Publications

Peer-Reviewed Publications (reverse chronological; corresponding author(s) is underlined; *these authors contributed equally; ®reviews/perspectives)

2026 | 2025 | 2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | Other Publications

2026

  • Soares, R. F., Chang, C.-H., Koerich, L. B., Malik, H. S., and Kuhn, G. C. S. (2026) Retention of a single Cenp-C gene in different syntenic locations in the montium group of Drosophila species. Heredity (under review). biorXiv doi: 10.64898/2025.12.11.693522.
  • Raman, P., Khan, H., Tsukiyama, T., and Malik, H. S. (2026) Dynamic evolution of EZHIP, an inhibitor of the Polycomb Repressive Complex 2 in mammals.  biorXiv doi: 10.64898/2025.12.12.693809.
  • Bhattacharya, T., Freeman, T. S., Alleman, E. M., Wang, F., Checik, L., Emerman, M., Myles, K. M., & Malik, H. S. (2026) A conserved in-frame stop codon acts as a multipotent defense mechanism in alphaviruses. Science Adv (under revision) biorXiv doi: 10.1101/2025.09.27.679005.
  • Langley, C. A., Lilly, M., Malik, H. S., and Emerman, M. (2026) Fitness Landscapes of APOBEC3G Antagonism by HIV-1 Vif proteins. Science Adv (under review) biorXiv doi: 10.1101/2025.10.20.683452.
  • Kenaston, M. W., Cherkashchenko, L., Skawinski, C. L. S., Fishburn, A. T., Peddamallu, V., Florio, C. J., Robertson, A. E., Bhattacharya, T., Young, J. M., Malik, H. S., and Shah, P. S. (2026) Yellow Fever Virus Interactomes Reveal Common and Divergent Strategies of Replication and Evolution for Mosquito-borne Flaviviruses. Cell (under revision) biorXiv doi: 10.1101/2025.06.14.659623.
  • Batra, J.*, Rutkowska, M.*, Zhou, Y., Ye, C., Adavikolanu, R., Young, J. M., Anand, D., Verma, S., Gordon, M., Malpotra, S., Cupic, A., Kehrer, T., Moen, J. M., Winters, D. M., Rojc, A., Mena, I., Aslam, S., Martinez-Romero, C., Viñas, I. C., Khalil, Z., Farrugia, K., Banerjee, A., Tussia-Cohen, D., Dos Santos, M., Maji, S., Muralidharan, M., Foussard, H., Chen, I. P., Fuchs, R., San Felipe, C. J., Zuliani-Alvarez, L., Choudhury, P., Obernier, K., Gracias, S., Suryawanshi, R., Ibáñez, C., Juste, J., Pache, L., Taha, T. Y., Jouvenet, N., Verba, K. A., Fraser, J. S., Demeret, C., Stroud, R. M., van Bakel, H., Ott, M., Hagai, T., Polacco, B., Swaney, D. L., Echeverria, I., Bouhaddou, M., Eckhardt, M., Malik, H. S., Martinez-Sobrido, L. Miorin, L., García-Sastre, A., and Krogan, N. J. (2026) Coronavirus protein interaction mapping in bat and human cells identifies molecular and genetic switches for immune evasion and replication. Cell Host Microbe (under revision) biorXiv doi: 10.1101/2025.07.26.666918.
  • Chang, C.-H., de la Cruz, A. F. A., Mejia Natividad, I., Noyola, A. C., & Malik, H. S. (2026) Rapid protamine evolution suppresses meiotic drive in Drosophila. Science Adv. (in revision) biorXiv doi: 10.1101/2025.09.03.674087.
  • Rathore, U.*, Dugan, E.*, Thornton, H., Kumar, V. E., Dajani, R., Burdick, R. C., Young, J. M., Steinhart, Z., Lao, R., Delviks-Frankenberry, K. A., Dureja, I., Pathak, N., Arce, M. M., Dann, E., Choi, W., McKetney, J., Umhoefer, J. M., Parulekar, S., Schmidt, R., Polacco, B., Neidleman, J., Montano, M., Nguyen, V. Q.,, Cheng, Y., Roan, N. R., Swaney, D. L., Kaake, R. M., Dodgson, S. E., Hiatt, J., Pathak, V. K., Malik, H. S., Krogan, N. J., & Marson, A. (2026) Systematic Discovery of Pro- and Anti-HIV Host Factors in Primary Human CD4+ T Cells. Cell (in press)

