faculty
Harmit Malik
hsmalik@fhcrc.org
Professor
Fred Hutch
,Basic Sciences
Gene Expression, Cell Cycle & Chromosome Biology
Genetics, Genomics & Evolution
Microbiology, Infection & Immunity
Evolutionary and functional studies of genetic conflicts
Faculty Contact Information
Building: Weintraub Building
Room: A2-205
Box: A2-025
Phone: 206-667-5204
Alt Phone: 206-667-4512
http://research.fhcrc.org/malik/en.html
Research Summary
My lab studies how eukaryotic genetics and epigenetics have been shaped by diverse genetic conflicts. Projects in the lab can be roughly classified into two types: extrinsic (between genomes) conflicts that shape genes involved in host-pathogen interactions, and intrinsic (within genome) conflicts that shape eukaryotic genomes. We use studies that combine insights from evolutionary biology together with molecular/ cellular biology, virology, and genetics. While our primary research organism is Drosophila, we study a variety of model and non-systems depending on the research question.
DEI Statement
My lab is committed to enhancing diversity by increasing the participation of individuals from diverse backgrounds, including those from underrepresented groups, in biomedical sciences. Two of the eleven students who have finished their Ph.D. studies in my lab are from underrepresented communities. We have trained nearly two dozen undergraduate students from underrepresented groups in post-baccalaureate or research technician positions, and in summer internships; the vast majority of these students went on to Ph.D. or M.D. or M.D./Ph.D. studies.
Training Summary
My lab is also involved in the training of graduate and postdoctoral trainees. Our work is interdisciplinary and our trainees are trained in evolutionary, computational, cell and molecular biology. I consider my trainees and their success as my most significant contribution to science. The Malik lab seeks graduate trainees who desire being in a lab full of diverse projects, where they can design and implement an independent research program. We aim to provide a supportive and enriching training environment that will enable students to achieve their goals.
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Publications
The following publications were retrieved from PubMed:
A functional map of HIV-host interactions in primary human T cells.
Hiatt J, Hultquist JF, McGregor MJ, Bouhaddou M, Leenay RT, Simons LM, Young JM, Haas P, Roth TL, Tobin V, Wojcechowskyj JA, Woo JM, Rathore U, Cavero DA, Shifrut E, Nguyen TT, Haas KM, Malik HS, Doudna JA, May AP, Marson A, Krogan NJ.
Nat Commun. 2022 Apr 1; 1(13)1752
Novel Classes and Evolutionary Turnover of Histone H2B Variants in the Mammalian Germline.
Raman P, Rominger MC, Young JM, Molaro A, Tsukiyama T, Malik HS.
Mol Biol Evol. 2022 Feb 3; 2(39)
Evolutionary Landscapes of Host-Virus Arms Races.
Tenthorey JL, Emerman M, Malik HS.
Annu Rev Immunol. 2022 Apr 26; (40)271-294
The novel anti-CRISPR AcrIIA22 relieves DNA torsion in target plasmids and impairs SpyCas9 activity.
Forsberg KJ, Schmidtke DT, Werther R, Uribe RV, Hausman D, Sommer MOA, Stoddard BL, Kaiser BK, Malik HS.
PLoS Biol. 2021 Oct; 10(19)e3001428
Schroeder CM, Tomlin SA, Mejia Natividad I, Valenzuela JR, Young JM, Malik HS.
Elife. 2021 Jul 20; (10)
Gametic specialization of centromeric histone paralogs in Drosophila virilis.
Kursel LE, McConnell H, de la Cruz AFA, Malik HS.
Life Sci Alliance. 2021 Jul; 7(4)
Putting the brakes on centromere drive in Mimulus.
Chang CH, Malik HS.
PLoS Genet. 2021 Apr; 4(17)e1009494
A balancing act between primate lentiviruses and their receptor.
Ohainle M, Malik HS.
Proc Natl Acad Sci U S A. 2021 May 18; 20(118)
Mushtaq I, Cheema HA, Malik HS, Waheed N.
J Ayub Med Coll Abbottabad. 2021 Jan-Mar; 1(33)14-19
Short H2A histone variants are expressed in cancer.
Chew GL, Bleakley M, Bradley RK, Malik HS, Henikoff S, Molaro A, Sarthy J.
