Nevan Krogan, PhD
Senior Investigator, Gladstone Institute of Data Science and Biotechnology

Other Professional Titles

Professor, Cellular and Molecular Pharmacology, California Institute for Quantitative Biomedical Research, UCSF

Phone

(415) 734-2980

Fax

(415) 514-9736

Assistant

Daryl Jones
(415) 734-2713
Jennifer Paloma
Kane JR, Stanley DJ, Hultquist JF, Johnson JR, Mietrach N, Binning JM, Jónsson SR, Barelier S, Newton BW, Johnson TL et al..  2015.  Lineage-Specific Viral Hijacking of Non-canonical E3 Ubiquitin Ligase Cofactors in the Evolution of Vif Anti-APOBEC3 Activity.. Cell Rep. 11(8):1236-50.
Sánchez A, Roguev A, Krogan NJ, Russell P.  2015.  Genetic Interaction Landscape Reveals Critical Requirements for Schizosaccharomyces pombe Brc1 in DNA Damage Response Mutants.. G3 (Bethesda). 5(5):953-62.
Patrick KL, Ryan CJ, Xu J, Lipp JJ, Nissen KE, Roguev A, Shales M, Krogan NJ, Guthrie C.  2015.  Genetic interaction mapping reveals a role for the SWI/SNF nucleosome remodeler in spliceosome activation in fission yeast.. PLoS Genet. 11(3):e1005074.
DePaula-Silva ABeatriz, Cassiday PA, Chumley J, Bosque A, Monteiro-Filho CMR, Mahon CS, Cone KR, Krogan NJ, Elde NC, Planelles V.  2015.  Determinants for degradation of SAMHD1, Mus81 and induction of G2 arrest in HIV-1 Vpr and SIVagm Vpr.. Virology. 477:10-7.
Mirrashidi KM, Elwell CA, Verschueren E, Johnson JR, Frando A, Von Dollen J, Rosenberg O, Gulbahce N, Jang G, Johnson T et al..  2015.  Global Mapping of the Inc-Human Interactome Reveals that Retromer Restricts Chlamydia Infection.. Cell Host Microbe. 18(1):109-21.
Jessulat M, Malty RH, Nguyen-Tran D-H, Deineko V, Aoki H, Vlasblom J, Omidi K, Jin K, Minic Z, Hooshyar M et al..  2015.  Spindle Checkpoint Factors Bub1 and Bub2 Promote DNA Double-Strand Break Repair by Nonhomologous End Joining.. Mol Cell Biol. 35(14):2448-63.
Davis ZH, Verschueren E, Jang GM, Kleffman K, Johnson JR, Park J, Von Dollen J, M Maher C, Johnson T, Newton W et al..  2015.  Global mapping of herpesvirus-host protein complexes reveals a transcription strategy for late genes.. Mol Cell. 57(2):349-60.
Ramage HR, G Kumar R, Verschueren E, Johnson JR, Von Dollen J, Johnson T, Newton B, Shah P, Horner J, Krogan NJ et al..  2015.  A combined proteomics/genomics approach links hepatitis C virus infection with nonsense-mediated mRNA decay.. Mol Cell. 57(2):329-40.
Eifler TT, Shao W, Bartholomeeusen K, Fujinaga K, Jäger S, Johnson JR, Luo Z, Krogan NJ, B Peterlin M.  2015.  Cyclin-dependent kinase 12 increases 3' end processing of growth factor-induced c-FOS transcripts.. Mol Cell Biol. 35(2):468-78.
Downey M, Johnson JR, Davey NE, Newton BW, Johnson TL, Galaang S, Seller CA, Krogan NJ, Toczyski DP.  2015.  Acetylome profiling reveals overlap in the regulation of diverse processes by sirtuins, gcn5, and esa1.. Mol Cell Proteomics. 14(1):162-76.
Martins MM, Zhou AY, Corella A, Horiuchi D, Yau C, Rakshandehroo T, Gordan JD, Levin RS, Johnson J, Jascur J et al..  2015.  Linking tumor mutations to drug responses via a quantitative chemical-genetic interaction map.. Cancer Discov. 5(2):154-67.
Blakely CM, Pazarentzos E, Olivas V, Asthana S, Yan JJiacheng, Tan I, Hrustanovic G, Chan E, Lin L, Neel DS et al..  2015.  NF-κB-activating complex engaged in response to EGFR oncogene inhibition drives tumor cell survival and residual disease in lung cancer.. Cell Rep. 11(1):98-110.
