2023
Zhao H, Syed AM, Khalid MM, Nguyen A, Ciling A, Wu D, Yau WM, Srinivasan S, Esposito D, Doudna JA, Piszczek G, Ott M, Schuck P. Assembly reactions of SARS-CoV-2 nucleocapsid protein with nucleic acid. bioRxiv [Preprint]. 2023 Nov 23:2023.11.22.568361. doi: 10.1101/2023.11.22.568361. PMID: 38045338; PMCID: PMC10690241.
Subramanian A, Wang L, Moss T, Voorhies M, Sangwan S, Stevenson E, Pulido EH, Kwok S, Chalkley RJ, Li KH, Krogan NJ, Swaney DL, Burlingame AL, Floor SN, Sil A, Walter P, Mukherjee S. A Legionella toxin exhibits tRNA mimicry and glycosyl transferase activity to target the translation machinery and trigger a ribotoxic stress response. Nat Cell Biol. 2023 Nov;25(11):1600-1615. doi: 10.1038/s41556-023-01248-z. Epub 2023 Oct 19. PMID: 37857833.
Haas KM, McGregor MJ, Bouhaddou M, Polacco BJ, Kim EY, Nguyen TT, Newton BW, Urbanowski M, Kim H, Williams MAP, Rezelj VV, Hardy A, Fossati A, Stevenson EJ, Sukerman E, Kim T, Penugonda S, Moreno E, Braberg H, Zhou Y, Metreveli G, Harjai B, Tummino TA, Melnyk JE, Soucheray M, Batra J, Pache L, Martin-Sancho L, Carlson-Stevermer J, Jureka AS, Basler CF, Shokat KM, Shoichet BK, Shriver LP, Johnson JR, Shaw ML, Chanda SK, Roden DM, Carter TC, Kottyan LC, Chisholm RL, Pacheco JA, Smith ME, Schrodi SJ, Albrecht RA, Vignuzzi M, Zuliani-Alvarez L, Swaney DL, Eckhardt M, Wolinsky SM, White KM, Hultquist JF, Kaake RM, García-Sastre A, Krogan NJ. Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets. Nat Commun. 2023 Sep 27;14(1):6030. doi: 10.1038/s41467-023-41442-z. PMID: 37758692; PMCID: PMC10533562.
Kehrer T, Cupic A, Ye C, Yildiz S, Bouhaddou M, Crossland NA, Barrall EA, Cohen P, Tseng A, Çağatay T, Rathnasinghe R, Flores D, Jangra S, Alam F, Mena I, Aslam S, Saqi A, Rutkowska M, Ummadi MR, Pisanelli G, Richardson RB, Veit EC, Fabius JM, Soucheray M, Polacco BJ, Ak B, Marin A, Evans MJ, Swaney DL, Gonzalez-Reiche AS, Sordillo EM, van Bakel H, Simon V, Zuliani-Alvarez L, Fontoura BMA, Rosenberg BR, Krogan NJ, Martinez-Sobrido L, García-Sastre A, Miorin L. Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis. Cell Host Microbe. 2023 Oct 11;31(10):1668-1684.e12. doi: 10.1016/j.chom.2023.08.003. Epub 2023 Sep 21. PMID: 37738983; PMCID: PMC10750313.
Bouhaddou M, Reuschl AK, Polacco BJ, Thorne LG, Ummadi MR, Ye C, Rosales R, Pelin A, Batra J, Jang GM, Xu J, Moen JM, Richards AL, Zhou Y, Harjai B, Stevenson E, Rojc A, Ragazzini R, Whelan MVX, Furnon W, De Lorenzo G, Cowton V, Syed AM, Ciling A, Deutsch N, Pirak D, Dowgier G, Mesner D, Turner JL, McGovern BL, Rodriguez ML, Leiva-Rebollo R, Dunham AS, Zhong X, Eckhardt M, Fossati A, Liotta NF, Kehrer T, Cupic A, Rutkowska M, Mena I, Aslam S, Hoffert A, Foussard H, Olwal CO, Huang W, Zwaka T, Pham J, Lyons M, Donohue L, Griffin A, Nugent R, Holden K, Deans R, Aviles P, Lopez-Martin JA, Jimeno JM, Obernier K, Fabius JM, Soucheray M, Hüttenhain R, Jungreis I, Kellis M, Echeverria I, Verba K, Bonfanti P, Beltrao P, Sharan R, Doudna JA, Martinez-Sobrido L, Patel AH, Palmarini M, Miorin L, White K, Swaney DL, Garcia-Sastre A, Jolly C, Zuliani-Alvarez L, Towers GJ, Krogan NJ. SARS-CoV-2 variants evolve convergent strategies to remodel the host response. Cell. 2023 Oct 12;186(21):4597-4614.e26. doi: 10.1016/j.cell.2023.08.026. Epub 2023 Sep 21. PMID: 37738970; PMCID: PMC10604369.
Steinbach AM, Bhadkamkar VL, Jimenez-Morales D, Stevenson E, Jang GM, Krogan NJ, Swaney DL, Mukherjee S. Cross-family small GTPase ubiquitination by the intracellular pathogen Legionella pneumophila. bioRxiv [Preprint]. 2023 Aug 3:2023.08.03.551750. doi: 10.1101/2023.08.03.551750. Update in: Mol Biol Cell. 2023 Dec 20;:mbcE23060260. PMID: 37577546; PMCID: PMC10418220.