Nat Commun. 2021 Jan 20; 1(12)490
P2RX7 at the Host-Pathogen Interface of Infectious Diseases.
Soare AY, Freeman TL, Min AK, Malik HS, Osota EO, Swartz TH.
Microbiol Mol Biol Rev. 2021 Feb 17; 1(85)
Kato K, Ahmad S, Zhu Z, Young JM, Mu X, Park S, Malik HS, Hur S.
Mol Cell. 2021 Feb 4; 3(81)599-613.e8
Biparental contributions of the H2A.B histone variant control embryonic development in mice.
Molaro A, Wood AJ, Janssens D, Kindelay SM, Eickbush MT, Wu S, Singh P, Muller CH, Henikoff S, Malik HS.
PLoS Biol. 2020 Dec; 12(18)e3001001
Kasinathan B, Colmenares SU 3rd, McConnell H, Young JM, Karpen GH, Malik HS.
Elife. 2020 Nov 10; (9)
Hays M, Young JM, Levan PF, Malik HS.
Elife. 2020 Oct 16; (9)
Tenthorey JL, Young C, Sodeinde A, Emerman M, Malik HS.
Elife. 2020 Sep 15; (9)
The pyrin inflammasome and the Yersinia effector interaction.
Malik HS, Bliska JB.
Immunol Rev. 2020 Sep; 1(297)96-107
Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O'Meara MJ, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Naing ZZC, Zhou Y, Peng S, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Shen W, Shi Y, Zhang Z, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Ramachandran R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Lin Y, Wankowicz SA, Bohn M, Trenker R, Young JM, Cavero D, Hiatt J, Roth T, Rathore U, Subramanian A, Noack J, Hubert M, Roesch F, Vallet T, Meyer B, White KM, Miorin L, Agard D, Emerman M, Ruggero D, García-Sastre A, Jura N, von Zastrow M, Taunton J, Schwartz O, Vignuzzi M, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor S, Fraser JS, Gross J, Sali A, Kortemme T, Beltrao P, Shokat K, Shoichet BK, Krogan NJ.
bioRxiv. 2020 Mar 22;
Retrocopying expands the functional repertoire of APOBEC3 antiviral proteins in primates.
Yang L, Emerman M, Malik HS, McLaughlin RN Jnr.
Elife. 2020 Jun 1; (9)
A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.
Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Meyer B, Roesch F, Vallet T, Mac Kain A, Miorin L, Moreno E, Naing ZZC, Zhou Y, Peng S, Shi Y, Zhang Z, Shen W, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Lyu J, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Rakesh R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Liboy-Lugo J, Lin Y, Huang XP, Liu Y, Wankowicz SA, Bohn M, Safari M, Ugur FS, Koh C, Savar NS, Tran QD, Shengjuler D, Fletcher SJ, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, Sharp PP, Wenzell NA, Kuzuoglu-Ozturk D, Wang HY, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Stroud RM, Frankel AD, Rosenberg OS, Verba KA, Agard DA, Ott M, Emerman M, Jura N, von Zastrow M, Verdin E, Ashworth A, Schwartz O, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor SN, Fraser JS, Gross JD, Sali A, Roth BL, Ruggero D, Taunton J, Kortemme T, Beltrao P, Vignuzzi M, García-Sastre A, Shokat KM, Shoichet BK, Krogan NJ.
Nature. 2020 Jul; 7816(583)459-468
Ancient Coretention of Paralogs of Cid Centromeric Histones and Cal1 Chaperones in Mosquito Species.
Kursel LE, Welsh FC, Malik HS.
Mol Biol Evol. 2020 Jul 1; 7(37)1949-1963
Dynamic Evolution of De Novo DNA Methyltransferases in Rodent and Primate Genomes.
Molaro A, Malik HS, Bourc'his D.
Mol Biol Evol. 2020 Jul 1; 7(37)1882-1892
Soare AY, Malik HS, Durham ND, Freeman TL, Alvarez R, Patel F, Satija N, Upadhyay C, Hioe CE, Chen BK, Swartz TH.
J Virol. 2020 Feb 28; 6(94)
Hybridization promotes asexual reproduction in Caenorhabditis nematodes.