Martin H, Shales M, Fernandez-Piñar P, Wei P, Molina M, Fiedler D, Shokat KM, Beltrao P, Lim W, Krogan NJ.  2015.  Differential genetic interactions of yeast stress response MAPK pathways.. Mol Syst Biol. 11(4):800.
Sidrauski C, Tsai JC, Kampmann M, Hearn BR, Vedantham P, Jaishankar P, Sokabe M, Mendez AS, Newton BW, Tang EL et al..  2015.  Pharmacological dimerization and activation of the exchange factor eIF2B antagonizes the integrated stress response.. Elife. 4:e07314.
Verschueren E, Von Dollen J, Cimermančič P, Gulbahce N, Sali A, Krogan NJ.  2015.  Scoring Large-Scale Affinity Purification Mass Spectrometry Datasets with MiST.. Curr Protoc Bioinformatics. 49:8.19.1-8.19.16.
Lin C, Yao E, Wang K, Nozawa Y, Shimizu H, Johnson JR, Chen J-N, Krogan NJ, Chuang P-T.  2014.  Regulation of Sufu activity by p66β and Mycbp provides new insight into vertebrate Hedgehog signaling.. Genes Dev. 28(22):2547-63.
Kabeche R, Roguev A, Krogan NJ, Moseley JB.  2014.  A Pil1-Sle1-Syj1-Tax4 functional pathway links eisosomes with PI(4,5)P2 regulation.. J Cell Sci. 127(Pt 6):1318-26.
Kim H-S, Mukhopadhyay R, Rothbart SB, Silva AC, Vanoosthuyse V, Radovani E, Kislinger T, Roguev A, Ryan CJ, Xu J et al..  2014.  Identification of a BET family bromodomain/casein kinase II/TAF-containing complex as a regulator of mitotic condensin function.. Cell Rep. 6(5):892-905.
Leung GP, Aristizabal MJ, Krogan NJ, Kobor MS.  2014.  Conditional genetic interactions of RTT107, SLX4, and HRQ1 reveal dynamic networks upon DNA damage in S. cerevisiae.. G3 (Bethesda). 4(6):1059-69.
Lu H, Li Z, Xue Y, Schulze-Gahmen U, Johnson JR, Krogan NJ, Alber T, Zhou Q.  2014.  AFF1 is a ubiquitous P-TEFb partner to enable Tat extraction of P-TEFb from 7SK snRNP and formation of SECs for HIV transactivation.. Proc Natl Acad Sci U S A. 111(1):E15-24.
Kriegenburg F, Jakopec V, Poulsen EG, Nielsen SVincents, Roguev A, Krogan NJ, Gordon C, Fleig U, Hartmann-Petersen R.  2014.  A chaperone-assisted degradation pathway targets kinetochore proteins to ensure genome stability.. PLoS Genet. 10(1):e1004140.
Anver S, Roguev A, Zofall M, Krogan NJ, Grewal SIS, Harmer SL.  2014.  Yeast X-chromosome-associated protein 5 (Xap5) functions with H2A.Z to suppress aberrant transcripts.. EMBO Rep. 15(8):894-902.
Braberg H, Alexander R, Shales M, Xu J, Franks-Skiba KE, Wu Q, Haber JE, Krogan NJ.  2014.  Quantitative analysis of triple-mutant genetic interactions.. Nat Protoc. 9(8):1867-81.
Martín GMas, King DA, Green EM, Garcia-Nieto PE, Alexander R, Collins SR, Krogan NJ, Gozani OP, Morrison AJ.  2014.  Set5 and Set1 cooperate to repress gene expression at telomeres and retrotransposons.. Epigenetics. 9(4):513-22.
Tosti E, Katakowski JA, Schaetzlein S, Kim H-S, Ryan CJ, Shales M, Roguev A, Krogan NJ, Palliser D, Keogh M-C et al..  2014.  Evolutionarily conserved genetic interactions with budding and fission yeast MutS identify orthologous relationships in mismatch repair-deficient cancer cells.. Genome Med. 6(9):68.
Moehle EA, Braberg H, Krogan NJ, Guthrie C.  2014.  Adventures in time and space: splicing efficiency and RNA polymerase II elongation rate.. RNA Biol. 11(4):313-9.
Mahon C, Krogan NJ, Craik CS, Pick E.  2014.  Cullin E3 ligases and their rewiring by viral factors.. Biomolecules. 4(4):897-930.
