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Blanchette M, Diallo AB, Green ED, Miller W, Haussler D. Computational reconstruction of ancestral DNA sequences. Methods Mol Biol 2008; 422:171-84. [PMID: 18629667 DOI: 10.1007/978-1-59745-581-7_11] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This chapter introduces the problem of ancestral sequence reconstruction: given a set of extant orthologous DNA genomic sequences (or even whole-genomes), together with a phylogenetic tree relating these sequences, predict the DNA sequence of all ancestral species in the tree. Blanchette et al. (1) have shown that for certain sets of species (in particular, for eutherian mammals), very accurate reconstruction can be obtained. We explain the main steps involved in this process, including multiple sequence alignment, insertion and deletion inference, substitution inference, and gene arrangement inference. We also describe a simulation-based procedure to assess the accuracy of the reconstructed sequences. The whole reconstruction process is illustrated using a set of mammalian sequences from the CFTR region.
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Rosenbloom K, Taylor J, Schaeffer S, Kent J, Haussler D, Miller W. Phylogenomic resources at the UCSC Genome Browser. Methods Mol Biol 2008; 422:133-44. [PMID: 18629665 DOI: 10.1007/978-1-59745-581-7_9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The UC Santa Cruz Genome Browser provides a number of resources that can be used for phylogenomic studies, including (1) whole-genome sequence data from a number of vertebrate species, (2) pairwise alignments of the human genome sequence to a number of other vertebrate genome, (3) a simultaneous alignment of 17 vertebrate genomes (most of them incompletely sequenced) that covers all of the human sequence, (4) several independent sets of multiple alignments covering 1% of the human genome (ENCODE regions), (5) extensive sequence annotation for interpreting those sequences and alignments, and (6) sequence, alignments, and annotations from certain other species, including an alignment of nine insect genomes. We illustrate the use of these resources in the context of assigning rare genomic changes to the branch of the phylogenetic tree where they appear to have occurred, or of looking for evidence supporting a particular possible tree topology. Sample source code for performing such studies is available.
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Karolchik D, Kuhn RM, Baertsch R, Barber GP, Clawson H, Diekhans M, Giardine B, Harte RA, Hinrichs AS, Hsu F, Kober KM, Miller W, Pedersen JS, Pohl A, Raney BJ, Rhead B, Rosenbloom KR, Smith KE, Stanke M, Thakkapallayil A, Trumbower H, Wang T, Zweig AS, Haussler D, Kent WJ. The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res 2007; 36:D773-9. [PMID: 18086701 PMCID: PMC2238835 DOI: 10.1093/nar/gkm966] [Citation(s) in RCA: 403] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The University of California, Santa Cruz, Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes. Seventeen new assemblies have been added to the database in the past year, for a total coverage of 19 vertebrate and 21 invertebrate species as of September 2007. For each assembly, the GBD contains a collection of annotation data aligned to the genomic sequence. Highlights of this year's additions include a 28-species human-based vertebrate conservation annotation, an enhanced UCSC Genes set, and more human variation, MGC, and ENCODE data. The database is optimized for fast interactive performance with a set of web-based tools that may be used to view, manipulate, filter and download the annotation data. New toolset features include the Genome Graphs tool for displaying genome-wide data sets, session saving and sharing, better custom track management, expanded Genome Browser configuration options and a Genome Browser wiki site. The downloadable GBD data, the companion Genome Browser toolset and links to documentation and related information can be found at: http://genome.ucsc.edu/.