Lamelza P, Young JM, Noble LM, Caro L, Isakharov A, Palanisamy M, Rockman MV, Malik HS, Ailion M.
PLoS Genet. 2019 Dec; 12(15)e1008520
Meiosis: How Gambling Chromosomes Beat the Rules.
Schroeder CM, Malik HS.
Curr Biol. 2019 Dec 2; 23(29)R1247-R1248
A Burst of Genetic Innovation in Drosophila Actin-Related Proteins for Testis-Specific Function.
Schroeder CM, Valenzuela JR, Mejia Natividad I, Hocky GM, Malik HS.
Mol Biol Evol. 2020 Mar 1; 3(37)757-772
Combinatorial mutagenesis of rapidly evolving residues yields super-restrictor antiviral proteins.
Colón-Thillet R, Hsieh E, Graf L, McLaughlin RN Jr, Young JM, Kochs G, Emerman M, Malik HS.
PLoS Biol. 2019 Oct; 10(17)e3000181
EvoChromo: towards a synthesis of chromatin biology and evolution.
Drinnenberg IA, Berger F, Elsässer SJ, Andersen PR, Ausió J, Bickmore WA, Blackwell AR, Erwin DH, Gahan JM, Gaut BS, Harvey ZH, Henikoff S, Kao JY, Kurdistani SK, Lemos B, Levine MT, Luger K, Malik HS, Martín-Durán JM, Peichel CL, Renfree MB, Rutowicz K, Sarkies P, Schmitz RJ, Technau U, Thornton JW, Warnecke T, Wolfe KH.
Development. 2019 Sep 26; 19(146)
Functional metagenomics-guided discovery of potent Cas9 inhibitors in the human microbiome.
Forsberg KJ, Bhatt IV, Schmidtke DT, Javanmardi K, Dillard KE, Stoddard BL, Finkelstein IJ, Kaiser BK, Malik HS.
Elife. 2019 Sep 10; (8)
Levin TC, Goldspiel BP, Malik HS.
Elife. 2019 May 28; (8)
The PLOS Biology XV Collection: 15 Years of Exceptional Science Highlighted across 12 Months.
Richardson LA, Schmid SL, Bhandoola A, Harly C, Hedenström A, Laub MT, Mace GM, Sengupta P, Stock AM, Read AF, Malik HS, Estelle M, Lowell S, Kimmelman J.
PLoS Biol. 2019 Feb; 2(17)e3000180
Microbial Genomics: The Expanding Universe of Bacterial Defense Systems.
Forsberg KJ, Malik HS.
Curr Biol. 2018 Apr 23; 8(28)R361-R364
Evolutionary origins and diversification of testis-specific short histone H2A variants in mammals.
Molaro A, Young JM, Malik HS.
Genome Res. 2018 Apr; 4(28)460-473
Electrocardiographic Manifestations In Paediatric Wilson Disease.
Batool Hamdani SS, Cheema HA, Saeed A, Malik HS, Sehar T.
J Ayub Med Coll Abbottabad. 2018 Jan-Mar; 1(30)22-25
The cellular mechanisms and consequences of centromere drive.
Kursel LE, Malik HS.
Curr Opin Cell Biol. 2018 Jun; (52)58-65
Genetics: Master Regulator or Master of Disguise?
Ailion M, Malik HS.
Curr Biol. 2017 Sep 11; 17(27)R844-R847
Kasinathan B, Ahmad K, Malik HS.
Genetics. 2017 Sep; 1(207)49-51
Malik HS, Cheema HA, Fayyaz Z, Hashmi MA, Parkash A, Waheed N, Mushtaq I, Anjum N.
J Ayub Med Coll Abbottabad. 2016 Jul-Sep; 3(28)518-522
Mushtaq I, Cheema HA, Malik HS, Waheed N, Hashmi MA, Malik HS.
J Ayub Med Coll Abbottabad. 2017 Jan-Mar; 1(29)78-82
Clinical Spectrum Of Solitary Rectal Ulcer In Children Presenting With Per-Rectal Bleed.
Anjum MN, Cheema HA, Malik HS, Hashmi MA.
J Ayub Med Coll Abbottabad. 2017 Jan-Mar; 1(29)74-77
wtf genes are prolific dual poison-antidote meiotic drivers.
