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Publications

*these authors contributed equally

  1. Zhao H, Syed AM, Khalid MM, Nguyen A, Ciling A, Wu D, Yau WM, Srinivasan S, Esposito D, Doudna JA,  Piszczek G, Melanie Ott M, Schuck P. Assembly of SARS-CoV-2 nucleocapsid protein with nucleic acid, Nucleic Acids Research, 2024. doi: 10.1093/nar/gkae256; bioRxiv, 2023. doi: 10.1101/2023.11.22.568361.

  2. Khalid MM*, Chen IP*, Soveg FW*, Taha TY, Tabata T, Suryawanshi RK, Syed AM, Ciling A, McCavitt-Malvido M, Schulze-Gahmen U, Hayashi J, Kim I-J, Fong SW, Batra J, Kumar GR, Laurent R, Ng LFP, Krogan NJ, Doudna JA, Verdin E, Ott M. Regulation of virion production by the ORF8 signal peptide across SARS-CoV-2 variants. bioRxiv, 2024. doi: 10.1101/2024.03.05.583578.

  3. Meyers NL, Ashuach T*, Lyons DE*, Khalid MM*, Simoneau CR, Erickson AL, Bouhaddou M, Nguyen TT, Kumar GR, Taha TY, Natarajan V, Baron JL, Neff N, Zanini F, Mahmoudi T, Quake SR, Krogan NJ, Cooper S, McDevitt TC, Yosef N, Ott M. Hepatitis C Virus Infects and Perturbs Liver Stem Cells. mBio, 2023. doi:10.1128/mbio.01318-23; bioRxiv, 2021. doi:10.1101/2021.10.26.465357.

  4. Glenn IS, Hall LN, Khalid MM, Ott M, Shoichet BK. Colloidal aggregation confounds cell-based Covid-19 antiviral screens. bioRxiv, 2023. doi: 10.1101/2023.10.27.564435.

  5. Suryawanshi RK, Taha TY, McCavitt-Malvido M, Silva I, Khalid MM, Syed AM, Irene P. Chen, Saldhi P, Sreekumar B, Montano M, Foresythe K, Tabata T, Kumar GR, Sotomayor-Gonzalez A, Servellita V, Gliwa A, Nguyen J, Kojima N, Arellanor T, Bussanich A, Hess V, Shacreaw M, Lopez L, Brobeck M, Turner F, Wang Y, Ghazarian S, Davis G, Rodriguez D, Doudna J, Spraggon L, Chiu CY, Ott M. Previous exposure to Spike-providing parental strains confers neutralizing immunity to XBB lineage and other SARS-CoV-2 recombinants in the context of vaccination. Emerging Microbes & Infections, 2023. doi:10.1080/22221751.2023.2270071.

  6. Kim IJ, Lee Yh, Khalid MM, Chen IP, Zhang Y, Ott M, Verdin E, SARS-CoV-2 protein ORF8 limits expression levels of Spike antigen and facilitates immune evasion of infected host cells. J Biol Chem., 2023. doi: https://doi.org/10.1016/j.jbc.2023.104955. bioRxiv, 2022. doi:10.1101/2022.11.09.515752.

  7. Taha TY, Chen IP, Hayashi JM, Tabata T, Walcott K, Kimmerly GR, Syed AM, Ciling A, Suryawanshi RK, Martin HS, Bach BH, Tsou CL, Montano M, Khalid MM, Sreekumar BK, Renuka Kumar G, Wyman S, Doudna JA, Ott M. Rapid assembly of SARS-CoV-2 genomes reveals attenuation of the Omicron BA.1 variant through NSP6. Nat Commun., 2023. doi: 10.1038/s41467-023-37787-0. bioRxiv, 2023. doi:10.1101/2023.01.31.525914.

