HARMIT MALIK

Summary

Affiliation: Fred Hutchinson Cancer Research Center
Country: USA

Publications

  1. pmc Protein kinase R reveals an evolutionary model for defeating viral mimicry
    Nels C Elde
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Nature 457:485-9. 2009
  2. pmc An evolutionary screen highlights canonical and noncanonical candidate antiviral genes within the primate TRIM gene family
    Ray Malfavon-Borja
    Department of Genome Sciences, University of Washington
    Genome Biol Evol 5:2141-54. 2013
  3. pmc Phylogenomic analysis reveals dynamic evolutionary history of the Drosophila heterochromatin protein 1 (HP1) gene family
    Mia T Levine
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
    PLoS Genet 8:e1002729. 2012
  4. pmc Convergent evolution of escape from hepaciviral antagonism in primates
    Maulik R Patel
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
    PLoS Biol 10:e1001282. 2012
  5. pmc The function and evolution of the restriction factor Viperin in primates was not driven by lentiviruses
    Efrem S Lim
    Department of Microbiology, Fred Hutchinson Cancer Research Center, University of Washington, Seattle, WA 98109 1024, USA
    Retrovirology 9:55. 2012
  6. pmc A unified phylogeny-based nomenclature for histone variants
    Paul B Talbert
    Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
    Epigenetics Chromatin 5:7. 2012
  7. pmc Absence of positive selection on centromeric histones in Tetrahymena suggests unsuppressed centromere: drive in lineages lacking male meiosis
    Nels C Elde
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    J Mol Evol 72:510-20. 2011
  8. pmc Diversifying selection and functional analysis of interleukin-4 suggests antagonism-driven evolution at receptor-binding interfaces
    Madoka Koyanagi
    Department of Immunology, St Jude Children s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
    BMC Evol Biol 10:223. 2010
  9. doi request reprint Major evolutionary transitions in centromere complexity
    Harmit S Malik
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Cell 138:1067-82. 2009
  10. doi request reprint The centromere-drive hypothesis: a simple basis for centromere complexity
    Harmit S Malik
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, Seattle, WA 98109, USA
    Prog Mol Subcell Biol 48:33-52. 2009

Collaborators

  • M Emerman
  • S Henikoff
  • Nels C Elde
  • Yuh Chwen G Lee
  • Frederick A Matsen
  • Stacy M Horner
  • Mia T Levine
  • Michael Gale
  • Yan Zhang
  • Tudor Moldoveanu
  • Joshua M Akey
  • J Madeoy
  • Jane E Jackman
  • Eric Phizicky
  • Thomas Eickbush
  • Sara L Sawyer
  • Danielle Vermaak
  • Julie A Kerns
  • Efrem S Lim
  • Lily I Wu
  • Joshua J Bayes
  • Molly OhAinle
  • Ray Malfavon-Borja
  • Paul B Talbert
  • Maulik R Patel
  • Madoka Koyanagi
  • Semih U Tareen
  • Eric E Smith
  • Shari M Kaiser
  • Monica A Rodriguez
  • Benjamin L Wiggins
  • Marcella D Cervantes
  • William D Burke
  • Prem L Bhalla
  • Kinga Kamieniarz
  • David John Tremethick
  • Benjamin Loppin
  • David Landsman
  • Ramesh Yelagandula
  • W Zacheus Cande
  • M Mitchell Smith
  • Bryan M Turner
  • Yueh Ming Loo
  • William M Bonner
  • BARBARA A HAMKALO
  • Bing Zhu
  • Sandra B Hake
  • Juan Ausio
  • José M Eirín-López
  • George A M Cross
  • Jan Postberg
  • Detlef Doenecke
  • William F Marzluff
  • Andreas G Ladurner
  • Robert Schneider
  • Liwang Cui
  • Heike Wollmann
  • Genevieve Almouzni
  • Eric Thompson
  • Sarah Holec
  • Simon W L Chan
  • Frederic Berger
  • Jakob Harm Waterborg
  • Saadi Khochbin
  • Maria Elena Torres-Padilla
  • Martin A Gorovsky
  • Steven E Jacobsen
  • Kami Ahmad
  • John R Pehrson
  • Brian P Chadwick
  • John A Latham
  • Mohan B Singh
  • Stefan I Dimitrov
  • Linda Chung
  • Mark Bix
  • Scott Brown
  • Melody M H Li
  • Meng Chao Yao
  • Xiaohui Xi
  • Stephen M Rich