Roguev A, Talbot D, Negri GLuca, Shales M, Cagney G, Bandyopadhyay S, Panning B, Krogan NJ.  2013.  Quantitative genetic-interaction mapping in mammalian cells.. Nat Methods. 10(5):432-7.
Bushman FD, Barton S, Bailey A, Greig C, Malani N, Bandyopadhyay S, Young J, Chanda S, Krogan NJ.  2013.  Bringing it all together: big data and HIV research.. AIDS. 27(5):835-8.
Haber JE, Braberg H, Wu Q, Alexander R, Haase J, Ryan C, Lipkin-Moore Z, Franks-Skiba KE, Johnson T, Shales M et al..  2013.  Systematic triple-mutant analysis uncovers functional connectivity between pathways involved in chromosome regulation.. Cell Rep. 3(6):2168-78.
Swaney DL, Beltrao P, Starita L, Guo A, Rush J, Fields S, Krogan NJ, Villén J.  2013.  Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.. Nat Methods. 10(7):676-82.
Chou S, Upton H, Bao K, Schulze-Gahmen U, Samelson AJ, He N, Nowak A, Lu H, Krogan NJ, Zhou Q et al..  2013.  HIV-1 Tat recruits transcription elongation factors dispersed along a flexible AFF4 scaffold.. Proc Natl Acad Sci U S A. 110(2):E123-31.
Guénolé A, Srivas R, Vreeken K, Wang ZZhong, Wang S, Krogan NJ, Ideker T, van Attikum H.  2013.  Dissection of DNA damage responses using multiconditional genetic interaction maps.. Mol Cell. 49(2):346-58.
Fraser JS, Gross JD, Krogan NJ.  2013.  From systems to structure: bridging networks and mechanism.. Mol Cell. 49(2):222-31.
Dutkowski J, Kramer M, Surma MA, Balakrishnan R, J Cherry M, Krogan NJ, Ideker T.  2013.  A gene ontology inferred from molecular networks.. Nat Biotechnol. 31(1):38-45.
Kim DYoung, Kwon E, Hartley PD, Crosby DC, Mann S, Krogan NJ, Gross JD.  2013.  CBFβ stabilizes HIV Vif to counteract APOBEC3 at the expense of RUNX1 target gene expression.. Mol Cell. 49(4):632-44.
Kliegman JI, Fiedler D, Ryan CJ, Xu Y-F, Su X-Y, Thomas D, Caccese MC, Cheng A, Shales M, Rabinowitz JD et al..  2013.  Chemical genetics of rapamycin-insensitive TORC2 in S. cerevisiae.. Cell Rep. 5(6):1725-36.
Ryan CJ, Cimermančič P, Szpiech ZA, Sali A, Hernandez RD, Krogan NJ.  2013.  High-resolution network biology: connecting sequence with function.. Nat Rev Genet. 14(12):865-79.
Surma MA, Klose C, Peng D, Shales M, Mrejen C, Stefanko A, Braberg H, Gordon DE, Vorkel D, Ejsing CS et al..  2013.  A lipid E-MAP identifies Ubx2 as a critical regulator of lipid saturation and lipid bilayer stress.. Mol Cell. 51(4):519-30.
Braberg H, Jin H, Moehle EA, Chan YA, Wang S, Shales M, Benschop JJ, Morris JH, Qiu C, Hu F et al..  2013.  From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II.. Cell. 154(4):775-88.
Aristizabal MJ, Negri GLuca, Benschop JJ, Holstege FCP, Krogan NJ, Kobor MS.  2013.  High-throughput genetic and gene expression analysis of the RNAPII-CTD reveals unexpected connections to SRB10/CDK8.. PLoS Genet. 9(8):e1003758.
Albin JS, Anderson JS, Johnson JR, Harjes E, Matsuo H, Krogan NJ, Harris RS.  2013.  Dispersed sites of HIV Vif-dependent polyubiquitination in the DNA deaminase APOBEC3F.. J Mol Biol. 425(7):1172-82.
Beltrao P, Bork P, Krogan NJ, van Noort V.  2013.  Evolution and functional cross-talk of protein post-translational modifications.. Mol Syst Biol. 9:714.
Schulze-Gahmen U, Upton H, Birnberg A, Bao K, Chou S, Krogan NJ, Zhou Q, Alber T.  2013.  The AFF4 scaffold binds human P-TEFb adjacent to HIV Tat.. Elife. 2:e00327.
Ryan CJ, Krogan NJ, Cunningham P, Cagney G.  2013.  All or nothing: protein complexes flip essentiality between distantly related eukaryotes.. Genome Biol Evol. 5(6):1049-59.