2025

  • Hsieh, Y-Y. P.*, O’Keefe, I. P.*, Sun, W. W., Wang, Z., Yang, H., Vu, L. M., Smalley, N. E., Ernst, R. K., Dandekar, A. A.**, & Malik, H. S.** (2025) Magnesium depletion unleashes two unusual modes of colistin resistance with different fitness costs. PLOS Biology (in press) biorXiv doi: 10.1101/2024.10.15.618514.
  • Takenaka, R., Albanese, E. H., Simmerman, S., Verghese, S., de la Cruz, A. F. A., Schmidt, C. A.*, Rieder, L. E.*, & Malik, H. S.* (2025) The Drosophila maternal-effect gene abnormal oocyte (ao) does not repress histone gene expression. Genetics iyag036.
  • Geiger, R. A., Khera, D., Tenthorey, J. L., Kochs. G., Graf, L., Emerman, M., & Malik, H. S. (2025) Heterozygous and generalist MxA super-restrictors overcome breadth-specificity tradeoffs in antiviral restriction. Science Adv. 11: eadu0062.
  • Bhattacharya, T., Alleman, E. M., Freeman, T. S., Noyola, A. C., Emerman, M., & Malik, H. S. (2025) A conserved opal termination codon optimizes a temperature-dependent tradeoff between protein production and processing in alphaviruses. Science Adv. 11: eads7933.
  • Tenthorey, J. L., Del Banco, S., Ramzan, I., Klingenberg, H., Liu, C., Emerman, M., & Malik, H. S. (2025) Indels allow antiviral proteins to evolve functional novelty inaccessible by missense mutations. Cell Genomics 5: 100818.
  • Langley, C. A., Dietzen, P. A., Emerman, M., Tenthorey, J. L., & Malik, H. S. (2025) Antiviral Mx proteins have an ancient origin and widespread distribution among eukaryotes. Proc. Natl. Acad. Sci. USA. 122: e2416811122.

2024

  • Hollis, J. A., Chan, M. C., Malik, H. S., & Campbell, M. G. (2024) Molecular exaptation by the integrin αI domain. Science Adv. 11: eadx9567.
  • Casado, A. C.*, Pothukuchi, P.*, Naydenova, K., Yip, M. C. J., Young, J. M., Boulanger, J., Dharamdasani, V., Harper, C., Hammoudi, P.-M., Otten, E. G., Boyle, K., Gogoi, M., Malik, H. S., & Randow, F. (2024) Recognition of phylogenetically diverse pathogens through enzymatically amplified recruitment of RNF213. EMBO Rep. 5: 4979-5005.
  • Hsieh, Y-Y. P., Sun, W. W., Young, J. M., Cheung, R., Hogan, D. A., Dandekar, A. A.*, & Malik, H. S.* (2024) Widespread fungal-bacterial competition for magnesium lowers bacterial susceptibility to polymyxin antibiotics. PLOS Biology 22: e3002694.
  • Henriques, W. S., Young, J. M., Nemudryi, A., Nemudraia, A., Wiedenheft, B.*, & Malik, H. S.* (2024) The diverse evolutionary histories of domesticated metaviral capsid genes in mammals. Mol. Biol. Evol. 41(4): msae061.

2023

  • ®Malik, H. S., & Mank, J. E. (2023) Editorial overview: Conflicts, conflicts everywhere. Curr. Opin. Genet. Dev. 83: 102131.
  • Bayer, A., Child, S. J., Malik, H. S., & Geballe, A. P. (2023) A single polymorphic residue in humans underlies species-specific restriction of HSV-1 by the antiviral protein MxB. J. Virol. 5: e0083023.
  • Chang, C.-H., Mejia Natividad, I., & Malik, H. S. (2023) Expansion and loss of sperm nuclear basic proteins in Drosophila correspond with genetic conflicts between sex chromosomes. eLife 12: e85249.
  • ®Malik, H. S. (2023) Driving lessons: a brief (personal) history of centromere drive. Genetics 222: iyac155.