Morrison HM, Craft J, Rivera-Lugo R, Johnson JR, Golovkine GR, Bell SL, Dodd CE, Van Dis E, Beatty WL, Margolis SR, Repasy T, Shaker I, Lee AY, Vance RE, Stanley SA, Watson RO, Krogan NJ, Portnoy DA, Penn BH, Cox JS. Deficiency in Galectin-3, -8, and -9 impairs immunity to chronic Mycobacterium tuberculosis infection but not acute infection with multiple intracellular pathogens. PLoS Pathog. 2023 Jun 23;19(6):e1011088. doi: 10.1371/journal.ppat.1011088. PMID: 37352334; PMCID: PMC10325092.
Muralidharan M, Krogan NJ, Bouhaddou M, Kim M. Current proteomics methods applicable to dissecting the DNA damage response. NAR Cancer. 2023 May 19;5(2):zcad020. doi: 10.1093/narcan/zcad020. PMID: 37213254; PMCID: PMC10198729.
Golovkine GR, Roberts AW, Morrison HM, Rivera-Lugo R, McCall RM, Nilsson H, Garelis NE, Repasy T, Cronce M, Budzik J, Van Dis E, Popov LM, Mitchell G, Zalpuri R, Jorgens D, Cox JS. Autophagy restricts Mycobacterium tuberculosis during acute infection in mice. Nat Microbiol. 2023 May;8(5):819-832. doi: 10.1038/s41564-023-01354-6. Epub 2023 Apr 10. PMID: 37037941.
Kim SK, Dickinson MS, Finer-Moore J, Guan Z, Kaake RM, Echeverria I, Chen J, Pulido EH, Sali A, Krogan NJ, Rosenberg OS, Stroud RM. Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13. Nat Struct Mol Biol. 2023 Mar;30(3):296-308. doi: 10.1038/s41594-022-00918-0. Epub 2023 Feb 13. PMID: 36782050; PMCID: PMC10312659.
2022
Peters CE, Schulze-Gahmen U, Eckhardt M, Jang GM, Xu J, Pulido EH, Bardine C, Craik CS, Ott M, Gozani O, Verba KA, Hüttenhain R, Carette JE, Krogan NJ. Structure-function analysis of enterovirus protease 2A in complex with its essential host factor SETD3. Nat Commun. 2022 Sep 8;13(1):5282. doi: 10.1038/s41467-022-32758-3. PMID: 36075902; PMCID: PMC9453702.
Johnson JR, Crosby DC, Hultquist JF, Kurland AP, Adhikary P, Li D, Marlett J, Swann J, Hüttenhain R, Verschueren E, Johnson TL, Newton BW, Shales M, Simon VA, Beltrao P, Frankel AD, Marson A, Cox JS, Fregoso OI, Young JAT, Krogan NJ. Global post-translational modification profiling of HIV-1-infected cells reveals mechanisms of host cellular pathway remodeling. Cell Rep. 2022 Apr 12;39(2):110690. doi: 10.1016/j.celrep.2022.110690. PMID: 35417684; PMCID: PMC9429972.
Van Dis E, Fox DM, Morrison HM, Fines DM, Babirye JP, McCann LH, Rawal S, Cox JS, Stanley SA. IFN-γ-independent control of M. tuberculosis requires CD4 T cell-derived GM-CSF and activation of HIF-1α. PLoS Pathog. 2022 Jul 25;18(7):e1010721. doi: 10.1371/journal.ppat.1010721. PMID: 35877763; PMCID: PMC9352196.
May DG, Martin-Sancho L, Anschau V, Liu S, Chrisopulos RJ, Scott KL, Halfmann CT, Díaz Peña R, Pratt D, Campos AR, Roux KJ. A BioID-Derived Proximity Interactome for SARS-CoV-2 Proteins. Viruses. 2022 Mar 15;14(3):611. doi: 10.3390/v14030611. PMID: 35337019; PMCID: PMC8951556.
Echeverria I, Braberg H, Krogan NJ, Sali A. Integrative structure determination of histones H3 and H4 using genetic interactions. FEBS J. 2023 May;290(10):2565-2575. doi: 10.1111/febs.16435. Epub 2022 Apr 3. PMID: 35298864; PMCID: PMC9481981.
Escalera A, Gonzalez-Reiche AS, Aslam S, Mena I, Laporte M, Pearl RL, Fossati A, Rathnasinghe R, Alshammary H, van de Guchte A, Farrugia K, Qin Y, Bouhaddou M, Kehrer T, Zuliani-Alvarez L, Meekins DA, Balaraman V, McDowell C, Richt JA, Bajic G, Sordillo EM, Dejosez M, Zwaka TP, Krogan NJ, Simon V, Albrecht RA, van Bakel H, García-Sastre A, Aydillo T. Mutations in SARS-CoV-2 variants of concern link to increased spike cleavage and virus transmission. Cell Host Microbe. 2022 Mar 9;30(3):373-387.e7. doi: 10.1016/j.chom.2022.01.006. Epub 2022 Jan 21. PMID: 35150638; PMCID: PMC8776496.
Hancock M, Peulen TO, Webb B, Poon B, Fraser JS, Adams P, Sali A. Integration of software tools for integrative modeling of biomolecular systems. J Struct Biol. 2022 Mar;214(1):107841. doi: 10.1016/j.jsb.2022.107841. Epub 2022 Feb 9. PMID: 35149213; PMCID: PMC9278553.