Detail Information

Publications40

  1. pmc Protein kinase R reveals an evolutionary model for defeating viral mimicry
    Nels C Elde
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Nature 457:485-9. 2009
    ....
  2. pmc An evolutionary screen highlights canonical and noncanonical candidate antiviral genes within the primate TRIM gene family
    Ray Malfavon-Borja
    Department of Genome Sciences, University of Washington
    Genome Biol Evol 5:2141-54. 2013
    ....
  3. pmc Phylogenomic analysis reveals dynamic evolutionary history of the Drosophila heterochromatin protein 1 (HP1) gene family
    Mia T Levine
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
    PLoS Genet 8:e1002729. 2012
    ....
  4. pmc Convergent evolution of escape from hepaciviral antagonism in primates
    Maulik R Patel
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
    PLoS Biol 10:e1001282. 2012
    ..Our analyses also provide a means by which primates might clear infections by extant hepaciviruses like HCV...
  5. pmc The function and evolution of the restriction factor Viperin in primates was not driven by lentiviruses
    Efrem S Lim
    Department of Microbiology, Fred Hutchinson Cancer Research Center, University of Washington, Seattle, WA 98109 1024, USA
    Retrovirology 9:55. 2012
    ..Since HIV-1 and other retroviruses depend on lipid domains of the host cell for budding and infectivity, we investigated the possibility that Viperin also restricts human immunodeficiency virus and other retroviruses...
  6. pmc A unified phylogeny-based nomenclature for histone variants
    Paul B Talbert
    Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
    Epigenetics Chromatin 5:7. 2012
    ..For clarity and searchability, we encourage the use of descriptors that are separate from the phylogeny-based variant name to indicate developmental and other properties of variants that may be independent of structure...
  7. pmc Absence of positive selection on centromeric histones in Tetrahymena suggests unsuppressed centromere: drive in lineages lacking male meiosis
    Nels C Elde
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    J Mol Evol 72:510-20. 2011
    ..Our study raises the possibility that taxa like ciliates, with only female meiosis, may therefore undergo unsuppressed centromere drive...
  8. pmc Diversifying selection and functional analysis of interleukin-4 suggests antagonism-driven evolution at receptor-binding interfaces
    Madoka Koyanagi
    Department of Immunology, St Jude Children s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
    BMC Evol Biol 10:223. 2010
    ..Reasoning that helminths may have evolved mechanisms to antagonize IL4 to maximize their dispersal, we explored mammalian IL4 evolution...
  9. doi request reprint Major evolutionary transitions in centromere complexity
    Harmit S Malik
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Cell 138:1067-82. 2009
    ....
  10. doi request reprint The centromere-drive hypothesis: a simple basis for centromere complexity
    Harmit S Malik
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, Seattle, WA 98109, USA
    Prog Mol Subcell Biol 48:33-52. 2009
    ..This chapter summarizes the mounting evidence in favor of the centromere-drive model, and its implications for centromere evolution in taxa with variations in meiosis...
  11. ncbi request reprint Phylogenetic analysis of ribonuclease H domains suggests a late, chimeric origin of LTR retrotransposable elements and retroviruses
    H S Malik
    Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Genome Res 11:1187-97. 2001
    ....
  12. pmc A hitchhiker's guide to survival finally makes CENs
    Harmit S Malik
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    J Cell Biol 174:747-9. 2006
    ....
  13. ncbi request reprint Genetic conflicts during meiosis and the evolutionary origins of centromere complexity
    H S Malik
    Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, A1 162, Seattle, WA 98109, USA
    Biochem Soc Trans 34:569-73. 2006
    ..CenH3s as well as other heterochromatin proteins have evolved under positive selection to suppress the deleterious consequences of 'centromere-drive' by restoring meiotic parity...
  14. ncbi request reprint Conflict begets complexity: the evolution of centromeres
    Harmit S Malik
    Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Curr Opin Genet Dev 12:711-8. 2002
    ....
  15. ncbi request reprint Ribonuclease H evolution in retrotransposable elements
    H S Malik
    Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 1024, USA
