Nevan Krogan, PhD

Bio

Honors and Awards

Publications

• Smoothened transduces hedgehog signals via activity-dependent sequestration of PKA catalytic subunits. Arveseth CD, Happ JT, Hedeen DS, Zhu JF, Capener JL, Klatt Shaw D, Deshpande I, Liang J, Xu J, Stubben SL, Nelson IB, Walker MF, Kawakami K, Inoue A, Krogan NJ, Grunwald DJ, Hüttenhain R, Manglik A, Myers BR. PLoS Biol. 2021 Apr 22; 19(4):e3001191.
• Chaperone-mediated autophagy prevents collapse of the neuronal metastable proteome. Bourdenx M, Martín-Segura A, Scrivo A, Rodriguez-Navarro JA, Kaushik S, Tasset I, Diaz A, Storm NJ, Xin Q, Juste YR, Stevenson E, Luengo E, Clement CC, Choi SJ, Krogan NJ, Mosharov EV, Santambrogio L, Grueninger F, Collin L, Swaney DL, Sulzer D, Gavathiotis E, Cuervo AM. Cell. 2021 Apr 14.
• The AMBRA1 E3 ligase adaptor regulates the stability of cyclin D. Chaikovsky AC, Li C, Jeng EE, Loebell S, Lee MC, Murray CW, Cheng R, Demeter J, Swaney DL, Chen SH, Newton BW, Johnson JR, Drainas AP, Shue YT, Seoane JA, Srinivasan P, He A, Yoshida A, Hipkins SQ, McCrea E, Poltorack CD, Krogan NJ, Diehl JA, Kong C, Jackson PK, Curtis C, Petrov DA, Bassik MC, Winslow MM, Sage J. Nature. 2021 Apr 14.
• Phospholipidosis is a shared mechanism underlying the in vitro antiviral activity of many repurposed drugs against SARS-CoV-2. 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. bioRxiv. 2021 Mar 24.
• Creating collaboration by breaking down scientific barriers. Fabius JM, Krogan NJ. Cell. 2021 Mar 18.
• Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution. Jungreis I, Nelson CW, Ardern Z, Finkel Y, Krogan NJ, Sato K, Ziebuhr J, Stern-Ginossar N, Pavesi A, Firth AE, Gorbalenya AE, Kellis M. Virology. 2021 Mar 17; 558:145-151.
• Evaluating a New Class of AKT/mTOR Activators for HIV Latency Reversing Activity Ex Vivo and In Vivo. Gramatica A, Schwarzer R, Brantley W, Varco-Merth B, Sperber HS, Hull PA, Montano M, Migueles SA, Rosenthal D, Hogan LE, Johnson JR, Packard TA, Grimmett ZW, Herzig E, Besnard E, Nekorchuk M, Hsiao F, Deeks SG, Snape M, Kiernan B, Roan NR, Lifson JD, Estes JD, Picker LJ, Verdin E, Krogan NJ, Henrich TJ, Connors M, Ott M, Pillai SK, Okoye AA, Greene WC. J Virol. 2021 Feb 03.
• SUMO is a pervasive regulator of meiosis. Bhagwat NR, Owens SN, Ito M, Boinapalli JV, Poa P, Ditzel A, Kopparapu S, Mahalawat M, Davies OR, Collins SR, Johnson JR, Krogan NJ, Hunter N. Elife. 2021 Jan 27; 10.
• Plitidepsin has potent preclinical efficacy against SARS-CoV-2 by targeting the host protein eEF1A. 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. Science. 2021 Jan 25.
• Host-directed therapies against early-lineage SARS-CoV-2 retain efficacy against B.1.1.7 variant. Reuschl AK, Thorne L, Zuliani Alvarez L, Bouhaddou M, Obernier K, Soucheray M, Turner J, Fabius J, Nguyen GT, Swaney D, Rosales R, White KM, Aviles P, Kirby IT, Melnyk JE, Shi Y, Zhang Z, Shokat K, Garcia-Sastre A, Jolly C, Towers GJ, Krogan NJ. bioRxiv. 2021 Jan 24.
• Proteomic Approaches to Study SARS-CoV-2 Biology and COVID-19 Pathology. Haas P, Muralidharan M, Krogan NJ, Kaake RM, Hüttenhain R. J Proteome Res. 2021 Jan 19.
• Mass spectrometry-based protein-protein interaction networks for the study of human diseases. Richards AL, Eckhardt M, Krogan NJ. Mol Syst Biol. 2021 Jan; 17(1):e8792.
• Genetic interaction mapping informs integrative structure determination of protein complexes. Braberg H, Echeverria I, Bohn S, Cimermancic P, Shiver A, Alexander R, Xu J, Shales M, Dronamraju R, Jiang S, Dwivedi G, Bogdanoff D, Chaung KK, Hüttenhain R, Wang S, Mavor D, Pellarin R, Schneidman D, Bader JS, Fraser JS, Morris J, Haber JE, Strahl BD, Gross CA, Dai J, Boeke JD, Sali A, Krogan NJ. Science. 2020 Dec 11; 370(6522).
• Genetic Screens Identify Host Factors for SARS-CoV-2 and Common Cold Coronaviruses. 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. Cell. 2020 Dec 09.
• An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike. Schoof M, Faust B, Saunders RA, Sangwan S, Rezelj V, Hoppe N, Boone M, Billesbølle CB, Puchades C, Azumaya CM, Kratochvil HT, Zimanyi M, Deshpande I, Liang J, Dickinson S, Nguyen HC, Chio CM, Merz GE, Thompson MC, Diwanji D, Schaefer K, Anand AA, Dobzinski N, Zha BS, Simoneau CR, Leon K, White KM, Chio US, Gupta M, Jin M, Li F, Liu Y, Zhang K, Bulkley D, Sun M, Smith AM, Rizo AN, Moss F, Brilot AF, Pourmal S, Trenker R, Pospiech T, Gupta S, Barsi-Rhyne B, Belyy V, Barile-Hill AW, Nock S, Liu Y, Krogan NJ, Ralston CY, Swaney DL, García-Sastre A, Ott M, Vignuzzi M, Walter P, Manglik A. Science. 2020 12 18; 370(6523):1473-1479.
• SARS-CoV-2 Orf6 hijacks Nup98 to block STAT nuclear import and antagonize interferon signaling. Miorin L, Kehrer T, Sanchez-Aparicio MT, Zhang K, Cohen P, Patel RS, Cupic A, Makio T, Mei M, Moreno E, Danziger O, White KM, Rathnasinghe R, Uccellini M, Gao S, Aydillo T, Mena I, Yin X, Martin-Sancho L, Krogan NJ, Chanda SK, Schotsaert M, Wozniak RW, Ren Y, Rosenberg BR, Fontoura BMA, García-Sastre A. Proc Natl Acad Sci U S A. 2020 11 10; 117(45):28344-28354.
• Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. 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, Nguyen P, Paulino J, Pawar KI, Peters JK, Pospiech TH, 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. Science. 2020 12 04; 370(6521).
• Functional genomic screens identify human host factors for SARS-CoV-2 and common cold coronaviruses. 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. bioRxiv. 2020 Sep 24.
• The E3 Ubiquitin-Protein Ligase Cullin 3 Regulates HIV-1 Transcription. Langer S, Yin X, Diaz A, Portillo AJ, Gordon DE, Rogers UH, Marlett JM, Krogan NJ, Young JAT, Pache L, Chanda SK. Cells. 2020 09 01; 9(9).
• Evaluation of SARS-CoV-2 serology assays reveals a range of test performance. Whitman JD, Hiatt J, Mowery CT, Shy BR, Yu R, Yamamoto TN, Rathore U, Goldgof GM, Whitty C, Woo JM, Gallman AE, Miller TE, Levine AG, Nguyen DN, Bapat SP, Balcerek J, Bylsma SA, Lyons AM, Li S, Wong AW, Gillis-Buck EM, Steinhart ZB, Lee Y, Apathy R, Lipke MJ, Smith JA, Zheng T, Boothby IC, Isaza E, Chan J, Acenas DD, Lee J, Macrae TA, Kyaw TS, Wu D, Ng DL, Gu W, York VA, Eskandarian HA, Callaway PC, Warrier L, Moreno ME, Levan J, Torres L, Farrington LA, Loudermilk RP, Koshal K, Zorn KC, Garcia-Beltran WF, Yang D, Astudillo MG, Bernstein BE, Gelfand JA, Ryan ET, Charles RC, Iafrate AJ, Lennerz JK, Miller S, Chiu CY, Stramer SL, Wilson MR, Manglik A, Ye CJ, Krogan NJ, Anderson MS, Cyster JG, Ernst JD, Wu AHB, Lynch KL, Bern C, Hsu PD, Marson A. Nat Biotechnol. 2020 10; 38(10):1174-1183.
• SARS-CoV-2 ORF9c Is a Membrane-Associated Protein that Suppresses Antiviral Responses in Cells. Dominguez Andres A, Feng Y, Campos AR, Yin J, Yang CC, James B, Murad R, Kim H, Deshpande AJ, Gordon DE, Krogan N, Pippa R, Ronai ZA. bioRxiv. 2020 Aug 19.
• An ultra-high affinity synthetic nanobody blocks SARS-CoV-2 infection by locking Spike into an inactive conformation. Schoof M, Faust B, Saunders RA, Sangwan S, Rezelj V, Hoppe N, Boone M, Billesbølle CB, Zimanyi M, Deshpande I, Liang J, Anand AA, Dobzinski N, Zha BS, Barsi-Rhyne B, Belyy V, Barile-Hill AW, Gupta S, Simoneau CR, Leon K, White KM, Nock S, Liu Y, Krogan NJ, Ralston CY, Swaney DL, García-Sastre A, Ott M, Vignuzzi M, Walter P, Manglik A. bioRxiv. 2020 Aug 10.
• Structural basis of CD4 downregulation by HIV-1 Nef. Kwon Y, Kaake RM, Echeverria I, Suarez M, Karimian Shamsabadi M, Stoneham C, Ramirez PW, Kress J, Singh R, Sali A, Krogan N, Guatelli J, Jia X. Nat Struct Mol Biol. 2020 09; 27(9):822-828.
• Envelope protein ubiquitination drives entry and pathogenesis of Zika virus. Giraldo MI, Xia H, Aguilera-Aguirre L, Hage A, van Tol S, Shan C, Xie X, Sturdevant GL, Robertson SJ, McNally KL, Meade-White K, Azar SR, Rossi SL, Maury W, Woodson M, Ramage H, Johnson JR, Krogan NJ, Morais MC, Best SM, Shi PY, Rajsbaum R. Nature. 2020 09; 585(7825):414-419.
• The Global Phosphorylation Landscape of SARS-CoV-2 Infection. 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. Cell. 2020 08 06; 182(3):685-712.e19.
• The kinase Isr1 negatively regulates hexosamine biosynthesis in S. cerevisiae. Alme EB, Stevenson E, Krogan NJ, Swaney DL, Toczyski DP. PLoS Genet. 2020 06; 16(6):e1008840.
• Hybrid Gene Origination Creates Human-Virus Chimeric Proteins during Infection. Ho JSY, Angel M, Ma Y, Sloan E, Wang G, Martinez-Romero C, Alenquer M, Roudko V, Chung L, Zheng S, Chang M, Fstkchyan Y, Clohisey S, Dinan AM, Gibbs J, Gifford R, Shen R, Gu Q, Irigoyen N, Campisi L, Huang C, Zhao N, Jones JD, van Knippenberg I, Zhu Z, Moshkina N, Meyer L, Noel J, Peralta Z, Rezelj V, Kaake R, Rosenberg B, Wang B, Wei J, Paessler S, Wise HM, Johnson J, Vannini A, Amorim MJ, Baillie JK, Miraldi ER, Benner C, Brierley I, Digard P, Luksza M, Firth AE, Krogan N, Greenbaum BD, MacLeod MK, van Bakel H, Garcìa-Sastre A, Yewdell JW, Hutchinson E, Marazzi I. Cell. 2020 06 25; 181(7):1502-1517.e23.
• Unbiased Proteomic Profiling Uncovers a Targetable GNAS/PKA/PP2A Axis in Small Cell Lung Cancer Stem Cells. Coles GL, Cristea S, Webber JT, Levin RS, Moss SM, He A, Sangodkar J, Hwang YC, Arand J, Drainas AP, Mooney NA, Demeter J, Spradlin JN, Mauch B, Le V, Shue YT, Ko JH, Lee MC, Kong C, Nomura DK, Ohlmeyer M, Swaney DL, Krogan NJ, Jackson PK, Narla G, Gordan JD, Shokat KM, Sage J. Cancer Cell. 2020 Jul 13; 38(1):129-143.e7.
• The Landscape of Human Cancer Proteins Targeted by SARS-CoV-2. Tutuncuoglu B, Cakir M, Batra J, Bouhaddou M, Eckhardt M, Gordon DE, Krogan NJ. Cancer Discov. 2020 07; 10(7):916-921.