Oom AL, Stoneham CA, Lewinski MK, Richards A, Wozniak JM, Shams-Ud-Doha K, Gonzalez DJ, Krogan NJ, Guatelli J. Comparative Analysis of T-Cell Spatial Proteomics and the Influence of HIV Expression. Mol Cell Proteomics. 2022 Mar;21(3):100194. doi: 10.1016/j.mcpro.2022.100194. Epub 2022 Jan 8. PMID: 35017099; PMCID: PMC8956815.
Braberg H, Echeverria I, Kaake RM, Sali A, Krogan NJ. From systems to structure - using genetic data to model protein structures. Nat Rev Genet. 2022 Jun;23(6):342-354. doi: 10.1038/s41576-021-00441-w. Epub 2022 Jan 10. PMID: 35013567; PMCID: PMC8744059.
Varona JF, Landete P, Lopez-Martin JA, Estrada V, Paredes R, Guisado-Vasco P, Fernandez de Orueta L, Torralba M, Fortun J, Vates R, Barberan J, Clotet B, Ancochea J, Carnevali D, Cabello N, Porras L, Gijon P, Monereo A, Abad D, Zuñiga S, Sola I, Rodon J, Vergara-Alert J, Izquierdo-Useros N, Fudio S, Pontes MJ, de Rivas B, Giron de Velasco P, Nieto A, Gomez J, Aviles P, Lubomirov R, Belgrano A, Sopesen B, White KM, Rosales R, Yildiz S, Reuschl AK, Thorne LG, Jolly C, Towers GJ, Zuliani-Alvarez L, Bouhaddou M, Obernier K, McGovern BL, Rodriguez ML, Enjuanes L, Fernandez-Sousa JM, Krogan NJ, Jimeno JM, Garcia-Sastre A. Preclinical and randomized phase I studies of plitidepsin in adults hospitalized with COVID-19. Life Sci Alliance. 2022 Jan 10;5(4):e202101200. doi: 10.26508/lsa.202101200. PMID: 35012962; PMCID: PMC8761492.
2021
Thorne LG, Bouhaddou M, Reuschl AK, Zuliani-Alvarez L, Polacco B, Pelin A, Batra J, Whelan MVX, Hosmillo M, Fossati A, Ragazzini R, Jungreis I, Ummadi M, Rojc A, Turner J, Bischof ML, Obernier K, Braberg H, Soucheray M, Richards A, Chen KH, Harjai B, Memon D, Hiatt J, Rosales R, McGovern BL, Jahun A, Fabius JM, White K, Goodfellow IG, Takeuchi Y, Bonfanti P, Shokat K, Jura N, Verba K, Noursadeghi M, Beltrao P, Kellis M, Swaney DL, García-Sastre A, Jolly C, Towers GJ, Krogan NJ. Evolution of enhanced innate immune evasion by SARS-CoV-2. Nature. 2022 Feb;602(7897):487-495. doi: 10.1038/s41586-021-04352-y. Epub 2021 Dec 23. Erratum in: Nature. 2022 Apr;604(7905):E14. PMID: 34942634; PMCID: PMC8850198.
Martin-Sancho L, Tripathi S, Rodriguez-Frandsen A, Pache L, Sanchez-Aparicio M, McGregor MJ, Haas KM, Swaney DL, Nguyen TT, Mamede JI, Churas C, Pratt D, Rosenthal SB, Riva L, Nguyen C, Beltran-Raygoza N, Soonthornvacharin S, Wang G, Jimenez-Morales D, De Jesus PD, Moulton HM, Stein DA, Chang MW, Benner C, Ideker T, Albrecht RA, Hultquist JF, Krogan NJ, García-Sastre A, Chanda SK. Restriction factor compendium for influenza A virus reveals a mechanism for evasion of autophagy. Nat Microbiol. 2021 Oct;6(10):1319-1333. doi: 10.1038/s41564-021-00964-2. Epub 2021 Sep 23. PMID: 34556855; PMCID: PMC9683089.
Cakir M, Obernier K, Forget A, Krogan NJ. Target Discovery for Host-Directed Antiviral Therapies: Application of Proteomics Approaches. mSystems. 2021 Oct 26;6(5):e0038821. doi: 10.1128/mSystems.00388-21. Epub 2021 Sep 14. PMID: 34519533; PMCID: PMC8547474.
Raveh B, Sun L, White KL, Sanyal T, Tempkin J, Zheng D, Bharath K, Singla J, Wang C, Zhao J, Li A, Graham NA, Kesselman C, Stevens RC, Sali A. Bayesian metamodeling of complex biological systems across varying representations. Proc Natl Acad Sci U S A. 2021 Aug 31;118(35):e2104559118. doi: 10.1073/pnas.2104559118. PMID: 34453000; PMCID: PMC8536362.
Kaake RM, Echeverria I, Kim SJ, Von Dollen J, Chesarino NM, Feng Y, Yu C, Ta H, Chelico L, Huang L, Gross J, Sali A, Krogan NJ. Characterization of an A3G-VifHIV-1-CRL5-CBFβ Structure Using a Cross-linking Mass Spectrometry Pipeline for Integrative Modeling of Host-Pathogen Complexes. Mol Cell Proteomics. 2021;20:100132. doi: 10.1016/j.mcpro.2021.100132. Epub 2021 Aug 11. PMID: 34389466; PMCID: PMC8459920.