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Miller W, Rosenbloom K, Hardison RC, Hou M, Taylor J, Raney B, Burhans R, King DC, Baertsch R, Blankenberg D, Kosakovsky Pond SL, Nekrutenko A, Giardine B, Harris RS, Tyekucheva S, Diekhans M, Pringle TH, Murphy WJ, Lesk A, Weinstock GM, Lindblad-Toh K, Gibbs RA, Lander ES, Siepel A, Haussler D, Kent WJ. 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genes Dev 2007; 17:1797-808. [PMID: 17984227 PMCID: PMC2099589 DOI: 10.1101/gr.6761107] [Citation(s) in RCA: 207] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2007] [Accepted: 08/30/2007] [Indexed: 01/17/2023]
Abstract
This article describes a set of alignments of 28 vertebrate genome sequences that is provided by the UCSC Genome Browser. The alignments can be viewed on the Human Genome Browser (March 2006 assembly) at http://genome.ucsc.edu, downloaded in bulk by anonymous FTP from http://hgdownload.cse.ucsc.edu/goldenPath/hg18/multiz28way, or analyzed with the Galaxy server at http://g2.bx.psu.edu. This article illustrates the power of this resource for exploring vertebrate and mammalian evolution, using three examples. First, we present several vignettes involving insertions and deletions within protein-coding regions, including a look at some human-specific indels. Then we study the extent to which start codons and stop codons in the human sequence are conserved in other species, showing that start codons are in general more poorly conserved than stop codons. Finally, an investigation of the phylogenetic depth of conservation for several classes of functional elements in the human genome reveals striking differences in the rates and modes of decay in alignability. Each functional class has a distinctive period of stringent constraint, followed by decays that allow (for the case of regulatory regions) or reject (for coding regions and ultraconserved elements) insertions and deletions.
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Kaufmann M, von Minckwitz G, Bear H, Buzdar A, McGale P, Bonnefoi H, Colleoni M, Denkert C, Eiermann W, Jackesz R, Makris A, Miller W, Pierga JY, Semiglazov V, Schneeweiss A, Souchon R, Stearns V, Untch M, Loibl S. Recommendations from an international expert panel on the use of neoadjuvant (primary) systemic treatment of operable breast cancer: new perspectives 2006. Ann Oncol 2007; 18:1927-34. [DOI: 10.1093/annonc/mdm201] [Citation(s) in RCA: 296] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Janecka JE, Miller W, Pringle TH, Wiens F, Zitzmann A, Helgen KM, Springer MS, Murphy WJ. Molecular and genomic data identify the closest living relative of primates. Science 2007; 318:792-4. [PMID: 17975064 DOI: 10.1126/science.1147555] [Citation(s) in RCA: 201] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
A full understanding of primate morphological and genomic evolution requires the identification of their closest living relative. In order to resolve the ancestral relationships among primates and their closest relatives, we searched multispecies genome alignments for phylogenetically informative rare genomic changes within the superordinal group Euarchonta, which includes the orders Primates, Dermoptera (colugos), and Scandentia (treeshrews). We also constructed phylogenetic trees from 14 kilobases of nuclear genes for representatives from most major primate lineages, both extant colugos, and multiple treeshrews, including the pentail treeshrew, Ptilocercus lowii, the only living member of the family Ptilocercidae. A relaxed molecular clock analysis including Ptilocercus suggests that treeshrews arose approximately 63 million years ago. Our data show that colugos are the closest living relatives of primates and indicate that their divergence occurred in the Cretaceous.
