Malik Lab

Malik Lab

Fred Hutch Logo

Publications

Peer-Reviewed Publications (reverse chronological; corresponding author(s) is underlined; *these authors contributed equally; ®reviews/perspectives; F1000highlighted by the Faculty of 1000 Biology; #cited >100 times in Google Scholar database)

2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | Other Publications

2024

2023

2022

2021

  • Chew GL, Bleakley M, Bradley RK, Malik HS, Henikoff S, Molaro A, Sarthy J. (2021) Short H2A histone variants are expressed in cancer.  Nat Commun, Jan 20;12(1):490.
  • Kato K, Ahmad S, Zhu Z, Young JM, Mu X, Park S, Malik HS, Hur S. (2021) Structural analysis of RIG-I-like receptors reveals ancient rules of engagament between diverse RNA helicases and TRIM ubiquitin ligases. Mol Cell, Feb 4;81(3):599-613.e8
  • Chang CH, Malik HS. (2021) Putting the brakes on centromere drive in Mimulus. PLoS Genet, Apr 22;17(4):e1009494.
  • Ohainle M, Malik HS. (2021) A balancing act between primate lentiviruses and their receptor. Proc Natl Acad Sci U S A, May 18;118(20):e2104741118.
  • Kursel LE, McConnell H, de la Cruz AFA, Malik HS. (2021) Gametic specialization of centromeric histone paralogs in Drosophila virilis. Life Sci Alliance, May 13;4(7):e202000992.
  • Forsberg KJ, Schmidtke DT, Werther R, Uribe RV, Hausman D, Sommer MOA, Stoddard BL, Kaiser BK, Malik HS. (2021) The novel anti-CRISPR Acr!!A22 relieves DNA torsion in target plasmids and impairs SpyCas9 activity PLoS Biol.  Oct 13;19(10):e3001428. doi: 10.1371/journal.pbio.3001428. eCollection 2021 Oct.
  • Schroeder CM, Tomlin SA, Mejia Natividad I, Valenzuela JR, Young JM, Malik HS. (2021) An Actin-related protein that is most highly expressed in Drosophila testes is critical for embryonic development  Elife.Jul 20;10:e71279. doi: 10.7554/eLife.71279.
  • Chew GL, Bleakley M, Bradley RK, Malik HS, Henikoff S, Molaro A, Sarthy J. (2021) Short H2A histone variants are expressed in cancer. Nat Commun, Jan 20;12(1):490.
  • Kato K, Ahmad S, Zhu Z, Young JM, Mu X, Park S, Malik HS, Hur S. (2021) Structural analysis of RIG-I-like receptors reveals ancient rules of engagament between diverse RNA helicases and TRIM ubiquitin ligases. Mol Cell, Feb 4;81(3):599-613.e8
  • Chang CH, Malik HS. (2021) Putting the brakes on centromere drive in Mimulus. PLoS Genet, Apr 22;17(4):e1009494.
  • Ohainle M, Malik HS. (2021) A balancing act between primate lentiviruses and their receptor. Proc Natl Acad Sci U S A, May 18;118(20):e2104741118.
  • Kursel LE, McConnell H, de la Cruz AFA, Malik HS. (2021) Gametic specialization of centromeric histone paralogs in Drosophila virilis. Life Sci Alliance, May 13;4(7):e202000992.