Tummino TA, Rezelj VV, Fischer B, Fischer A, O'Meara MJ, Monel B, Vallet T, White KM, Zhang Z, Alon A, Schadt H, O'Donnell HR, Lyu J, Rosales R, McGovern BL, Rathnasinghe R, Jangra S, Schotsaert M, Galarneau JR, Krogan NJ, Urban L, Shokat KM, Kruse AC, García-Sastre A, Schwartz O, Moretti F, Vignuzzi M, Pognan F, Shoichet BK. Drug-induced phospholipidosis confounds drug repurposing for SARS-CoV-2. Science. 2021 Jul 30;373(6554):541-547. doi: 10.1126/science.abi4708. Epub 2021 Jun 22. PMID: 34326236; PMCID: PMC8501941.
Bell SL, Lopez KL, Cox JS, Patrick KL, Watson RO. Galectin-8 Senses Phagosomal Damage and Recruits Selective Autophagy Adapter TAX1BP1 To Control Mycobacterium tuberculosis Infection in Macrophages. mBio. 2021 Aug 31;12(4):e0187120. doi: 10.1128/mBio.01871-20. Epub 2021 Jul 6. PMID: 34225486; PMCID: PMC8406326.
Souilmi Y, Lauterbur ME, Tobler R, Huber CD, Johar AS, Moradi SV, Johnston WA, Krogan NJ, Alexandrov K, Enard D. An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia. Curr Biol. 2021 Aug 23;31(16):3504-3514.e9. doi: 10.1016/j.cub.2021.05.067. Epub 2021 Jun 24. Erratum in: Curr Biol. 2021 Aug 23;31(16):3704. PMID: 34171302; PMCID: PMC8223470.
Thorne LG, Bouhaddou M, Reuschl AK, Zuliani-Alvarez L, Polacco B, Pelin A, Batra J, Whelan MVX, Ummadi M, Rojc A, Turner J, Obernier K, Braberg H, Soucheray M, Richards A, Chen KH, Harjai B, Memon D, Hosmillo M, Hiatt J, Jahun A, Goodfellow IG, Fabius JM, Shokat K, Jura N, Verba K, Noursadeghi M, Beltrao P, Swaney DL, Garcia-Sastre A, Jolly C, Towers GJ, Krogan NJ. Evolution of enhanced innate immune evasion by the SARS-CoV-2 B.1.1.7 UK variant. bioRxiv [Preprint]. 2021 Jun 7:2021.06.06.446826. doi: 10.1101/2021.06.06.446826. Update in: Nature. 2021 Dec 23;: PMID: 34127972; PMCID: PMC8202424.
Gupta M, Azumaya CM, Moritz M, Pourmal S, Diallo A, Merz GE, Jang G, Bouhaddou M, Fossati A, Brilot AF, Diwanji D, Hernandez E, Herrera N, Kratochvil HT, Lam VL, Li F, Li Y, Nguyen HC, Nowotny C, Owens TW, Peters JK, Rizo AN, Schulze-Gahmen U, Smith AM, Young ID, Yu Z, Asarnow D, Billesbølle C, Campbell MG, Chen J, Chen KH, Chio US, Dickinson MS, Doan L, Jin M, Kim K, Li J, Li YL, Linossi E, Liu Y, Lo M, Lopez J, Lopez KE, Mancino A, Moss FR 3rd, Paul MD, Pawar KI, Pelin A, Pospiech TH Jr, Puchades C, Remesh SG, Safari M, Schaefer K, Sun M, Tabios MC, Thwin AC, Titus EW, Trenker R, Tse E, Tsui TKM, Wang F, Zhang K, Zhang Y, Zhao J, Zhou F, Zhou Y, Zuliani-Alvarez L; QCRG Structural Biology Consortium; Agard DA, Cheng Y, Fraser JS, Jura N, Kortemme T, Manglik A, Southworth DR, Stroud RM, Swaney DL, Krogan NJ, Frost A, Rosenberg OS, Verba KA. CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes. bioRxiv [Preprint]. 2021 May 11:2021.05.10.443524. doi: 10.1101/2021.05.10.443524. PMID: 34013269; PMCID: PMC8132225.
Hiatt J, Cavero DA, McGregor MJ, Zheng W, Budzik JM, Roth TL, Haas KM, Wu D, Rathore U, Meyer-Franke A, Bouzidi MS, Shifrut E, Lee Y, Kumar VE, Dang EV, Gordon DE, Wojcechowskyj JA, Hultquist JF, Fontaine KA, Pillai SK, Cox JS, Ernst JD, Krogan NJ, Marson A. Efficient generation of isogenic primary human myeloid cells using CRISPR-Cas9 ribonucleoproteins. Cell Rep. 2021 May 11;35(6):109105. doi: 10.1016/j.celrep.2021.109105. PMID: 33979618; PMCID: PMC8188731.
Sali A. From integrative structural biology to cell biology. J Biol Chem. 2021 Jan-Jun;296:100743. doi: 10.1016/j.jbc.2021.100743. Epub 2021 May 4. PMID: 33957123; PMCID: PMC8203844.
Martin-Sancho L, Lewinski MK, Pache L, Stoneham CA, Yin X, Becker ME, Pratt D, Churas C, Rosenthal SB, Liu S, Weston S, De Jesus PD, O'Neill AM, Gounder AP, Nguyen C, Pu Y, Curry HM, Oom AL, Miorin L, Rodriguez-Frandsen A, Zheng F, Wu C, Xiong Y, Urbanowski M, Shaw ML, Chang MW, Benner C, Hope TJ, Frieman MB, García-Sastre A, Ideker T, Hultquist JF, Guatelli J, Chanda SK. Functional landscape of SARS-CoV-2 cellular restriction. Mol Cell. 2021 Jun 17;81(12):2656-2668.e8. doi: 10.1016/j.molcel.2021.04.008. Epub 2021 Apr 13. PMID: 33930332; PMCID: PMC8043580.