  8. Hysenaj L, Little S, Kulhanek K, Magnen M, Bahl K, Gbenedio OM, Prinz M, Rodriguez L, Andersen C, Rao AA, Shen A, Lone J-C, Lupin-Jimenez LC, Bonser LR, Serwas NK, Mick E, Khalid MM, Taha TY, Kumar R, Li JZ, Ding VW, Matsumoto S, Maishan M, Sreekumar B, Simoneau C, Nazarenko I, Tomlinson MG, Khan K, von Gottberg A, Sigal A, Looney MR, Fragiadakis GK, Jablons DM, Langelier CR, Matthay M, Krummel M, Erle DJ, Combes AJ, Sil A, Ott M, Kratz JR, Roose JP. SARS-CoV-2 infection of airway organoids reveals conserved use of Tetraspanin-8 by Ancestral, Delta, and Omicron variants. Stem Cell Reports, 2023. doi: 10.1016/j.stemcr.2023.01.011. SSRN, 2022. doi:10.2139/ssrn.4198511.

  9. Leon KE*, Khalid MM*, Flynn RA, Fontaine KA, Nguyen TT, Kumar GR, Simoneau CR, Tomar S, Jimenez-Morales D, Dunlap M, Kaye J, Shah PS, Finkbeiner S, Krogan NJ, Bertozzi C, Carette JE, Ott M. Nuclear accumulation of host transcripts during Zika Virus Infection. PLoS Pathogens, 2023. doi: 10.1371/journal.ppat.1011070. bioRxiv, 2020. doi:10.1101/2020.12.03.410837.

  10. Simoneau CR, Chen PY, Xing GK, Khalid MM, Meyers NL, Hayashi JM, Taha TY, Leon KE, Ashuach T, Fontaine KA, Rodriguez L, Joehnk B, Walcott K, Vasudevan S, Fang X, Maishan M, Schultz S, Roose J, Matthay MA, Sil A, Arjomandi M, Yosef N, Ott M. NF-κB inhibitor alpha has a cross-variant role during SARS CoV-2 infection in ACE2-overexpressing human airway organoids. bioRxiv, 2022. doi: 10.1101/2022.08.02.502100. (Under review for publication)

  11. Syed AM, Ciling A, Taha TY, Chen IP, Khalid MM, Sreekumar B, Chen PY, Kumar GR, Suryawanshi R, Silva I, Milbes B, Kojima N, Hess V, Shacreaw M, Lopez L, Brobeck M, Turner F, Spraggon L, Tabata T, Ott M, Doudna JA. Omicron mutations enhance infectivity and reduce antibody neutralization of SARS-CoV-2 virus-like particles. PNAS, 2022. doi: 10.1073/pnas.2200592119. medRxiv, 2022. doi:10.1101/2021.12.20.21268048.

  12. Chen IP, Longbotham JE, McMahon S, Suryawanshi RK, Khalid MM, Taha TY, Tabata T, Hayashi JM, Soveg FW, Carlson-Stevermer J, Gupta M, Zhang MY, Lam VL, Li Y, Yu Z, Titus EW, Diallo A, Oki J, Holden K, Krogan N, Fujimori DG, Ott M. Viral E protein neutralizes BET protein-mediated post-entry antagonism of SARS-CoV-2. Cell Rep, 2022. doi: 10.1016/j.celrep.2022.111088. bioRxiv, 2021. doi:10.1101/2021.11.14.468537.

  13. Suryawanshi RK, Chen IP, Ma T, Syed AM, Brazer N, Saldhi P, Simoneau CR, Ciling A, Khalid MM, Sreekumar B, Chen PY, Kumar GR, Montano M, Gascon R, Tsou CL, Garcia-Knight MA, Sotomayor-Gonzalez A, Servellita V, Gliwa A, Nguyen J, Silva I, Milbes B, Kojima N, Hess V, Shacreaw M, Lopez L, Brobeck M, Turner F, Soveg FW, George AF, Fang X, Maishan M, Matthay M, Morris MK, Wadford D, Hanson C, Greene WC, Andino R, Spraggon L, Roan NR, Chiu CY, Doudna JA, Ott M. Limited cross-variant immunity from SARS-CoV-2 Omicron without vaccination. Nature, 2022. doi: 10.1038/s41586-022-04865-0. medRxiv, 2022. doi:10.1101/2022.01.13.22269243.