2020

  • Molaro A, Wood AJ, Janssens D, Kindelay SM, Eickbush MT, Wu S, Singh P, Muller CH, Henikoff S, Malik HS. (2020) Biparental contributions of the H2A.B histone variant control embryonic development in mice. PLoS Biol, Dec 23;18(12):e3001001
  • Kasinathan B, Colmenares SU 3rd, McConnell H, Young JM, Karpen GH, Malik HS. (2020) Innovation of heterochromatin functions drives rapid evolution of essential ZAD-ZNF genes in Drosophila. Elife, Nov 10;9:e63368
  • Hays M, Young JM, Levan PF, Malik HS. (2020) A natural variant of the essential host gene MMS21 restricts the parasitic 2-micron plasmid in Saccharomyces cerevisiae. Elife, Oct 16;9:e62337
  • Tenthorey JL, Young C, Sodeinde A, Emerman M, Malik HS. (2020) Mutational resilience of antiviral restriction favors primate TRIM5α in host-virus evolutionary arms races. Elife, Sep 15;9:e59988. doi: 10.7554/eLife.59988.
  • D. Gordon, G. Jang, M. Bouhaddou, J. Xu, K. Obernier, K. White, M. O’Meara, V. Rezelj, J. Guo, D. Swaney, T. Tummino, R. Hüttenhain, R. Kaake, A. Richards, B. Tutuncuoglu, H. Foussard, J. Batra, K. Haas, M. Modak, M. Kim, P. Haas, B. Polacco, H. Braberg, J. Fabius, M. Eckhardt, M. Soucheray, M. Bennett, M. Cakir, M. McGregor, Q. Li, B. Meyer, F. Roesch, T. Vallet, A. Kain, L. Miorin, E. Moreno, Z. Naing, Y. Zhou, S. Peng, Y. Shi, Z. Zhang, W. Shen, I. Kirby, J. Melnyk, J. Chorba, K. Lou, S. Dai, I. Barrio-Hernandez, D. Memon, C. Hernandez-Armenta, J. Lyu, C. Mathy, T. Perica, K. Pilla, S. Ganesan, D. Saltzberg, R. Rakesh, X. Liu, S. Rosenthal, L. Calviello, S. Venkataramanan, J. Liboy-Lugo, Y. Lin, X. Huang, Y. Liu, S. Wankowicz, M. Bohn, M. Safari, F. Ugur, C. Koh, N. Savar, Q. Tran, D. Shengjuler, . Fletcher, M. O’Neal, Y. Cai, J. Chang, D. Broadhurst, S. Klippsten, P. Sharp, N. Wenzell, D. Kuzuoglu-Ozturk, H. Wang, R. Trenker, J. Young, D. Cavero, J. Hiatt, T. Roth, U. Rathore, A. Subramanian, J. Noack, M. Hubert, R. Stroud, A. Frankel, O. Rosenberg, K. Verba, D. Agard, M. Ott, M. Emerman, N. Jura, M. von Zastrow, E. Verdin, A. Ashworth, O. Schwartz, C. d’Enfert, S. Mukherjee, M. Jacobson, H. Malik, D. Fujimori, T. Ideker, C. Craik, S. Floor, J. Fraser, J. Gross, A. Sali, B. Roth, D. Ruggero, J. Taunton, T. Kortemme, P. Beltrao, M. Vignuzzi, A.García-Sastre, K. Shokat, B. Shoichet & N. Krogan (2020) A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature, 583, 459-468.
  • Molaro A, Malik HS, Bourc'his (2020) Dynamic Evolution of De Novo DNA Methyltransferases in Rodent and Primate Genomes. D.Mol Biol Evol., 37(7):1882-1892
  • Kursel LE, Welsh FC, Malik HS. (2020) Ancient Coretention of Paralogs of Cid Centromeric Histones and Cal1 Chaperones in Mosquito Species. Mol Biol Evol., 37(7):1949-1963

2019

  • Lamelza P, Young JM, Noble LM, Caro L, Isakharov A, Palanisamy M, Rockman MV, Malik H. S., Ailion M (2019) Hybridization promotes asexual reproduction in Caenorhabditis nematodes. PLoS Genet. Dec 16;15(12):e1008520. doi: 10.1371/journal.pgen.1008520.
  • Schroeder CM, Malik H. S. (2019) Meiosis: How Gambling Chromosomes Beat the Rules. Curr Biol. Dec 2;29(23):R1247-R1248. doi: 10.1016/j.cub.2019.10.056.
  • Schroeder CM, Valenzuela JR, Natividad IM, Hocky GM, Malik H. S. (2019) A burst of genetic innovation in Drosophila actin-related proteins for testis-specific function. Mol Biol Evol. Nov 7. pii: msz262. doi: 10.1093/molbev/msz262. [Epub ahead of print]
  • Colón-Thillet R, Hsieh E, Graf L, McLaughlin RN Jr, Young JM, Kochs G, Emerman M, Malik H. S. (2019) Microbial Genomics: Combinatorial mutagenesis of rapidly evolving residues yields super-restrictor antiviral proteins. PLoS Biol. 2019 Oct 1;17(10):e3000181. doi: 10.1371/journal.pbio.3000181.
  • 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 H. S., Martín-Durán JM, Peichel CL, Renfree MB, Rutowicz K, Sarkies P, Schmitz RJ, Technau U, Thornton JW, Warnecke T, Wolfe KH. (2019) EvoChromo: towards a synthesis of chromatin biology and evolution. Development. Sep 26;146(19). pii: dev178962. doi: 10.1242/dev.178962.
  • KForsberg KJ, Bhatt IV, Schmidtke DT, Javanmardi K, Dillard KE, Stoddard BL, Finkelstein IJ, Kaiser BK, Malik H. S. (2019) Functional metagenomics-guided discovery of potent Cas9 inhibitors in the human microbiome. Elife. Sep 10;8. pii: e46540. doi: 10.7554/eLife.46540.
  • Levin TC, Goldspiel BP, Malik H. S. (2019) Density-dependent resistance protects Legionella pneumophila from its own antimicrobial metabolite, HGA. Elife. May 28;8. pii: e46086. doi: 10.7554/eLife.46086