Schuller M, Correy GJ, Gahbauer S, Fearon D, Wu T, Díaz RE, Young ID, Carvalho Martins L, Smith DH, Schulze-Gahmen U, Owens TW, Deshpande I, Merz GE, Thwin AC, Biel JT, Peters JK, Moritz M, Herrera N, Kratochvil HT; QCRG Structural Biology Consortium; Aimon A, Bennett JM, Brandao Neto J, Cohen AE, Dias A, Douangamath A, Dunnett L, Fedorov O, Ferla MP, Fuchs MR, Gorrie-Stone TJ, Holton JM, Johnson MG, Krojer T, Meigs G, Powell AJ, Rack JGM, Rangel VL, Russi S, Skyner RE, Smith CA, Soares AS, Wierman JL, Zhu K, O'Brien P, Jura N, Ashworth A, Irwin JJ, Thompson MC, Gestwicki JE, von Delft F, Shoichet BK, Fraser JS, Ahel I. Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking. Sci Adv. 2021 Apr 14;7(16):eabf8711. doi: 10.1126/sciadv.abf8711. PMID: 33853786; PMCID: PMC8046379.
Tummino TA, Rezelj VV, Fischer B, Fischer A, O'Meara MJ, Monel B, Vallet T, Zhang Z, Alon A, O'Donnell HR, Lyu J, Schadt H, White KM, Krogan NJ, Urban L, Shokat KM, Kruse AC, García-Sastre A, Schwartz O, Moretti F, Vignuzzi M, Pognan F, Shoichet BK. Phospholipidosis is a shared mechanism underlying the in vitro antiviral activity of many repurposed drugs against SARS-CoV-2. bioRxiv [Preprint]. 2021 Mar 24:2021.03.23.436648. doi: 10.1101/2021.03.23.436648. PMID: 33791693; PMCID: PMC8010720.
Fabius JM, Krogan NJ. Creating collaboration by breaking down scientific barriers. Cell. 2021 Apr 29;184(9):2271-2275. doi: 10.1016/j.cell.2021.02.022. Epub 2021 Mar 24. PMID: 33765441; PMCID: PMC8630979.
Reuschl AK, Thorne LG, Zuliani-Alvarez L, Bouhaddou M, Obernier K, Hiatt J, Soucheray M, Turner J, Fabius JM, Nguyen GT, Swaney DL, Rosales R, White KM, Avilés P, Kirby IT, Melnyk JE, Shi Y, Zhang Z, Shokat KM, García-Sastre A, Jolly C, Towers GJ, Krogan NJ. Host-directed therapies against early-lineage SARS-CoV-2 retain efficacy against B.1.1.7 variant. bioRxiv [Preprint]. 2021 Feb 4:2021.01.24.427991. doi: 10.1101/2021.01.24.427991. PMID: 33501437; PMCID: PMC7836107.
White KM, Rosales R, Yildiz S, Kehrer T, Miorin L, Moreno E, Jangra S, Uccellini MB, Rathnasinghe R, Coughlan L, Martinez-Romero C, Batra J, Rojc A, Bouhaddou M, Fabius JM, Obernier K, Dejosez M, Guillén MJ, Losada A, Avilés P, Schotsaert M, Zwaka T, Vignuzzi M, Shokat KM, Krogan NJ, García-Sastre A. Plitidepsin has potent preclinical efficacy against SARS-CoV-2 by targeting the host protein eEF1A. Science. 2021 Feb 26;371(6532):926-931. doi: 10.1126/science.abf4058. Epub 2021 Jan 25. PMID: 33495306; PMCID: PMC7963220.
Haas P, Muralidharan M, Krogan NJ, Kaake RM, Hüttenhain R. Proteomic Approaches to Study SARS-CoV-2 Biology and COVID-19 Pathology. J Proteome Res. 2021 Feb 5;20(2):1133-1152. doi: 10.1021/acs.jproteome.0c00764. Epub 2021 Jan 19. PMID: 33464917; PMCID: PMC7839417.
Richards AL, Eckhardt M, Krogan NJ. Mass spectrometry-based protein-protein interaction networks for the study of human diseases. Mol Syst Biol. 2021 Jan;17(1):e8792. doi: 10.15252/msb.20188792. PMID: 33434350; PMCID: PMC7803364.
Wang R, Simoneau CR, Kulsuptrakul J, Bouhaddou M, Travisano KA, Hayashi JM, Carlson-Stevermer J, Zengel JR, Richards CM, Fozouni P, Oki J, Rodriguez L, Joehnk B, Walcott K, Holden K, Sil A, Carette JE, Krogan NJ, Ott M, Puschnik AS. Genetic Screens Identify Host Factors for SARS-CoV-2 and Common Cold Coronaviruses. Cell. 2021 Jan 7;184(1):106-119.e14. doi: 10.1016/j.cell.2020.12.004. Epub 2020 Dec 9. PMID: 33333024; PMCID: PMC7723770.
Shivram H, Cress BF, Knott GJ, Doudna JA. Controlling and enhancing CRISPR systems. Nat Chem Biol. 2021 Jan;17(1):10-19. doi: 10.1038/s41589-020-00700-7. Epub 2020 Dec 16. PMID: 33328654; PMCID: PMC8101458.