Nuckolls NL, Bravo Núñez MA, Eickbush MT, Young JM, Lange JJ, Yu JS, Smith GR, Jaspersen SL, Malik HS, Zanders SE.
Elife. 2017 Jun 20; (6)
Rapidly Evolving Toll-3/4 Genes Encode Male-Specific Toll-Like Receptors in Drosophila.
Levin TC, Malik HS.
Mol Biol Evol. 2017 Sep 1; 9(34)2307-2323
Corrigendum: Evolution of a transcriptional regulator from a transmembrane nucleoporin.
Franks TM, Benner C, Narvaiza I, Marchetto MCN, Young JM, Malik HS, Gage FH, Hetzer MW.
Genes Dev. 2017 Apr 15; 8(31)845
Kursel LE, Malik HS.
Mol Biol Evol. 2017 Jun 1; 6(34)1445-1462
Cheng CY, Young JM, Lin CG, Chao JL, Malik HS, Yao MC.
Genes Dev. 2016 Dec 15; 24(30)2724-2736
Genetic conflicts: the usual suspects and beyond.
McLaughlin RN Jr, Malik HS.
J Exp Biol. 2017 Jan 1; Pt 1(220)6-17
Did a Single Amino Acid Change Make Ebola Virus More Virulent?
Bedford T, Malik HS.
Cell. 2016 Nov 3; 4(167)892-894
Patel MR, Miriyala GK, Littleton AJ, Yang H, Trinh K, Young JM, Kennedy SR, Yamashita YM, Pallanck LJ, Malik HS.
Elife. 2016 Aug 2; (5)
Daugherty MD, Schaller AM, Geballe AP, Malik HS.
Elife. 2016 May 31; (5)
Evolution of a transcriptional regulator from a transmembrane nucleoporin.
Franks TM, Benner C, Narvaiza I, Marchetto MC, Young JM, Malik HS, Gage FH, Hetzer MW.
Genes Dev. 2016 May 15; 10(30)1155-71
Conservation and Innovation of APOBEC3A Restriction Functions during Primate Evolution.
McLaughlin RN Jr, Gable JT, Wittkopp CJ, Emerman M, Malik HS.
Mol Biol Evol. 2016 Aug; 8(33)1889-901
Recurrent Gene Duplication Diversifies Genome Defense Repertoire in Drosophila.
Levine MT, Vander Wende HM, Hsieh E, Baker EP, Malik HS.
Mol Biol Evol. 2016 Jul; 7(33)1641-53
Evolutionary Turnover of Kinetochore Proteins: A Ship of Theseus?
Drinnenberg IA, Henikoff S, Malik HS.
Trends Cell Biol. 2016 Jul; 7(26)498-510
Hide and seek: how chromatin-based pathways silence retroelements in the mammalian germline.
Molaro A, Malik HS.
Curr Opin Genet Dev. 2016 Apr; (37)51-58
An essential cell cycle regulation gene causes hybrid inviability in Drosophila.
Phadnis N, Baker EP, Cooper JC, Frizzell KA, Hsieh E, de la Cruz AF, Shendure J, Kitzman JO, Malik HS.
Science. 2015 Dec 18; 6267(350)1552-5
Evolutionary Analyses Suggest a Function of MxB Immunity Proteins Beyond Lentivirus Restriction.
Mitchell PS, Young JM, Emerman M, Malik HS.
PLoS Pathog. 2015 Dec; 12(11)e1005304
Chromosome segregation: human female meiosis breaks all the rules.
Zanders SE, Malik HS.
Curr Biol. 2015 Aug 3; 15(25)R654-6
BIOSAFETY. Safeguarding gene drive experiments in the laboratory.
Akbari OS, Bellen HJ, Bier E, Bullock SL, Burt A, Church GM, Cook KR, Duchek P, Edwards OR, Esvelt KM, Gantz VM, Golic KG, Gratz SJ, Harrison MM, Hayes KR, James AA, Kaufman TC, Knoblich J, Malik HS, Matthews KA, O'Connor-Giles KM, Parks AL, Perrimon N, Port F, Russell S, Ueda R, Wildonger J.
Science. 2015 Aug 28; 6251(349)927-9
Mitotic fidelity requires transgenerational action of a testis-restricted HP1.
Levine MT, Vander Wende HM, Malik HS.