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Abraham J, Abreu P, Aglietta M, Aguirre C, Allard D, Allekotte I, Allen J, Allison P, Alvarez C, Alvarez-Muñiz J, Ambrosio M, Anchordoqui L, Andringa S, Anzalone A, Aramo C, Argirò S, Arisaka K, Armengaud E, Arneodo F, Arqueros F, Asch T, Asorey H, Assis P, Atulugama BS, Aublin J, Ave M, Avila G, Bäcker T, Badagnani D, Barbosa AF, Barnhill D, Barroso SLC, Bauleo P, Beatty J, Beau T, Becker BR, Becker KH, Bellido JA, BenZvi S, Berat C, Bergmann T, Bernardini P, Bertou X, Biermann PL, Billoir P, Blanch-Bigas O, Blanco F, Blasi P, Bleve C, Blümer H, Boháčová M, Bonifazi C, Bonino R, Boratav M, Brack J, Brogueira P, Brown WC, Buchholz P, Bueno A, Busca NG, Caballero-Mora KS, Cai B, Camin DV, Caruso R, Carvalho W, Castellina A, Catalano O, Cataldi G, Cazón-Boado L, Cester R, Chauvin J, Chiavassa A, Chinellato JA, Chou A, Chye J, Clark PDJ, Clay RW, Colombo E, Conceição R, Connolly B, Contreras F, Coppens J, Cordier A, Cotti U, Coutu S, Covault CE, Creusot A, Cronin J, Dagoret-Campagne S, Daumiller K, Dawson BR, de Almeida RM, De Donato C, de Jong SJ, De La Vega G, de Mello Junior WJM, de Mello Neto JRT, De Mitri I, de Souza V, del Peral L, Deligny O, Selva AD, Fratte CD, Dembinski H, Di Giulio C, Diaz JC, Dobrigkeit C, D'Olivo JC, Dornic D, Dorofeev A, Anjos JCD, Dova MT, D'Urso D, DuVernois MA, Engel R, Epele L, Erdmann M, Escobar CO, Etchegoyen A, Luis PFS, Falcke H, Farrar G, Fauth AC, Fazzini N, Fernández A, Ferrer F, Ferry S, Fick B, Filevich A, Filipčič A, Fleck I, Fonte R, Fracchiolla CE, Fulgione W, García B, García Gámez D, Garcia-Pinto D, Garrido X, Geenen H, Gelmini G, Gemmeke H, Ghia PL, Giller M, Glass H, Gold MS, Golup G, Albarracin FG, Berisso MG, Herrero RG, Gonçalves P, do Amaral MG, Gonzalez D, Gonzalez JG, González M, Góra D, Gorgi A, Gouffon P, Grassi V, Grillo A, Grunfeld C, Guardincerri Y, Guarino F, Guedes GP, Gutiérrez J, Hague JD, Hamilton JC, Hansen P, Harari D, Harmsma S, Harton JL, Haungs A, Hauschildt T, Healy MD, Hebbeker T, Heck D, Hojvat C, Holmes VC, Homola P, Hörandel J, Horneffer A, Horvat M, Hrabovský M, Huege T, Iarlori M, Insolia A, Ionita F, Italiano A, Kaducak M, Kampert KH, Keilhauer B, Kemp E, Kieckhafer RM, Klages HO, Kleifges M, Kleinfeller J, Knapik R, Knapp J, Koang DH, Kopmann A, Krieger A, Krömer O, Kümpel D, Kunka N, Kusenko A, La Rosa G, Lachaud C, Lago BL, Lebrun D, LeBrun P, Lee J, de Oliveira MAL, Letessier-Selvon A, Leuthold M, Lhenry-Yvon I, López R, Lopez Agüera A, Bahilo JL, Maccarone MC, Macolino C, Maldera S, Malek M, Mancarella G, Manceñido ME, Mandat D, Mantsch P, Mariazzi AG, Maris IC, Martello D, Martínez J, Bravo OM, Mathes HJ, Matthews J, Matthews JAJ, Matthiae G, Maurizio D, Mazur PO, McCauley T, McEwen M, McNeil RR, Medina MC, Medina-Tanco G, Meli A, Melo D, Menichetti E, Menschikov A, Meurer C, Meyhandan R, Micheletti MI, Miele G, Miller W, Mollerach S, Monasor M, Ragaigne DM, Montanet F, Morales B, Morello C, Moreno E, Moreno JC, Morris C, Mostafá M, Muller MA, Mussa R, Navarra G, Navarro JL, Navas S, Nellen L, Newman-Holmes C, Newton D, Thi TN, Nierstenhöfer N, Nitz D, Nosek D, Nožka L, Oehlschläger J, Ohnuki T, Olinto A, Olmos-Gilbaja VM, Ortiz M, Ostapchenko S, Otero L, Selmi-Dei DP, Palatka M, Pallotta J, Parente G, Parizot E, Parlati S, Pastor S, Patel M, Paul T, Pavlidou V, Payet K, Pech M, Pȩkala J, Pelayo R, Pepe IM, Perrone L, Petrera S, Petrinca P, Petrov Y, Ngoc D, Ngoc D, Thi TNP, Pichel A, Piegaia R, Pierog T, Pimenta M, Pinto T, Pirronello V, Pisanti O, Platino M, Pochon J, Porter TA, Privitera P, Prouza M, Quel EJ, Rautenberg J, Reucroft S, Revenu B, Rezende FAS, Řídký J, Riggi S, Risse M, Rivière C, Rizi V, Roberts M, Robledo