Bracken CJ, Lim SA, Solomon P, Rettko NJ, Nguyen DP, Zha BS, Schaefer K, Byrnes JR, Zhou J, Lui I, Liu J, Pance K; QCRG Structural Biology Consortium; Zhou XX, Leung KK, Wells JA. Bi-paratopic and multivalent VH domains block ACE2 binding and neutralize SARS-CoV-2. Nat Chem Biol. 2021 Jan;17(1):113-121. doi: 10.1038/s41589-020-00679-1. Epub 2020 Oct 20. PMID: 33082574; PMCID: PMC8356808.
2020
Bouhaddou M, Memon D, Meyer B, White KM, Rezelj VV, Correa Marrero M, Polacco BJ, Melnyk JE, Ulferts S, Kaake RM, Batra J, Richards AL, Stevenson E, Gordon DE, Rojc A, Obernier K, Fabius JM, Soucheray M, Miorin L, Moreno E, Koh C, Tran QD, Hardy A, Robinot R, Vallet T, Nilsson-Payant BE, Hernandez-Armenta C, Dunham A, Weigang S, Knerr J, Modak M, Quintero D, Zhou Y, Dugourd A, Valdeolivas A, Patil T, Li Q, Hüttenhain R, Cakir M, Muralidharan M, Kim M, Jang G, Tutuncuoglu B, Hiatt J, Guo JZ, Xu J, Bouhaddou S, Mathy CJP, Gaulton A, Manners EJ, Félix E, Shi Y, Goff M, Lim JK, McBride T, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, De Wit E, Leach AR, Kortemme T, Shoichet B, Ott M, Saez-Rodriguez J, tenOever BR, Mullins RD, Fischer ER, Kochs G, Grosse R, García-Sastre A, Vignuzzi M, Johnson JR, Shokat KM, Swaney DL, Beltrao P, Krogan NJ. The Global Phosphorylation Landscape of SARS-CoV-2 Infection. Cell. 2020 Jun 28;. doi: 10.1016/j.cell.2020.06.034. [Epub ahead of print] PubMed PMID: 32645325; PubMed Central PMCID: PMC7321036.
Budzik JM, Swaney DL, Jimenez-Morales D, Johnson JR, Garelis NE, Repasy T, Roberts AW, Popov LM, Parry TJ, Pratt D, Ideker T, Krogan NJ, Cox JS. Dynamic post-translational modification profiling of Mycobacterium tuberculosis-infected primary macrophages. Elife. 2020 Jan 17;9. doi: 10.7554/eLife.51461. PubMed PMID: 31951200; PubMed Central PMCID: PMC7030789.
Eckhardt M, Hultquist JF, Kaake RM, Hüttenhain R, Krogan NJ. A systems approach to infectious disease. Nat Rev Genet. 2020 Jun;21(6):339-354. doi: 10.1038/s41576-020-0212-5. Epub 2020 Feb 14. Review. PubMed PMID: 32060427.
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. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. 2020 Apr 30;. doi: 10.1038/s41586-020-2286-9. [Epub ahead of print] PubMed PMID: 32353859; NIHMSID:NIHMS1587111.
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, Soucheray M, McGregor M, Cakir Z, Jang G, O'Meara MJ, Tummino TA, Zhang Z, Foussard H, Rojc A, Zhou Y, Kuchenov D, Hüttenhain R, Xu J, Eckhardt M, Swaney DL, Fabius JM, Ummadi M, Tutuncuoglu B, Rathore U, Modak M, Haas P, Haas KM, Naing ZZC, Pulido EH, Shi Y, Barrio-Hernandez I, Memon D, Petsalaki E, Dunham A, Marrero MC, Burke D, Koh C, Vallet T, Silvas JA, Azumaya CM, Billesbølle C, Brilot AF, Campbell MG, Diallo A, Dickinson MS, Diwanji D, Herrera N, Hoppe N, Kratochvil HT, Liu Y, Merz GE, Moritz M, Nguyen HC, Nowotny C, Puchades C, Rizo AN, Schulze-Gahmen U, Smith AM, Sun M, Young ID, Zhao J, Asarnow D, Biel J, Bowen A, Braxton JR, Chen J, Chio CM, Chio US, Deshpande I, Doan L, Faust B, Flores S, Jin M, Kim K, Lam VL, Li F, Li J, Li YL, Li Y, Liu X, Lo M, Lopez KE, Melo AA, Moss FR 3rd, Nguyen P, Paulino J, Pawar KI, Peters JK, Pospiech TH Jr, Safari M, Sangwan S, Schaefer K, Thomas PV, Thwin AC, Trenker R, Tse E, Tsui TKM, Wang F, Whitis N, Yu Z, Zhang K, Zhang Y, Zhou F, Saltzberg D, Hodder AJ, Shun-Shion AS, Williams DM, White KM, Rosales R, Kehrer T, Miorin L, Moreno E, Patel AH, Rihn S, Khalid MM, Vallejo-Gracia A, Fozouni P, Simoneau CR, Roth TL, Wu D, Karim MA, Ghoussaini M, Dunham I, Berardi F, Weigang S, Chazal M, Park J, Logue J, McGrath M, Weston S, Haupt R, Hastie CJ, Elliott M, Brown F, Burness KA, Reid E, Dorward M, Johnson C, Wilkinson SG, Geyer A, Giesel DM, Baillie C, Raggett S, Leech H, Toth R, Goodman N, Keough KC, Lind AL, Klesh RJ, Hemphill KR, Carlson-Stevermer J, Oki J, Holden K, Maures T, Pollard KS, Sali A, Agard DA, Cheng Y, Fraser JS, Frost A, Jura N, Kortemme T, Manglik A, Southworth DR, Stroud RM, Alessi DR, Davies P, Frieman MB, Ideker T, Abate C, Jouvenet N, Kochs G, Shoichet B, 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 Oct 15;. doi: 10.1126/science.abe9403. [Epub ahead of print] PubMed PMID: 33060197.