Elife. 2015 Jul 7; (4)e07378
R2d2 and Hyperdrive Mechanisms (in Mouse Meiosis).
Zanders SE, Malik HS.
PLoS Genet. 2015 Feb; 2(11)e1004950
Transferred interbacterial antagonism genes augment eukaryotic innate immune function.
Chou S, Daugherty MD, Peterson SB, Biboy J, Yang Y, Jutras BL, Fritz-Laylin LK, Ferrin MA, Harding BN, Jacobs-Wagner C, Yang XF, Vollmer W, Malik HS, Mougous JD.
Nature. 2015 Feb 5; 7537(518)98-101
Evolutionary cell biology: two origins, one objective.
Lynch M, Field MC, Goodson HV, Malik HS, Pereira-Leal JB, Roos DS, Turkewitz AP, Sazer S.
Proc Natl Acad Sci U S A. 2014 Dec 2; 48(111)16990-4
Mobile genetic elements and genome evolution 2014.
Singh PK, Bourque G, Craig NL, Dubnau JT, Feschotte C, Flasch DA, Gunderson KL, Malik HS, Moran JV, Peters JE, Slotkin RK, Levin HL.
Mob DNA. 2014; (5)26
Genetic conflicts: stronger centromeres win tug-of-war in female meiosis.
Ross BD, Malik HS.
Curr Biol. 2014 Oct 6; 19(24)R966-8
Recurrent loss of CenH3 is associated with independent transitions to holocentricity in insects.
Drinnenberg IA, deYoung D, Henikoff S, Malik HS.
Elife. 2014 Sep 23; (3)
McLaughlin RN Jr, Young JM, Yang L, Neme R, Wichman HA, Malik HS.
PLoS Genet. 2014 Sep; 9(10)e1004531
How a virus blocks a cellular emergency access lane to the nucleus, STAT!
Daugherty MD, Malik HS.
Cell Host Microbe. 2014 Aug 13; 2(16)150-152
Genome rearrangements and pervasive meiotic drive cause hybrid infertility in fission yeast.
Zanders SE, Eickbush MT, Yu JS, Kang JW, Fowler KR, Smith GR, Malik HS.
Elife. 2014 Jun 24; (3)e02630
Rapid evolution of PARP genes suggests a broad role for ADP-ribosylation in host-virus conflicts.
Daugherty MD, Young JM, Kerns JA, Malik HS.
PLoS Genet. 2014; 5(10)e1004403
Molecular basis for specific recognition of bacterial ligands by NAIP/NLRC4 inflammasomes.
Tenthorey JL, Kofoed EM, Daugherty MD, Malik HS, Vance RE.
Mol Cell. 2014 Apr 10; 1(54)17-29
Malfavon-Borja R, Sawyer SL, Wu LI, Emerman M, Malik HS.
Genome Biol Evol. 2013; 11(5)2141-54
Host gene evolution traces the evolutionary history of ancient primate lentiviruses.
Compton AA, Malik HS, Emerman M.
Philos Trans R Soc Lond B Biol Sci. 2013 Sep 19; 1626(368)20120496
Carter JJ, Daugherty MD, Qi X, Bheda-Malge A, Wipf GC, Robinson K, Roman A, Malik HS, Galloway DA.
Proc Natl Acad Sci U S A. 2013 Jul 30; 31(110)12744-9
Stepwise evolution of essential centromere function in a Drosophila neogene.
Ross BD, Rosin L, Thomae AW, Hiatt MA, Vermaak D, de la Cruz AF, Imhof A, Mellone BG, Malik HS.
Science. 2013 Jun 7; 6137(340)1211-4
An evolutionary perspective on the broad antiviral specificity of MxA.
Mitchell PS, Emerman M, Malik HS.
Curr Opin Microbiol. 2013 Aug; 4(16)493-9
A rapidly evolving genomic toolkit for Drosophila heterochromatin.
Levine MT, Malik HS.
Fly (Austin). 2013 Jul-Sep; 3(7)137-41
Birth, decay, and reconstruction of an ancient TRIMCyp gene fusion in primate genomes.
Malfavon-Borja R, Wu LI, Emerman M, Malik HS.
