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  • Genomic analysis of nCoV spread. Situation report 2020-01-23. 

    Bedford, Trevor; Neher, Richard; Hadfield, James; Hodcroft, Emma; Ilcisin, Misja; Muller, Nicola (2020-01-23)
    Using 24 public shared novel coronavirus (nCoV) genomes, we examined genetic diversity to infer date of common ancestor and rate of spread. We find: 24 sampled genomes are nearly identical, differing by 0-3 mutations This ...
  • Resolving multicopy duplications de novo using polyploid phasing 

    Chaisson, Mark J; Mukherjee, Sudipto; Kannan, Sreeram; Eichler, Evan E (Springer, 2017-05)
    While the rise of single-molecule sequencing systems has enabled an unprecedented rise in the ability to assemble complex regions of the genome, long segmental duplications in the genome still remain a challenging ...
  • The evolution and population diversity of human-specific segmental duplications 

    Dennis, Megan Y; Harshman, Lana; Nelson, Bradley J; Penn, Osnat; Cantsilieris, Stuart; Huddleston, John; Antonacci, Francesca; Penewit, Kelsi; Denman, Laura; Raja, Archana; Baker, Carl; Mark, Kenneth; Malig, Maika; Janke, Nicolette; Espinoza, Claudia; Stessman, Holly A; Nuttle, Xander; Hoekzema, Kendra; Graves, Tina A; Wilson, Richard K; Eichler, Evan E (Nature Ecology & Evolution, 2017-02-17)
    Segmental duplications contribute significantly to the evolution, adaptation and diseaseassociated instability of the human genome. The largest and most identical duplications suffer from the poorest characterization, ...
  • Evolutionary conservation of regulated longevity assurance mechanisms 

    McElwee, Joshua J.; Schuster, Eugene; Blanc, Eric; Piper, Matthew D.; Thomas, James H.; Patel, Dhaval S.; Selman, Colin; Withers, Dominic J.; Thorton, Janet M.; Partridge, Linda; Gems, David (2007)
    Background: To what extent are the determinants of aging in animal species universal? Insulin/insulin-like growth factor (IGF)-1 signaling (IIS) is an evolutionarily conserved (public) regulator of longevity; yet it remains ...
  • The Caenorhabditis chemoreceptor gene families 

    Thomas, James H.; Robertson, Hugh M. (2008)
    Background: Chemoreceptor proteins mediate the first step in the transduction of environmental chemical stimuli, defining the breadth of detection and conferring stimulus specificity. Animal genomes contain families of ...
  • Multiple origins of resistance-conferring mutations in Plasmodium vivax dihydrofolate reductase 

    Hawkins, Vivian N.; Auliff, Alyson; Prajapati, Surendra Kumar; Rungsihirunrat, Kanchana; Hapuarachchi, Hapuarachchige C.; Maestre, Amanda; O'Neil, Michael T.; Cheng, Qin; Joshi, Hema; Nabangchang, Kesara; Sibley, Carol Hopkins (2008)
    Background: In order to maximize the useful therapeutic life of antimalarial drugs, it is crucial to understand the mechanisms by which parasites resistant to antimalarial drugs are selected and spread in natural populations. ...
  • World Antimalarial Resistance Network (WARN) IV: Clinical pharmacology 

    Barnes, Karen I.; Lindegardh, Niklas; Ogundahunsi, Olumide; Olliaro, Piero; Plowe, Christopher V.; Randrianarievelojosia, Milijaona; Gbotosho, Grace O.; Watkins, William M.; Sibley, Carol Hopkins; White, Nicholas J. (2007)
    A World Antimalarial Resistance Network (WARN) database has the potential to improve the treatment of malaria, through informing current drug selection and use and providing a prompt warning of when treatment policies need ...
  • World Antimalarial Resistance Network (WARN) III: Molecular markers for drug resistant malaria 