Mast FD, Navare AT, van der Sloot AM, Coulombe-Huntington J, Rout MP, Baliga NS, Kaushansky A, Chait BT, Aderem A, Rice CM, Sali A, Tyers M, Aitchison JD. Crippling life support for SARS-CoV-2 and other viruses through synthetic lethality. J Cell Biol. 2020 Oct 5;219(10):e202006159. doi: 10.1083/jcb.202006159. PMID: 32785687; PMCID: PMC7659715.
Tutuncuoglu B, Cakir M, Batra J, Bouhaddou M, Eckhardt M, Gordon DE, Krogan NJ. The Landscape of Human Cancer Proteins Targeted by SARS-CoV-2. Cancer Discov. 2020 Jul;10(7):916-921. doi: 10.1158/2159-8290.CD-20-0559. Epub 2020 May 22. PubMed PMID: 32444466; PubMed Central PMCID: PMC7357668.
Wang F, Liu Y, Yu Z, Li S, Feng S, Cheng Y, Agard DA. General and robust covalently linked graphene oxide affinity grids for high-resolution cryo-EM. Proc Natl Acad Sci U S A. 2020 Sep 29;117(39):24269-24273. doi: 10.1073/pnas.2009707117. Epub 2020 Sep 10. PMID: 32913054; PMCID: PMC7533693.
Wang R, Simoneau CR, Kulsuptrakul J, Bouhaddou M, Travisano K, Hayashi JM, Carlson-Stevermer J, Oki J, Holden K, Krogan NJ, Ott M, Puschnik AS. Functional genomic screens identify human host factors for SARS-CoV-2 and common cold coronaviruses. bioRxiv [Preprint]. 2020 Sep 24:2020.09.24.312298. doi: 10.1101/2020.09.24.312298. PMID: 32995787; PMCID: PMC7523113.
Wolff G, Limpens RWAL, Zevenhoven-Dobbe JC, Laugks U, Zheng S, de Jong AWM, Koning RI, Agard DA, Grünewald K, Koster AJ, Snijder EJ, Bárcena M. A molecular pore spans the double membrane of the coronavirus replication organelle. Science. 2020 Sep 11;369(6509):1395-1398. doi: 10.1126/science.abd3629. Epub 2020 Aug 6. PubMed PMID: 32763915.
2019
Fay A, Czudnochowski N, Rock JM, Johnson JR, Krogan NJ, Rosenberg O, Glickman MS. Two Accessory Proteins Govern MmpL3 Mycolic Acid Transport in Mycobacteria. MBio. 2019 Jun 25;10(3). doi: 10.1128/mBio.00850-19. PubMed PMID: 31239378; PubMed Central PMCID: PMC6593404.
Hüttenhain R, Xu J, Burton LA, Gordon DE, Hultquist JF, Johnson JR, Satkamp L, Hiatt J, Rhee DY, Baek K, Crosby DC, Frankel AD, Marson A, Harper JW, Alpi AF, Schulman BA, Gross JD, Krogan NJ. ARIH2 Is a Vif-Dependent Regulator of CUL5-Mediated APOBEC3G Degradation in HIV Infection. Cell Host Microbe. 2019 Jul 10;26(1):86-99.e7. doi: 10.1016/j.chom.2019.05.008. Epub 2019 Jun 25. PubMed PMID: 31253590; NIHMSID:NIHMS1533232.
Jeng EE, Bhadkamkar V, Ibe NU, Gause H, Jiang L, Chan J, Jian R, Jimenez-Morales D, Stevenson E, Krogan NJ, Swaney DL, Snyder MP, Mukherjee S, Bassik MC. Systematic Identification of Host Cell Regulators of Legionella pneumophila Pathogenesis Using a Genome-wide CRISPR Screen. Cell Host Microbe. 2019 Oct 9;26(4):551-563.e6. doi: 10.1016/j.chom.2019.08.017. Epub 2019 Sep 17. PubMed PMID: 31540829; PubMed Central PMCID: PMC6800164.
Li M, Johnson JR, Truong B, Kim G, Weinbren N, Dittmar M, Shah PS, Von Dollen J, Newton BW, Jang GM, Krogan NJ, Cherry S, Ramage H. Identification of antiviral roles for the exon-junction complex and nonsense-mediated decay in flaviviral infection. Nat Microbiol. 2019 Jun;4(6):985-995. doi: 10.1038/s41564-019-0375-z. Epub 2019 Mar 4. PubMed PMID: 30833725; PubMed Central PMCID: PMC6533143.
Leenay RT, Aghazadeh A, Hiatt J, Tse D, Roth TL, Apathy R, Shifrut E, Hultquist JF, Krogan N, Wu Z, Cirolia G, Canaj H, Leonetti MD, Marson A, May AP, Zou J. Large dataset enables prediction of repair after CRISPR-Cas9 editing in primary T cells. Nat Biotechnol. 2019 Jul 29;. doi: 10.1038/s41587-019-0203-2. [Epub ahead of print] PubMed PMID: 31359007.