  14. Matsui Y, Li L, Prahl M, Cassidy AG, Ozarslan N, Golan Y, Gonzalez VJ, Lin CY, Jigmeddagva U, Chidboy MA, Montano M, Taha TY, Khalid MM, Sreekumar B, Hayashi JM, Chen PY, Kumar GR, Warrier L, Wu AH, Song D, Jegatheesan P, Rai DS, Govindaswami B, Needens J, Rincon M, Myatt L, Asiodu IV, Flaherman VJ, Afshar Y, Jacoby VL, Murtha AP, Robinson JF, Ott M, Greene WC, Gaw SL. Neutralizing antibody activity against SARS-CoV-2 variants in gestational age-matched mother-infant dyads after infection or vaccination. JCI Insight, 2022. doi: 10.1172/jci.insight.157354. medRxiv, 2021. doi:10.1101/2021.12.09.21267557.

  15. Servellita V, Syed AM, Morris MK, Brazer N, Saldhi P, Garcia-Knight M, Sreekumar B, Khalid MM, Ciling A, Chen PY, Kumar GR, Gliwa AS, Nguyen J, Sotomayor-Gonzalez A, Zhang Y, Frias E, Prostko J, Hackett J Jr, Andino R, Wadford DA, Hanson C, Doudna J, Ott M, Chiu CY. Neutralizing immunity in vaccine breakthrough infections from the SARS-CoV-2 Omicron and Delta variants. Cell, 2022. doi: 10.1016/j.cell.2022.03.019. medRXiv, 2022. doi:10.1101/2022.01.25.22269794.

  16. Jahan I*, Hayat S*, Khalid MM*, Ahammad RU, Asad A, Islam B, Mohammad QD, Jacobs BC, Islam Z. Association of mannose-binding lectin 2 gene polymorphisms with Guillain-Barré syndrome. Sci Rep, 2022. doi: 10.1038/s41598-022-09621-y.

  17. Khalid MM. Exploring the Molecular Mechanisms of SARS-CoV2 and ZIKV Pathogenesis. Erasmus University Rotterdam, 2022. Doctoral Thesis. ISBN: 978-94-6361-624-9. Publisher: Optima Grafische Communicatie, Rotterdam.

  18. Syed AM, Taha TY, Tabata T, Chen IP, Ciling A, Khalid MM, Sreekumar B, Chen PY, Hayashi JM, Soczek KM, Ott M, Doudna JA. Rapid assessment of SARS-CoV-2-evolved variants using virus-like particles. Science, 2021. doi: 10.1126/science.abl6184. bioRxiv, 2021. doi:10.1101/2021.08.05.455082.

  19. De Crignis E, Hossain T, Romal S, Carofiglio F, Moulos P, Khalid MM, Rao S, Bazrafshan A, Verstegen MM, Pourfarzad F, Koutsothanassis C, Gehart H, Kan TW, Palstra RJ, Boucher C, IJzermans JN, Huch M, Boj SF, Vries R, Clevers H, van der Laan LJ, Hatzis P, Mahmoudi T. Application of human liver organoids as a patient-derived primary model for HBV infection and related hepatocellular carcinoma. eLife, 2021. doi: 10.7554/eLife.60747. bioRxiv, 2020. doi:10.1101/568147.

  20. Deng X*, Garcia-Knight MA*, Khalid MM*, Servellita V*, Wang C*, Morris MK, Sotomayor-González A, Glasner DR, Reyes KR, Gliwa AS, Reddy NP, Martin CSS, Federman S, Cheng J, Balcerek J,Taylor J, Streithorst JA,Miller S, Sreekumar B, Chen PY, Schulze-Gahmen U, Taha TY, Hayashi JM, Siomoneau CR, Kumar GR,  McMahon S, Lidsky PV, Xiao Y, Hemarajata P, Green NM, Espinosa A, Kath C, Haw M, Bell J, Hacker JK, Hanson C, Wadford DA, Anaya C, Ferguson D, Frankino PA, Shivram H, Lareau LF, Wyman SK, Ott M, Andino R, Chiu CY. Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant. Cell, 2021. doi: 10.1016/j.cell.2021.04.025. medRxiv, 2021. doi:10.1101/2021.03.07.21252647.

