG007497/HG/NHGRI NIH HHS/ -- U41 HG007635/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2015 Jan 29;517(7536):608-11. doi: 10.1038/nature13907. Epub 2014 Nov 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA. ; 1] Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA [2] Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA. ; Dipartimento di Biologia, Universita degli Studi di Bari 'Aldo Moro', Bari 70125, Italy. ; Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA. ; Pacific Biosciences of California, Inc., Menlo Park, California 94025, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25383537" target="_blank"〉PubMed〈/a〉
    Keywords: Chromosome Inversion/genetics ; Chromosomes, Human, Pair 10/genetics ; Cloning, Molecular ; GC Rich Sequence/genetics ; Genetic Variation/*genetics ; Genome, Human/*genetics ; *Genomics ; Haploidy ; Humans ; Mutagenesis, Insertional/genetics ; Reference Standards ; Sequence Analysis, DNA/*methods ; Tandem Repeat Sequences/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1980-02-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hunkapiller, M W -- Hood, L E -- New York, N.Y. -- Science. 1980 Feb 1;207(4430):523-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7352258" target="_blank"〉PubMed〈/a〉
    Keywords: *Amino Acid Sequence ; Animals ; Humans ; Mice ; *Proteins/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1980-06-27
    Description: The acetylcholine receptor from the electric ray Torpedo californica is composed of five subunits; two are identical and the other three are structurally related to them. Microsequence analysis of the four polypeptides demonstrates amino acid homology among the subunits. Further sequence analysis of both membrane-bound and Triton-solubilized, chromatographically purified receptor gave the stoichiometry of the four subunits (40,000:50,000:60,000:65,000 daltons) as 2:1:1:1, indicating that this protein is a pentameric complex with a molecular weight of 255,000 daltons. Genealogical analysis suggests that divergence from a common ancestral gene occurred early in the evolution of the receptor. This shared ancestry argues that each of the four subunits plays a functional role in the receptor's physiological action.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Raftery, M A -- Hunkapiller, M W -- Strader, C D -- Hood, L E -- New York, N.Y. -- Science. 1980 Jun 27;208(4451):1454-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7384786" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylcholine/metabolism ; Amino Acid Sequence ; Animals ; Electric Organ/*analysis ; Fishes ; Macromolecular Substances ; Molecular Weight ; Protein Conformation ; *Receptors, Cholinergic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 1980-02-01
    Description: Mouse interferons of three size classes (A, 35,000 to 40,000 daltons; B, 26,000 to 33,000 daltons; and C, 20,000 daltons) were purified from Ehrlich ascites tumor cells infected with Newcastle disease virus. The sequences of the first 24 amino acids (No. 17 has not been identified) of interferons A and B are identical. The sequence of the first 20 amino acids of interferon C differs from that of A and B in 18 positions. There is partial homology in amino terminal sequence between mouse interferons A (or B) and a human fibroblast interferon and between mouse interferon C and a human lymphoblastoid interferon.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Taira, H -- Broeze, R J -- Jayaram, B M -- Lengyel, P -- Hunkapiller, M W -- Hood, L E -- New York, N.Y. -- Science. 1980 Feb 1;207(4430):528-30.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7352261" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Biological Evolution ; Carcinoma, Ehrlich Tumor/analysis ; Cells, Cultured ; Glycoproteins/analysis ; *Interferons/genetics ; Mice ; Molecular Weight
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 1983-07-15
    Description: The transforming protein of a primate sarcoma virus and a platelet-derived growth factor are derived from the same or closely related cellular genes. This conclusion is based on the demonstration of extensive sequence similarity between the transforming protein derived from the simian sarcoma virus onc gene, v-sis, and a human platelet-derived growth factor. The mechanism by which v-sis transforms cells could involve the constitutive expression of a protein with functions similar or identical to those of a factor active transiently during normal cell growth.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Doolittle, R F -- Hunkapiller, M W -- Hood, L E -- Devare, S G -- Robbins, K C -- Aaronson, S A -- Antoniades, H N -- CA30101/CA/NCI NIH HHS/ -- RR00757/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 1983 Jul 15;221(4607):275-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6304883" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Cebidae ; Cell Transformation, Neoplastic/metabolism ; Genes ; Growth Substances/*genetics/physiology ; Humans ; *Oncogenes ; Peptides/*genetics/physiology ; Platelet-Derived Growth Factor ; Retroviridae/*genetics ; Sarcoma Virus, Woolly Monkey/*genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1984-10-19