• Test performance evaluation of SARS-CoV-2 serological assays. Whitman JD, Hiatt J, Mowery CT, Shy BR, Yu R, Yamamoto TN, Rathore U, Goldgof GM, Whitty C, Woo JM, Gallman AE, Miller TE, Levine AG, Nguyen DN, Bapat SP, Balcerek J, Bylsma SA, Lyons AM, Li S, Wong AW, Gillis-Buck EM, Steinhart ZB, Lee Y, Apathy R, Lipke MJ, Smith JA, Zheng T, Boothby IC, Isaza E, Chan J, Acenas DD, Lee J, Macrae TA, Kyaw TS, Wu D, Ng DL, Gu W, York VA, Eskandarian HA, Callaway PC, Warrier L, Moreno ME, Levan J, Torres L, Farrington LA, Loudermilk R, Koshal K, Zorn KC, Garcia-Beltran WF, Yang D, Astudillo MG, Bernstein BE, Gelfand JA, Ryan ET, Charles RC, Iafrate AJ, Lennerz JK, Miller S, Chiu CY, Stramer SL, Wilson MR, Manglik A, Ye CJ, Krogan NJ, Anderson MS, Cyster JG, Ernst JD, Wu AHB, Lynch KL, Bern C, Hsu PD, Marson A. medRxiv. 2020 May 17.
• mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1. Du Y, Hultquist JF, Zhou Q, Olson A, Tseng Y, Zhang TH, Hong M, Tang K, Chen L, Meng X, McGregor MJ, Dai L, Gong D, Martin-Sancho L, Chanda S, Li X, Bensenger S, Krogan NJ, Sun R. Nat Commun. 2020 05 15; 11(1):2449.
• A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. 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. Nature. 2020 07; 583(7816):459-468.
• A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing. Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O'Meara MJ, 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, Naing ZZC, Zhou Y, Peng S, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Shen W, Shi Y, Zhang Z, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Ramachandran R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Lin Y, Wankowicz SA, Bohn M, Trenker R, Young JM, Cavero D, Hiatt J, Roth T, Rathore U, Subramanian A, Noack J, Hubert M, Roesch F, Vallet T, Meyer B, White KM, Miorin L, Agard D, Emerman M, Ruggero D, García-Sastre A, Jura N, von Zastrow M, Taunton J, Schwartz O, Vignuzzi M, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor S, Fraser JS, Gross J, Sali A, Kortemme T, Beltrao P, Shokat K, Shoichet BK, Krogan NJ. bioRxiv. 2020 Mar 22.
• Cyclophilin A Prevents HIV-1 Restriction in Lymphocytes by Blocking Human TRIM5a Binding to the Viral Core. Selyutina A, Persaud M, Simons LM, Bulnes-Ramos A, Buffone C, Martinez-Lopez A, Scoca V, Di Nunzio F, Hiatt J, Marson A, Krogan NJ, Hultquist JF, Diaz-Griffero F. Cell Rep. 2020 03 17; 30(11):3766-3777.e6.
• A Quantitative Genetic Interaction Map of HIV Infection. Gordon DE, Watson A, Roguev A, Zheng S, Jang GM, Kane J, Xu J, Guo JZ, Stevenson E, Swaney DL, Franks-Skiba K, Verschueren E, Shales M, Crosby DC, Frankel AD, Marson A, Marazzi I, Cagney G, Krogan NJ. Mol Cell. 2020 04 16; 78(2):197-209.e7.
• A systems approach to infectious disease. Eckhardt M, Hultquist JF, Kaake RM, Hüttenhain R, Krogan NJ. Nat Rev Genet. 2020 06; 21(6):339-354.
• Dynamic post-translational modification profiling of Mycobacterium tuberculosis-infected primary macrophages. 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. Elife. 2020 Jan 17; 9.
• Splicing Defects of the Profilin Gene Alter Actin Dynamics in an S. pombe SMN Mutant. Antoine M, Patrick KL, Soret J, Duc P, Rage F, Cacciottolo R, Nissen KE, Cauchi RJ, Krogan NJ, Guthrie C, Gachet Y, Bordonné R. iScience. 2020 Jan 24; 23(1):100809.
• The functional landscape of the human phosphoproteome. Ochoa D, Jarnuczak AF, Viéitez C, Gehre M, Soucheray M, Mateus A, Kleefeldt AA, Hill A, Garcia-Alonso L, Stein F, Krogan NJ, Savitski MM, Swaney DL, Vizcaíno JA, Noh KM, Beltrao P. Nat Biotechnol. 2020 03; 38(3):365-373.
• Mutations in ANKLE2, a ZIKA Virus Target, Disrupt an Asymmetric Cell Division Pathway in Drosophila Neuroblasts to Cause Microcephaly. Link N, Chung H, Jolly A, Withers M, Tepe B, Arenkiel BR, Shah PS, Krogan NJ, Aydin H, Geckinli BB, Tos T, Isikay S, Tuysuz B, Mochida GH, Thomas AX, Clark RD, Mirzaa GM, Lupski JR, Bellen HJ. Dev Cell. 2019 12 16; 51(6):713-729.e6.
• Mapping genetic interactions in cancer: a road to rational combination therapies. Tutuncuoglu B, Krogan NJ. Genome Med. 2019 10 22; 11(1):62.
• UNC93B1 recruits syntenin-1 to dampen TLR7 signalling and prevent autoimmunity. Majer O, Liu B, Kreuk LSM, Krogan N, Barton GM. Nature. 2019 11; 575(7782):366-370.
• Systematic Identification of Host Cell Regulators of Legionella pneumophila Pathogenesis Using a Genome-wide CRISPR Screen. 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. Cell Host Microbe. 2019 10 09; 26(4):551-563.e6.
• Enterovirus pathogenesis requires the host methyltransferase SETD3. Diep J, Ooi YS, Wilkinson AW, Peters CE, Foy E, Johnson JR, Zengel J, Ding S, Weng KF, Laufman O, Jang G, Xu J, Young T, Verschueren E, Kobluk KJ, Elias JE, Sarnow P, Greenberg HB, Hüttenhain R, Nagamine CM, Andino R, Krogan NJ, Gozani O, Carette JE. Nat Microbiol. 2019 12; 4(12):2523-2537.
• Regulation of Skn7-dependent, oxidative stress-induced genes by the RNA polymerase II-CTD phosphatase, Fcp1, and Mediator kinase subunit, Cdk8, in yeast. Aristizabal MJ, Dever K, Negri GL, Shen M, Hawe N, Benschop JJ, Holstege FCP, Krogan NJ, Sadowski I, Kobor MS. J Biol Chem. 2019 11 01; 294(44):16080-16094.
• Anti-CRISPR-Associated Proteins Are Crucial Repressors of Anti-CRISPR Transcription. Stanley SY, Borges AL, Chen KH, Swaney DL, Krogan NJ, Bondy-Denomy J, Davidson AR. Cell. 2019 09 05; 178(6):1452-1464.e13.
• Synthetic Essentiality of Metabolic Regulator PDHK1 in PTEN-Deficient Cells and Cancers. Chatterjee N, Pazarentzos E, Mayekar MK, Gui P, Allegakoen DV, Hrustanovic G, Olivas V, Lin L, Verschueren E, Johnson JR, Hofree M, Yan JJ, Newton BW, Dollen JV, Earnshaw CH, Flanagan J, Chan E, Asthana S, Ideker T, Wu W, Suzuki J, Barad BA, Kirichok Y, Fraser JS, Weiss WA, Krogan NJ, Tulpule A, Sabnis AJ, Bivona TG. Cell Rep. 2019 08 27; 28(9):2317-2330.e8.
• Large dataset enables prediction of repair after CRISPR-Cas9 editing in primary T cells. 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. Nat Biotechnol. 2019 09; 37(9):1034-1037.
• PEAK3/C19orf35 pseudokinase, a new NFK3 kinase family member, inhibits CrkII through dimerization. Lopez ML, Lo M, Kung JE, Dudkiewicz M, Jang GM, Von Dollen J, Johnson JR, Krogan NJ, Pawlowski K, Jura N. Proc Natl Acad Sci U S A. 2019 07 30; 116(31):15495-15504.
• Mapping the protein-protein and genetic interactions of cancer to guide precision medicine. Bouhaddou M, Eckhardt M, Chi Naing ZZ, Kim M, Ideker T, Krogan NJ. Curr Opin Genet Dev. 2019 02; 54:110-117.
• Dynamic BAF chromatin remodeling complex subunit inclusion promotes temporally distinct gene expression programs in cardiogenesis. Hota SK, Johnson JR, Verschueren E, Thomas R, Blotnick AM, Zhu Y, Sun X, Pennacchio LA, Krogan NJ, Bruneau BG. Development. 2019 07 05; 146(19).
• ARIH2 Is a Vif-Dependent Regulator of CUL5-Mediated APOBEC3G Degradation in HIV Infection. 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. . 2019 07 10; 26(1):86-99.e7.
• Two Accessory Proteins Govern MmpL3 Mycolic Acid Transport in Mycobacteria. Fay A, Czudnochowski N, Rock JM, Johnson JR, Krogan NJ, Rosenberg O, Glickman MS. mBio. 2019 06 25; 10(3).
• Heart failure drug proscillaridin A targets MYC overexpressing leukemia through global loss of lysine acetylation. Da Costa EM, Armaos G, McInnes G, Beaudry A, Moquin-Beaudry G, Bertrand-Lehouillier V, Caron M, Richer C, St-Onge P, Johnson JR, Krogan N, Sai Y, Downey M, Rafei M, Boileau M, Eppert K, Flores-Díaz E, Haman A, Hoang T, Sinnett D, Beauséjour C, McGraw S, Raynal NJ. J Exp Clin Cancer Res. 2019 Jun 13; 38(1):251.
• Chaperone-mediated reflux of secretory proteins to the cytosol during endoplasmic reticulum stress. Igbaria A, Merksamer PI, Trusina A, Tilahun F, Johnson JR, Brandman O, Krogan NJ, Weissman JS, Papa FR. Proc Natl Acad Sci U S A. 2019 06 04; 116(23):11291-11298.
• Crosstalk between RNA Pol II C-Terminal Domain Acetylation and Phosphorylation via RPRD Proteins. 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. Mol Cell. 2019 06 20; 74(6):1164-1174.e4.
• SIRT3 controls brown fat thermogenesis by deacetylation regulation of pathways upstream of UCP1. Sebaa R, Johnson J, Pileggi C, Norgren M, Xuan J, Sai Y, Tong Q, Krystkowiak I, Bondy-Chorney E, Davey NE, Krogan N, Downey M, Harper ME. Mol Metab. 2019 07; 25:35-49.
• Identification of antiviral roles for the exon-junction complex and nonsense-mediated decay in flaviviral infection. 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. Nat Microbiol. 2019 06; 4(6):985-995.
• CRISPR-Cas9 genome engineering of primary CD4+ T cells for the interrogation of HIV-host factor interactions. Hultquist JF, Hiatt J, Schumann K, McGregor MJ, Roth TL, Haas P, Doudna JA, Marson A, Krogan NJ. Nat Protoc. 2019 01; 14(1):1-27.
• Neuronal Apolipoprotein E4 Expression Results in Proteome-Wide Alterations and Compromises Bioenergetic Capacity by Disrupting Mitochondrial Function. Orr AL, Kim C, Jimenez-Morales D, Newton BW, Johnson JR, Krogan NJ, Swaney DL, Mahley RW. J Alzheimers Dis. 2019; 68(3):991-1011.
• TCO, a Putative Transcriptional Regulator in Arabidopsis, Is a Target of the Protein Kinase CK2. Weinman LM, Running KLD, Carey NS, Stevenson EJ, Swaney DL, Chow BY, Krogan NJ, Krogan NT. Int J Mol Sci. 2018 Dec 28; 20(1).
• Genetic analysis reveals functions of atypical polyubiquitin chains. Meza Gutierrez F, Simsek D, Mizrak A, Deutschbauer A, Braberg H, Johnson J, Xu J, Shales M, Nguyen M, Tamse-Kuehn R, Palm C, Steinmetz LM, Krogan NJ, Toczyski DP. Elife. 2018 12 14; 7.
• Comparative Flavivirus-Host Protein Interaction Mapping Reveals Mechanisms of Dengue and Zika Virus Pathogenesis. 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. Cell. 2018 12 13; 175(7):1931-1945.e18.
• Protein Interaction Mapping Identifies RBBP6 as a Negative Regulator of Ebola Virus Replication. 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. Cell. 2018 12 13; 175(7):1917-1930.e13.
• Virus and host interactions critical for filoviral RNA synthesis as therapeutic targets. Basler CF, Krogan NJ, Leung DW, Amarasinghe GK. Antiviral Res. 2019 02; 162:90-100.
• The Yeast DNA Damage Checkpoint Kinase Rad53 Targets the Exoribonuclease, Xrn1. Lao JP, Ulrich KM, Johnson JR, Newton BW, Vashisht AA, Wohlschlegel JA, Krogan NJ, Toczyski DP. G3 (Bethesda). 2018 12 10; 8(12):3931-3944.
• Proteasome lid bridges mitochondrial stress with Cdc53/Cullin1 NEDDylation status. Bramasole L, Sinha A, Gurevich S, Radzinski M, Klein Y, Panat N, Gefen E, Rinaldi T, Jimenez-Morales D, Johnson J, Krogan NJ, Reis N, Reichmann D, Glickman MH, Pick E. Redox Biol. 2019 01; 20:533-543.
• The Cellular NMD Pathway Restricts Zika Virus Infection and Is Targeted by the Viral Capsid Protein. Fontaine KA, Leon KE, Khalid MM, Tomar S, Jimenez-Morales D, Dunlap M, Kaye JA, Shah PS, Finkbeiner S, Krogan NJ, Ott M. mBio. 2018 11 06; 9(6).
• Multiple Routes to Oncogenesis Are Promoted by the Human Papillomavirus-Host Protein Network. Eckhardt M, Zhang W, Gross AM, Von Dollen J, Johnson JR, Franks-Skiba KE, Swaney DL, Johnson TL, Jang GM, Shah PS, Brand TM, Archambault J, Kreisberg JF, Grandis JR, Ideker T, Krogan NJ. Cancer Discov. 2018 11; 8(11):1474-1489.