Majer O, Liu B, Kreuk LSM, Krogan N, Barton GM. UNC93B1 recruits syntenin-1 to dampen TLR7 signalling and prevent autoimmunity. Nature. 2019 Sep 23;. doi: 10.1038/s41586-019-1612-6. [Epub ahead of print] PubMed PMID: 31546246.
Majer O, Liu B, Woo BJ, Kreuk LSM, Van Dis E, Barton GM. Release from UNC93B1 reinforces the compartmentalized activation of select TLRs. Nature. 2019 Sep 23;. doi: 10.1038/s41586-019-1611-7. [Epub ahead of print] PubMed PMID: 31546247.
Poweleit N, Czudnochowski N, Nakagawa R, Trinidad DD, Murphy KC, Sassetti CM, Rosenberg OS. The structure of the endogenous ESX-3 secretion system. Elife. 2019 Dec 30;8. doi: 10.7554/eLife.52983. PubMed PMID: 31886769; PubMed Central PMCID: PMC6986878.
Roberts AW, Popov LM, Mitchell G, Ching KL, Licht DJ, Golovkine G, Barton GM, Cox JS. Cas9 conditionally-immortalized macrophages as a tool for bacterial pathogenesis and beyond. Elife. 2019 Jun 17;8. doi: 10.7554/eLife.45957. PubMed PMID: 31204998; PubMed Central PMCID: PMC6579556.x
2018
Batra J, Hultquist JF, Liu D, Shtanko O, Von Dollen J, Satkamp L, Jang GM, Luthra P, Schwarz TM, Small GI, Arnett E, Anantpadma M, Reyes A, Leung DW, Kaake R, Haas P, Schmidt CB, Schlesinger LS, LaCount DJ, Davey RA, Amarasinghe GK, Basler CF, Krogan NJ. Protein Interaction Mapping Identifies RBBP6 as a Negative Regulator of Ebola Virus Replication. Cell. 2018 Dec 13;175(7):1917-1930.e13. doi: 10.1016/j.cell.2018.08.044. PubMed PMID: 30550789; PubMed Central PMCID: PMC6366944.
Palovcak E, Wang F, Zheng SQ, Yu Z, Li S, Betegon M, Bulkley D, Agard DA, Cheng Y. A simple and robust procedure for preparing graphene-oxide cryo-EM grids. J Struct Biol. 2018 Oct;204(1):80-84. doi: 10.1016/j.jsb.2018.07.007. Epub 2018 Jul 11. PubMed PMID: 30017701; PubMed Central PMCID: PMC6119484.
Penn BH, Netter Z, Johnson JR, Von Dollen J, Jang GM, Johnson T, Ohol YM, Maher C, Bell SL, Geiger K, Golovkine G, Du X, Choi A, Parry T, Mohapatra BC, Storck MD, Band H, Chen C, Jäger S, Shales M, Portnoy DA, Hernandez R, Coscoy L, Cox JS, Krogan NJ. An Mtb-Human Protein-Protein Interaction Map Identifies a Switch between Host Antiviral and Antibacterial Responses. Mol Cell. 2018 Aug 16;71(4):637-648.e5. doi: 10.1016/j.molcel.2018.07.010. PubMed PMID: 30118682; PubMed Central PMCID: PMC6329589.
Shah PS, Link N, Jang GM, Sharp PP, Zhu T, Swaney DL, Johnson JR, Von Dollen J, Ramage HR, Satkamp L, Newton B, Hüttenhain R, Petit MJ, Baum T, Everitt A, Laufman O, Tassetto M, Shales M, Stevenson E, Iglesias GN, Shokat L, Tripathi S, Balasubramaniam V, Webb LG, Aguirre S, Willsey AJ, Garcia-Sastre A, Pollard KS, Cherry S, Gamarnik AV, Marazzi I, Taunton J, Fernandez-Sesma A, Bellen HJ, Andino R, Krogan NJ. Comparative Flavivirus-Host Protein Interaction Mapping Reveals Mechanisms of Dengue and Zika Virus Pathogenesis. Cell. 2018 Dec 13;175(7):1931-1945.e18. doi: 10.1016/j.cell.2018.11.028. PubMed PMID: 30550790; PubMed Central PMCID: PMC6474419.
Wipperman MF, Heaton BE, Nautiyal A, Adefisayo O, Evans H, Gupta R, van Ditmarsch D, Soni R, Hendrickson R, Johnson J, Krogan N, Glickman MS. Mycobacterial Mutagenesis and Drug Resistance Are Controlled by Phosphorylation- and Cardiolipin-Mediated Inhibition of the RecA Coprotease. Mol Cell. 2018 Oct 4;72(1):152-161.e7. doi: 10.1016/j.molcel.2018.07.037. Epub 2018 Aug 30. PubMed PMID: 30174294; PubMed Central PMCID: PMC6389330.
Yu MK, Ma J, Ono K, Zheng F, Fong SH, Gary A, Chen J, Demchak B, Pratt D, Ideker T. DDOT: A Swiss Army Knife for Investigating Data-Driven Biological Ontologies. Cell Syst. 2019 Mar 27;8(3):267-273.e3. doi: 10.1016/j.cels.2019.02.003. Epub 2019 Mar 13. PubMed PMID: 30878356; NIHMSID:NIHMS1026021.