    Plowe, Christopher V.; Roper, Cally; Barnwell, John W.; Happi, Christian T.; Joshi, Hema H.; Mbacham, Wilfred; Meshnick, Steven R.; Mugittu, Kefas; Naidoo, Inbarani; Price, Ric N.; Shafer, Robert W.; Sibley, Carol Hopkins; Sutherland, Colin J.; Zimmerman, Peter A.; Rosenthal, Phillip J. (2007)
    Molecular markers for drug resistant malaria represent public health tools of great but mostly unrealized potential value. A key reason for the failure of molecular resistance markers to live up to their potential is that ...
  • World Antimalarial Resistance Network (WARN) II: In vitro antimalarial drug susceptibility 

    Bacon, David J.; Jambou, Ronan; Fandeur, Thierry; Le Bras, Jacques; Wongsrichanalai, Chansuda; Fukuda, Mark M.; Ringwald, Pascal; Sibley, Carol Hopkins; Kyle, Dennis E. (2007)
    Intrinsic resistance of Plasmodium falciparum is clearly a major determinant of the clinical failure of antimalarial drugs. However, complex interactions between the host, the parasite and the drug obscure the ability to ...
  • The rationale and plan for creating a World Antimalarial Resistance Network (WARN) 

    Sibley, Carol Hopkins; Barnes, Karen I.; Plowe, Christopher V. (2007)
    Drug resistant malaria was a major factor contributing to the failure of a worldwide campaign to eradicate malaria in the last century, and now threatens the large investment being made by the global community in the rollout ...
  • A database of antimalarial drug resistance 

    Sibley, Carol Hopkins; Ringwald, Pascal (2006)
    A large investment is required to develop, license and deploy a new antimalarial drug. Too often, that investment has been rapidly devalued by the selection of parasite populations resistant to the drug action. To understand ...
  • Interaction of an atypical Plasmodium falciparum ETRAMP with human apolipoproteins 

    Vignali, Marissa; McKinlay, Anastasia; LaCount, Douglas J.; Chettier, Rakesh; Bell, Russell; Sahasrabudhe, Sudhir; Hughes, Robert E.; Fields, Stanley (2008)
    Background: In order to establish a successful infection in the human host, the malaria parasite Plasmodium falciparum must establish interactions with a variety of human proteins on the surface of different cell types, ...
  • Hominoid chromosomal rearrangements on 17q map to complex regions of segmental duplication 

    Cardone, Maria Francesca; Jiang, Zhaoshi; D'Addabbo, Pietro; Archidiacono, Nicoletta; Rocchi, Mariano; She, Xinwei; Eichler, Evan E.; Ventura, Mario. (2008)
    Background: Chromosomal rearrangements, such as translocations and inversions, are recurrent phenomena during evolution, and both of them are involved in reproductive isolation and speciation. To better understand the ...
  • Independent centromere formation in a capricious, gene-free domain of chromosome 13q21 in Old World monkeys and pigs 

    Cardone, Maria Francesca; Alonso, Alicia; Pazienza, Michele; Ventura, Mario; Montermurro, Gabriella; Carbone, Lucia; De Jong, Pieter J.; Stanyon, Roscoe; D'Addabbo, Pietro; Archidiacono, Nicoletta; She, Xinwei; Eichler, Evan E.; Warburton, Peter E.; Rocchi, Mariano (2006)
    Background: Evolutionary centromere repositioning and human analphoid neocentromeres occurring in clinical cases are, very likely, two stages of the same phenomenon whose properties still remain substantially obscure. ...
  • The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements 

    Marques-Bonet, Tom�s; Cheng, Ze; She, Xinwei; Eichler, Evan E.; Navarro, Arcadi (2008)
    Background: It has been suggested that chromosomal rearrangements harbor the molecular footprint of the biological phenomena which they induce, in the form, for instance, of changes in the sequence divergence rates of ...
  • On the number of founding germ cells in humans 

    Zheng, Chang-Jiang; Luebeck, E. Georg; Byers, Breck E.; Moolgavkar, Suresh H. (2005)
    Background: The number of founding germ cells (FGCs) in mammals is of fundamental significance to the fidelity of gene transmission between generations, but estimates from various methods vary widely. In this paper we ...