• EpCAM homo-oligomerization is not the basis for its role in cell-cell adhesion. Gaber A, Kim SJ, Kaake RM, Bencina M, Krogan N, Šali A, Pavšic M, Lenarcic B. Sci Rep. 2018 09 05; 8(1):13269.
• Influenza virus infection causes global RNAPII termination defects. Zhao N, Sebastiano V, Moshkina N, Mena N, Hultquist J, Jimenez-Morales D, Ma Y, Rialdi A, Albrecht R, Fenouil R, Sánchez-Aparicio MT, Ayllon J, Ravisankar S, Haddad B, Ho JSY, Low D, Jin J, Yurchenko V, Prinjha RK, Tarakhovsky A, Squatrito M, Pinto D, Allette K, Byun M, Smith ML, Sebra R, Guccione E, Tumpey T, Krogan N, Greenbaum B, van Bakel H, García-Sastre A, Marazzi I. Nat Struct Mol Biol. 2018 09; 25(9):885-893.
• CRL4AMBRA1 targets Elongin C for ubiquitination and degradation to modulate CRL5 signaling. Chen SH, Jang GM, Hüttenhain R, Gordon DE, Du D, Newton BW, Johnson JR, Hiatt J, Hultquist JF, Johnson TL, Liu YL, Burton LA, Ye J, Reichermeier KM, Stroud RM, Marson A, Debnath J, Gross JD, Krogan NJ. EMBO J. 2018 09 14; 37(18).
• Mycobacterial Mutagenesis and Drug Resistance Are Controlled by Phosphorylation- and Cardiolipin-Mediated Inhibition of the RecA Coprotease. 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. Mol Cell. 2018 10 04; 72(1):152-161.e7.
• An Mtb-Human Protein-Protein Interaction Map Identifies a Switch between Host Antiviral and Antibacterial Responses. 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. Mol Cell. 2018 08 16; 71(4):637-648.e5.
• Quantitative Yeast Genetic Interaction Profiling of Bacterial Effector Proteins Uncovers a Role for the Human Retromer in Salmonella Infection. Patrick KL, Wojcechowskyj JA, Bell SL, Riba MN, Jing T, Talmage S, Xu P, Cabello AL, Xu J, Shales M, Jimenez-Morales D, Ficht TA, de Figueiredo P, Samuel JE, Li P, Krogan NJ, Watson RO. Cell Syst. 2018 09 26; 7(3):323-338.e6.
• The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders. Willsey AJ, Morris MT, Wang S, Willsey HR, Sun N, Teerikorpi N, Baum TB, Cagney G, Bender KJ, Desai TA, Srivastava D, Davis GW, Doudna J, Chang E, Sohal V, Lowenstein DH, Li H, Agard D, Keiser MJ, Shoichet B, von Zastrow M, Mucke L, Finkbeiner S, Gan L, Sestan N, Ward ME, Huttenhain R, Nowakowski TJ, Bellen HJ, Frank LM, Khokha MK, Lifton RP, Kampmann M, Ideker T, State MW, Krogan NJ. Cell. 2018 07 26; 174(3):505-520.
• Sympathetic inputs regulate adaptive thermogenesis in brown adipose tissue through cAMP-Salt inducible kinase axis. Paulo E, Wu D, Wang Y, Zhang Y, Wu Y, Swaney DL, Soucheray M, Jimenez-Morales D, Chawla A, Krogan NJ, Wang B. Sci Rep. 2018 Jul 20; 8(1):11001.
• The HIV-1 Tat protein recruits a ubiquitin ligase to reorganize the 7SK snRNP for transcriptional activation. Faust TB, Li Y, Bacon CW, Jang GM, Weiss A, Jayaraman B, Newton BW, Krogan NJ, D'Orso I, Frankel AD. Elife. 2018 05 30; 7.
• The H3K36me2 Methyltransferase Nsd1 Demarcates PRC2-Mediated H3K27me2 and H3K27me3 Domains in Embryonic Stem Cells. Streubel G, Watson A, Jammula SG, Scelfo A, Fitzpatrick DJ, Oliviero G, McCole R, Conway E, Glancy E, Negri GL, Dillon E, Wynne K, Pasini D, Krogan NJ, Bracken AP, Cagney G. Mol Cell. 2018 04 19; 70(2):371-379.e5.
• SIRT1 Deacetylates Tau and Reduces Pathogenic Tau Spread in a Mouse Model of Tauopathy. Min SW, Sohn PD, Li Y, Devidze N, Johnson JR, Krogan NJ, Masliah E, Mok SA, Gestwicki JE, Gan L. J Neurosci. 2018 04 11; 38(15):3680-3688.
• Proteome Imbalance of Mitochondrial Electron Transport Chain in Brown Adipocytes Leads to Metabolic Benefits. Masand R, Paulo E, Wu D, Wang Y, Swaney DL, Jimenez-Morales D, Krogan NJ, Wang B. Cell Metab. 2018 03 06; 27(3):616-629.e4.
• How many human proteoforms are there? Aebersold R, Agar JN, Amster IJ, Baker MS, Bertozzi CR, Boja ES, Costello CE, Cravatt BF, Fenselau C, Garcia BA, Ge Y, Gunawardena J, Hendrickson RC, Hergenrother PJ, Huber CG, Ivanov AR, Jensen ON, Jewett MC, Kelleher NL, Kiessling LL, Krogan NJ, Larsen MR, Loo JA, Ogorzalek Loo RR, Lundberg E, MacCoss MJ, Mallick P, Mootha VK, Mrksich M, Muir TW, Patrie SM, Pesavento JJ, Pitteri SJ, Rodriguez H, Saghatelian A, Sandoval W, Schlüter H, Sechi S, Slavoff SA, Smith LM, Snyder MP, Thomas PM, Uhlén M, Van Eyk JE, Vidal M, Walt DR, White FM, Williams ER, Wohlschlager T, Wysocki VH, Yates NA, Young NL, Zhang B. Nat Chem Biol. 2018 02 14; 14(3):206-214.
• Cross-talk Signaling between HER3 and HPV16 E6 and E7 Mediates Resistance to PI3K Inhibitors in Head and Neck Cancer. Brand TM, Hartmann S, Bhola NE, Li H, Zeng Y, O'Keefe RA, Ranall MV, Bandyopadhyay S, Soucheray M, Krogan NJ, Kemp C, Duvvuri U, LaVallee T, Johnson DE, Ozbun MA, Bauman JE, Grandis JR. Cancer Res. 2018 05 01; 78(9):2383-2395.
• Genetic Interaction Mapping in Schizosaccharomyces pombe Using the Pombe Epistasis Mapper (PEM) System and a ROTOR HDA Colony Replicating Robot in a 1536 Array Format. Roguev A, Xu J, Krogan N. Cold Spring Harb Protoc. 2018 02 01; 2018(2).
• Genetic Interaction Score (S-Score) Calculation, Clustering, and Visualization of Genetic Interaction Profiles for Yeast. Roguev A, Ryan CJ, Xu J, Colson I, Hartsuiker E, Krogan N. Cold Spring Harb Protoc. 2018 02 01; 2018(2).
• High-Throughput Quantitative Genetic Interaction Mapping in the Fission Yeast Schizosaccharomyces pombe. Roguev A, Ryan CJ, Hartsuiker E, Krogan NJ. Cold Spring Harb Protoc. 2018 02 01; 2018(2).
• SMARCA2-regulated host cell factors are required for MxA restriction of influenza A viruses. Dornfeld D, Dudek AH, Vausselin T, Günther SC, Hultquist JF, Giese S, Khokhlova-Cubberley D, Chew YC, Pache L, Krogan NJ, Garcia-Sastre A, Schwemmle M, Shaw ML. Sci Rep. 2018 02 01; 8(1):2092.
• Fab-based inhibitors reveal ubiquitin independent functions for HIV Vif neutralization of APOBEC3 restriction factors. Binning JM, Smith AM, Hultquist JF, Craik CS, Caretta Cartozo N, Campbell MG, Burton L, La Greca F, McGregor MJ, Ta HM, Bartholomeeusen K, Peterlin BM, Krogan NJ, Sevillano N, Cheng Y, Gross JD. PLoS Pathog. 2018 01; 14(1):e1006830.
• DNA Preparation from Schizosaccharomyces pombe. Roguev A, Xu J, Krogan NJ. Cold Spring Harb Protoc. 2018 01 02; 2018(1).
• Transformation of Schizosaccharomyces pombe in a 96-Well Format. Roguev A, Xu J, Krogan NJ. Cold Spring Harb Protoc. 2018 01 02; 2018(1).
• Evolutionary Proteomics Uncovers Ancient Associations of Cilia with Signaling Pathways. Sigg MA, Menchen T, Lee C, Johnson J, Jungnickel MK, Choksi SP, Garcia G, Busengdal H, Dougherty GW, Pennekamp P, Werner C, Rentzsch F, Florman HM, Krogan N, Wallingford JB, Omran H, Reiter JF. Dev Cell. 2017 12 18; 43(6):744-762.e11.
• Metabolic reprogramming of human CD8+ memory T cells through loss of SIRT1. Jeng MY, Hull PA, Fei M, Kwon HS, Tsou CL, Kasler H, Ng CP, Gordon DE, Johnson J, Krogan N, Verdin E, Ott M. J Exp Med. 2018 01 02; 215(1):51-62.
• Mutations in the X-linked ATP6AP2 cause a glycosylation disorder with autophagic defects. Rujano MA, Cannata Serio M, Panasyuk G, Péanne R, Reunert J, Rymen D, Hauser V, Park JH, Freisinger P, Souche E, Guida MC, Maier EM, Wada Y, Jäger S, Krogan NJ, Kretz O, Nobre S, Garcia P, Quelhas D, Bird TD, Raskind WH, Schwake M, Duvet S, Foulquier F, Matthijs G, Marquardt T, Simons M. J Exp Med. 2017 Dec 04; 214(12):3707-3729.
• Protein Moonlighting Revealed by Noncatalytic Phenotypes of Yeast Enzymes. Espinosa-Cantú A, Ascencio D, Herrera-Basurto S, Xu J, Roguev A, Krogan NJ, DeLuna A. Genetics. 2018 01; 208(1):419-431.
• The Host E3-Ubiquitin Ligase TRIM6 Ubiquitinates the Ebola Virus VP35 Protein and Promotes Virus Replication. Bharaj P, Atkins C, Luthra P, Giraldo MI, Dawes BE, Miorin L, Johnson JR, Krogan NJ, Basler CF, Freiberg AN, Rajsbaum R. J Virol. 2017 09 15; 91(18).
• A BAG3 chaperone complex maintains cardiomyocyte function during proteotoxic stress. Judge LM, Perez-Bermejo JA, Truong A, Ribeiro AJ, Yoo JC, Jensen CL, Mandegar MA, Huebsch N, Kaake RM, So PL, Srivastava D, Pruitt BL, Krogan NJ, Conklin BR. JCI Insight. 2017 Jul 20; 2(14).
• Virus-Like Vesicles of Kaposi's Sarcoma-Associated Herpesvirus Activate Lytic Replication by Triggering Differentiation Signaling. Gong D, Dai X, Xiao Y, Du Y, Chapa TJ, Johnson JR, Li X, Krogan NJ, Deng H, Wu TT, Sun R. J Virol. 2017 08 01; 91(15).
• The Tyrosine Kinase Inhibitor Gefitinib Restricts Mycobacterium tuberculosis Growth through Increased Lysosomal Biogenesis and Modulation of Cytokine Signaling. Sogi KM, Lien KA, Johnson JR, Krogan NJ, Stanley SA. ACS Infect Dis. 2017 08 11; 3(8):564-574.
• SMYD2-Mediated Histone Methylation Contributes to HIV-1 Latency. Boehm D, Jeng M, Camus G, Gramatica A, Schwarzer R, Johnson JR, Hull PA, Montano M, Sakane N, Pagans S, Godin R, Deeks SG, Krogan NJ, Greene WC, Ott M. . 2017 May 10; 21(5):569-579.e6.
• Genetic interaction mapping in mammalian cells using CRISPR interference. Du D, Roguev A, Gordon DE, Chen M, Chen SH, Shales M, Shen JP, Ideker T, Mali P, Qi LS, Krogan NJ. Nat Methods. 2017 Jun; 14(6):577-580.
• The RNA Exosome Syncs IAV-RNAPII Transcription to Promote Viral Ribogenesis and Infectivity. Rialdi A, Hultquist J, Jimenez-Morales D, Peralta Z, Campisi L, Fenouil R, Moshkina N, Wang ZZ, Laffleur B, Kaake RM, McGregor MJ, Haas K, Pefanis E, Albrecht RA, Pache L, Chanda S, Jen J, Ochando J, Byun M, Basu U, García-Sastre A, Krogan N, van Bakel H, Marazzi I. Cell. 2017 05 04; 169(4):679-692.e14.
• An Approach to Spatiotemporally Resolve Protein Interaction Networks in Living Cells. Lobingier BT, Hüttenhain R, Eichel K, Miller KB, Ting AY, von Zastrow M, Krogan NJ. Cell. 2017 04 06; 169(2):350-360.e12.
• The histone variant H2A.Z promotes splicing of weak introns. Nissen KE, Homer CM, Ryan CJ, Shales M, Krogan NJ, Patrick KL, Guthrie C. Genes Dev. 2017 04 01; 31(7):688-701.