  21. Weinberg ZY, Hilburger CE, Kim M, Cao L, Khalid M, Elmes S, Diwanji D, Hernandez E, Lopez J, Schaefer K, Smith AM, Zhou F; QCRG Structural Biology Consortium, Kumar RG, Ott M, Baker D, El-Samad H. Sentinel cells enable genetic detection of SARS-CoV-2 Spike protein. bioRxiv, 2021. doi: 10.1101/2021.04.20.440678.

  22. Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM, Weckstein AR, Owens TW, Gupta M, Pourmal S, Titus EW, Cakir M, , …… Khalid MM, Vallejo-Gracia A, Fozouni P, Simoneau CR, ….. Ott M, Palmarini M, Shokat KM, García-Sastre A, Rassen JA, Grosse R, Rosenberg OS, Verba KA, Basler CF, Vignuzzi M, Peden AA, Beltrao P, Krogan NJ. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science, 2020. doi: 10.1126/science.abe9403.

  23. Ali I, Ruiz DG, Ni Z, Johnson JR, Zhang H, Li PC, Khalid MM, Conrad RJ, Guo X, Min J, Greenblatt J, Jacobson M, Krogan NJ, Ott M. Crosstalk between RNA Pol II C-Terminal Domain Acetylation and Phosphorylation via RPRD Proteins. Molecular Cell, 2019. doi:10.1016/j.molcel.2019.04.008. bioRxiv, 2019. doi:10.1101/442491

  24. Jahan I, Ahammad RU, Khalid MM, Rahman MI, Hayat S, Islam B, Mohammad QD, Islam Z. Toll‐like receptor‐4 299Gly allele is associated with Guillain‐Barré syndrome in Bangladesh. Annals of Clinical and Translational Neurology, 2019. doi:10.1002/acn3.744.

  25. Fontaine KA, Leon KE, Khalid MM, Tomar S, Jimenez-Morales D, Dunlap M, Kaye JA, Shah PS, Finkbeiner S, Krogan NJ, Ott M. The Cellular NMD Pathway Restricts Zika Virus Infection and Is Targeted by the Viral Capsid Protein. mBio, 2018. doi:10.1128/mBio.02126-18. bioRxiv, 2018. doi:10.1101/290296.

  26. Rahman MI, Jahan I, Khalid MM, Jahan I, Ahammad RU, Nahar S, Islam Z. CD1A and CD1E gene polymorphisms are not associated with susceptibility to Guillain-Barré syndrome in the Bangladeshi population. J Neuroimmunol, 2018. doi:10.1016/j.jneuroim.2017.11.013.

  27. Jahan I, Ahammad RU, Farzana KS, Khalid MM, Islam MB, Rahman MI, Nahar S, Kabir Y, Mohmmad QD, Islam Z. Tumor necrosis factor-alpha -863C/A polymorphism is associated with Guillain-Barré syndrome in Bangladesh. J Neuroimmunol, 2017. doi:10.1016/j.jneuroim.2017.06.005.

  28. Stoszko M, De Crignis E, Rokx C, Khalid MM, Lungu C, Palstra RJ, Kan TW, Boucher C, Verbon A, Dykhuizen EC, Mahmoudi T. Small Molecule Inhibitors of BAF; A Promising Family of Compounds in HIV-1 Latency Reversal. EBioMedicine, 2016. doi:10.1016/j.ebiom.2015.11.047.

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Submitted or manuscript in preparation

*these authors contributed equally

  1. Syed A, Ciling A, Chen IP, Carlson CR, Adly A, Martin H, Taha TY, Khalid MM, Bouhaddou M, Ummadi M, Moen J ,Krogan N, Morgan DO,Ott M,Doudna JA. SARS-CoV-2 evolution balances conflicting roles of N protein phosphorylation. (Under review for publication) Available at SSRN: https://ssrn.com/abstract=4472729 or http://dx.doi.org/10.2139/ssrn.4472729.

  2. Hayashi JM, Taha TY, Chen IP, Syed A, Khalid MM, Simoneau CR, Chen PY, Leon KE, Krogan NJ, Wang Z, Puschnik AS, Doudna JA, Ott M. Circulating cholesterol fuels SARS-CoV-2 replication via ORF3a. (Under review for publication)

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