2018

  • Molaro A., Young J. M., Malik, H. S. (2018) Evolutionary origins and diversification of testis-specific short histone H2A variants in mammals. Genome Res Apr;28(4):460-473. doi: 10.1101/gr.229799.117. Epub 2018 Mar 16.
  • Forsberg KJ, Malik H. S. (2018) Microbial Genomics: The Expanding Universe of Bacterial Defense Systems. Curr Biol. Apr 23;28(8):R361-R364. doi: 10.1016/j.cub.2018.02.053.
  • Schroeder CM, Malik H. S. (2018) Kindr Motors Drive in Meiosis. Cell. May 3;173(4):813-815. doi: 10.1016/j.cell.2018.04.021.
  • Kursel LE, Malik H. S. (2018) The cellular mechanisms and consequences of centromere drive. Curr Opin Cell Biol. Jun;52:58-65. doi: 10.1016/j.ceb.2018.01.011. Epub 2018 Feb 16. Review.
  • Molaro A, Malik H. S. (2018) Culture shock. Elife. Dec 18;6. pii: e33312. doi: 10.7554/eLife.33312.

2017

  • ®McLaughlin, R. N. & Malik, H. S. (2017) Genetic conflicts: the usual suspects and beyond. J. Exp. Biol. 220: 6-17.
  • Kursel, L. E. & Malik, H. S. (2017) Recurrent gene duplication leads to diverse repertoires of centromeric histones in Drosophila species. Mol. Biol. Evol. 34: 1445-1462.
  • Nuckolls, N. L., Núñez, M. A. B., Eickbush, M. T., Young, J. M., Lange, J. L., Yu, J. S., Smith, G. R., Jaspersen, S. L. Malik, H. S. & Zanders, S. E. (2017) wtf genes are prolific dual poison-antidote meiotic drivers. eLife 6: pii: e26033.
  • Insight: Shropshire, J. D. & Rokas, A. (2017) Heredity: the gene family that cheats Mendel. eLife 6: pii: e28567.
  • Levin, T. C. & Malik, H. S. (2017) Rapidly evolving Toll-3/4 genes encode male-specific Toll-like receptors in Drosophila. Mol. Biol. Evol. (epub ahead of print). doi: 10.1093/molbev/msx168.
  • ®Bull, J. J. & Malik, H. S. (2017) The gene drive bubble: New realities. (Perspective) PLOS Genetics (in press).
  • ®Kasinathan, B., Ahmad, K. & Malik, H. S. (2017) Waddington redux: de novo mutations underlie the genetic assimilation of stress-induced phenocopies in Drosophila melanogaster. (Commentary) Genetics (in press).
  • ®Ailion, M. & Malik, H. S. (2017) Genetics: master regulator or master of disguise. (Dispatch) Curr Biol. (in press).

2016

  • ®Molaro, A. & Malik, H. S. (2016) Hide and seek: how chromatin-based pathways silence retroelements in the mammalian germline. Curr. Opin. Genet. Dev. 37: 51-58.
  • ®Drinnenberg, I. A., Henikoff, S. & Malik, H. S. (2016) Evolutionary turnover of kinetochore proteins: a ship of Theseus? Trends Cell Biol. 26: 498-510.
  • Levine, M. T., Vander Wende, H. M., Hsieh, E., Baker, E. P. & Malik, H. S. (2016) Recurrent gene duplication diversifies genome defense repertoire in Drosophila. Mol. Biol. Evol. 33: 1641-53 (MBE Fast Track).
  • McLaughlin, R. N., Gable, J. T., Wittkopp, C. J., Emerman, M. & Malik, H. S. (2016) Conservation and innovation of APOBEC3A restriction functions during primate evolution. Mol. Biol. Evol. 33: 1889-901 (MBE Fast Track).
  • Franks, T. M., Benner, C., Narvaiza, I., Marchetto, M. C., Young, J. M., Malik, H. S., Gage, F. H. & Hetzer, M. W. (2016) Evolution of a transcriptional regulator from a transmembrane nuceloporin. Genes Dev. 30: 1155-71.
  • Daugherty, M. D., Schaller, A. M., Geballe, A. P. & Malik, H. S. (2016) Evolution-guided functional analyses reveal diverse antiviral specificities encoded by IFIT1 genes in mammals. eLife 5: e14228.
  • ®Kursel, L. E. & Malik, H. S. (2016) Centromeres (Primer). Curr Biol. 26: R487-90.
  • Patel, M. R., Miriyala, G.K.*, Littleton, A. J.*, Yang, H., Trinh, K., Young, J. M., Kennedy, S. R., Yamashita, Y. M., Pallanck, L. J. & Malik, H. S. (2016) A mitochondrial DNA hypomorph of cytochrome oxidase specifically impairs male fertility in Drosophila melanogaster. eLife 5: e16923.
  • ®Goodin, M. M.*, Hatfull, G. F.* & Malik, H. S.* (2016) A diversified portfolio. (Editorial comment) Annu. Rev. Virol. 3: vi-vii.
  • ®Bedford, T. & Malik, H. S. (2016) Did a single amino acid change make Ebola virus more virulent? (Leading Edge preview) Cell 167: 892-894.
  • Cheng, C.-Y.*, Young, J. M.*, Lin, C.-Y.G., Chao, J.-L., Malik, H. S. & Yao, M.-C. (2016) The piggyBac transposon-derived genes TPB1 and TPB6 mediate essential transposon-like excision during the developmental rearrangement of key genes in Tetrahymena thermophila. Genes Dev. 30: 2724-2736.