C, Rodriguez G, Frías DR, Martino JR, Rojo JR, Rodriguez-Cabo I, Ros G, Rosado J, Roth M, Rouillé-d'Orfeuil B, Roulet E, Rovero AC, Salamida F, Salazar H, Salina G, Sánchez F, Santander M, Santo CE, Santos EM, Sarazin F, Sarkar S, Sato R, Scherini V, Schieler H, Schmidt F, Schmidt T, Scholten O, Schovánek P, Schüssler F, Sciutto SJ, Scuderi M, Segreto A, Semikoz D, Settimo M, Shellard RC, Sidelnik I, Siffert BB, Sigl G, De Grande NS, Smiałkowski A, šmída R, Smith AGK, Smith BE, Snow GR, Sokolsky P, Sommers P, Sorokin J, Spinka H, Squartini R, Strazzeri E, Stutz A, Suarez F, Suomijärvi T, Supanitsky AD, Sutherland MS, Swain J, Szadkowski Z, Takahashi J, Tamashiro A, Tamburro A, Taşcău O, Tcaciuc R, Thomas D, Ticona R, Tiffenberg J, Timmermans C, Tkaczyk W, Peixoto CJT, Tomé B, Tonachini A, Torresi D, Travnicek P, Tripathi A, Tristram G, Tscherniakhovski D, Tueros M, Tunnicliffe V, Ulrich R, Unger M, Urban M, Galicia JFV, Valiño I, Valore L, van den Berg AM, van Elewyck V, Vázquez RA, Veberič D, Veiga A, Velarde A, Venters T, Verzi V, Videla M, Villaseñor L, Vorobiov S, Voyvodic L, Wahlberg H, Wainberg O, Waldenmaier T, Walker P, Warner D, Watson AA, Westerhoff S, Wieczorek G, Wiencke L, Wilczyńska B, Wilczyński H, Wileman C, Winnick MG, Wu H, Wundheiler B, Xu J, Yamamoto T, Younk P, Zas E, Zavrtanik D, Zavrtanik M, Zech A, Zepeda A, Ziolkowski M. Correlation of the Highest-Energy Cosmic Rays with Nearby Extragalactic Objects. Science 2007; 318:938-43. [DOI: 10.1126/science.1151124] [Citation(s) in RCA: 560] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Gilbert MTP, Tomsho LP, Rendulic S, Packard M, Drautz DI, Sher A, Tikhonov A, Dalén L, Kuznetsova T, Kosintsev P, Campos PF, Higham T, Collins MJ, Wilson AS, Shidlovskiy F, Buigues B, Ericson PGP, Germonpré M, Götherström A, Iacumin P, Nikolaev V, Nowak-Kemp M, Willerslev E, Knight JR, Irzyk GP, Perbost CS, Fredrikson KM, Harkins TT, Sheridan S, Miller W, Schuster SC. Whole-Genome Shotgun Sequencing of Mitochondria from Ancient Hair Shafts. Science 2007; 317:1927-30. [PMID: 17901335 DOI: 10.1126/science.1146971] [Citation(s) in RCA: 191] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Although the application of sequencing-by-synthesis techniques to DNA extracted from bones has revolutionized the study of ancient DNA, it has been plagued by large fractions of contaminating environmental DNA. The genetic analyses of hair shafts could be a solution: We present 10 previously unexamined Siberian mammoth (Mammuthus primigenius) mitochondrial genomes, sequenced with up to 48-fold coverage. The observed levels of damage-derived sequencing errors were lower than those observed in previously published frozen bone samples, even though one of the specimens was >50,000 14C years old and another had been stored for 200 years at room temperature. The method therefore sets the stage for molecular-genetic analysis of museum collections.
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109
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Miller W, Succi S. Lattice gas modeling of nanowhisker growth. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2007; 76:031601. [PMID: 17930250 DOI: 10.1103/physreve.76.031601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2007] [Indexed: 05/25/2023]
Abstract
Building upon the ideas of Gerischer et al., we have developed a cellular automaton for the growth dynamics of nanowhiskers. We present two models for the whisker growth. The first is a simple extension of the surface model, whereas the second includes diffusion on the rim of the whiskers. Results for one-dimensional calculations are presented and discussed, together with a comparison between the two models and with experimental results as well.