2022

  • Caro, L.*, Raman, P.*, Steiner, F.A., Ailion, M., & Malik, H. S. (2022) Recurrent but short-lived dupplications of centromeric proteins in holocentric Caenorhabditis species. Mol. Biol. Evol. 39: msac206
  • Hiatt, J., Hultquist, J. F., McGregor, M. J., Bouhaddou, M., Leenay, R. T., Simons, L. M., Young, J. M., Haas, P., Roth, T. L., Tobin, V., Wojcechowskyj, J. A., Woo, J. M., Rathore, U., Cavero, D. A., Shifrut, E., Nguyen, T. T., Haas, K. M., Malik, H. S., Doudna, J. A., May, A. P., Marson, A., & Krogan, N. J. (2022) A functional map of HIV-host interactions in primary human T cells. Nat. Comm. 13: 1752.
  • Raman, P., Rominger, M. C., Young, J. M., Molaro, A., Tsukiyama, T. & Malik, H. S. (2022) Novel classes and evolutionary turnover of histone H2B variants in the mammalian germline. Mol. Biol. Evol. 39: msac019.
  • ®Tenthorey, J. T., Emerman, M., & Malik, H. S. (2022) Evolutionary landscapes of host virus arms races. (Review) Ann. Rev. Immunol. 40:271-294

2021

  • Forsberg, K. J., Schmidtke, D. T., Werther, R., Hausman, D., Stoddard, B. L., Kaiser, B. K., & Malik, H. S. (2021) The novel anti-CRISPR AcrIIA22 relieves DNA torsion in target plasmids and impairs SpyCas9 activity. PLOS Biology 19: e3001428. 
  • Schroeder, C. M., Tomlin, S. A., Mejia Natividad, I., Valenzuela, J. R., & Malik, H. S. (2021) A rapidly evolving actin mediates fertility and developmental tradeoffs in Drosophila. eLife 10: e71279.
  • Kursel, L. E., McConnell, H., de la Cruz, A. F. A., & Malik, H. S. (2021) An actin-related protein that is most highly expressed in Drosophila testes is critical for embryonic development. Life Science Alliance 4: e202000992.
  • ®Ohainle, M. & Malik, H. S. (2021) A balancing act between primate lentiviruses and their receptor. (Commentary) Proc. Natl. Acad. Sci. USA 118: e2104741118.
  • ®Chang, C.-H. & Malik, H. S. (2021) Putting the brakes on centromere drive in Mimulus. (Perspective) PLOS Genetics 17: e1009494.
  • Kato, K., Ahmad, S., Zhu, A., Young, J. M., Mu, X., Park, S., Malik, H. S., & Hur, S. (2021) Structural analysis of RIG-I-like receptors reveals ancient rules of engagement between diverse RNA helicases and TRIM ubiquitin ligases. Mol. Cell 81: 599-613.
  • Chew, G.-L., Bleakley, M., Bradley, R. K., Malik, H. S., Henikoff, S., Molaro, A. & Sarthy, J. (2021) Short H2A histone variants are expressed in cancers. Nat. Comm. 12: 490.

2020

  • Molaro, A., Wood, A. J., Janssens, D., Kindelay, S. M., Eickbush, M. T., Wu, S., Singh, P., Muller, C. H., Henikoff, S., & Malik, H. S. (2020) Biparental contributions of the H2A.B histone variant control embryonic development in mice. PLOS Biology 18: e3001001
  • Kasinathan, B., Colmenares, S. U., McConnell, H., Young, J. M., Karpen, G. H., & Malik, H. S. (2020) Innovation of heterochromatin functions drives rapid evolution of essential ZAD-ZNF genes in Drosophila. eLife 9: e63368.
  • Hays, M., Young, J. M., Levan, P., & Malik, H. S. (2020) A natural variant of the essential host gene MMS21 restricts the parasitic 2-micron plasmid in Saccharomyces cerevisiae. eLife 9: e62337.
  • Tenthorey, J. L., Young, C. L., Sodeinde, A., Emerman, M.* & Malik, H. S.* (2020) Mutational resilience of antiviral restriction favors primate TRIM5α in host-virus evolutionary arms races. eLife 9: e59988.
  • Gordon, D. E.*, Jang, G. M.*, Bouhaddou, M.*, Xu, J., … Malik, H. S. (author #108 of 125 authors) … Beltrao, P.**, Vignuzzi, M.**, García-Sastre, A.**, Shokat, K. M.**, Shoichet, B. K.**, & Krogan, N. J. (2020) A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature 583: 459-468.
  • Yang, L., Emerman, M., Malik, H. S., & McLaughlin, R. N. (2020) Retrocopying expands the functional repertoire of APOBEC3 antiviral proteins in primates. eLife 9: e58436.
  • Kursel, L. E., Welsh, F. C., & Malik, H. S. (2020) Ancient co-retention of paralogs of Cid centromeric histones and Cal1 chaperones in mosquito species. Mol. Biol. Evol. 37: 1949-1963.
  • Molaro, A., Malik, H. S., & Bourc’his, D. (2020) Dynamic evolution of de novo DNA methyltransferases in rodent and primate genomes. Mol. Biol. Evol. 37: 1882-1892.
  • Schroeder, C. M., Valenzuela, J. R., Mejia Natividad, I., Hocky, G. M., & Malik, H. S. (2020) A burst of genetic innovation in Drosophila actin-related proteins for testis-specific function. Mol. Biol. Evol. 37: 757-772.