Millán-Zambrano G, Rodríguez-Gil A, Peñate X, de Miguel-Jiménez L, Morillo-Huesca M, Krogan NJ, Chávez S.  2013.  The prefoldin complex regulates chromatin dynamics during transcription elongation.. PLoS Genet. 9(9):e1003776.
Lu C, Luo Z, Jäger S, Krogan NJ, B Peterlin M.  2012.  Moloney leukemia virus type 10 inhibits reverse transcription and retrotransposition of intracisternal a particles.. J Virol. 86(19):10517-23.
Sánchez A, Sharma S, Rozenzhak S, Roguev A, Krogan NJ, Chabes A, Russell P.  2012.  Replication fork collapse and genome instability in a deoxycytidylate deaminase mutant.. Mol Cell Biol. 32(21):4445-54.
Li M, Shandilya SMD, Carpenter MA, Rathore A, Brown WL, Perkins AL, Harki DA, Solberg J, Hook DJ, Pandey KK et al..  2012.  First-in-class small molecule inhibitors of the single-strand DNA cytosine deaminase APOBEC3G.. ACS Chem Biol. 7(3):506-17.
Ryan CJ, Roguev A, Patrick K, Xu J, Jahari H, Tong Z, Beltrao P, Shales M, Qu H, Collins SR et al..  2012.  Hierarchical modularity and the evolution of genetic interactomes across species.. Mol Cell. 46(5):691-704.
Beltrao P, Albanèse V, Kenner LR, Swaney DL, Burlingame A, Villén J, Lim WA, Fraser JS, Frydman J, Krogan NJ.  2012.  Systematic functional prioritization of protein posttranslational modifications.. Cell. 150(2):413-25.
Jäger S, Kim DYoung, Hultquist JF, Shindo K, LaRue RS, Kwon E, Li M, Anderson BD, Yen L, Stanley D et al..  2012.  Vif hijacks CBF-β to degrade APOBEC3G and promote HIV-1 infection.. Nature. 481(7381):371-5.
Jäger S, Cimermančič P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K et al..  2012.  Global landscape of HIV-human protein complexes.. Nature. 481(7381):365-70.
Armakola M, Higgins MJ, Figley MD, Barmada SJ, Scarborough EA, Diaz Z, Fang X, Shorter J, Krogan NJ, Finkbeiner S et al..  2012.  Inhibition of RNA lariat debranching enzyme suppresses TDP-43 toxicity in ALS disease models.. Nat Genet. 44(12):1302-9.
Stanley DJ, Bartholomeeusen K, Crosby DC, Kim DYoung, Kwon E, Yen L, Cartozo NCaretta, Li M, Jäger S, Mason-Herr J et al..  2012.  Inhibition of a NEDD8 Cascade Restores Restriction of HIV by APOBEC3G.. PLoS Pathog. 8(12):e1003085.
Naji S, Ambrus G, Cimermančič P, Reyes JR, Johnson JR, Filbrandt R, Huber MD, Vesely P, Krogan NJ, Yates JR et al..  2012.  Host cell interactome of HIV-1 Rev includes RNA helicases involved in multiple facets of virus production.. Mol Cell Proteomics. 11(4):M111.015313.
Beltrao P, Ryan C, Krogan NJ.  2012.  Comparative interaction networks: bridging genotype to phenotype.. Adv Exp Med Biol. 751:139-56.
Ideker T, Krogan NJ.  2012.  Differential network biology.. Mol Syst Biol. 8:565.
Moehle EA, Ryan CJ, Krogan NJ, Kress TL, Guthrie C.  2012.  The yeast SR-like protein Npl3 links chromatin modification to mRNA processing.. PLoS Genet. 8(11):e1003101.
Hunkapiller J, Shen Y, Diaz A, Cagney G, McCleary D, Ramalho-Santos M, Krogan NJ, Ren B, Song JS, Reiter JF.  2012.  Polycomb-like 3 promotes polycomb repressive complex 2 binding to CpG islands and embryonic stem cell self-renewal.. PLoS Genet. 8(3):e1002576.
Wang AY, Aristizabal MJ, Ryan C, Krogan NJ, Kobor MS.  2011.  Key functional regions in the histone variant H2A.Z C-terminal docking domain.. Mol Cell Biol. 31(18):3871-84.
Karotki L, Huiskonen JT, Stefan CJ, Ziółkowska NE, Roth R, Surma MA, Krogan NJ, Emr SD, Heuser J, Grünewald K et al..  2011.  Eisosome proteins assemble into a membrane scaffold.. J Cell Biol. 195(5):889-902.