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Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, Taylor J, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Brown JB, Bickel P, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Stone EA, Rosenbloom KR, Kent WJ, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VVB, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Hinrichs A, Trumbower H, Clawson H, Zweig A, Kuhn RM, Barber G, Harte R, Karolchik D, Field MA, Moore RA, Matthewson CA, Schein JE, Marra MA, Antonarakis SE, Batzoglou S, Goldman N, Hardison R, Haussler D, Miller W, Pachter L, Green ED, Sidow A. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res 2007; 17:760-74. [PMID: 17567995 PMCID: PMC1891336 DOI: 10.1101/gr.6034307] [Citation(s) in RCA: 170] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation, alignment, and evolutionary constraint analyses of 23 mammalian species for all ENCODE targets. Alignments were generated using four different methods; comparisons of these methods reveal large-scale consistency but substantial differences in terms of small genomic rearrangements, sensitivity (sequence coverage), and specificity (alignment accuracy). We describe the quantitative and qualitative trade-offs concomitant with alignment method choice and the levels of technical error that need to be accounted for in applications that require multisequence alignments. Using the generated alignments, we identified constrained regions using three different methods. While the different constraint-detecting methods are in general agreement, there are important discrepancies relating to both the underlying alignments and the specific algorithms. However, by integrating the results across the alignments and constraint-detecting methods, we produced constraint annotations that were found to be robust based on multiple independent measures. Analyses of these annotations illustrate that most classes of experimentally annotated functional elements are enriched for constrained sequences; however, large portions of each class (with the exception of protein-coding sequences) do not overlap constrained regions. The latter elements might not be under primary sequence constraint, might not be constrained across all mammals, or might have expendable molecular functions. Conversely, 40% of the constrained sequences do not overlap any of the functional elements that have been experimentally identified. Together, these findings demonstrate and quantify how many genomic functional elements await basic molecular characterization.
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King DC, Taylor J, Zhang Y, Cheng Y, Lawson HA, Martin J, Chiaromonte F, Miller W, Hardison RC. Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data. Genome Res 2007; 17:775-86. [PMID: 17567996 PMCID: PMC1891337 DOI: 10.1101/gr.5592107] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Identification of functional genomic regions using interspecies comparison will be most effective when the full span of relationships between genomic function and evolutionary constraint are utilized. We find that sets of putative transcriptional regulatory sequences, defined by ENCODE experimental data, have a wide span of evolutionary histories, ranging from stringent constraint shown by deep phylogenetic comparisons to recent selection on lineage-specific elements. This diversity of evolutionary histories can be captured, at least in part, by the suite of available comparative genomics tools, especially after correction for regional differences in the neutral substitution rate. Putative transcriptional regulatory regions show alignability in different clades, and the genes associated with them are enriched for distinct functions. Some of the putative regulatory regions show evidence for recent selection, including a primate-specific, distal promoter that may play a novel role in regulation.
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Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res 2007; 17:960-4. [PMID: 17568012 PMCID: PMC1891355 DOI: 10.1101/gr.5578007] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The standardization and sharing of data and tools are the biggest challenges of large collaborative projects such as the Encyclopedia of DNA Elements (ENCODE). Here we describe a compact Web application, Galaxy2(ENCODE), that effectively addresses these issues. It provides an intuitive interface for the deposition and access of data, and features a vast number of analysis tools including operations on genomic intervals, utilities for manipulation of multiple sequence alignments, and molecular evolution algorithms. By providing a direct link between data and analysis tools, Galaxy2(ENCODE) allows addressing biological questions that are beyond the reach of existing software. We use Galaxy2(ENCODE) to show that the ENCODE regions contain >2000 unannotated transcripts under strong purifying selection that are likely functional. We also show that the ENCODE regions are representative of the entire genome by estimating the rate of nucleotide substitution and comparing it to published data. Although each of these analyses is complex, none takes more than 15 min from beginning to end. Finally, we demonstrate how new tools can be added to Galaxy2(ENCODE) with almost no effort. Every section of the manuscript is supplemented with QuickTime screencasts. Galaxy2(ENCODE) and the screencasts can be accessed at http://g2.bx.psu.edu.