• PJA2 ubiquitinates the HIV-1 Tat protein with atypical chain linkages to activate viral transcription. Faust TB, Li Y, Jang GM, Johnson JR, Yang S, Weiss A, Krogan NJ, Frankel AD. Sci Rep. 2017 03 27; 7:45394.
• Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. Shen JP, Zhao D, Sasik R, Luebeck J, Birmingham A, Bojorquez-Gomez A, Licon K, Klepper K, Pekin D, Beckett AN, Sanchez KS, Thomas A, Kuo CC, Du D, Roguev A, Lewis NE, Chang AN, Kreisberg JF, Krogan N, Qi L, Ideker T, Mali P. Nat Methods. 2017 Jun; 14(6):573-576.
• Chlamydia interfere with an interaction between the mannose-6-phosphate receptor and sorting nexins to counteract host restriction. Elwell CA, Czudnochowski N, von Dollen J, Johnson JR, Nakagawa R, Mirrashidi K, Krogan NJ, Engel JN, Rosenberg OS. Elife. 2017 03 02; 6.
• Systems-based analysis of RIG-I-dependent signalling identifies KHSRP as an inhibitor of RIG-I receptor activation. Soonthornvacharin S, Rodriguez-Frandsen A, Zhou Y, Galvez F, Huffmaster NJ, Tripathi S, Balasubramaniam VR, Inoue A, de Castro E, Moulton H, Stein DA, Sánchez-Aparicio MT, De Jesus PD, Nguyen Q, König R, Krogan NJ, García-Sastre A, Yoh SM, Chanda SK. Nat Microbiol. 2017 Mar 01; 2:17022.
• Suppression of C9orf72 RNA repeat-induced neurotoxicity by the ALS-associated RNA-binding protein Zfp106. Celona B, Dollen JV, Vatsavayai SC, Kashima R, Johnson JR, Tang AA, Hata A, Miller BL, Huang EJ, Krogan NJ, Seeley WW, Black BL. Elife. 2017 01 10; 6.
• Inhibition of CRISPR-Cas9 with Bacteriophage Proteins. Rauch BJ, Silvis MR, Hultquist JF, Waters CS, McGregor MJ, Krogan NJ, Bondy-Denomy J. Cell. 2017 Jan 12; 168(1-2):150-158.e10.
• A genome-wide CRISPR screen identifies a restricted set of HIV host dependency factors. Park RJ, Wang T, Koundakjian D, Hultquist JF, Lamothe-Molina P, Monel B, Schumann K, Yu H, Krupzcak KM, Garcia-Beltran W, Piechocka-Trocha A, Krogan NJ, Marson A, Sabatini DM, Lander ES, Hacohen N, Walker BD. Nat Genet. 2017 Feb; 49(2):193-203.
• The mTOR Complex Controls HIV Latency. Besnard E, Hakre S, Kampmann M, Lim HW, Hosmane NN, Martin A, Bassik MC, Verschueren E, Battivelli E, Chan J, Svensson JP, Gramatica A, Conrad RJ, Ott M, Greene WC, Krogan NJ, Siliciano RF, Weissman JS, Verdin E. . 2016 Dec 14; 20(6):785-797.
• G Protein-Coupled Receptor Endocytosis Confers Uniformity in Responses to Chemically Distinct Ligands. Tsvetanova NG, Trester-Zedlitz M, Newton BW, Riordan DP, Sundaram AB, Johnson JR, Krogan NJ, von Zastrow M. Mol Pharmacol. 2017 Feb; 91(2):145-156.
• A Herpesvirus Protein Selectively Inhibits Cellular mRNA Nuclear Export. Gong D, Kim YH, Xiao Y, Du Y, Xie Y, Lee KK, Feng J, Farhat N, Zhao D, Shu S, Dai X, Chanda SK, Rana TM, Krogan NJ, Sun R, Wu TT. . 2016 Nov 09; 20(5):642-653.
• Combined Action of Histone Reader Modules Regulates NuA4 Local Acetyltransferase Function but Not Its Recruitment on the Genome. Steunou AL, Cramet M, Rossetto D, Aristizabal MJ, Lacoste N, Drouin S, Côté V, Paquet E, Utley RT, Krogan N, Robert F, Kobor MS, Côté J. Mol Cell Biol. 2016 11 15; 36(22):2768-2781.
• Microcephaly Proteins Wdr62 and Aspm Define a Mother Centriole Complex Regulating Centriole Biogenesis, Apical Complex, and Cell Fate. Jayaraman D, Kodani A, Gonzalez DM, Mancias JD, Mochida GH, Vagnoni C, Johnson J, Krogan N, Harper JW, Reiter JF, Yu TW, Bae BI, Walsh CA. Neuron. 2016 Nov 23; 92(4):813-828.
• A Cas9 Ribonucleoprotein Platform for Functional Genetic Studies of HIV-Host Interactions in Primary Human T Cells. Hultquist JF, Schumann K, Woo JM, Manganaro L, McGregor MJ, Doudna J, Simon V, Krogan NJ, Marson A. Cell Rep. 2016 10 25; 17(5):1438-1452.
• The Dengue Virus NS5 Protein Intrudes in the Cellular Spliceosome and Modulates Splicing. De Maio FA, Risso G, Iglesias NG, Shah P, Pozzi B, Gebhard LG, Mammi P, Mancini E, Yanovsky MJ, Andino R, Krogan N, Srebrow A, Gamarnik AV. PLoS Pathog. 2016 08; 12(8):e1005841.
• A Chemical-Genomic Screen of Neglected Antibiotics Reveals Illicit Transport of Kasugamycin and Blasticidin S. Shiver AL, Osadnik H, Kritikos G, Li B, Krogan N, Typas A, Gross CA. PLoS Genet. 2016 06; 12(6):e1006124.
• Non-degradative Ubiquitination of Protein Kinases. Ball KA, Johnson JR, Lewinski MK, Guatelli J, Verschueren E, Krogan NJ, Jacobson MP. PLoS Comput Biol. 2016 06; 12(6):e1004898.
• A scaffold protein connects type IV pili with the Chp chemosensory system to mediate activation of virulence signaling in Pseudomonas aeruginosa. Inclan YF, Persat A, Greninger A, Von Dollen J, Johnson J, Krogan N, Gitai Z, Engel JN. Mol Microbiol. 2016 08; 101(4):590-605.
• Nonsense-mediated decay regulates key components of homologous recombination. Janke R, Kong J, Braberg H, Cantin G, Yates JR, Krogan NJ, Heyer WD. Nucleic Acids Res. 2016 06 20; 44(11):5218-30.
• CRISPR Interference Efficiently Induces Specific and Reversible Gene Silencing in Human iPSCs. Mandegar MA, Huebsch N, Frolov EB, Shin E, Truong A, Olvera MP, Chan AH, Miyaoka Y, Holmes K, Spencer CI, Judge LM, Gordon DE, Eskildsen TV, Villalta JE, Horlbeck MA, Gilbert LA, Krogan NJ, Sheikh SP, Weissman JS, Qi LS, So PL, Conklin BR. Cell Stem Cell. 2016 Apr 07; 18(4):541-53.
• Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems. Yu MK, Kramer M, Dutkowski J, Srivas R, Licon K, Kreisberg J, Ng CT, Krogan N, Sharan R, Ideker T. Cell Syst. 2016 Feb 24; 2(2):77-88.
• Targeting Viral Proteostasis Limits Influenza Virus, HIV, and Dengue Virus Infection. Heaton NS, Moshkina N, Fenouil R, Gardner TJ, Aguirre S, Shah PS, Zhao N, Manganaro L, Hultquist JF, Noel J, Sachs D, Hamilton J, Leon PE, Chawdury A, Tripathi S, Melegari C, Campisi L, Hai R, Metreveli G, Gamarnik AV, García-Sastre A, Greenbaum B, Simon V, Fernandez-Sesma A, Krogan NJ, Mulder LCF, van Bakel H, Tortorella D, Taunton J, Palese P, Marazzi I. Immunity. 2016 Jan 19; 44(1):46-58.
• Meta- and Orthogonal Integration of Influenza "OMICs" Data Defines a Role for UBR4 in Virus Budding. Tripathi S, Pohl MO, Zhou Y, Rodriguez-Frandsen A, Wang G, Stein DA, Moulton HM, DeJesus P, Che J, Mulder LC, Yángüez E, Andenmatten D, Pache L, Manicassamy B, Albrecht RA, Gonzalez MG, Nguyen Q, Brass A, Elledge S, White M, Shapira S, Hacohen N, Karlas A, Meyer TF, Shales M, Gatorano A, Johnson JR, Jang G, Johnson T, Verschueren E, Sanders D, Krogan N, Shaw M, König R, Stertz S, García-Sastre A, Chanda SK. . 2015 Dec 09; 18(6):723-35.
• CDK11 in TREX/THOC Regulates HIV mRNA 3' End Processing. Pak V, Eifler TT, Jäger S, Krogan NJ, Fujinaga K, Peterlin BM. . 2015 Nov 11; 18(5):560-70.
• Discovery and functional characterization of a neomorphic PTEN mutation. Costa HA, Leitner MG, Sos ML, Mavrantoni A, Rychkova A, Johnson JR, Newton BW, Yee MC, De La Vega FM, Ford JM, Krogan NJ, Shokat KM, Oliver D, Halaszovich CR, Bustamante CD. Proc Natl Acad Sci U S A. 2015 Nov 10; 112(45):13976-81.
• Critical role of acetylation in tau-mediated neurodegeneration and cognitive deficits. Min SW, Chen X, Tracy TE, Li Y, Zhou Y, Wang C, Shirakawa K, Minami SS, Defensor E, Mok SA, Sohn PD, Schilling B, Cong X, Ellerby L, Gibson BW, Johnson J, Krogan N, Shamloo M, Gestwicki J, Masliah E, Verdin E, Gan L. Nat Med. 2015 Oct; 21(10):1154-62.
• Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes. Johnson JR, Santos SD, Johnson T, Pieper U, Strumillo M, Wagih O, Sali A, Krogan NJ, Beltrao P. PLoS Comput Biol. 2015 Aug; 11(8):e1004362.
• Systems Analyses Reveal Shared and Diverse Attributes of Oct4 Regulation in Pluripotent Cells. Ding L, Paszkowski-Rogacz M, Winzi M, Chakraborty D, Theis M, Singh S, Ciotta G, Poser I, Roguev A, Chu WK, Choudhary C, Mann M, Stewart AF, Krogan N, Buchholz F. Cell Syst. 2015 Aug 26; 1(2):141-51.
• Centriolar satellites assemble centrosomal microcephaly proteins to recruit CDK2 and promote centriole duplication. Kodani A, Yu TW, Johnson JR, Jayaraman D, Johnson TL, Al-Gazali L, Sztriha L, Partlow JN, Kim H, Krup AL, Dammermann A, Krogan NJ, Walsh CA, Reiter JF. Elife. 2015 Aug 22; 4.
• Comparative mapping of host-pathogen protein-protein interactions. Shah PS, Wojcechowskyj JA, Eckhardt M, Krogan NJ. Curr Opin Microbiol. 2015 Oct; 27:62-8.
• Prb1 Protease Activity Is Required for Its Recognition by the F-Box Protein Saf1. Mark KG, Meza-Gutierrez F, Johnson JR, Newton BW, Krogan NJ, Toczyski DP. Biochemistry. 2015 Jul 28; 54(29):4423-6.
• Global Mapping of the Inc-Human Interactome Reveals that Retromer Restricts Chlamydia Infection. Mirrashidi KM, Elwell CA, Verschueren E, Johnson JR, Frando A, Von Dollen J, Rosenberg O, Gulbahce N, Jang G, Johnson T, Jäger S, Gopalakrishnan AM, Sherry J, Dunn JD, Olive A, Penn B, Shales M, Cox JS, Starnbach MN, Derre I, Valdivia R, Krogan NJ, Engel J. . 2015 Jul 08; 18(1):109-21.
• The cancer cell map initiative: defining the hallmark networks of cancer. Krogan NJ, Lippman S, Agard DA, Ashworth A, Ideker T. Mol Cell. 2015 May 21; 58(4):690-8.
• Lineage-Specific Viral Hijacking of Non-canonical E3 Ubiquitin Ligase Cofactors in the Evolution of Vif Anti-APOBEC3 Activity. Kane JR, Stanley DJ, Hultquist JF, Johnson JR, Mietrach N, Binning JM, Jónsson SR, Barelier S, Newton BW, Johnson TL, Franks-Skiba KE, Li M, Brown WL, Gunnarsson HI, Adalbjornsdóttir A, Fraser JS, Harris RS, Andrésdóttir V, Gross JD, Krogan NJ. Cell Rep. 2015 May 26; 11(8):1236-50.
• Spindle Checkpoint Factors Bub1 and Bub2 Promote DNA Double-Strand Break Repair by Nonhomologous End Joining. Jessulat M, Malty RH, Nguyen-Tran DH, Deineko V, Aoki H, Vlasblom J, Omidi K, Jin K, Minic Z, Hooshyar M, Burnside D, Samanfar B, Phanse S, Freywald T, Prasad B, Zhang Z, Vizeacoumar F, Krogan NJ, Freywald A, Golshani A, Babu M. Mol Cell Biol. 2015 Jul; 35(14):2448-63.
• Differential genetic interactions of yeast stress response MAPK pathways. Martin H, Shales M, Fernandez-Piñar P, Wei P, Molina M, Fiedler D, Shokat KM, Beltrao P, Lim W, Krogan NJ. Mol Syst Biol. 2015 Apr 17; 11(4):800.