2015

  • Phadnis, N., Baker, E. P., Cooper, J. C., Frizzell, K. A., Hsieh, E., de la Cruz, A. F. A., Shendure, J., Kitzman, J. O. & Malik, H. S. (2015) An essential cell cycle regulation gene causes hybrid inviability in Drosophila. Science 350: 1552-5.
  • Mitchell, P. S., Young, J. A., Emerman, M. & Malik, H. S. (2015) Evolutionary Analyses Suggest a Function of MxB Immunity Proteins Beyond Lentivirus Restriction. PLOS Pathogens 11: e1005304.
  • ® Zanders, S. E. & Malik, H. S. (2015) Chromosome segregation: human female meiosis breaks all the rules. Curr. Biol. 25: R654-6.
  • ® Akbari, O.S., Bellen, H. J., Bier, E., Bullock, S.L., Burt, A., Church, G. M., Cook, K. R., Duchek, P., Edwards, O. R., Esvelt, K. M., Gantz, V. M., Golic, K. G., Gratz, S. J., Harrison, M. M., Hayes, K. R., James, A. A., Kaufman, T. C., Knoblich, J., Malik, H. S., Matthews, K. A., O'Connor-Giles, K. M., Parks, A. L., Perrimon, N., Port, F., Russell, S., Ueda, R. & Wildonger, J. (2015) Safeguarding gene drive experiments in the laboratory. Science 349: 927-9.
  • Li, J. J., Cao, C., Fixsen, S. M., Young, J. M., Ono, C., Bando, H., Elde, N. C., Katsuma, S., Dever, T. E., Sicheri, F. (2015) Baculovirus protein PK2 subverts eIF2α kinase function by mimicry of its kinase domain C-lobe. Proc Natl. Acad. Sci. USA 112: E4364-73
  • ® McLaughlin, R. N. & Malik, H. S. (2015) LINE-1 retroelements get ZAPped! (Perspective) PLOS Genetics 11: e1005364.
  • Levine, M. T., Vander Wende H. M. & Malik, H. S. (2015) Mitotic fidelity requires the transgenerational action of a testis-restricted HP1. eLife, 4: e07378.
    • Research Highlight: Baumann, K. (2015) Chromosomes: transgenerational remodeling of sperm DNA. Nat. Rev. Mol. Cell Biol. 16: 453.
    • Editor’s choice: Purnell, B. (2015) Biparental control in remodeling sperm. Science 349: 599.
  • ® Zanders, S. & Malik, H. S. (2015) R2D2 and Hyperdrive mechanisms (in mouse meiosis). (Perspective) PLOS Genetics 11: e1004950.
  • Chou, S.* Daugherty, M. D.*, Peterson, S. B., Biboy, J. Yang, Y., Jutras, B. L., Fritz-Laylin, L. K., Ferrin, M.A., Harding, B. L., Jacobs-Wagner, C., Yang, X. F., Vollmer, W., Malik, H. S. & Mougous, J. D. (2015) Transferred interbacterial antagonism genes augment eukaryotic innate immune function. Nature 518: 98-101.
    • Preview: Dunning Hotopp J. C. & Estes, A. E. (2014) Biology wars: the eukaryotes strike back. Cell Host Microbe 16: 701-703. 