Charles GM, Chen C, Shih SC, Collins SR, Beltrao P, Zhang X, Sharma T, Tan S, Burlingame AL, Krogan NJ et al..  2011.  Site-specific acetylation mark on an essential chromatin-remodeling complex promotes resistance to replication stress.. Proc Natl Acad Sci U S A. 108(26):10620-5.
Temkin P, Lauffer B, Jäger S, Cimermančič P, Krogan NJ, von Zastrow M.  2011.  SNX27 mediates retromer tubule entry and endosome-to-plasma membrane trafficking of signalling receptors.. Nat Cell Biol. 13(6):715-21.
Nichols RJ, Sen S, Choo YJin, Beltrao P, Zietek M, Chaba R, Lee S, Kazmierczak KM, Lee KJ, Wong A et al..  2011.  Phenotypic landscape of a bacterial cell.. Cell. 144(1):143-56.
Jäger S, Gulbahce N, Cimermančič P, Kane J, He N, Chou S, D'Orso I, Fernandes J, Jang G, Frankel AD et al..  2011.  Purification and characterization of HIV-human protein complexes.. Methods. 53(1):13-9.
Stewart EV, Nwosu CC, Tong Z, Roguev A, Cummins TD, Kim D-U, Hayles J, Park H-O, Hoe K-L, Powell DW et al..  2011.  Yeast SREBP cleavage activation requires the Golgi Dsc E3 ligase complex.. Mol Cell. 42(2):160-71.
Ryan C, Greene D, Guénolé A, van Attikum H, Krogan NJ, Cunningham P, Cagney G.  2011.  Improved functional overview of protein complexes using inferred epistatic relationships.. BMC Syst Biol. 5:80.
Fahey ME, Bennett MJ, Mahon C, Jäger S, Pache L, Kumar D, Shapiro A, Rao K, Chanda SK, Craik CS et al..  2011.  GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data.. BMC Bioinformatics. 12:298.
Ryan C, Cagney G, Krogan NJ, Cunningham P, Greene D.  2011.  Imputing and predicting quantitative genetic interactions in epistatic MAPs.. Methods Mol Biol. 781:353-61.
Zheng J, Benschop JJ, Shales M, Kemmeren P, Greenblatt J, Cagney G, Holstege F, Li H, Krogan NJ.  2010.  Epistatic relationships reveal the functional organization of yeast transcription factors.. Mol Syst Biol. 6:420.
Beltrao P, Cagney G, Krogan NJ.  2010.  Quantitative genetic interactions reveal biological modularity.. Cell. 141(5):739-45.
He N, Liu M, Hsu J, Xue Y, Chou S, Burlingame A, Krogan NJ, Alber T, Zhou Q.  2010.  HIV-1 Tat and host AFF4 recruit two transcription elongation factors into a bifunctional complex for coordinated activation of HIV-1 transcription.. Mol Cell. 38(3):428-38.
Lefebvre C, Rajbhandari P, Alvarez MJ, Bandaru P, Lim WKeat, Sato M, Wang K, Sumazin P, Kustagi M, Bisikirska BC et al..  2010.  A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers.. Mol Syst Biol. 6:377.
Aguilar PS, Fröhlich F, Rehman M, Shales M, Ulitsky I, Olivera-Couto A, Braberg H, Shamir R, Walter P, Mann M et al..  2010.  A plasma-membrane E-MAP reveals links of the eisosome with sphingolipid metabolism and endosomal trafficking.. Nat Struct Mol Biol. 17(7):901-8.
Lenassi M, Cagney G, Liao M, Vaupotic T, Bartholomeeusen K, Cheng Y, Krogan NJ, Plemenitas A, B Peterlin M.  2010.  HIV Nef is secreted in exosomes and triggers apoptosis in bystander CD4+ T cells.. Traffic. 11(1):110-22.
Walker E, Chang WY, Hunkapiller J, Cagney G, Garcha K, Torchia J, Krogan NJ, Reiter JF, Stanford WL.  2010.  Polycomb-like 2 associates with PRC2 and regulates transcriptional networks during mouse embryonic stem cell self-renewal and differentiation.. Cell Stem Cell. 6(2):153-66.
Bandyopadhyay S, Mehta M, Kuo D, Sung M-K, Chuang R, Jaehnig EJ, Bodenmiller B, Licon K, Copeland W, Shales M et al..  2010.  Rewiring of genetic networks in response to DNA damage.. Science. 330(6009):1385-9.
