Publications

HPMI Publications

2020-2021

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.

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.

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.

2019-2020
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.

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.

Wang F, Yu Z, Betegon M, Campbell MG, Aksel T, Zhao J, Li S, Douglas SM, Cheng Y, Agard DA. Amino and PEG-amino graphene oxide grids enrich and protect samples for high-resolution single particle cryo-electron microscopy. J Struct Biol. 2020 Feb 1;209(2):107437. doi: 10.1016/j.jsb.2019.107437. Epub 2019 Dec 19. PubMed PMID: 31866389.

2018-19
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.

Read about it in the news!

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.

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