2014

  • ® Phadnis, N. & Malik, H. S. (2014) Speciation via Autoimmunity: A Dangerous Mix. Cell. 159(6):1247-9
  • ® Lynch, M., Field, M. C., Goodson, H. V., Malik, H. S., Pereira-Leal, J. B., Roos, D. S., Turkewitz, A. P., and Sazer, S. (2014) Evolutionary Cell Biology: Two Origins, One Objective (Perspective). Proc Natl. Acad. Sci. USA 111: 16990-4.
  • ® Ross, B. D. and Malik, H. S. (2014) Genetic conflicts: stronger centromeres win tug-of-war in female meiosis (Dispatch). Curr. Biol. 24: R966-R968.
  • Drinnenberg, I. A., DeYoung, D., Henikoff, S.* & Malik, H. S.* (2014) Recurrent loss of CenH3 is associated with independent transitions to holocentricity in insects. eLife, 3: e03676.
  • McLaughlin, R. N.*, Young, J. M.*, Yang, L., Neme, R., Wichman, H. A. & Malik, H. S. (2014) Positive Selection and Multiple Losses of the LINE-1-derived L1TD1 Gene in Mammals Suggest a Dual Role in Genome Defense and Pluripotency. PLOS Genetics 10: e1004531.
  • ® Daugherty, M. D. and Malik, H. S. (2014) How a virus blocks an emergency access lane to the nucleus, STAT! (Preview) Cell Host Microbe 16: 150-152.
  • Zanders, S. E., Eickbush, M. T., Yu, J. S., Kang, J. W., Fowler, K. R., Smith, G. R. & Malik, H. S. (2014) Genome rearrangements and pervasive meiotic drive cause hybrid infertility in fission yeast. elife. 3:e02630.
    • Insight: Bomblies, K. (2014) Meiotic drivers: cheaters divide and conquer. eLife 3: e03371.
    • Editor’s Choice: Zahn, L. M. (2014) Speciation: putting the genetic breaks on breeding. Science 345: 281.
  • Daugherty, M. D., Young, J. M., Kerns, J. A. & Malik, H. S. (2014) Rapid Evolution of PARP Genes Suggests a Broad Role for ADP-Ribosylation in Host-Virus Conflicts. PLOS Genet. 10:e1004403.
  • Tenthorey, J. L., Kofoed, E. M., Daugherty, M. D., Malik, H. S. & Vance, R. E. (2014) Molecular Basis for Specific Recognition of Bacterial Ligands by NAIP/NLRC4 Inflammasomes. Mol Cell. 54: 17-29.

2013

  • Malfavon-Borja, R. C., Sawyer, S. L., Wu, L. I., Emerman, M. & Malik, H. S. (2013) An evolutionary screen highlights canonical and non-canonical candidate antiviral genes within the primate TRIM gene family. Genome Biol. Evol. 5: 2141-2154.
  • ® Compton, A. A., Malik, H. S. & Emerman, M. (2013) Host Gene Evolution Traces the Evolutionary History of Ancient Primate Lentiviruses. Philos. Trans. Royal Soc. B 368: 20120496.
  • ® Mitchell, P. S., Emerman, M. & Malik, H. S. (2013) An evolutionary perspective on the broad antiviral specificity of MxA. Curr. Opin. Microbiol. 16: 493-499.
  • Carter, J. J.*, Daugherty, M. D.*, Qi, X., Bheda-Malge, A., Wipf, G. C., Robinson, K., Roman, A., Malik, H. S.  & Galloway, D. A. (2013) Identification of an overprinting gene in Merkel cell polyomavirus provides evolutionary insight into the birth of viral genes. Proc. Natl. Acad. Sci USA 10: 12744-12749.
  • Ross, B. D., Rosin, L.*, Thomae, A.*, Hiatt, M. A.*, Vermaak, D.*, de la Cruz, A. F. A., Imhof, A., Mellone, B. G. & Malik, H. S. (2013) Stepwise evolution of essential centromeric function in a Drosophila neogene. Science 340: 1211-1214. Fred Hutch Science Spotlight
    • Research Highlight: Burgess, D. J. (2013) Evolution: reconstructing essentiality. Nat. Rev. Genet. 14: 442.
  • ® Levine, M. & Malik. H. S. (2013) A rapidly evolving genetic toolkit for Drosophila heterochromatin. Fly 7: 3.
  • Malfavon-Borja, R. C., Wu, L. I., Emerman, M. & Malik, H. S. (2013) Birth, decay, and reconstruction of an ancient TRIMCyp gene fusion in primate genomes. (PNAS Plus) Proc. Natl. Acad. Sci USA 110: E583-92. Fred Hutch Science Spotlight