Proc Natl Acad Sci U S A. 2013 Feb 12; 7(110)E583-92
Rules of engagement: molecular insights from host-virus arms races.
Daugherty MD, Malik HS.
Annu Rev Genet. 2012; (46)677-700
Mitchell PS, Patzina C, Emerman M, Haller O, Malik HS, Kochs G.
Cell Host Microbe. 2012 Oct 18; 4(12)598-604
Extensive evolutionary and functional diversity among mammalian AIM2-like receptors.
Brunette RL, Young JM, Whitley DG, Brodsky IE, Malik HS, Stetson DB.
J Exp Med. 2012 Oct 22; 11(209)1969-83
Poxviruses deploy genomic accordions to adapt rapidly against host antiviral defenses.
Elde NC, Child SJ, Eickbush MT, Kitzman JO, Rogers KS, Shendure J, Geballe AP, Malik HS.
Cell. 2012 Aug 17; 4(150)831-41
Levine MT, McCoy C, Vermaak D, Lee YC, Hiatt MA, Matsen FA, Malik HS.
PLoS Genet. 2012; 6(8)e1002729
Lim ES, Wu LI, Malik HS, Emerman M.
Retrovirology. 2012 Jun 26; (9)55
A unified phylogeny-based nomenclature for histone variants.
Talbert PB, Ahmad K, Almouzni G, Ausió J, Berger F, Bhalla PL, Bonner WM, Cande WZ, Chadwick BP, Chan SW, Cross GA, Cui L, Dimitrov SI, Doenecke D, Eirin-López JM, Gorovsky MA, Hake SB, Hamkalo BA, Holec S, Jacobsen SE, Kamieniarz K, Khochbin S, Ladurner AG, Landsman D, Latham JA, Loppin B, Malik HS, Marzluff WF, Pehrson JR, Postberg J, Schneider R, Singh MB, Smith MM, Thompson E, Torres-Padilla ME, Tremethick DJ, Turner BM, Waterborg JH, Wollmann H, Yelagandula R, Zhu B, Henikoff S.
Epigenetics Chromatin. 2012 Jun 21; (5)7
Convergent evolution of escape from hepaciviral antagonism in primates.
Patel MR, Loo YM, Horner SM, Gale M Jr, Malik HS.
PLoS Biol. 2012; 3(10)e1001282
Retroviruses push the envelope for mammalian placentation.
Malik HS
Proc Natl Acad Sci U S A. 2012 Feb 14; 7(109)2184-5
Lim ES, Fregoso OI, McCoy CO, Matsen FA, Malik HS, Emerman M.
Cell Host Microbe. 2012 Feb 16; 2(11)194-204
Birth, death, and replacement of karyopherins in Drosophila.
Phadnis N, Hsieh E, Malik HS.
Mol Biol Evol. 2012 May; 5(29)1429-40
Paleovirology - ghosts and gifts of viruses past.
Patel MR, Emerman M, Malik HS.
Curr Opin Virol. 2011 Oct; 4(1)304-9
The breadth of antiviral activity of Apobec3DE in chimpanzees has been driven by positive selection.
Duggal NK, Malik HS, Emerman M.
J Virol. 2011 Nov; 21(85)11361-71
Elde NC, Roach KC, Yao MC, Malik HS.
J Mol Evol. 2011 Jun; 5-6(72)510-20
Koyanagi M, Kerns JA, Chung L, Zhang Y, Brown S, Moldoveanu T, Malik HS, Bix M.
BMC Evol Biol. 2010 Jul 22; (10)223
Lim ES, Malik HS, Emerman M.
J Virol. 2010 Jul; 14(84)7124-34
Paleovirology--modern consequences of ancient viruses.
Emerman M, Malik HS.
PLoS Biol. 2010 Feb 9; 2(8)e1000301
Accelerated evolution of the Prdm9 speciation gene across diverse metazoan taxa.
Oliver PL, Goodstadt L, Bayes JJ, Birtle Z, Roach KC, Phadnis N, Beatson SA, Lunter G, Malik HS, Ponting CP.
PLoS Genet. 2009 Dec; 12(5)e1000753
Moran JV, Malik HS.
EMBO Rep. 2009 Dec; 12(10)1306-10
Altered heterochromatin binding by a hybrid sterility protein in Drosophila sibling species.
