Nevan Krogan, PhD

Bio

Honors and Awards

Publications

• 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. 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. Science. 2020 12 04; 370(6521).
• Functional genomic screens identify human host factors for SARS-CoV-2 and common cold coronaviruses. 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).
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• 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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