2012

  • Daugherty, M. D. and Malik, H. S. (2012) Rules of engagement: molecular insights from host-virus arms races. (Review) Ann. Rev. Genet. 46: 677-700.
  • Mitchell, P. S., Patzina, C., Emerman, M., Haller, O., Malik, H. S., Kochs, G. (2012) Evolution-guided identification of antiviral specificity determinants in the broadly acting interferon-induced innate immunity factor MxA. Cell Host Microbe 12: 598-604.  Fred Hutch Science Spotlight
  • Elde, N. C., Child, S. J., Eickbush, M. T., Kitzman, J. O., Rogers, K. S., Shendure, J., Geballe, A. P. and Malik, H. S. (2012) Poxviruses deploy genomic accordions to adapt rapidly against host antiviral defenses. Cell 150: 831-841.  Fred Hutch News Releases
  • Brunette, R. L., Young, J. M., Whitley, D. G., Brodsky, I. E., Malik, H. S., Stetson, D. B. (2012) Extensive evolutionary and functional diversity among mammalian AIM2-like receptors. J. Exp. Med. 209: 1969-1983.
  • Lim, E. S., Wu, Li. I., Malik, H. S. and Emerman, M. (2012) The function and evolution of the restriction factor Viperin in primates was not driven by lentiviruses. Retrovirology 9:55.
  • Levine, M. T., McCoy, C., Vermaak, D., Lee, G., Hiatt, M. A., Matsen, F. A. and Malik, H. S. (2012) Phylogenomic analysis of the Drosophila heterochromatin protein 1 (HP1) gene family suggests dynamic evolution of germline heterochromatin function. PLoS Genetics 8: e1002729 (12 pages).
  • ® Talbert, P.B., Ahmad, K., Almouzni, G., Ausió J., Berger, F., Bhalla, P. B., Bonner, W. M., Cande, W. Z., Chadwick, B. P., Chan, S. W. L., Cross, G. A. M., Cui, L., Dimitrov, S. I., Doenecke, D., Eirin-López, J. M., Gorovsky, M. A., Hake, S. A., Hamkalo, B. A., Holec, S., Jacobsen, S. E., Kamieniarz, K., Khochbin, S., Ladurner, A. G., Landsman, D., Latham, J. A., Loppin, B., Malik, H. S., Marzluff, W. F., Pehrson, J. R., Postberg, J., Singh, M. B., Schneider, R., Smith, M. M., Thompson, E., Torres-Padilla, M.-E., Tremethick, D. J., Turner, B. M., Waterborg, J. H., Wollmann, H., Yelagandula, R., Zhu, B. and Henikoff, S. (2012) A Unified Phylogeny-based Nomenclature for Histone Variants. Epigenetics Chromatin 5:7.
  • Roach, K. C., Ross, B. D. and Malik, H. S. (2012) Rapid evolution of centromeres and centromeric/ kinetochore proteins. in "Evolution in the Fast Lane: Rapidly Evolving Genes and Genetic Systems" (eds: Rama Singh, Jianping Xu & Rob Kulathinal), pp. 83-93, Oxford University Press.
  • Phadnis, N., Hsieh, E. and Malik, H. S. (2012) Birth, death and replacement of karyopherins in Drosophila. Mol. Biol. Evol. 29: 1429-1440.
  • Patel, M. R., Loo, Y-M.*, Horner, S. M.*, Gale, M. Jr. and Malik, H. S. (2012) Recurrent escape of antiviral factor MAVS from hepaciviral antagonism in primates. PLoS Biology 10: e1001282 (11 pages). F1000 
    • Synopsis: (2012) War archives: how some primates fought off ancient viruses. PLoS Biology 10: e1001285.
  • Lim, E. S., Fregoso, O. I., McCoy, C. O., Matsen, F. A., Malik, H. S. and Emerman, M. (2012) SAMHD1-degrading activity preceded the birth of Vpx in primate lentiviruses. Cell Host Microbe 11: 194-204.  Fred Hutch News Releases
    • Preview: Planelles, V. (2012) SAMHD1 joins the Red Queen's court. Cell Host Microbe 11: 103- 105.

2011

  • Phadnis N. (2011) Genetic architecture of male sterility and segregation distortion in Drosophila pseudoobscura Bogota-USA hybrids. Genetics 189: 1001-1009.
  • ® Roach, K. C., Ross, B. D. and Malik, H. S. (2011) Adaptive Evolution of Centromeric Proteins. Encyclopedia of Life Sciences [doi: 10.1002/9780470015902.a0022868], John Wiley & Sons Publishing Co.
  • ® Patel, M. R., Emerman, M. and Malik, H. S. (2011) Paleovirology: ghosts and gifts of viruses past. Curr. Opin. Virol. 1: 304-309.
  • Duggal, N. K., Malik, H. S. and Emerman, M. (2011) Positive selection of Apobec3DE in chimpanzees has driven breadth in anti-viral activity. J. Virol. 85: 11361-11371.
  • Elde, N. C., Roach, K. C., Yao, M.-C., and Malik, H. S. (2011) Absence of positive selection on centromeric histones in Tetrahymena suggests unsuppressed centromere-drive in lineages lacking male meiosis. J. Mol. Evol. 72: 510-520.