Kapitzky L, Beltrao P, Berens TJ, Gassner N, Zhou C, Wüster A, Wu J, M Babu M, Elledge SJ, Toczyski D et al..  2010.  Cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action.. Mol Syst Biol. 6:451.
Mehta M, Braberg H, Wang S, Lozsa A, Shales M, Solache A, Krogan NJ, Keogh M-C.  2010.  Individual lysine acetylations on the N terminus of Saccharomyces cerevisiae H2A.Z are highly but not differentially regulated.. J Biol Chem. 285(51):39855-65.
van Wageningen S, Kemmeren P, Lijnzaad P, Margaritis T, Benschop JJ, de Castro IJ, van Leenen D, Koerkamp MJAGroot, Ko CW, Miles AJ et al..  2010.  Functional overlap and regulatory links shape genetic interactions between signaling pathways.. Cell. 143(6):991-1004.
Collins SR, Roguev A, Krogan NJ.  2010.  Quantitative genetic interaction mapping using the E-MAP approach.. Methods Enzymol. 470:205-31.
Fischbach MA, Krogan NJ.  2010.  The next frontier of systems biology: higher-order and interspecies interactions.. Genome Biol. 11(5):208.
Collins SR, Weissman JS, Krogan NJ.  2009.  From information to knowledge: new technologies for defining gene function.. Nat Methods. 6(10):721-23.
R Wiseman L, Chin K-T, Haynes CM, Stanhill A, Xu C-F, Roguev A, Krogan NJ, Neubert TA, Ron D.  2009.  Thioredoxin-related Protein 32 is an arsenite-regulated Thiol Reductase of the proteasome 19 S particle.. J Biol Chem. 284(22):15233-45.
Bushman FD, Malani N, Fernandes J, D'Orso I, Cagney G, Diamond TL, Zhou H, Hazuda DJ, Espeseth AS, König R et al..  2009.  Host cell factors in HIV replication: meta-analysis of genome-wide studies.. PLoS Pathog. 5(5):e1000437.
Fiedler D, Braberg H, Mehta M, Chechik G, Cagney G, Mukherjee P, Silva AC, Shales M, Collins SR, van Wageningen S et al..  2009.  Functional organization of the S. cerevisiae phosphorylation network.. Cell. 136(5):952-63.
Beltrao P, Trinidad JC, Fiedler D, Roguev A, Lim WA, Shokat KM, Burlingame AL, Krogan NJ.  2009.  Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species.. PLoS Biol. 7(6):e1000134.
Wang H, Kakaradov B, Collins SR, Karotki L, Fiedler D, Shales M, Shokat KM, Walther TC, Krogan NJ, Koller D.  2009.  A complex-based reconstruction of the Saccharomyces cerevisiae interactome.. Mol Cell Proteomics. 8(6):1361-81.
Lee S-I, Dudley AM, Drubin D, Silver PA, Krogan NJ, Pe'er D, Koller D.  2009.  Learning a prior on regulatory potential from eQTL data.. PLoS Genet. 5(1):e1000358.
Khanna M, Van Bakel H, Tang X, Calarco JA, Babak T, Guo G, Emili A, Greenblatt JF, Hughes TR, Krogan NJ et al..  2009.  A systematic characterization of Cwc21, the yeast ortholog of the human spliceosomal protein SRm300.. RNA. 15(12):2174-85.
Kim H-S, Vanoosthuyse V, Fillingham J, Roguev A, Watt S, Kislinger T, Treyer A, Carpenter LRocco, Bennett CS, Emili A et al..  2009.  An acetylated form of histone H2A.Z regulates chromosome architecture in Schizosaccharomyces pombe.. Nat Struct Mol Biol. 16(12):1286-93.
Hannum G, Srivas R, Guénolé A, van Attikum H, Krogan NJ, Karp RM, Ideker T.  2009.  Genome-wide association data reveal a global map of genetic interactions among protein complexes.. PLoS Genet. 5(12):e1000782.
Selth LA, Lorch Y, Ocampo-Hafalla MT, Mitter R, Shales M, Krogan NJ, Kornberg RD, Svejstrup JQ.  2009.  An rtt109-independent role for vps75 in transcription-associated nucleosome dynamics.. Mol Cell Biol. 29(15):4220-34.
Ulitsky I, Krogan NJ, Shamir R.  2009.  Towards accurate imputation of quantitative genetic interactions.. Genome Biol. 10(12):R140.