• Pharmacological dimerization and activation of the exchange factor eIF2B antagonizes the integrated stress response. Sidrauski C, Tsai JC, Kampmann M, Hearn BR, Vedantham P, Jaishankar P, Sokabe M, Mendez AS, Newton BW, Tang EL, Verschueren E, Johnson JR, Krogan NJ, Fraser CS, Weissman JS, Renslo AR, Walter P. Elife. 2015 Apr 15; 4:e07314.
• NF-κB-activating complex engaged in response to EGFR oncogene inhibition drives tumor cell survival and residual disease in lung cancer. Blakely CM, Pazarentzos E, Olivas V, Asthana S, Yan JJ, Tan I, Hrustanovic G, Chan E, Lin L, Neel DS, Newton W, Bobb KL, Fouts TR, Meshulam J, Gubens MA, Jablons DM, Johnson JR, Bandyopadhyay S, Krogan NJ, Bivona TG. Cell Rep. 2015 Apr 07; 11(1):98-110.
• Genetic interaction mapping reveals a role for the SWI/SNF nucleosome remodeler in spliceosome activation in fission yeast. Patrick KL, Ryan CJ, Xu J, Lipp JJ, Nissen KE, Roguev A, Shales M, Krogan NJ, Guthrie C. PLoS Genet. 2015 Mar; 11(3):e1005074.
• Genetic Interaction Landscape Reveals Critical Requirements for Schizosaccharomyces pombe Brc1 in DNA Damage Response Mutants. Sánchez A, Roguev A, Krogan NJ, Russell P. G3 (Bethesda). 2015 Mar 19; 5(5):953-62.
• Scoring Large-Scale Affinity Purification Mass Spectrometry Datasets with MiST. Verschueren E, Von Dollen J, Cimermancic P, Gulbahce N, Sali A, Krogan NJ. Curr Protoc Bioinformatics. 2015 Mar 09; 49:8.19.1-8.19.16.
• A combined proteomics/genomics approach links hepatitis C virus infection with nonsense-mediated mRNA decay. Ramage HR, Kumar GR, Verschueren E, Johnson JR, Von Dollen J, Johnson T, Newton B, Shah P, Horner J, Krogan NJ, Ott M. Mol Cell. 2015 Jan 22; 57(2):329-340.
• Determinants for degradation of SAMHD1, Mus81 and induction of G2 arrest in HIV-1 Vpr and SIVagm Vpr. DePaula-Silva AB, Cassiday PA, Chumley J, Bosque A, Monteiro-Filho CMR, Mahon CS, Cone KR, Krogan N, Elde NC, Planelles V. Virology. 2015 Mar; 477:10-17.
• Global mapping of herpesvirus-host protein complexes reveals a transcription strategy for late genes. Davis ZH, Verschueren E, Jang GM, Kleffman K, Johnson JR, Park J, Von Dollen J, Maher MC, Johnson T, Newton W, Jäger S, Shales M, Horner J, Hernandez RD, Krogan NJ, Glaunsinger BA. Mol Cell. 2015 Jan 22; 57(2):349-60.
• Linking tumor mutations to drug responses via a quantitative chemical-genetic interaction map. Martins MM, Zhou AY, Corella A, Horiuchi D, Yau C, Rakhshandehroo T, Gordan JD, Levin RS, Johnson J, Jascur J, Shales M, Sorrentino A, Cheah J, Clemons PA, Shamji AF, Schreiber SL, Krogan NJ, Shokat KM, McCormick F, Goga A, Bandyopadhyay S. Cancer Discov. 2015 02; 5(2):154-67.
• Regulation of Sufu activity by p66ß and Mycbp provides new insight into vertebrate Hedgehog signaling. Lin C, Yao E, Wang K, Nozawa Y, Shimizu H, Johnson JR, Chen JN, Krogan NJ, Chuang PT. Genes Dev. 2014 Nov 15; 28(22):2547-63.
• Cyclin-dependent kinase 12 increases 3' end processing of growth factor-induced c-FOS transcripts. Eifler TT, Shao W, Bartholomeeusen K, Fujinaga K, Jäger S, Johnson JR, Luo Z, Krogan NJ, Peterlin BM. Mol Cell Biol. 2015 Jan; 35(2):468-78.
• Acetylome profiling reveals overlap in the regulation of diverse processes by sirtuins, gcn5, and esa1. Downey M, Johnson JR, Davey NE, Newton BW, Johnson TL, Galaang S, Seller CA, Krogan N, Toczyski DP. Mol Cell Proteomics. 2015 Jan; 14(1):162-76.
• Cullin E3 ligases and their rewiring by viral factors. Mahon C, Krogan NJ, Craik CS, Pick E. Biomolecules. 2014 Oct 13; 4(4):897-930.
• Evolutionarily conserved genetic interactions with budding and fission yeast MutS identify orthologous relationships in mismatch repair-deficient cancer cells. Tosti E, Katakowski JA, Schaetzlein S, Kim HS, Ryan CJ, Shales M, Roguev A, Krogan NJ, Palliser D, Keogh MC, Edelmann W. Genome Med. 2014; 6(9):68.
• Quantitative analysis of triple-mutant genetic interactions. Braberg H, Alexander R, Shales M, Xu J, Franks-Skiba KE, Wu Q, Haber JE, Krogan NJ. Nat Protoc. 2014 Aug; 9(8):1867-81.
• Yeast X-chromosome-associated protein 5 (Xap5) functions with H2A.Z to suppress aberrant transcripts. Anver S, Roguev A, Zofall M, Krogan NJ, Grewal SI, Harmer SL. . 2014 Aug; 15(8):894-902.
• Genetic interaction analysis of point mutations enables interrogation of gene function at a residue-level resolution: exploring the applications of high-resolution genetic interaction mapping of point mutations. Braberg H, Moehle EA, Shales M, Guthrie C, Krogan NJ. Bioessays. 2014 Jul; 36(7):706-13.
• Adventures in time and space: splicing efficiency and RNA polymerase II elongation rate. Moehle EA, Braberg H, Krogan NJ, Guthrie C. RNA Biol. 2014; 11(4):313-9.
• Conditional genetic interactions of RTT107, SLX4, and HRQ1 reveal dynamic networks upon DNA damage in S. cerevisiae. Leung GP, Aristizabal MJ, Krogan NJ, Kobor MS. G3 (Bethesda). 2014 Apr 02; 4(6):1059-69.
• Identification of a BET family bromodomain/casein kinase II/TAF-containing complex as a regulator of mitotic condensin function. Kim HS, Mukhopadhyay R, Rothbart SB, Silva AC, Vanoosthuyse V, Radovani E, Kislinger T, Roguev A, Ryan CJ, Xu J, Jahari H, Hardwick KG, Greenblatt JF, Krogan NJ, Fillingham JS, Strahl BD, Bouhassira EE, Edelmann W, Keogh MC. Cell Rep. 2014 Mar 13; 6(5):892-905.
• A chaperone-assisted degradation pathway targets kinetochore proteins to ensure genome stability. Kriegenburg F, Jakopec V, Poulsen EG, Nielsen SV, Roguev A, Krogan N, Gordon C, Fleig U, Hartmann-Petersen R. PLoS Genet. 2014 Jan; 10(1):e1004140.
• Set5 and Set1 cooperate to repress gene expression at telomeres and retrotransposons. Martín GM, King DA, Green EM, Garcia-Nieto PE, Alexander R, Collins SR, Krogan NJ, Gozani OP, Morrison AJ. Epigenetics. 2014 Apr; 9(4):513-22.
• A Pil1-Sle1-Syj1-Tax4 functional pathway links eisosomes with PI(4,5)P2 regulation. Kabeche R, Roguev A, Krogan NJ, Moseley JB. J Cell Sci. 2014 Mar 15; 127(Pt 6):1318-26.
• AFF1 is a ubiquitous P-TEFb partner to enable Tat extraction of P-TEFb from 7SK snRNP and formation of SECs for HIV transactivation. Lu H, Li Z, Xue Y, Schulze-Gahmen U, Johnson JR, Krogan NJ, Alber T, Zhou Q. Proc Natl Acad Sci U S A. 2014 Jan 07; 111(1):E15-24.
• Evolution and functional cross-talk of protein post-translational modifications. Beltrao P, Bork P, Krogan NJ, van Noort V. Mol Syst Biol. 2013; 9:714.
• Chemical genetics of rapamycin-insensitive TORC2 in S. cerevisiae. Kliegman JI, Fiedler D, Ryan CJ, Xu YF, Su XY, Thomas D, Caccese MC, Cheng A, Shales M, Rabinowitz JD, Krogan NJ, Shokat KM. Cell Rep. 2013 Dec 26; 5(6):1725-36.
• IFI16 DNA sensor is required for death of lymphoid CD4 T cells abortively infected with HIV. Monroe KM, Yang Z, Johnson JR, Geng X, Doitsh G, Krogan NJ, Greene WC. Science. 2014 Jan 24; 343(6169):428-32.
• High-resolution network biology: connecting sequence with function. Ryan CJ, Cimermancic P, Szpiech ZA, Sali A, Hernandez RD, Krogan NJ. Nat Rev Genet. 2013 Dec; 14(12):865-79.
• The prefoldin complex regulates chromatin dynamics during transcription elongation. Millán-Zambrano G, Rodríguez-Gil A, Peñate X, de Miguel-Jiménez L, Morillo-Huesca M, Krogan N, Chávez S. PLoS Genet. 2013; 9(9):e1003776.
• High-throughput genetic and gene expression analysis of the RNAPII-CTD reveals unexpected connections to SRB10/CDK8. Aristizabal MJ, Negri GL, Benschop JJ, Holstege FC, Krogan NJ, Kobor MS. PLoS Genet. 2013 Aug; 9(8):e1003758.
• From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II. Braberg H, Jin H, Moehle EA, Chan YA, Wang S, Shales M, Benschop JJ, Morris JH, Qiu C, Hu F, Tang LK, Fraser JS, Holstege FC, Hieter P, Guthrie C, Kaplan CD, Krogan NJ. Cell. 2013 Aug 15; 154(4):775-88.
• A lipid E-MAP identifies Ubx2 as a critical regulator of lipid saturation and lipid bilayer stress. Surma MA, Klose C, Peng D, Shales M, Mrejen C, Stefanko A, Braberg H, Gordon DE, Vorkel D, Ejsing CS, Farese R, Simons K, Krogan NJ, Ernst R. Mol Cell. 2013 Aug 22; 51(4):519-30.
• Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation. Swaney DL, Beltrao P, Starita L, Guo A, Rush J, Fields S, Krogan NJ, Villén J. Nat Methods. 2013 Jul; 10(7):676-82.
• Systematic triple-mutant analysis uncovers functional connectivity between pathways involved in chromosome regulation. Haber JE, Braberg H, Wu Q, Alexander R, Haase J, Ryan C, Lipkin-Moore Z, Franks-Skiba KE, Johnson T, Shales M, Lenstra TL, Holstege FC, Johnson JR, Bloom K, Krogan NJ. Cell Rep. 2013 Jun 27; 3(6):2168-78.
• Bringing it all together: big data and HIV research. Bushman FD, Barton S, Bailey A, Greig C, Malani N, Bandyopadhyay S, Young J, Chanda S, Krogan N. AIDS. 2013 Mar 13; 27(5):835-8.
• The AFF4 scaffold binds human P-TEFb adjacent to HIV Tat. Schulze-Gahmen U, Upton H, Birnberg A, Bao K, Chou S, Krogan NJ, Zhou Q, Alber T. Elife. 2013 Mar 05; 2:e00327.
• Quantitative genetic-interaction mapping in mammalian cells. Roguev A, Talbot D, Negri GL, Shales M, Cagney G, Bandyopadhyay S, Panning B, Krogan NJ. Nat Methods. 2013 May; 10(5):432-7.
• From systems to structure: bridging networks and mechanism. Fraser JS, Gross JD, Krogan NJ. Mol Cell. 2013 Jan 24; 49(2):222-31.
• CBFß stabilizes HIV Vif to counteract APOBEC3 at the expense of RUNX1 target gene expression. Kim DY, Kwon E, Hartley PD, Crosby DC, Mann S, Krogan NJ, Gross JD. Mol Cell. 2013 Feb 21; 49(4):632-44.
• Dispersed sites of HIV Vif-dependent polyubiquitination in the DNA deaminase APOBEC3F. Albin JS, Anderson JS, Johnson JR, Harjes E, Matsuo H, Krogan NJ, Harris RS. J Mol Biol. 2013 Apr 12; 425(7):1172-82.
• A gene ontology inferred from molecular networks. Dutkowski J, Kramer M, Surma MA, Balakrishnan R, Cherry JM, Krogan NJ, Ideker T. Nat Biotechnol. 2013 Jan; 31(1):38-45.
• All or nothing: protein complexes flip essentiality between distantly related eukaryotes. Ryan CJ, Krogan NJ, Cunningham P, Cagney G. Genome Biol Evol. 2013; 5(6):1049-59.
• Dissection of DNA damage responses using multiconditional genetic interaction maps. Guénolé A, Srivas R, Vreeken K, Wang ZZ, Wang S, Krogan NJ, Ideker T, van Attikum H. Mol Cell. 2013 Jan 24; 49(2):346-58.