2010

  • Koyanagi, M., Kerns, J. A., Chung, L., Zhang, Y., Brown, S., Malik, H. S. and Bix, M. (2010) Diversifying selection and functional analysis of interleukin-4 suggests antagonism-driven evolution at receptor-binding interfaces. BMC Evol. Biol. 10: 223 (13 pages).
  • Lim, E. S., Malik, H. S. and Emerman, M. (2010) Ancient adaptive evolution of Tetherin shaped Vpu and Nef functions in human immunodeficiency virus and primate lentiviruses. J. Virol. 84: 7124-7134.
  • Emerman, M. and Malik, H. S. (2010) Paleovirology: modern consequences of ancient viruses. (Essay) PLoS Biology 8: e1000301 (5 pages).

2009

  • Oliver, P. L.*, Goodstadt, L.*, Bayes, J. J., Birtle, Z., Roach, K. C., Phadnis, N., Beatson, S. A., Lunter, G., Malik, H. S. and Ponting, C. P. (2009) Accelerated evolution of the Prdm9 speciation gene across diverse metazoan taxa. PLoS Genetics 5: e1000753 (14 pages). F1000
  • Moran, J. V. and Malik, H. S. (2009) Diamonds and rust: how transposable elements influence mammalian genomes. (Meeting report) EMBO Rep. 10: 1306-1310.
  • Bayes, J. J., and Malik, H. S. (2009) Altered heterochromatin binding by a hybrid sterility protein in Drosophila species. Science 326: 1538-1541.
    • Research Highlight: Swami, M. (2009) Speciation: new insights into hybrid sterility. Nat. Rev. Genet. 10: 820.
  • Elde, N. C. and Malik, H. S. (2009) The evolutionary conundrum of pathogen mimicry. Nat. Rev. Microbiol. 7: 787-797. (cover article). F1000
  • ® Vermaak, D. and Malik, H. S. (2009) Multiple roles of Heterochromatin Protein 1 genes in Drosophila. Annu. Rev. Genet. 43: 467-492.
  • Malik, H. S. and Henikoff, S. (2009) Major evolutionary transitions in centromere complexity. (Leading Edge Perspective) Cell 138: 1067-1082.
  • ® Vermaak, D., Bayes, J.J. and Malik, H. S. (2009) Surrogate approaches to study evolution of non- coding DNA elements that organize eukaryotic genomes. J. Hered. 100: 624-636.
  • ® Malik, H. S. (2009) The centromere-drive hypothesis: a simple basis for centromere complexity. Prog. Mol. Subcell. Biol. 48:33-52 (also published as a book chapter in “Centromere- Structure and Evolution”, ed: Durdica Ugarkovic, Springer-Verlag Publishing, Series).
  • Tareen, S. U., Sawyer, S. L., Malik, H. S. and Emerman, M. (2009) An Expanded Clade of Rodent Trim5 Genes. Virology 385: 473-483. F1000
  • Smith, E. E. and Malik, H. S. (2009) The apolipoprotein L family of programmed cell death and immunity genes rapidly evolved in primates at discrete sites of host-pathogen interactions. Genome Res. 19: 850-858. F1000
  • Elde, N. C., Child, S. J., Geballe, A. P. and Malik, H. S. (2009) Protein Kinase R reveals an evolutionary model for defeating viral mimicry. Nature 457: 485-489. F1000
  • LaRue, R. S., Andrésdóttir, V., Blanchard, Y., Conticello, S. G., Derse, D., Emerman, M., Greene, W. C., Jónsson, S. R., Landau, N. R., Löchelt, M., Malik, H. S., Malim, M. H., Münk, C., O'Brien, S. J., Pathak, V. K., Strebel, K., Wain-Hobson, S., Yu, X. F., Yuhki, N. and Harris, R. S. (2009) Guidelines for naming nonprimate APOBEC3 genes and proteins. (Guest Commentary) J. Virol 83: 494-497.

2008

  • OhAinle, M., Kerns, J. A., Malik, H. S. and Emerman, M. (2008) Antiviral Activity of APOBEC3H was Lost Twice in Recent Human Evolution. Cell Host & Microbe 4: 249-259.
    • Preview: Jern, P. and Coffin, J. M. (2008) Host-retrovirus arms race: trimming the budget. Cell Host & Microbe 4: 196-197.
  • ® Bayes, J. J. and Malik, H. S. (2008) The evolution of centromeric DNA sequences. Encyclopedia of Life Sciences [doi: 10.1002/9780470015902.a0020827], John Wiley & Sons Publishing Co. (also published in “The Handbook of Human Evolution”, ed: David N. Cooper and Hildegard Kehrer-Sawatzki, Wiley Publishing Co.)
  • Kerns, J. A., Emerman, M., and Malik, H. S. (2008) Positive selection and increased antiviral activity associated with the PARP-containing isoform of human Zinc-finger Antiviral Protein. PLoS Genetics 4: e21 (9 pages).