Gong Y, Kakihara Y, Krogan NJ, Greenblatt J, Emili A, Zhang Z, Houry WA.  2009.  An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell.. Mol Syst Biol. 5:275.
Typas A, Nichols RJ, Siegele DA, Shales M, Collins SR, Lim B, Braberg H, Yamamoto N, Takeuchi R, Wanner BL et al..  2008.  High-throughput, quantitative analyses of genetic interactions in E. coli.. Nat Methods. 5(9):781-7.
Nagai S, Dubrana K, Tsai-Pflugfelder M, Davidson MB, Roberts TM, Brown GW, Varela E, Hediger F, Gasser SM, Krogan NJ.  2008.  Functional targeting of DNA damage to a nuclear pore-associated SUMO-dependent ubiquitin ligase.. Science. 322(5901):597-602.
Roguev A, Bandyopadhyay S, Zofall M, Zhang K, Fischer T, Collins SR, Qu H, Shales M, Park H-O, Hayles J et al..  2008.  Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast.. Science. 322(5900):405-10.
Roguev A, Krogan NJ.  2008.  BAC to the future: functional genomics in mammals.. Nat Methods. 5(5):383-4.
Fillingham J, Recht J, Silva AC, Suter B, Emili A, Stagljar I, Krogan NJ, C Allis D, Keogh M-C, Greenblatt JF.  2008.  Chaperone control of the activity and specificity of the histone H3 acetyltransferase Rtt109.. Mol Cell Biol. 28(13):4342-53.
Kress TL, Krogan NJ, Guthrie C.  2008.  A single SR-like protein, Npl3, promotes pre-mRNA splicing in budding yeast.. Mol Cell. 32(5):727-34.
Wilmes GM, Bergkessel M, Bandyopadhyay S, Shales M, Braberg H, Cagney G, Collins SR, Whitworth GB, Kress TL, Weissman JS et al..  2008.  A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing.. Mol Cell. 32(5):735-46.
Casey FP, Cagney G, Krogan NJ, Shields DC.  2008.  Optimal stepwise experimental design for pairwise functional interaction studies.. Bioinformatics. 24(23):2733-9.
Greene D, Cagney G, Krogan NJ, Cunningham P.  2008.  Ensemble non-negative matrix factorization methods for clustering protein-protein interactions.. Bioinformatics. 24(15):1722-8.
Breslow DK, Cameron DM, Collins SR, Schuldiner M, Stewart-Ornstein J, Newman HW, Braun S, Madhani HD, Krogan NJ, Weissman JS.  2008.  A comprehensive strategy enabling high-resolution functional analysis of the yeast genome.. Nat Methods. 5(8):711-8.
Bandyopadhyay S, Kelley R, Krogan NJ, Ideker T.  2008.  Functional maps of protein complexes from quantitative genetic interaction data.. PLoS Comput Biol. 4(4):e1000065.
Shevchenko A, Roguev A, Schaft D, Buchanan L, Habermann B, Sakalar C, Thomas H, Krogan NJ, Shevchenko A, A Stewart F.  2008.  Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment.. Genome Biol. 9(11):R167.
Roguev A, Wiren M, Weissman JS, Krogan NJ.  2007.  High-throughput genetic interaction mapping in the fission yeast Schizosaccharomyces pombe.. Nat Methods. 4(10):861-6.
Roguev A, Krogan NJ.  2007.  SIN-fully silent: HDAC complexes in fission yeast.. Nat Struct Mol Biol. 14(5):358-9.
Collins SR, Kemmeren P, Zhao X-C, Greenblatt JF, Spencer F, Holstege FCP, Weissman JS, Krogan NJ.  2007.  Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae.. Mol Cell Proteomics. 6(3):439-50.
Wyce A, Xiao T, Whelan KA, Kosman C, Walter W, Eick D, Hughes TR, Krogan NJ, Strahl BD, Berger SL.  2007.  H2B ubiquitylation acts as a barrier to Ctk1 nucleosomal recruitment prior to removal by Ubp8 within a SAGA-related complex.. Mol Cell. 27(2):275-88.
Xiao T, Shibata Y, Rao B, R Laribee N, O'Rourke R, Buck MJ, Greenblatt JF, Krogan NJ, Lieb JD, Strahl BD.  2007.  The RNA polymerase II kinase Ctk1 regulates positioning of a 5' histone methylation boundary along genes.. Mol Cell Biol. 27(2):721-31.