• Inhibition of a NEDD8 Cascade Restores Restriction of HIV by APOBEC3G. Stanley DJ, Bartholomeeusen K, Crosby DC, Kim DY, Kwon E, Yen L, Cartozo NC, Li M, Jäger S, Mason-Herr J, Hayashi F, Yokoyama S, Krogan NJ, Harris RS, Peterlin BM, Gross JD. PLoS Pathog. 2012 Dec; 8(12):e1003085.
• HIV-1 Tat recruits transcription elongation factors dispersed along a flexible AFF4 scaffold. Chou S, Upton H, Bao K, Schulze-Gahmen U, Samelson AJ, He N, Nowak A, Lu H, Krogan NJ, Zhou Q, Alber T. Proc Natl Acad Sci U S A. 2013 Jan 08; 110(2):E123-31.
• The yeast SR-like protein Npl3 links chromatin modification to mRNA processing. Moehle EA, Ryan CJ, Krogan NJ, Kress TL, Guthrie C. PLoS Genet. 2012; 8(11):e1003101.
• Inhibition of RNA lariat debranching enzyme suppresses TDP-43 toxicity in ALS disease models. Armakola M, Higgins MJ, Figley MD, Barmada SJ, Scarborough EA, Diaz Z, Fang X, Shorter J, Krogan NJ, Finkbeiner S, Farese RV, Gitler AD. Nat Genet. 2012 Dec; 44(12):1302-9.
• Replication fork collapse and genome instability in a deoxycytidylate deaminase mutant. Sánchez A, Sharma S, Rozenzhak S, Roguev A, Krogan NJ, Chabes A, Russell P. Mol Cell Biol. 2012 Nov; 32(21):4445-54.
• Systematic functional prioritization of protein posttranslational modifications. Beltrao P, Albanèse V, Kenner LR, Swaney DL, Burlingame A, Villén J, Lim WA, Fraser JS, Frydman J, Krogan NJ. Cell. 2012 Jul 20; 150(2):413-25.
• Moloney leukemia virus type 10 inhibits reverse transcription and retrotransposition of intracisternal a particles. Lu C, Luo Z, Jäger S, Krogan NJ, Peterlin BM. J Virol. 2012 Oct; 86(19):10517-23.
• Hierarchical modularity and the evolution of genetic interactomes across species. Ryan CJ, Roguev A, Patrick K, Xu J, Jahari H, Tong Z, Beltrao P, Shales M, Qu H, Collins SR, Kliegman JI, Jiang L, Kuo D, Tosti E, Kim HS, Edelmann W, Keogh MC, Greene D, Tang C, Cunningham P, Shokat KM, Cagney G, Svensson JP, Guthrie C, Espenshade PJ, Ideker T, Krogan NJ. Mol Cell. 2012 Jun 08; 46(5):691-704.
• Genetic and Proteomic Dissection of TDP43 Toxicity in S. cerevisiae. Matthew James Higgins, Nevan J Krogan, Robert V Farese. The FASEB Journal. 2012 Apr 1; 26:745.1-745.1.
• Physical host-pathogen networks. Nevan Krogan. The FASEB Journal. 2012 Apr 1; 26:89.1-89.1.
• Polycomb-like 3 promotes polycomb repressive complex 2 binding to CpG islands and embryonic stem cell self-renewal. Hunkapiller J, Shen Y, Diaz A, Cagney G, McCleary D, Ramalho-Santos M, Krogan N, Ren B, Song JS, Reiter JF. PLoS Genet. 2012; 8(3):e1002576.
• Differential network biology. Ideker T, Krogan NJ. Mol Syst Biol. 2012 Jan 17; 8:565.
• First-in-class small molecule inhibitors of the single-strand DNA cytosine deaminase APOBEC3G. Li M, Shandilya SM, Carpenter MA, Rathore A, Brown WL, Perkins AL, Harki DA, Solberg J, Hook DJ, Pandey KK, Parniak MA, Johnson JR, Krogan NJ, Somasundaran M, Ali A, Schiffer CA, Harris RS. ACS Chem Biol. 2012 Mar 16; 7(3):506-17.
• Comparative interaction networks: bridging genotype to phenotype. Beltrao P, Ryan C, Krogan NJ. Adv Exp Med Biol. 2012; 751:139-56.
• Global landscape of HIV-human protein complexes. Jäger S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K, Hernandez H, Jang GM, Roth SL, Akiva E, Marlett J, Stephens M, D'Orso I, Fernandes J, Fahey M, Mahon C, O'Donoghue AJ, Todorovic A, Morris JH, Maltby DA, Alber T, Cagney G, Bushman FD, Young JA, Chanda SK, Sundquist WI, Kortemme T, Hernandez RD, Craik CS, Burlingame A, Sali A, Frankel AD, Krogan NJ. Nature. 2011 Dec 21; 481(7381):365-70.
• Vif hijacks CBF-ß to degrade APOBEC3G and promote HIV-1 infection. Jäger S, Kim DY, Hultquist JF, Shindo K, LaRue RS, Kwon E, Li M, Anderson BD, Yen L, Stanley D, Mahon C, Kane J, Franks-Skiba K, Cimermancic P, Burlingame A, Sali A, Craik CS, Harris RS, Gross JD, Krogan NJ. Nature. 2011 Dec 21; 481(7381):371-5.
• Host cell interactome of HIV-1 Rev includes RNA helicases involved in multiple facets of virus production. Naji S, Ambrus G, Cimermancic P, Reyes JR, Johnson JR, Filbrandt R, Huber MD, Vesely P, Krogan NJ, Yates JR, Saphire AC, Gerace L. Mol Cell Proteomics. 2012 Apr; 11(4):M111.015313.
• RNA polymerase II carboxyl-terminal domain phosphorylation regulates protein stability of the Set2 methyltransferase and histone H3 di- and trimethylation at lysine 36. Fuchs SM, Kizer KO, Braberg H, Krogan NJ, Strahl BD. J Biol Chem. 2012 Jan 27; 287(5):3249-56.
• Eisosome proteins assemble into a membrane scaffold. Karotki L, Huiskonen JT, Stefan CJ, Ziólkowska NE, Roth R, Surma MA, Krogan NJ, Emr SD, Heuser J, Grünewald K, Walther TC. J Cell Biol. 2011 Nov 28; 195(5):889-902.
• Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs. Casey F, Krogan N, Shields DC, Cagney G. BMC Syst Biol. 2011 Aug 22; 5:133.
• Key functional regions in the histone variant H2A.Z C-terminal docking domain. Wang AY, Aristizabal MJ, Ryan C, Krogan NJ, Kobor MS. Mol Cell Biol. 2011 Sep; 31(18):3871-84.
• GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data. Fahey ME, Bennett MJ, Mahon C, Jäger S, Pache L, Kumar D, Shapiro A, Rao K, Chanda SK, Craik CS, Frankel AD, Krogan NJ. BMC Bioinformatics. 2011 Jul 22; 12:298.
• Site-specific acetylation mark on an essential chromatin-remodeling complex promotes resistance to replication stress. Charles GM, Chen C, Shih SC, Collins SR, Beltrao P, Zhang X, Sharma T, Tan S, Burlingame AL, Krogan NJ, Madhani HD, Narlikar GJ. Proc Natl Acad Sci U S A. 2011 Jun 28; 108(26):10620-5.
• Improved functional overview of protein complexes using inferred epistatic relationships. Ryan C, Greene D, Guénolé A, van Attikum H, Krogan NJ, Cunningham P, Cagney G. BMC Syst Biol. 2011 May 23; 5:80.
• SNX27 mediates retromer tubule entry and endosome-to-plasma membrane trafficking of signalling receptors. Temkin P, Lauffer B, Jäger S, Cimermancic P, Krogan NJ, von Zastrow M. Nat Cell Biol. 2011 Jun; 13(6):715-21.
• Yeast SREBP cleavage activation requires the Golgi Dsc E3 ligase complex. Stewart EV, Nwosu CC, Tong Z, Roguev A, Cummins TD, Kim DU, Hayles J, Park HO, Hoe KL, Powell DW, Krogan NJ, Espenshade PJ. Mol Cell. 2011 Apr 22; 42(2):160-71.
• Imputing and predicting quantitative genetic interactions in epistatic MAPs. Ryan C, Cagney G, Krogan N, Cunningham P, Greene D. Methods Mol Biol. 2011; 781:353-61.
• Phenotypic landscape of a bacterial cell. Nichols RJ, Sen S, Choo YJ, Beltrao P, Zietek M, Chaba R, Lee S, Kazmierczak KM, Lee KJ, Wong A, Shales M, Lovett S, Winkler ME, Krogan NJ, Typas A, Gross CA. Cell. 2011 Jan 07; 144(1):143-56.
• Cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action. Kapitzky L, Beltrao P, Berens TJ, Gassner N, Zhou C, Wüster A, Wu J, Babu MM, Elledge SJ, Toczyski D, Lokey RS, Krogan NJ. Mol Syst Biol. 2010 Dec 21; 6:451.
• Functional overlap and regulatory links shape genetic interactions between signaling pathways. van Wageningen S, Kemmeren P, Lijnzaad P, Margaritis T, Benschop JJ, de Castro IJ, van Leenen D, Groot Koerkamp MJ, Ko CW, Miles AJ, Brabers N, Brok MO, Lenstra TL, Fiedler D, Fokkens L, Aldecoa R, Apweiler E, Taliadouros V, Sameith K, van de Pasch LA, van Hooff SR, Bakker LV, Krogan NJ, Snel B, Holstege FC. Cell. 2010 Dec 10; 143(6):991-1004.
• Rewiring of genetic networks in response to DNA damage. Bandyopadhyay S, Mehta M, Kuo D, Sung MK, Chuang R, Jaehnig EJ, Bodenmiller B, Licon K, Copeland W, Shales M, Fiedler D, Dutkowski J, Guénolé A, van Attikum H, Shokat KM, Kolodner RD, Huh WK, Aebersold R, Keogh MC, Krogan NJ, Ideker T. Science. 2010 Dec 03; 330(6009):1385-9.
• Individual lysine acetylations on the N terminus of Saccharomyces cerevisiae H2A.Z are highly but not differentially regulated. Mehta M, Braberg H, Wang S, Lozsa A, Shales M, Solache A, Krogan NJ, Keogh MC. J Biol Chem. 2010 Dec 17; 285(51):39855-65.
• Epistatic relationships reveal the functional organization of yeast transcription factors. Zheng J, Benschop JJ, Shales M, Kemmeren P, Greenblatt J, Cagney G, Holstege F, Li H, Krogan NJ. Mol Syst Biol. 2010 Oct 05; 6:420.
• Purification and characterization of HIV-human protein complexes. Jäger S, Gulbahce N, Cimermancic P, Kane J, He N, Chou S, D'Orso I, Fernandes J, Jang G, Frankel AD, Alber T, Zhou Q, Krogan NJ. Methods. 2011 Jan; 53(1):13-9.
• A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers. Lefebvre C, Rajbhandari P, Alvarez MJ, Bandaru P, Lim WK, Sato M, Wang K, Sumazin P, Kustagi M, Bisikirska BC, Basso K, Beltrao P, Krogan N, Gautier J, Dalla-Favera R, Califano A. Mol Syst Biol. 2010 Jun 08; 6:377.
• A plasma-membrane E-MAP reveals links of the eisosome with sphingolipid metabolism and endosomal trafficking. Aguilar PS, Fröhlich F, Rehman M, Shales M, Ulitsky I, Olivera-Couto A, Braberg H, Shamir R, Walter P, Mann M, Ejsing CS, Krogan NJ, Walther TC. Nat Struct Mol Biol. 2010 Jul; 17(7):901-8.
• Quantitative genetic interactions reveal biological modularity. Beltrao P, Cagney G, Krogan NJ. Cell. 2010 May 28; 141(5):739-45.
• HIV-1 Tat and host AFF4 recruit two transcription elongation factors into a bifunctional complex for coordinated activation of HIV-1 transcription. He N, Liu M, Hsu J, Xue Y, Chou S, Burlingame A, Krogan NJ, Alber T, Zhou Q. Mol Cell. 2010 May 14; 38(3):428-38.
• The next frontier of systems biology: higher-order and interspecies interactions. Fischbach MA, Krogan NJ. Genome Biol. 2010; 11(5):208.
• Genome-wide screens in yeast reveal that diverse cellular pathways influence the toxicity of various neurodegenerative disease-associated misfolded proteins. Dale Matthew Cameron, Jean Savare, Matthew Higgins, Vicente Sancenon Galarza, Angela Sia, Sean Collins, Michael Shales, Nevan Krogan, Robert Farese, Paul Muchowski, Jonathan Weissman. The FASEB Journal. 2010 Apr 1; 24:684.1-684.1.
• Quantitative genetic interaction mapping using the E-MAP approach. Collins SR, Roguev A, Krogan NJ. Methods Enzymol. 2010; 470:205-31.
• Polycomb-like 2 associates with PRC2 and regulates transcriptional networks during mouse embryonic stem cell self-renewal and differentiation. Walker E, Chang WY, Hunkapiller J, Cagney G, Garcha K, Torchia J, Krogan NJ, Reiter JF, Stanford WL. Cell Stem Cell. 2010 Feb 05; 6(2):153-66.
• HIV Nef is secreted in exosomes and triggers apoptosis in bystander CD4+ T cells. Lenassi M, Cagney G, Liao M, Vaupotic T, Bartholomeeusen K, Cheng Y, Krogan NJ, Plemenitas A, Peterlin BM. Traffic. 2010 Jan; 11(1):110-22.