2019

  • Lamelza, P., Young, J. M., Noble, L. M., Caro, L., Isakharov, A., Palanisamy, M., Rockman, M. V., Malik, H. S., & Ailion, M. (2019) Hybridization promotes asexual reproduction in Caenorhabditis nematodes. PLOS Genetics 15: e1008520.
  • ®Schroeder, C. M., & Malik, H. S. (2019) Meiosis: How Gambling Chromosomes Beat the Rules (Dispatch). Current Biol. 29: R1247-R1248. 
  • Colón-Thillet, R., Hsieh, E.*, Graf, L.*, Mclaughlin, R. N., Kochs, G., Emerman, M., & Malik, H. S. (2019) Combinatorial mutagenesis of rapidly evolving residues yields super-restrictor antiviral proteins. PLOS Biology 17: e3000181.
  • ®Drinnenberg, I. A., Berger, F., Elsässer, S. J., Andersen, P. R., Ausió, J., Bickmore, W. A., Blackwell, A. R., Erwin, D. H., Gahan, J. M., Gaut, B. S., Harvey, Z. H., Henikoff, S., Kao, J. Y., Kurdistani, S. K., Lemos, B., Levine, M. T., Luger, K., Malik, H. S., Martín-Durán, J. M., Peichel, C. L., Renfree, M. B., Rutowicz, K., Sarkies, P., Schmitz, R. J., Technau, U., Thornton, J. W., Warnecke, T., & Wolfe, K. H. (2019) EvoChromo: towards a synthesis of chromatin biology and evolution. Development 146: dev178962 (doi: 10.1242/dev.178962) 
  • Forsberg, K. J., Bhatt, I. V.*, Schmidtke, D. T.*, Stoddard, B. L., Kaiser, B., K., & Malik, H. S. (2019) Functional metagenomics-guided discovery of potent Cas9 inhibitors in the human microbiome. eLife 8: e46540. 
  • Levin, T. C., Goldspiel, B. P., & Malik, H. S. (2019) Density-dependent resistance protects Legionella pneumophila from its own antimicrobial metabolite, HGA. eLife 8: e46086.
  • ®Richardson, L. A., Schmid, S. L., Bhandoola, A., Harly, C., Hedenström, A., Laub, M. T., Mace, G. M., Sengupta, P., Stock, A. M., Read, A. F., Malik, H. S., Estelle, M., Lowell, S., & Kimmelman, J. (2019) The PLOS Biology XV Collection: 15 years of exceptional science highlighted over 12 months. PLOS Biology 17: e3000180

2018

  • ®Schroeder, C. M. & Malik, H. S. (2018) Kindr motors drive in meiosis. Cell 173: 813-815.
  • ®Forsberg, K. J. & Malik, H. S. (2018) Microbial genomics: the expanding world of bacterial defense systems. Curr. Biol. 28: R361-R364.
  • Molaro, A., Young, J. M., & Malik, H. S. (2018) Evolutionary origins and diversification of testis-specific short histone H2A variants in mammals. Genome Res. 28: 460-473.
  • ®Kursel, L. E. & Malik, H. S. (2018) The cellular mechanisms and consequences of centromere drive. Curr. Opin. Cell Biol. 52: 58-65.