    Description: The techniques used for the characterization of protein and peptide structure have undergone great changes that have improved the speed, reliability, and applicability of the process. High-performance liquid chromatography and gel electrophoresis have made the purification of proteins and peptides a routine procedure, even when the compound of interest is a minor component of a complex biological mixture. The chemistry and instrumentation used in amino acid analysis and amino acid sequencing now permit the analysis of as little as 5 to 50 picomoles of samples. This represents an increase in sensitivity of more than a thousandfold over the last 10 years and has made possible the structural analysis of a wide variety of scarce but important compounds.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hunkapiller, M W -- Strickler, J E -- Wilson, K J -- New York, N.Y. -- Science. 1984 Oct 19;226(4672):304-11.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6385254" target="_blank"〉PubMed〈/a〉
    Keywords: *Amino Acid Sequence ; Amino Acids/analysis ; Chemical Fractionation ; Chemistry Techniques, Analytical/*methods ; Chromatography ; Chromatography, High Pressure Liquid ; Chromatography, Ion Exchange ; Electrophoresis, Polyacrylamide Gel ; Isoelectric Focusing ; Peptide Hydrolases ; Peptides/analysis ; Proteins/*analysis/isolation & purification
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1983-05-27
    Description: Human platelet-derived growth factor (PDGF) obtained from outdated human platelets was subjected to amino-terminal amino acid sequence analysis by automated Edman degradation. Despite the apparent presence of limited proteolytic degradation of the protein derived from this method, the sequence analysis reveals two primary peptide sequences and suggests that active PDGF is composed of two, possibly homologous, peptides linked by a disulfide bond or bonds.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Antoniades, H N -- Hunkapiller, M W -- CA30101/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1983 May 27;220(4600):963-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6844921" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Electrophoresis, Polyacrylamide Gel ; Growth Substances/genetics/*metabolism ; Humans ; Molecular Weight ; Peptides/genetics/*metabolism ; Platelet-Derived Growth Factor
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
    Publication Date: 1984-03-09
    Description: The complete amino acid sequence of rat transforming growth factor type 1 has been determined. This growth factor, obtained from retrovirus-transformed fibroblasts, is structurally and functionally related to mouse epidermal growth factor and human urogastrone. Production of this polypeptide by various neoplastic cells might contribute to the continued expression of the transformed phenotype.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marquardt, H -- Hunkapiller, M W -- Hood, L E -- Todaro, G J -- New York, N.Y. -- Science. 1984 Mar 9;223(4640):1079-82.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6320373" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Cell Line ; *Cell Transformation, Neoplastic ; DNA/biosynthesis ; Epidermal Growth Factor/*metabolism/pharmacology ; Humans ; Idoxuridine/metabolism ; Mice ; Peptide Biosynthesis ; Peptides/*metabolism/pharmacology ; Rats ; Receptor, Epidermal Growth Factor ; Receptors, Cell Surface/metabolism ; Structure-Activity Relationship ; Transforming Growth Factors
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
    Publication Date: 1982-12-17
    Description: The nicotinic acetylcholine receptor has been purified from fetal calf muscle. Amino terminal amino acid sequence data indicate that the mammalian receptor is formed from closely related but distinct subunits. A cytoskeletal component, actin, may be associated with the receptor.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Conti-Tronconi, B M -- Gotti, C M -- Hunkapiller, M W -- Raftery, M A -- GM-06965/GM/NIGMS NIH HHS/ -- NS-10294/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 1982 Dec 17;218(4578):1227-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7146904" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/isolation & purification ; Amino Acid Sequence ; Animals ; Cattle ; Macromolecular Substances ; Molecular Weight ; Receptors, Cholinergic/*isolation & purification
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
    Publication Date: 1980-02-01
    Description: The purification of human fibroblast interferon has been simplified to a two-step procedure consisting of affinity chromatography on Blue Sepharose and sodium dodecyl sulfate polyacrlamide gel electrophoresis. A preliminary amino acid composition and the sequence of the 13 amino-terminal residues of homogeneous interferon prepared by this method is reported.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Knight, E Jr -- Hunkapiller, M W -- Korant, B D -- Hardy, R W -- Hood, L E -- New York, N.Y. -- Science. 1980 Feb 1;207(4430):525-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7352259" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acids/analysis ; Cells, Cultured ; Fibroblasts/*analysis ; Humans ; *Interferons
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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