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113
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Miller W. Performing armchair roundoff analyses of statistical algorithms. COMMUN STAT-SIMUL C 2007. [DOI: 10.1080/03610917808812074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Batist G, Miller W, Mayer L, Janoff A, Swenson C, Louie A, Chi K, Chia S, Gelmon K. Ratiometric dosing of irinotecan (IRI) and floxuridine (FLOX) in a phase I trial: A new approach for enhancing the activity of combination chemotherapy. J Clin Oncol 2007. [DOI: 10.1200/jco.2007.25.18_suppl.2549] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
2549 Background: Like many pairs of chemotherapy agents, the combination of IRI and FLOX displays ratio-dependent activity in vitro. CPX-1, a liposome formulation of IRI:FLOX, was developed to maintain a synergistic 1:1 molar ratio in vivo, was highly active in preclinical models, and was evaluated in a phase 1 trial (CLTR0104–101). Methods: Doses were escalated from 30U/m2 (1U= 1 mg IRI + 0.36 mg FLOX) to 270 U/m2 given on day 1 and 15 of each 28 day cycle. Adult patients (pts) with advanced solid tumors, ECOG PS<2, adequate bone marrow, liver, and renal function were eligible; 4 pts per cohort. After defining the MTD, additional pts with CRC were enrolled (extension phase). IRI completed greater than 12 months prior to this trial was allowed in the absence of resistance to IRI. PK was done on day 1 and 15 of the 1st cycle. Results: Safety: The dose escalation phase enrolled 24 pts in 6 cohorts and added 2 pts in the 5th cohort (210U/m2; the MTD) after noting dose limiting diarrhea (3 pts) and neutropenia (1 pt) including one death from dehydration and renal failure due to prolonged diarrhea (gr3) & vomiting (gr2) at 270U/m2. An additional 7 pts with CRC received 210U/m2 in the extension phase. Grade 3/4 adverse events included diarrhea, nausea, vomiting, neutropenia and thrombocytopenia with most occurring at 270U/m2. No new toxicities were observed for this combination. Response: 30/33 pts were evaluable with 2 confirmed PRs (NSCLC and CRC), 21 SD and 7 PD. Median PFS was 5.4 mos. (0.3–11.8 mos.) in 15 pts w/CRC. PK: All pts maintained synergistic plasma IRI:FLOX ratios for 24h. IRI and FLOX AUCs (0-inf) were greater for CPX-1 than expected for conventional drugs. AUCs for SN-38 and 5FU at 210U/m2 were 0.8 ± 0.1 and 10 ± 8.7 μg-hr/mL, respectively, indicating bioavailability for both drugs. Conclusion: CPX-1 was well tolerated in the outpatient setting and evidence of anti-tumor activity was obtained. This is the first clinical evaluation of ratiometric dosing in which a synergistic drug ratio, pre-selected in vitro based on optimal anti-tumor activity, was maintained systemically to enhance therapeutic benefit. [Table: see text]
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Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SCJ, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CWH, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JNS, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PIW, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VVB, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007; 447:799-816. [PMID: 17571346 PMCID: PMC2212820 DOI: 10.1038/nature05874] [Citation(s) in RCA: 3798] [Impact Index Per Article: 223.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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Chang YW, Miller W, Palta J. SU-FF-T-384: Statistical Analysis of a System for Radiation Treatment Positioning Accuracy. Med Phys 2007. [DOI: 10.1118/1.2761109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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117
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Miller W, Zalenski R, Hong Y, Levy P, Compton S. In-hospital Course of Initial CPR Survivors. Acad Emerg Med 2007. [DOI: 10.1197/j.aem.2007.03.1188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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118
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Khan A, Compton S, Miller W, Dehorn S, Calcaterra S, Levy P. Delirium Tremens: An Analysis of Factors Associated with Mortality. Acad Emerg Med 2007. [DOI: 10.1197/j.aem.2007.03.834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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119
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Han K, Konkel MK, Xing J, Wang H, Lee J, Meyer TJ, Huang CT, Sandifer E, Hebert K, Barnes EW, Hubley R, Miller W, Smit AFA, Ullmer B, Batzer MA. Mobile DNA in Old World monkeys: a glimpse through the rhesus macaque genome. Science 2007; 316:238-40. [PMID: 17431169 DOI: 10.1126/science.1139462] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The completion of the draft sequence of the rhesus macaque genome allowed us to study the genomic composition and evolution of transposable elements in this representative of the Old World monkey lineage, a group of diverse primates closely related to humans. The L1 family of long interspersed elements appears to have evolved as a single lineage, and Alu elements have evolved into four currently active lineages. We also found evidence of elevated horizontal transmissions of retroviruses and the absence of DNA transposon activity in the Old World monkey lineage. In addition, approximately 100 precursors of composite SVA (short interspersed element, variable number of tandem repeat, and Alu) elements were identified, with the majority being shared by the common ancestor of humans and rhesus macaques. Mobile elements compose roughly 50% of primate genomes, and our findings illustrate their diversity and strong influence on genome evolution between closely related species.