• Genome-wide association data reveal a global map of genetic interactions among protein complexes. Hannum G, Srivas R, Guénolé A, van Attikum H, Krogan NJ, Karp RM, Ideker T. PLoS Genet. 2009 Dec; 5(12):e1000782.
• Towards accurate imputation of quantitative genetic interactions. Ulitsky I, Krogan NJ, Shamir R. Genome Biol. 2009; 10(12):R140.
• An acetylated form of histone H2A.Z regulates chromosome architecture in Schizosaccharomyces pombe. Kim HS, Vanoosthuyse V, Fillingham J, Roguev A, Watt S, Kislinger T, Treyer A, Carpenter LR, Bennett CS, Emili A, Greenblatt JF, Hardwick KG, Krogan NJ, Bähler J, Keogh MC. Nat Struct Mol Biol. 2009 Dec; 16(12):1286-93.
• From information to knowledge: new technologies for defining gene function. Collins SR, Weissman JS, Krogan NJ. Nat Methods. 2009 Oct; 6(10):721-23.
• A systematic characterization of Cwc21, the yeast ortholog of the human spliceosomal protein SRm300. Khanna M, Van Bakel H, Tang X, Calarco JA, Babak T, Guo G, Emili A, Greenblatt JF, Hughes TR, Krogan NJ, Blencowe BJ. RNA. 2009 Dec; 15(12):2174-85.
• An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell. Gong Y, Kakihara Y, Krogan N, Greenblatt J, Emili A, Zhang Z, Houry WA. Mol Syst Biol. 2009; 5:275.
• Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species. Beltrao P, Trinidad JC, Fiedler D, Roguev A, Lim WA, Shokat KM, Burlingame AL, Krogan NJ. PLoS Biol. 2009 Jun 16; 7(6):e1000134.
• Host cell factors in HIV replication: meta-analysis of genome-wide studies. Bushman FD, Malani N, Fernandes J, D'Orso I, Cagney G, Diamond TL, Zhou H, Hazuda DJ, Espeseth AS, König R, Bandyopadhyay S, Ideker T, Goff SP, Krogan NJ, Frankel AD, Young JA, Chanda SK. PLoS Pathog. 2009 May; 5(5):e1000437.
• An rtt109-independent role for vps75 in transcription-associated nucleosome dynamics. Selth LA, Lorch Y, Ocampo-Hafalla MT, Mitter R, Shales M, Krogan NJ, Kornberg RD, Svejstrup JQ. Mol Cell Biol. 2009 Aug; 29(15):4220-34.
• Thioredoxin-related Protein 32 is an arsenite-regulated Thiol Reductase of the proteasome 19 S particle. Wiseman RL, Chin KT, Haynes CM, Stanhill A, Xu CF, Roguev A, Krogan NJ, Neubert TA, Ron D. J Biol Chem. 2009 May 29; 284(22):15233-45.
• Functional organization of the S. cerevisiae phosphorylation network. Fiedler D, Braberg H, Mehta M, Chechik G, Cagney G, Mukherjee P, Silva AC, Shales M, Collins SR, van Wageningen S, Kemmeren P, Holstege FC, Weissman JS, Keogh MC, Koller D, Shokat KM, Krogan NJ. Cell. 2009 Mar 06; 136(5):952-63.
• Learning a prior on regulatory potential from eQTL data. Lee SI, Dudley AM, Drubin D, Silver PA, Krogan NJ, Pe'er D, Koller D. PLoS Genet. 2009 Jan; 5(1):e1000358.
• A complex-based reconstruction of the Saccharomyces cerevisiae interactome. Wang H, Kakaradov B, Collins SR, Karotki L, Fiedler D, Shales M, Shokat KM, Walther TC, Krogan NJ, Koller D. Mol Cell Proteomics. 2009 Jun; 8(6):1361-81.
• Systematic characterization of the protein interaction network and protein complexes in Saccharomyces cerevisiae using tandem affinity purification and mass spectrometry. Babu M, Krogan NJ, Awrey DE, Emili A, Greenblatt JF. Methods Mol Biol. 2009; 548:187-207.
• A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing. Wilmes GM, Bergkessel M, Bandyopadhyay S, Shales M, Braberg H, Cagney G, Collins SR, Whitworth GB, Kress TL, Weissman JS, Ideker T, Guthrie C, Krogan NJ. Mol Cell. 2008 Dec 05; 32(5):735-46.
• A single SR-like protein, Npl3, promotes pre-mRNA splicing in budding yeast. Kress TL, Krogan NJ, Guthrie C. Mol Cell. 2008 Dec 05; 32(5):727-34.
• Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment. Shevchenko A, Roguev A, Schaft D, Buchanan L, Habermann B, Sakalar C, Thomas H, Krogan NJ, Shevchenko A, Stewart AF. Genome Biol. 2008; 9(11):R167.
• Functional targeting of DNA damage to a nuclear pore-associated SUMO-dependent ubiquitin ligase. Nagai S, Dubrana K, Tsai-Pflugfelder M, Davidson MB, Roberts TM, Brown GW, Varela E, Hediger F, Gasser SM, Krogan NJ. Science. 2008 Oct 24; 322(5901):597-602.
• Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. Roguev A, Bandyopadhyay S, Zofall M, Zhang K, Fischer T, Collins SR, Qu H, Shales M, Park HO, Hayles J, Hoe KL, Kim DU, Ideker T, Grewal SI, Weissman JS, Krogan NJ. Science. 2008 Oct 17; 322(5900):405-10.
• Optimal stepwise experimental design for pairwise functional interaction studies. Casey FP, Cagney G, Krogan NJ, Shields DC. Bioinformatics. 2008 Dec 01; 24(23):2733-9.
• High-throughput, quantitative analyses of genetic interactions in E. coli. Typas A, Nichols RJ, Siegele DA, Shales M, Collins SR, Lim B, Braberg H, Yamamoto N, Takeuchi R, Wanner BL, Mori H, Weissman JS, Krogan NJ, Gross CA. Nat Methods. 2008 Sep; 5(9):781-7.
• A comprehensive strategy enabling high-resolution functional analysis of the yeast genome. Breslow DK, Cameron DM, Collins SR, Schuldiner M, Stewart-Ornstein J, Newman HW, Braun S, Madhani HD, Krogan NJ, Weissman JS. Nat Methods. 2008 Aug; 5(8):711-8.
• Ensemble non-negative matrix factorization methods for clustering protein-protein interactions. Greene D, Cagney G, Krogan N, Cunningham P. Bioinformatics. 2008 Aug 01; 24(15):1722-8.
• Chaperone control of the activity and specificity of the histone H3 acetyltransferase Rtt109. Fillingham J, Recht J, Silva AC, Suter B, Emili A, Stagljar I, Krogan NJ, Allis CD, Keogh MC, Greenblatt JF. Mol Cell Biol. 2008 Jul; 28(13):4342-53.
• BAC to the future: functional genomics in mammals. Roguev A, Krogan NJ. Nat Methods. 2008 May; 5(5):383-4.
• Functional maps of protein complexes from quantitative genetic interaction data. Bandyopadhyay S, Kelley R, Krogan NJ, Ideker T. PLoS Comput Biol. 2008 Apr 18; 4(4):e1000065.
• High-throughput genetic interaction mapping in the fission yeast Schizosaccharomyces pombe. Roguev A, Wiren M, Weissman JS, Krogan NJ. Nat Methods. 2007 Oct; 4(10):861-6.
• Association with the origin recognition complex suggests a novel role for histone acetyltransferase Hat1p/Hat2p. Suter B, Pogoutse O, Guo X, Krogan N, Lewis P, Greenblatt JF, Rine J, Emili A. BMC Biol. 2007 Sep 19; 5:38.
• Mec1/Tel1 phosphorylation of the INO80 chromatin remodeling complex influences DNA damage checkpoint responses. Morrison AJ, Kim JA, Person MD, Highland J, Xiao J, Wehr TS, Hensley S, Bao Y, Shen J, Collins SR, Weissman JS, Delrow J, Krogan NJ, Haber JE, Shen X. Cell. 2007 Aug 10; 130(3):499-511.
• Mutations in yhiT enable utilization of exogenous pyrimidine intermediates in Salmonella enterica serovar Typhimurium. Zaharik ML, Lamb SS, Baker KE, Krogan NJ, Neuhard J, Kelln RA. Microbiology (Reading). 2007 Aug; 153(Pt 8):2472-2482.
• H2B ubiquitylation acts as a barrier to Ctk1 nucleosomal recruitment prior to removal by Ubp8 within a SAGA-related complex. Wyce A, Xiao T, Whelan KA, Kosman C, Walter W, Eick D, Hughes TR, Krogan NJ, Strahl BD, Berger SL. Mol Cell. 2007 Jul 20; 27(2):275-88.
• Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast. Gupta R, Kus B, Fladd C, Wasmuth J, Tonikian R, Sidhu S, Krogan NJ, Parkinson J, Rotin D. Mol Syst Biol. 2007; 3:116.
• SIN-fully silent: HDAC complexes in fission yeast. Roguev A, Krogan NJ. Nat Struct Mol Biol. 2007 May; 14(5):358-9.
• Backup without redundancy: genetic interactions reveal the cost of duplicate gene loss. Ihmels J, Collins SR, Schuldiner M, Krogan NJ, Weissman JS. Mol Syst Biol. 2007; 3:86.
• CCR4/NOT complex associates with the proteasome and regulates histone methylation. Laribee RN, Shibata Y, Mersman DP, Collins SR, Kemmeren P, Roguev A, Weissman JS, Briggs SD, Krogan NJ, Strahl BD. Proc Natl Acad Sci U S A. 2007 Apr 03; 104(14):5836-41.
• Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Collins SR, Miller KM, Maas NL, Roguev A, Fillingham J, Chu CS, Schuldiner M, Gebbia M, Recht J, Shales M, Ding H, Xu H, Han J, Ingvarsdottir K, Cheng B, Andrews B, Boone C, Berger SL, Hieter P, Zhang Z, Brown GW, Ingles CJ, Emili A, Allis CD, Toczyski DP, Weissman JS, Greenblatt JF, Krogan NJ. Nature. 2007 Apr 12; 446(7137):806-10.
• Investigating the in vivo activity of the DeaD protein using protein-protein interactions and the translational activity of structured chloramphenicol acetyltransferase mRNAs. Butland G, Krogan NJ, Xu J, Yang WH, Aoki H, Li JS, Krogan N, Menendez J, Cagney G, Kiani GC, Jessulat MG, Datta N, Ivanov I, Abouhaidar MG, Emili A, Greenblatt J, Ganoza MC, Golshani A. J Cell Biochem. 2007 Feb 15; 100(3):642-52.
• Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Collins SR, Kemmeren P, Zhao XC, Greenblatt JF, Spencer F, Holstege FC, Weissman JS, Krogan NJ. Mol Cell Proteomics. 2007 Mar; 6(3):439-50.
• Genetic Interaction mapping of essential genes in Saccharomyces cerevisiae. Jiahao Huang, Nevan Krogan, Maya Schuldiner. The FASEB Journal. 2007 Jan 1; 21(6):a1004-a1004.
• Quantitative genetic analysis in Saccharomyces cerevisiae using epistatic miniarray profiles (E-MAPs) and its application to chromatin functions. Schuldiner M, Collins SR, Weissman JS, Krogan NJ. Methods. 2006 Dec; 40(4):344-52.
• The RNA polymerase II kinase Ctk1 regulates positioning of a 5' histone methylation boundary along genes. Xiao T, Shibata Y, Rao B, Laribee RN, O'Rourke R, Buck MJ, Greenblatt JF, Krogan NJ, Lieb JD, Strahl BD. Mol Cell Biol. 2007 Jan; 27(2):721-31.
• GammaH2AX and its role in DNA double-strand break repair. Fillingham J, Keogh MC, Krogan NJ. Biochem Cell Biol. 2006 Aug; 84(4):568-77.
• PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs. Pitre S, Dehne F, Chan A, Cheetham J, Duong A, Emili A, Gebbia M, Greenblatt J, Jessulat M, Krogan N, Luo X, Golshani A. BMC Bioinformatics. 2006 Jul 27; 7:365.
• Signals and systems. Krogan NJ, Hughes TR. Genome Biol. 2006; 7(4):313.
• A genome-wide screen identifies the evolutionarily conserved KEOPS complex as a telomere regulator. Downey M, Houlsworth R, Maringele L, Rollie A, Brehme M, Galicia S, Guillard S, Partington M, Zubko MK, Krogan NJ, Emili A, Greenblatt JF, Harrington L, Lydall D, Durocher D. Cell. 2006 Mar 24; 124(6):1155-68.
• Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrín-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete MM, Vlasblom J, Wu S, Orsi C, Collins SR, Chandran S, Haw R, Rilstone JJ, Gandi K, Thompson NJ, Musso G, St Onge P, Ghanny S, Lam MH, Butland G, Altaf-Ul AM, Kanaya S, Shilatifard A, O'Shea E, Weissman JS, Ingles CJ, Hughes TR, Parkinson J, Gerstein M, Wodak SJ, Emili A, Greenblatt JF. Nature. 2006 Mar 30; 440(7084):637-43.
• The Saccharomyces cerevisiae histone H2A variant Htz1 is acetylated by NuA4. Keogh MC, Mennella TA, Sawa C, Berthelet S, Krogan NJ, Wolek A, Podolny V, Carpenter LR, Greenblatt JF, Baetz K, Buratowski S. Genes Dev. 2006 Mar 15; 20(6):660-5.