Bayes JJ, Malik HS.
Science. 2009 Dec 11; 5959(326)1538-41
Multiple roles for heterochromatin protein 1 genes in Drosophila.
Vermaak D, Malik HS.
Annu Rev Genet. 2009; (43)467-92
The evolutionary conundrum of pathogen mimicry.
Elde NC, Malik HS.
Nat Rev Microbiol. 2009 Nov; 11(7)787-97
Major evolutionary transitions in centromere complexity.
Malik HS, Henikoff S.
Cell. 2009 Sep 18; 6(138)1067-82
Vermaak D, Bayes JJ, Malik HS.
J Hered. 2009 Sep-Oct; 5(100)624-36
The centromere-drive hypothesis: a simple basis for centromere complexity.
Malik HS
Prog Mol Subcell Biol. 2009; (48)33-52
Smith EE, Malik HS.
Genome Res. 2009 May; 5(19)850-8
An expanded clade of rodent Trim5 genes.
Tareen SU, Sawyer SL, Malik HS, Emerman M.
Virology. 2009 Mar 15; 2(385)473-83
Protein kinase R reveals an evolutionary model for defeating viral mimicry.
Elde NC, Child SJ, Geballe AP, Malik HS.
Nature. 2009 Jan 22; 7228(457)485-9
Guidelines for naming nonprimate APOBEC3 genes and proteins.
LaRue RS, Andrésdóttir V, Blanchard Y, Conticello SG, Derse D, Emerman M, Greene WC, Jónsson SR, Landau NR, Löchelt M, Malik HS, Malim MH, Münk C, O'Brien SJ, Pathak VK, Strebel K, Wain-Hobson S, Yu XF, Yuhki N, Harris RS.
J Virol. 2009 Jan; 2(83)494-7
Antiretroelement activity of APOBEC3H was lost twice in recent human evolution.
OhAinle M, Kerns JA, Li MM, Malik HS, Emerman M.
Cell Host Microbe. 2008 Sep 11; 3(4)249-59
Wiggins BL, Malik HS.
Fly (Austin). 2007 May-Jun; 3(1)155-63
Kerns JA, Emerman M, Malik HS.
PLoS Genet. 2008 Jan; 1(4)e21
Discordant evolution of the adjacent antiretroviral genes TRIM22 and TRIM5 in mammals.
Sawyer SL, Emerman M, Malik HS.
PLoS Pathog. 2007 Dec; 12(3)e197
Rodriguez MA, Vermaak D, Bayes JJ, Malik HS.
Proc Natl Acad Sci U S A. 2007 Sep 25; 39(104)15412-7
Restriction of an extinct retrovirus by the human TRIM5alpha antiviral protein.
Kaiser SM, Malik HS, Emerman M.
Science. 2007 Jun 22; 5832(316)1756-8
Sawyer SL, Malik HS.
Proc Natl Acad Sci U S A. 2006 Nov 21; 47(103)17614-9
Genetic conflicts during meiosis and the evolutionary origins of centromere complexity.
Malik HS, Bayes JJ.
Biochem Soc Trans. 2006 Aug; Pt 4(34)569-73
Adaptive evolution and antiviral activity of the conserved mammalian cytidine deaminase APOBEC3H.
OhAinle M, Kerns JA, Malik HS, Emerman M.
J Virol. 2006 Apr; 8(80)3853-62
Sawyer SL, Wu LI, Akey JM, Emerman M, Malik HS.
Curr Biol. 2006 Jan 10; 1(16)95-100
Cervantes MD, Xi X, Vermaak D, Yao MC, Malik HS.
Mol Biol Cell. 2006 Jan; 1(17)485-97
Positive selection of Iris, a retroviral envelope-derived host gene in Drosophila melanogaster.
Malik HS, Henikoff S.
PLoS Genet. 2005 Oct; 4(1)e44
Vermaak D, Henikoff S, Malik HS.
PLoS Genet. 2005 Jul; 1(1)96-108
Ribonuclease H evolution in retrotransposable elements.
Malik HS
Cytogenet Genome Res. 2005; 1-4(110)392-401
Sawyer SL, Wu LI, Emerman M, Malik HS.
Proc Natl Acad Sci U S A. 2005 Feb 22; 8(102)2832-7
Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G.