2007

  • Sawyer, S. L., Emerman, M., and Malik, H. S. (2007) Discordant evolution of the TRIM5 and TRIM22 anti-retroviral genes in primates. PLoS Pathogens 3: e197 (12 pages).
    • News & Commentary: Liberles, D. A. (2008) Gene duplication: Red queens, linkage, redundancy and synfunctionalization. Heredity 101: 299–300.
  • Rodriguez, M. A.*, Vermaak, D.*, Bayes, J. J.*, and Malik, H. S. (2007) Species-specific positive selection of the male-specific lethal (MSL) complex that participates in dosage compensation in Drosophila melanogaster. Proc. Natl. Acad. Sci. 104: 15412–15417. F1000
  • Wiggins, B. L. and Malik, H. S. (2007) Molecular evolution of Drosophila Cdc6, an essential DNA replication-licensing gene, suggests an adaptive choice of DNA replication origins. Fly 1(3): 155-163.
  • Kaiser, S. M., Malik, H. S., and Emerman, M. (2007) Restriction of an Extinct Retrovirus by the Human TRIM5a Antiviral Protein. Science 316: 1756-1758. F1000
    • Perspective: Cohen, J. (2007) Fossil Virus Gives Clues to HIV Susceptibility. ScienceNOW Daily News.

2006

  • Sawyer, S. L. and Malik, H. S. (2006) Positive selection of yeast non-homologous end joining (NHEJ) proteins and a retrotransposon-conflict hypothesis. Proc. Natl. Acad. Sci. USA 103: 17614-17619.
  • ® Malik, H. S. and Bayes, J. J. (2006) Genetic conflicts during female meiosis and the evolutionary origins of centromere complexity. Biochem. Soc. Trans. 34: 569-573.
  • OhAinle, M., Kerns, J. A., Malik, H. S. and Emerman, M. (2006) Adaptive Evolution and Antiviral Activity of the Conserved Mammalian Cytidine Deaminase APOBEC3H. J. Virol. 80: 3853-3862. F1000
  • Sawyer, S. L., Wu, L. I., Akey, J. M., Emerman, M.* and Malik, H. S.* (2006) High Frequency Persistence of an Impaired Allele of the Retroviral Defense Gene TRIM5α in Humans. Curr. Biol. 16: 95-100.
  • Cervantes, M. D., Xi, X., Vermaak, D., Yao, M-C.* and Malik, H. S.* (2006) The CNA1 histone of the ciliate Tetrahymena thermophila is essential for chromosome segregation in the germline micronucleus. Mol. Biol. Cell. 17: 485-497.

2005

  • Malik, H. S. and Henikoff, S. (2005) Positive selection of Iris, a retroviral envelope-derived host gene in Drosophila melanogaster. PLoS Genetics. 1: e44 (14 pages).
  • ® Malik, H. S. (2005) Ribonuclease H evolution in retrotransposable elements. Special Issue on “Retrotransposable Elements and Genome Evolution”, Cytogen. Genome Res. 110: 392-401 (issue also published separately as a book).
  • Vermaak, D., Henikoff, S. and Malik, H.S. (2005) Positive selection drives the evolution of rhino, an oogenesis-specific member of the Heterochromatin protein 1 (HP1) family in Drosophila. PLoS Genetics. 1: e9 (13 pages).
  • Malik, H. S. (2005) Mimulus finds centromeres in the driver’s seat (Research Focus). Trends Ecol. Evol. 20: 151-154.
  • Sawyer, S. L., Wu, L. I., Emerman, M. and Malik, H. S. (2005) Positive selection in primate TRIM5a identifies a critical species-specific retroviral restriction domain. Proc. Natl. Acad. Sci. USA 102: 2832-2837. #
    • Perspective: Yang, Z. (2005) The power of phylogenetic comparison in revealing protein function. Proc. Natl. Acad. Sci. USA 102: 3179-3180.

2004

  • Sawyer, S. L., Emerman, M. and Malik, H. S. (2004) Ancient adaptive evolution of the primate antiviral DNA editing enzyme, APOBEC3G. PLoS Biology 2: e275 (8 pages). #
    • Synopsis: (2004) Evolution of a Primate Defense against Intragenomic Infiltrators, PLoS Biology 2: e292.
    • Primer: Holmes, E. C. (2004) Adaptation and Immunity. PLoS Biology 2: e307.

Other Publications

  • Malik, H. S. (2012) Retroviruses push the envelope for mammalian placentation. (Commentary) Proc. Natl. Acad. Sci. USA 109: 2184-2185.
  • Levine, M. T. and Malik, H. S. (2011) Learning to protect your genome on the fly. (Preview) Cell 147:1440-1441.
  • Malik, H. S. (2006) A hitchhiker’s guide to survival finally makes CENs (Comment). J. Cell Biol. 174: 747-749.
  • Malik, H. S. (2007) Genes get diabolical (Book review). Nat Genet. 39: 577.

 

Fundraise
Quick Links