2017

  • ®Molaro, A., & Malik, H. S. (2017) Sex chromosomes: culture shock. eLife 6: e33312.
  • ®Ailion, M., & Malik, H. S. (2017) Genetics: Master regulator or master of disguise. Curr. Biol. 27: R844-R847.
  • ®Kasinathan, R., Ahmad, K., & Malik, H. S. (2017) Waddington redux: de novo mutations underlie the genetic assimilation of stress-induced phenocopies in Drosophila melanogaster. Genetics 207: 49-51.
  • ®Bull, J. J. & Malik, H. S. (2017) The gene drive bubble: new realities (Perspective). PLOS Genetics 13: e1006850.
  • Levin, T. C. & Malik, H. S. (2017) Rapidly evolving Toll-3/4 genes encode male-specific Toll-like receptors in Drosophila. Mol. Biol. Evol. 34: 2307-2323.
  • 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: e26033.
  • 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.
  • ®McLaughlin, R. N. & Malik, H. S. (2017) Genetic conflicts: the usual suspects and beyond. J. Exp. Biol. 220: 6-17.

2016

  • 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.
  • ®Bedford, T. & Malik, H. S. (2016) Did a single amino acid change make Ebola virus more virulent? (Leading Edge preview) Cell 167: 892-894.
  • ®Goodin, M. M.*, Hatfull, G. F.* & Malik, H. S.* (2016) A diversified portfolio. (Editorial comment) Annu. Rev. Virol. 3: vi-vii.
  • 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.
  • ®Kursel, L. E. & Malik, H. S. (2016) Centromeres (Primer). Curr Biol. 26: R487-90.
  • 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.
  • 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 nucleoporin. Genes Dev. 30: 1155-71.
  • 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*).
  • 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*).
  • ®Drinnenberg, I. A., Henikoff, S. & Malik, H. S. (2016) Evolutionary turnover of kinetochore proteins: a ship of Theseus? Trends Cell Biol. 26: 498-510.
  • ®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.

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. & Malik, H. S. (2012) Phylogenomic Analysis Reveals Dynamic Evolutionary History of the Drosophila Heterochromatin Protein 1 (HP1) Gene Family. PLOS Genetics 8: e1002729.
  • ® 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. & Malik, H. S. (2012) Convergent Evolution of Escape from Hepaciviral Antagonism in Primates. PLOS Biology 10: e1001282.
  • Lim, E. S., Fregoso, O. I., McCoy, C. O., Matsen, F. A., Malik, H. S. & Emerman, M. (2012) The Ability of Primate Lentiviruses to Degrade the Monocyte Restriction Factor SAMHD1 Preceded the Birth of the Viral Accessory Protein Vpx. Cell Host Microbe 11: 194-204.

2011

  • ® 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. & Malik, H. S. (2011) Paleovirology: ghosts and gifts of viruses past. (Review) Curr. Opin. Virol. 1: 304-309.
  • Duggal, N. K., Malik, H. S. & Emerman, M. (2011) The Breadth of Antiviral Activity of Apobec3DE in Chimpanzees Has Been Driven by Positive Selection. 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. & Bix, M. (2010) Diversifying selection and functional analysis of interleukin-4 suggests antagonism-driven evolution at receptor-binding interfaces BMC Evol. Biol. 10: 223.
  • Lim, E. S., Malik, H. S. & 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. & Malik, H. S. (2010) Paleovirology: modern consequences of ancient viruses. (Essay) PLOS Biology 8: e1000301.