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Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, Hardison RC, Makova KD, Miller W, Milosavljevic A, Palermo RE, Siepel A, Sikela JM, Attaway T, Bell S, Bernard KE, Buhay CJ, Chandrabose MN, Dao M, Davis C, Delehaunty KD, Ding Y, Dinh HH, Dugan-Rocha S, Fulton LA, Gabisi RA, Garner TT, Godfrey J, Hawes AC, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Kirkness EF, Cree A, Fowler RG, Lee S, Lewis LR, Li Z, Liu YS, Moore SM, Muzny D, Nazareth LV, Ngo DN, Okwuonu GO, Pai G, Parker D, Paul HA, Pfannkoch C, Pohl CS, Rogers YH, Ruiz SJ, Sabo A, Santibanez J, Schneider BW, Smith SM, Sodergren E, Svatek AF, Utterback TR, Vattathil S, Warren W, White CS, Chinwalla AT, Feng Y, Halpern AL, Hillier LW, Huang X, Minx P, Nelson JO, Pepin KH, Qin X, Sutton GG, Venter E, Walenz BP, Wallis JW, Worley KC, Yang SP, Jones SM, Marra MA, Rocchi M, Schein JE, Baertsch R, Clarke L, Csürös M, Glasscock J, Harris RA, Havlak P, Jackson AR, Jiang H, Liu Y, Messina DN, Shen Y, Song HXZ, Wylie T, Zhang L, Birney E, Han K, Konkel MK, Lee J, Smit AFA, Ullmer B, Wang H, Xing J, Burhans R, Cheng Z, Karro JE, Ma J, Raney B, She X, Cox MJ, Demuth JP, Dumas LJ, Han SG, Hopkins J, Karimpour-Fard A, Kim YH, Pollack JR, Vinar T, Addo-Quaye C, Degenhardt J, Denby A, Hubisz MJ, Indap A, Kosiol C, Lahn BT, Lawson HA, Marklein A, Nielsen R, Vallender EJ, Clark AG, Ferguson B, Hernandez RD, Hirani K, Kehrer-Sawatzki H, Kolb J, Patil S, Pu LL, Ren Y, Smith DG, Wheeler DA, Schenck I, Ball EV, Chen R, Cooper DN, Giardine B, Hsu F, Kent WJ, Lesk A, Nelson DL, O'brien WE, Prüfer K, Stenson PD, Wallace JC, Ke H, Liu XM, Wang P, Xiang AP, Yang F, Barber GP, Haussler D, Karolchik D, Kern AD, Kuhn RM, Smith KE, Zwieg AS. Evolutionary and biomedical insights from the rhesus macaque genome. Science 2007; 316:222-34. [PMID: 17431167 DOI: 10.1126/science.1139247] [Citation(s) in RCA: 989] [Impact Index Per Article: 58.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The rhesus macaque (Macaca mulatta) is an abundant primate species that diverged from the ancestors of Homo sapiens about 25 million years ago. Because they are genetically and physiologically similar to humans, rhesus monkeys are the most widely used nonhuman primate in basic and applied biomedical research. We determined the genome sequence of an Indian-origin Macaca mulatta female and compared the data with chimpanzees and humans to reveal the structure of ancestral primate genomes and to identify evidence for positive selection and lineage-specific expansions and contractions of gene families. A comparison of sequences from individual animals was used to investigate their underlying genetic diversity. The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species.