• Transcription-linked kinases that regulate histone lysine methylation states. Brian D Strahl, R. Nicholas Laribee, Tiaojiang Xiao, Nevan J Krogan, Yoichiro Shibata, Timothy R Hughes, Jack F Greenblatt. The FASEB Journal. 2006 Mar 1; 20(5):a850-a850.
• Systems-level analyses identify extensive coupling among gene expression machines. Maciag K, Altschuler SJ, Slack MD, Krogan NJ, Emili A, Greenblatt JF, Maniatis T, Wu LF. Mol Syst Biol. 2006; 2:2006.0003.
• A strategy for extracting and analyzing large-scale quantitative epistatic interaction data. Collins SR, Schuldiner M, Krogan NJ, Weissman JS. Genome Biol. 2006; 7(7):R63.
• Functional genomics of the yeast DNA-damage response. Cagney G, Alvaro D, Reid RJ, Thorpe PH, Rothstein R, Krogan NJ. Genome Biol. 2006; 7(9):233.
• A phosphatase complex that dephosphorylates gammaH2AX regulates DNA damage checkpoint recovery. Keogh MC, Kim JA, Downey M, Fillingham J, Chowdhury D, Harrison JC, Onishi M, Datta N, Galicia S, Emili A, Lieberman J, Shen X, Buratowski S, Haber JE, Durocher D, Greenblatt JF, Krogan NJ. Nature. 2006 Jan 26; 439(7075):497-501.
• Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Keogh MC, Kurdistani SK, Morris SA, Ahn SH, Podolny V, Collins SR, Schuldiner M, Chin K, Punna T, Thompson NJ, Boone C, Emili A, Weissman JS, Hughes TR, Strahl BD, Grunstein M, Greenblatt JF, Buratowski S, Krogan NJ. Cell. 2005 Nov 18; 123(4):593-605.
• Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. Schuldiner M, Collins SR, Thompson NJ, Denic V, Bhamidipati A, Punna T, Ihmels J, Andrews B, Boone C, Greenblatt JF, Weissman JS, Krogan NJ. Cell. 2005 Nov 04; 123(3):507-19.
• Identification and characterization of Elf1, a conserved transcription elongation factor in Saccharomyces cerevisiae. Prather D, Krogan NJ, Emili A, Greenblatt JF, Winston F. Mol Cell Biol. 2005 Nov; 25(22):10122-35.
• BUR kinase selectively regulates H3 K4 trimethylation and H2B ubiquitylation through recruitment of the PAF elongation complex. Laribee RN, Krogan NJ, Xiao T, Shibata Y, Hughes TR, Greenblatt JF, Strahl BD. Curr Biol. 2005 Aug 23; 15(16):1487-93.
• Esf2p, a U3-associated factor required for small-subunit processome assembly and compaction. Hoang T, Peng WT, Vanrobays E, Krogan N, Hiley S, Beyer AL, Osheim YN, Greenblatt J, Hughes TR, Lafontaine DL. Mol Cell Biol. 2005 Jul; 25(13):5523-34.
• Navigating the chaperone network: an integrative map of physical and genetic interactions mediated by the hsp90 chaperone. Zhao R, Davey M, Hsu YC, Kaplanek P, Tong A, Parsons AB, Krogan N, Cagney G, Mai D, Greenblatt J, Boone C, Emili A, Houry WA. Cell. 2005 Mar 11; 120(5):715-27.
• Maintenance of low histone ubiquitylation by Ubp10 correlates with telomere-proximal Sir2 association and gene silencing. Emre NC, Ingvarsdottir K, Wyce A, Wood A, Krogan NJ, Henry KW, Li K, Marmorstein R, Greenblatt JF, Shilatifard A, Berger SL. Mol Cell. 2005 Feb 18; 17(4):585-94.
• The Shwachman-Bodian-Diamond syndrome protein family is involved in RNA metabolism. Savchenko A, Krogan N, Cort JR, Evdokimova E, Lew JM, Yee AA, Sánchez-Pulido L, Andrade MA, Bochkarev A, Watson JD, Kennedy MA, Greenblatt J, Hughes T, Arrowsmith CH, Rommens JM, Edwards AM. J Biol Chem. 2005 May 13; 280(19):19213-20.
• Interaction network containing conserved and essential protein complexes in Escherichia coli. Butland G, Peregrín-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A. Nature. 2005 Feb 03; 433(7025):531-7.
• H2B ubiquitin protease Ubp8 and Sgf11 constitute a discrete functional module within the Saccharomyces cerevisiae SAGA complex. Ingvarsdottir K, Krogan NJ, Emre NC, Wyce A, Thompson NJ, Emili A, Hughes TR, Greenblatt JF, Berger SL. Mol Cell Biol. 2005 Feb; 25(3):1162-72.
• Histone H2B ubiquitylation is associated with elongating RNA polymerase II. Xiao T, Kao CF, Krogan NJ, Sun ZW, Greenblatt JF, Osley MA, Strahl BD. Mol Cell Biol. 2005 Jan; 25(2):637-51.
• Proteasome involvement in the repair of DNA double-strand breaks. Krogan NJ, Lam MH, Fillingham J, Keogh MC, Gebbia M, Li J, Datta N, Cagney G, Buratowski S, Emili A, Greenblatt JF. Mol Cell. 2004 Dec 22; 16(6):1027-34.
• INO80 and gamma-H2AX interaction links ATP-dependent chromatin remodeling to DNA damage repair. Morrison AJ, Highland J, Krogan NJ, Arbel-Eden A, Greenblatt JF, Haber JE, Shen X. Cell. 2004 Dec 17; 119(6):767-75.
• The functional landscape of mouse gene expression. Zhang W, Morris QD, Chang R, Shai O, Bakowski MA, Mitsakakis N, Mohammad N, Robinson MD, Zirngibl R, Somogyi E, Laurin N, Eftekharpour E, Sat E, Grigull J, Pan Q, Peng WT, Krogan N, Greenblatt J, Fehlings M, van der Kooy D, Aubin J, Bruneau BG, Rossant J, Blencowe BJ, Frey BJ, Hughes TR. J Biol. 2004; 3(5):21.
• The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II. Kim M, Krogan NJ, Vasiljeva L, Rando OJ, Nedea E, Greenblatt JF, Buratowski S. Nature. 2004 Nov 25; 432(7016):517-22.
• Interaction of Fcp1 phosphatase with elongating RNA polymerase II holoenzyme, enzymatic mechanism of action, and genetic interaction with elongator. Kong SE, Kobor MS, Krogan NJ, Somesh BP, Søgaard TM, Greenblatt JF, Svejstrup JQ. J Biol Chem. 2005 Feb 11; 280(6):4299-306.
• Regulation of chromosome stability by the histone H2A variant Htz1, the Swr1 chromatin remodeling complex, and the histone acetyltransferase NuA4. Krogan NJ, Baetz K, Keogh MC, Datta N, Sawa C, Kwok TC, Thompson NJ, Davey MG, Pootoolal J, Hughes TR, Emili A, Buratowski S, Hieter P, Greenblatt JF. Proc Natl Acad Sci U S A. 2004 Sep 14; 101(37):13513-8.
• Exploration of essential gene functions via titratable promoter alleles. Mnaimneh S, Davierwala AP, Haynes J, Moffat J, Peng WT, Zhang W, Yang X, Pootoolal J, Chua G, Lopez A, Trochesset M, Morse D, Krogan NJ, Hiley SL, Li Z, Morris Q, Grigull J, Mitsakakis N, Roberts CJ, Greenblatt JF, Boone C, Kaiser CA, Andrews BJ, Hughes TR. Cell. 2004 Jul 09; 118(1):31-44.
• Bromodomain factor 1 (Bdf1) is phosphorylated by protein kinase CK2. Sawa C, Nedea E, Krogan N, Wada T, Handa H, Greenblatt J, Buratowski S. Mol Cell Biol. 2004 Jun; 24(11):4734-42.
• Escherichia coli mRNAs with strong Shine/Dalgarno sequences also contain 5' end sequences complementary to domain # 17 on the 16S ribosomal RNA. Golshani A, Krogan NJ, Xu J, Pacal M, Yang XC, Ivanov I, Providenti MA, Ganoza MC, Ivanov IG, AbouHaidar MG. Biochem Biophys Res Commun. 2004 Apr 16; 316(4):978-83.
• ESF1 is required for 18S rRNA synthesis in Saccharomyces cerevisiae. Peng WT, Krogan NJ, Richards DP, Greenblatt JF, Hughes TR. Nucleic Acids Res. 2004; 32(6):1993-9.
• Global mapping of the yeast genetic interaction network. Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M, Chen Y, Cheng X, Chua G, Friesen H, Goldberg DS, Haynes J, Humphries C, He G, Hussein S, Ke L, Krogan N, Li Z, Levinson JN, Lu H, Ménard P, Munyana C, Parsons AB, Ryan O, Tonikian R, Roberts T, Sdicu AM, Shapiro J, Sheikh B, Suter B, Wong SL, Zhang LV, Zhu H, Burd CG, Munro S, Sander C, Rine J, Greenblatt J, Peter M, Bretscher A, Bell G, Roth FP, Brown GW, Andrews B, Bussey H, Boone C. Science. 2004 Feb 06; 303(5659):808-13.
• The ctf13-30/CTF13 genomic haploinsufficiency modifier screen identifies the yeast chromatin remodeling complex RSC, which is required for the establishment of sister chromatid cohesion. Baetz KK, Krogan NJ, Emili A, Greenblatt J, Hieter P. Mol Cell Biol. 2004 Feb; 24(3):1232-44.
• High-definition macromolecular composition of yeast RNA-processing complexes. Krogan NJ, Peng WT, Cagney G, Robinson MD, Haw R, Zhong G, Guo X, Zhang X, Canadien V, Richards DP, Beattie BK, Lalev A, Zhang W, Davierwala AP, Mnaimneh S, Starostine A, Tikuisis AP, Grigull J, Datta N, Bray JE, Hughes TR, Emili A, Greenblatt JF. Mol Cell. 2004 Jan 30; 13(2):225-39.
• Transitions in RNA polymerase II elongation complexes at the 3' ends of genes. Kim M, Ahn SH, Krogan NJ, Greenblatt JF, Buratowski S. EMBO J. 2004 Jan 28; 23(2):354-64.
• A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1. Krogan NJ, Keogh MC, Datta N, Sawa C, Ryan OW, Ding H, Haw RA, Pootoolal J, Tong A, Canadien V, Richards DP, Wu X, Emili A, Hughes TR, Buratowski S, Greenblatt JF. Mol Cell. 2003 Dec; 12(6):1565-76.
• A Bayesian networks approach for predicting protein-protein interactions from genomic data. Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M. Science. 2003 Oct 17; 302(5644):449-53.
• A panoramic view of yeast noncoding RNA processing. Peng WT, Robinson MD, Mnaimneh S, Krogan NJ, Cagney G, Morris Q, Davierwala AP, Grigull J, Yang X, Zhang W, Mitsakakis N, Ryan OW, Datta N, Jojic V, Pal C, Canadien V, Richards D, Beattie B, Wu LF, Altschuler SJ, Roweis S, Frey BJ, Emili A, Greenblatt JF, Hughes TR. Cell. 2003 Jun 27; 113(7):919-33.
• Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Krogan NJ, Kim M, Tong A, Golshani A, Cagney G, Canadien V, Richards DP, Beattie BK, Emili A, Boone C, Shilatifard A, Buratowski S, Greenblatt J. Mol Cell Biol. 2003 Jun; 23(12):4207-18.
• The Paf1 complex is required for histone H3 methylation by COMPASS and Dot1p: linking transcriptional elongation to histone methylation. Krogan NJ, Dover J, Wood A, Schneider J, Heidt J, Boateng MA, Dean K, Ryan OW, Golshani A, Johnston M, Greenblatt JF, Shilatifard A. Mol Cell. 2003 Mar; 11(3):721-9.
• Bre1, an E3 ubiquitin ligase required for recruitment and substrate selection of Rad6 at a promoter. Wood A, Krogan NJ, Dover J, Schneider J, Heidt J, Boateng MA, Dean K, Golshani A, Zhang Y, Greenblatt JF, Johnston M, Shilatifard A. Mol Cell. 2003 Jan; 11(1):267-74.
• RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach. Krogan NJ, Kim M, Ahn SH, Zhong G, Kobor MS, Cagney G, Emili A, Shilatifard A, Buratowski S, Greenblatt JF. Mol Cell Biol. 2002 Oct; 22(20):6979-92.
• COMPASS, a histone H3 (Lysine 4) methyltransferase required for telomeric silencing of gene expression. Krogan NJ, Dover J, Khorrami S, Greenblatt JF, Schneider J, Johnston M, Shilatifard A. J Biol Chem. 2002 Mar 29; 277(13):10753-5.
• Characterization of a six-subunit holo-elongator complex required for the regulated expression of a group of genes in Saccharomyces cerevisiae. Krogan NJ, Greenblatt JF. Mol Cell Biol. 2001 Dec; 21(23):8203-12.
• COMPASS: a complex of proteins associated with a trithorax-related SET domain protein. Miller T, Krogan NJ, Dover J, Erdjument-Bromage H, Tempst P, Johnston M, Greenblatt JF, Shilatifard A. Proc Natl Acad Sci U S A. 2001 Nov 06; 98(23):12902-7.
• A combination of three mutations, dcd, pyrH, and cdd, establishes thymidine (Deoxyuridine) auxotrophy in thyA+ strains of Salmonella typhimurium. Krogan NJ, Zaharik ML, Neuhard J, Kelln RA. J Bacteriol. 1998 Nov; 180(22):5891-5.

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