    Cytogenet Genome Res 110:392-401. 2005
    ..It appears that all LTR retrotransposons are as old as, or younger than, the "youngest" lineages of non-LTR retroelements, suggesting that LTR retrotransposons arose late in eukaryotes...
  16. pmc Positive selection of Iris, a retroviral envelope-derived host gene in Drosophila melanogaster
    Harmit S Malik
    Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
    PLoS Genet 1:e44. 2005
    ..We propose a model in which Iris has "switched sides," having been recruited by host genomes to combat baculoviruses and retroviruses, which employ homologous envelope genes to mediate infection...
  17. pmc A surrogate approach to study the evolution of noncoding DNA elements that organize eukaryotic genomes
    Danielle Vermaak
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    J Hered 100:624-36. 2009
    ..These insights also help to explain why the same elements (e.g., centromeres and replication origins), which are so complex in some eukaryotic genomes, can be simple and well defined in other where similar conflicts do not exist...
  18. pmc Recurrent evolution of DNA-binding motifs in the Drosophila centromeric histone
    Harmit S Malik
    Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Proc Natl Acad Sci U S A 99:1449-54. 2002
    ..The recurrent evolution of these motifs in CenH3 suggests a packaging function for the N-terminal tail, which results in a unique chromatin organization at the primary constriction, the cytological marker of centromeres...
  19. pmc Molecular evolution of Drosophila Cdc6, an essential DNA replication-licensing gene, suggests an adaptive choice of replication origins
    Benjamin L Wiggins
    Molecular and Cellular Biology Program, University of Washington Seattle, Washington 98109, USA
    Fly (Austin) 1:155-63. 2007
    ..Our results suggest that choice of origin firing may be significantly altered in closely related species, as each set of replication proteins optimizes to its own genomic landscape...
  20. pmc Positive selection of yeast nonhomologous end-joining genes and a retrotransposon conflict hypothesis
    Sara L Sawyer
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Proc Natl Acad Sci U S A 103:17614-9. 2006
    ....
  21. ncbi request reprint The evolutionary conundrum of pathogen mimicry
    Nels C Elde
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Nat Rev Microbiol 7:787-97. 2009
    ..Even in these instances, mimicry may alter the evolutionary course of fundamental cellular processes in host organisms...
  22. pmc Species-specific positive selection of the male-specific lethal complex that participates in dosage compensation in Drosophila
    Monica A Rodriguez
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Proc Natl Acad Sci U S A 104:15412-7. 2007
    ....
  23. pmc Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G
    Sara L Sawyer
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
    PLoS Biol 2:E275. 2004
    ..Despite being only recently discovered, editing of RNA and DNA may thus represent an ancient form of host defense in primate genomes...
  24. doi request reprint Multiple roles for heterochromatin protein 1 genes in Drosophila
    Danielle Vermaak
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Annu Rev Genet 43:467-92. 2009
    ....
  25. pmc The apolipoprotein L family of programmed cell death and immunity genes rapidly evolved in primates at discrete sites of host-pathogen interactions
    Eric E Smith
    Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Genome Res 19:850-8. 2009
    ..Hence, the dynamic APOL gene family appears to be an important link between programmed cell death of host cells and immunity to pathogens...
  26. pmc Positive selection of primate TRIM5alpha identifies a critical species-specific retroviral restriction domain
    Sara L Sawyer
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Proc Natl Acad Sci U S A 102:2832-7. 2005
    ..Our study highlights the power of evolutionary analyses, in which positive selection identifies not only the age of genetic conflict but also the interaction interface where this conflict plays out...
  27. pmc Discordant evolution of the adjacent antiretroviral genes TRIM22 and TRIM5 in mammals
    Sara L Sawyer
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
    PLoS Pathog 3:e197. 2007
    ..Astonishingly, this same loop is under positive selection in the multiple cow TRIM5 genes as well, indicating that this small structural loop may be a viral recognition motif spanning a hundred million years of mammalian evolution...