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Murphy WJ, Pringle TH, Crider TA, Springer MS, Miller W. Using genomic data to unravel the root of the placental mammal phylogeny. Genes Dev 2007; 17:413-21. [PMID: 17322288 PMCID: PMC1832088 DOI: 10.1101/gr.5918807] [Citation(s) in RCA: 316] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2006] [Accepted: 12/20/2006] [Indexed: 11/24/2022]
Abstract
The phylogeny of placental mammals is a critical framework for choosing future genome sequencing targets and for resolving the ancestral mammalian genome at the nucleotide level. Despite considerable recent progress defining superordinal relationships, several branches remain poorly resolved, including the root of the placental tree. Here we analyzed the genome sequence assemblies of human, armadillo, elephant, and opossum to identify informative coding indels that would serve as rare genomic changes to infer early events in placental mammal phylogeny. We also expanded our species sampling by including sequence data from >30 ongoing genome projects, followed by PCR and sequencing validation of each indel in additional taxa. Our data provide support for a sister-group relationship between Afrotheria and Xenarthra (the Atlantogenata hypothesis), which is in turn the sister-taxon to Boreoeutheria. We failed to recover any indels in support of a basal position for Xenarthra (Epitheria), which is suggested by morphology and a recent retroposon analysis, or a hypothesis with Afrotheria basal (Exafricoplacentalia), which is favored by phylogenetic analysis of large nuclear gene data sets. In addition, we identified two retroposon insertions that also support Atlantogenata and none for the alternative hypotheses. A revised molecular timescale based on these phylogenetic inferences suggests Afrotheria and Xenarthra diverged from other placental mammals approximately 103 (95-114) million years ago. We discuss the impacts of this topology on earlier phylogenetic reconstructions and repeat-based inferences of phylogeny.
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Hardison RC, King DC, Taylor J, Wang H, Zhang Y, Zhou Y, Cheng Y, Dorman C, Dore LC, Weiss MJ, Chiaromonte F, Miller W. Comparative genomics to find function in noncoding DNA. Blood Cells Mol Dis 2007. [DOI: 10.1016/j.bcmd.2006.10.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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123
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Zhou Y, Cheng Y, Wang H, Zhang Y, King DC, Taylor J, Chiaromonte F, Dorman C, Miller W, Dore LC, Weiss MJ, Hardison RC. Validation of predicted erythroid cis-regulatory modules. Blood Cells Mol Dis 2007. [DOI: 10.1016/j.bcmd.2006.10.158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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124
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Hardison R, Giardine B, Riemer C, Miller W, Chui D, Wajcman H, Patrinos G. HbVar database for human hemoglobin variants and thalassemia mutations. Blood Cells Mol Dis 2007. [DOI: 10.1016/j.bcmd.2006.10.109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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125
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Giardine B, van Baal S, Kaimakis P, Riemer C, Miller W, Samara M, Kollia P, Anagnou NP, Chui DHK, Wajcman H, Hardison RC, Patrinos GP. HbVar database of human hemoglobin variants and thalassemia mutations: 2007 update. Hum Mutat 2007; 28:206. [PMID: 17221864 DOI: 10.1002/humu.9479] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
HbVar (http://globin.bx.psu.edu/hbvar) is a locus-specific database (LSDB) developed in 2001 by a multi-center academic effort to provide timely information on the genomic sequence changes leading to hemoglobin variants and all types of thalassemia and hemoglobinopathies. Database records include extensive phenotypic descriptions, biochemical and hematological effects, associated pathology, and ethnic occurrence, accompanied by mutation frequencies and references. In addition to the regular updates to entries, we report significant advances and updates, which can be useful not only for HbVar users but also for other LSDB development and curation in general. The query page provides more functionality but in a simpler, more user-friendly format and known single nucleotide polymorphisms in the human alpha- and beta-globin loci are provided automatically. Population-specific beta-thalassemia mutation frequencies for 31 population groups have been added and/or modified and the previously reported delta- and alpha-thalassemia mutation frequency data from 10 population groups have also been incorporated. In addition, an independent flat-file database, named XPRbase (http://www.goldenhelix.org/xprbase), has been developed and linked to the main HbVar web page to provide a succinct listing of 51 experimental protocols available for globin gene mutation screening. These updates significantly augment the database profile and quality of information provided, which should increase the already high impact of the HbVar database, while its combination with the UCSC powerful genome browser and the ITHANET web portal paves the way for drawing connections of clinical importance, that is from genome to function to phenotype.
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