Sawyer SL, Emerman M, Malik HS.
PLoS Biol. 2004 Sep; 9(2)E275
Jackman JE, Montange RK, Malik HS, Phizicky EM.
RNA. 2003 May; 5(9)574-85
Conflict begets complexity: the evolution of centromeres.
Malik HS, Henikoff S.
Curr Opin Genet Dev. 2002 Dec; 6(12)711-8
Ancient lineages of non-LTR retrotransposons in the primitive eukaryote, Giardia lamblia.
Burke WD, Malik HS, Rich SM, Eickbush TH.
Mol Biol Evol. 2002 May; 5(19)619-30
Recurrent evolution of DNA-binding motifs in the Drosophila centromeric histone.
Malik HS, Vermaak D, Henikoff S.
Proc Natl Acad Sci U S A. 2002 Feb 5; 3(99)1449-54
The centromere paradox: stable inheritance with rapidly evolving DNA.
Henikoff S, Ahmad K, Malik HS.
Science. 2001 Aug 10; 5532(293)1098-102
Malik HS, Eickbush TH.
Genome Res. 2001 Jul; 7(11)1187-97
Adaptive evolution of Cid, a centromere-specific histone in Drosophila.
Malik HS, Henikoff S.
Genetics. 2001 Mar; 3(157)1293-8
Ten-kilodalton domain in Ty3 Gag3-Pol3p between PR and RT is dispensable for Ty3 transposition.
Claypool JA, Malik HS, Eickbush TH, Sandmeyer SB.
J Virol. 2001 Feb; 3(75)1557-60
Poised for contagion: evolutionary origins of the infectious abilities of invertebrate retroviruses.
Malik HS, Henikoff S, Eickbush TH.
Genome Res. 2000 Sep; 9(10)1307-18
Dual recognition-incision enzymes might be involved in mismatch repair and meiosis.
Malik HS, Henikoff S.
Trends Biochem Sci. 2000 Sep; 9(25)414-8
Putative telomerase catalytic subunits from Giardia lamblia and Caenorhabditis elegans.
Malik HS, Burke WD, Eickbush TH.
Gene. 2000 Jun 27; 2(251)101-8
NeSL-1, an ancient lineage of site-specific non-LTR retrotransposons from Caenorhabditis elegans.
Malik HS, Eickbush TH.
Genetics. 2000 Jan; 1(154)193-203
Yang J, Malik HS, Eickbush TH.
Proc Natl Acad Sci U S A. 1999 Jul 6; 14(96)7847-52
The age and evolution of non-LTR retrotransposable elements.
Malik HS, Burke WD, Eickbush TH.
Mol Biol Evol. 1999 Jun; 6(16)793-805
Burke WD, Malik HS, Jones JP, Eickbush TH.
Mol Biol Evol. 1999 Apr; 4(16)502-11
Modular evolution of the integrase domain in the Ty3/Gypsy class of LTR retrotransposons.
Malik HS, Eickbush TH.
J Virol. 1999 Jun; 6(73)5186-90
Malik HS, Eickbush TH.
Genetics. 1999 Feb; 2(151)653-65
Spinelli SL, Malik HS, Consaul SA, Phizicky EM.
Proc Natl Acad Sci U S A. 1998 Nov 24; 24(95)14136-41
Malik HS, Eickbush TH.
Mol Biol Evol. 1998 Sep; 9(15)1123-34
Determining the evolutionary potential of a gene.
Hall BG, Malik HS.
Mol Biol Evol. 1998 Aug; 8(15)1055-61
Are retrotransposons long-term hitchhikers?
Burke WD, Malik HS, Lathe WC 3rd, Eickbush TH.
Nature. 1998 Mar 12; 6672(392)141-2
Evolutionary specialization of the nuclear targeting apparatus.
Malik HS, Eickbush TH, Goldfarb DS.
Proc Natl Acad Sci U S A. 1997 Dec 9; 25(94)13738-42
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Lab Information
Location: Fred Hutch
Building: Weintraub
Room: A2-205
Box: A2-025
Phone: 206-667-4512
http://research.fhcrc.org/malik/en.html
Building: Weintraub
Room: A2-205
Box: A2-025
Phone: 206-667-4512
http://research.fhcrc.org/malik/en.html