2009

  • Oliver, P. L.*, Goodstadt, L.*, Bayes, J. J., Birtle, Z., Roach, K. C., Phadnis, N., Beatson, S. A., Lunter, G., Malik, H. S. & Ponting, C. P. (2009) Accelerated evolution of the Prdm9 speciation gene across diverse metazoan taxa. PLOS Genetics 5: e1000753.
  • ®Moran, J. V. & Malik, H. S. (2009) Diamonds and rust: how transposable elements influence mammalian genomes. (Meeting report) EMBO Rep. 10: 1306-1310.
  • Bayes, J. J., & Malik, H. S. (2009) Altered heterochromatin binding by a hybrid sterility protein in Drosophila species. Science 326: 1538-1541.
  • ®Elde, N. C. & Malik, H. S. (2009) The evolutionary conundrum of pathogen mimicry. Nat. Rev. Microbiol. 7: 787-797 (cover).
  • ®Vermaak, D. & Malik, H. S. (2009) Multiple roles of Heterochromatin Protein 1 genes in Drosophila. (Review) Annu. Rev. Genet. 43: 467-492.
  • ®Malik, H. S. & Henikoff, S. (2009) Major evolutionary transitions in centromere complexity. (Review) Cell 138: 1067-1082.
  • ®Vermaak, D., Bayes, J.J. & Malik, H. S. (2009) Surrogate approaches to study evolution of non-coding DNA elements that organize eukaryotic genomes. (Review) J. Hered. 100: 624-636.
  • ®Malik, H. S. (2009) The centromere-drive hypothesis: a simple basis for centromere complexity. (Review) Prog. Mol. Subcell. Biol. 48:33-52 (also published as a book chapter in “Centromere-Structure and Evolution”, ed: Durdica Ugarkovic, Springer-Verlag Series).
  • Tareen, S. U., Sawyer, S. L., Malik, H. S. & Emerman, M. (2009) An Expanded Clade of Rodent Trim5 Genes. Virology 385:473-483.
  • Smith, E. E. & 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.
  • Elde, N. C., Child, S. J., Geballe, A. P. & Malik, H. S. (2009) Protein Kinase R reveals an evolutionary model for defeating viral mimicry. Nature 457: 485-489.
  • ®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. & Harris, R. S. (2009) Guidelines for naming nonprimate APOBEC3 genes and proteins. (Commentary) J. Virol 83: 494-497.

2008

  • OhAinle, M., Kerns, J. A., Malik, H. S. & Emerman, M. (2008) Antiretroelement activity of APOBEC3H was lost twice in recent human evolution. Cell Host Microbe 4: 249-259. 
  • ®Bayes, J. J. & Malik, H. S. (2008) The evolution of centromeric DNA sequences. (Review) Encyclopedia of Life Sciences, John Wiley & Sons Publishing Co.  
  • Kerns, J. A., Emerman, M., & 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.

2007

  • Sawyer, S. L., Emerman, M., & Malik, H. S. (2007) Discordant evolution of the adjacent antiretroviral genes TRIM22 and TRIM5 in mammals. PLOS Pathogens 3: e197.
  • Rodriguez, M. A.*, Vermaak, D.*, Bayes, J. J.*, & 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.
  • Wiggins, B. L. & 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: 155-163.
  • Kaiser, S. M., Malik, H. S., & Emerman, M. (2007) Restriction of an Extinct Retrovirus by the Human TRIM5a Antiviral Protein. Science 316: 1756-1758.

2006

  • Sawyer, S. L. & 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. & Bayes, J. J. (2006) Genetic conflicts during female meiosis and the evolutionary origins of centromere complexity. (Review) Biochem. Soc. Trans. 34: 569-573.
  • OhAinle, M., Kerns, J. A., Malik, H. S. & Emerman, M. (2006) Adaptive Evolution and Antiviral Activity of the Conserved Mammalian Cytidine Deaminase APOBEC3H. J. Virol. 80: 3853-3862.
  • Sawyer, S. L., Wu, L. I., Akey, J. M., Emerman, M.* & 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.* & 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. & Henikoff, S. (2005) Positive selection of Iris, a retroviral envelope-derived host gene in Drosophila melanogaster. PLOS Genetics 1: e44.
  • ®Malik, H. S. (2005) Ribonuclease H evolution in retrotransposable elements. (Review) Special Issue on “Retrotransposable Elements and Genome Evolution”, Cytogen. Genome Res. 110: 392-401.
  • Vermaak, D., Henikoff, S. & 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.
  • ®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. & 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.

2004

  • Sawyer, S. L., Emerman, M. & Malik, H. S. (2004) Ancient adaptive evolution of the primate antiviral DNA editing enzyme, Apobec3G. PLOS Biology 2: e275. 

Other Publications

  • ®Phadnis, N. & Malik. H. S. (2013) The molecular and evolutionary basis of hybrid sterility: from Odysseus to Overdrive. Book chapter in “Speciation: Natural Processes, Genetics and Biodiversity” (ed: Pawel Michalak) Nova Publishers. 
  • 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.