  28. ncbi request reprint Centromeres: selfish drivers
    Steven Henikoff
    Fred Hutchinson Cancer Research Center and the Howard Hughes Medical Institute, 1100 Fairview Avenue North, Seattle, Washington 98109, USA
    Nature 417:227. 2002
  29. pmc The CNA1 histone of the ciliate Tetrahymena thermophila is essential for chromosome segregation in the germline micronucleus
    Marcella D Cervantes
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Mol Biol Cell 17:485-97. 2006
    ..This study reveals a strong dependence of the germline micronucleus on centromeric histones for proper chromosome segregation...
  30. pmc Altered heterochromatin binding by a hybrid sterility protein in Drosophila sibling species
    Joshua J Bayes
    Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98185, USA
    Science 326:1538-41. 2009
    ..These results reveal that rapid heterochromatin evolution affects the onset of hybrid sterility...
  31. ncbi request reprint Phylogenomics of the nucleosome
    Harmit S Malik
    Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Nat Struct Biol 10:882-91. 2003
    ..How these diverse functions have evolved from ancestral forms can be addressed by applying phylogenetic tools to increasingly abundant sequence data...
  32. pmc Ancient adaptive evolution of tetherin shaped the functions of Vpu and Nef in human immunodeficiency virus and primate lentiviruses
    Efrem S Lim
    Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, P O Box 10924, Seattle, WA 98109 1024, USA
    J Virol 84:7124-34. 2010
    ..Our combined evolutionary and functional studies have allowed us to reconstruct the host-pathogen interactions that have shaped Tetherin and its lentivirus-encoded antagonists...
  33. pmc Positive selection and increased antiviral activity associated with the PARP-containing isoform of human zinc-finger antiviral protein
    Julie A Kerns
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
    PLoS Genet 4:e21. 2008
    ..The striking congruence between our evolutionary predictions and cellular infectivity assays strongly validates such a combined approach to study intrinsic immunity genes...
  34. pmc An expanded clade of rodent Trim5 genes
    Semih U Tareen
    Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
    Virology 385:473-83. 2009
    ..Sampling six rodent Trim5 genes failed to reveal antiviral activities against a set of eight retroviral challenges, although we predict that such activities exist...
  35. ncbi request reprint Restriction of an extinct retrovirus by the human TRIM5alpha antiviral protein
    Shari M Kaiser
    Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
    Science 316:1756-8. 2007
    ....
  36. ncbi request reprint High-frequency persistence of an impaired allele of the retroviral defense gene TRIM5alpha in humans
    Sara L Sawyer
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Curr Biol 16:95-100. 2006
    ..The unexpectedly high frequency of an impaired retroviral restriction allele among humans is likely to have a significant impact on our ability to ward off future retroviral challenges...
  37. pmc Antiretroelement activity of APOBEC3H was lost twice in recent human evolution
    Molly OhAinle
    Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
    Cell Host Microbe 4:249-59. 2008
    ....
  38. pmc Identification of the yeast gene encoding the tRNA m1G methyltransferase responsible for modification at position 9
    Jane E Jackman
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York 14642, USA
    RNA 9:574-85. 2003
    ..Trm10p homologs are found widely in eukaryotes and many archaea, with multiple homologs in several metazoans, including at least three in humans...
  39. ncbi request reprint Ancient lineages of non-LTR retrotransposons in the primitive eukaryote, Giardia lamblia
    William D Burke
    Department of Biology, University of Rochester, Rochester, NY 14627, USA
    Mol Biol Evol 19:619-30. 2002
    ..Genie 2 elements do not appear to be site specific in their insertion. An unusual aspect of Genie 2 is that all copies contain inverted repeats up to 172 bp in length...
  40. pmc Adaptive evolution and antiviral activity of the conserved mammalian cytidine deaminase APOBEC3H
    Molly OhAinle
    Molecular and Cellular Biology Program, University of Washington, Seattle 98109, USA
    J Virol 80:3853-62. 2006
    ..The consequences of the lack of antiviral activity of human APOBEC3H are likely to be relevant to the current-day abilities of humans to combat retroviral challenges...

Research Grants6