Butland G, Krogan NJ, Xu J, Yang W-H, Aoki H, Li JS, Krogan N, Menendez J, Cagney G, Kiani GC et al..  2007.  Investigating the in vivo activity of the DeaD protein using protein-protein interactions and the translational activity of structured chloramphenicol acetyltransferase mRNAs.. J Cell Biochem. 100(3):642-52.
Morrison AJ, Kim J-A, Person MD, Highland J, Xiao J, Wehr TS, Hensley S, Bao Y, Shen J, Collins SR et al..  2007.  Mec1/Tel1 phosphorylation of the INO80 chromatin remodeling complex influences DNA damage checkpoint responses.. Cell. 130(3):499-511.
Zaharik ML, Lamb SS, Baker KE, Krogan NJ, Neuhard J, Kelln RA.  2007.  Mutations in yhiT enable utilization of exogenous pyrimidine intermediates in Salmonella enterica serovar Typhimurium.. Microbiology. 153(Pt 8):2472-82.
R Laribee N, Shibata Y, Mersman DP, Collins SR, Kemmeren P, Roguev A, Weissman JS, Briggs SD, Krogan NJ, Strahl BD.  2007.  CCR4/NOT complex associates with the proteasome and regulates histone methylation.. Proc Natl Acad Sci U S A. 104(14):5836-41.
Collins SR, Miller KM, Maas NL, Roguev A, Fillingham J, Chu CS, Schuldiner M, Gebbia M, Recht J, Shales M et al..  2007.  Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map.. Nature. 446(7137):806-10.
Gupta R, Kus B, Fladd C, Wasmuth J, Tonikian R, Sidhu S, Krogan NJ, Parkinson J, Rotin D.  2007.  Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast.. Mol Syst Biol. 3:116.
Ihmels J, Collins SR, Schuldiner M, Krogan NJ, Weissman JS.  2007.  Backup without redundancy: genetic interactions reveal the cost of duplicate gene loss.. Mol Syst Biol. 3:86.
Suter B, Pogoutse O, Guo X, Krogan NJ, Lewis P, Greenblatt JF, Rine J, Emili A.  2007.  Association with the origin recognition complex suggests a novel role for histone acetyltransferase Hat1p/Hat2p.. BMC Biol. 5:38.
Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP et al..  2006.  Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.. Nature. 440(7084):637-43.
Downey M, Houlsworth R, Maringele L, Rollie A, Brehme M, Galicia S, Guillard S, Partington M, Zubko MK, Krogan NJ et al..  2006.  A genome-wide screen identifies the evolutionarily conserved KEOPS complex as a telomere regulator.. Cell. 124(6):1155-68.
Keogh M-C, Mennella TA, Sawa C, Berthelet S, Krogan NJ, Wolek A, Podolny V, Carpenter LRocco, Greenblatt JF, Baetz K et al..  2006.  The Saccharomyces cerevisiae histone H2A variant Htz1 is acetylated by NuA4.. Genes Dev. 20(6):660-5.
Keogh M-C, Kim J-A, Downey M, Fillingham J, Chowdhury D, Harrison JC, Onishi M, Datta N, Galicia S, Emili A et al..  2006.  A phosphatase complex that dephosphorylates gammaH2AX regulates DNA damage checkpoint recovery.. Nature. 439(7075):497-501.
Fillingham J, Keogh M-C, Krogan NJ.  2006.  GammaH2AX and its role in DNA double-strand break repair.. Biochem Cell Biol. 84(4):568-77.
Cagney G, Alvaro D, Reid RJD, Thorpe PH, Rothstein R, Krogan NJ.  2006.  Functional genomics of the yeast DNA-damage response.. Genome Biol. 7(9):233.
Pitre S, Dehne F, Chan A, Cheetham J, Duong A, Emili A, Gebbia M, Greenblatt J, Jessulat M, Krogan NJ et al..  2006.  PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs.. BMC Bioinformatics. 7:365.
Maciag K, Altschuler SJ, Slack MD, Krogan NJ, Emili A, Greenblatt JF, Maniatis T, Wu LF.  2006.  Systems-level analyses identify extensive coupling among gene expression machines.. Mol Syst Biol. 2:2006.0003.
Collins SR, Schuldiner M, Krogan NJ, Weissman JS.  2006.  A strategy for extracting and analyzing large-scale quantitative epistatic interaction data.. Genome Biol. 7(7):R63.
Krogan NJ, Hughes TR.  2006.  Signals and systems.. Genome Biol. 7(4):313.
Schuldiner M, Collins SR, Thompson NJ, Denic V, Bhamidipati A, Punna T, Ihmels J, Andrews B, Boone C, Greenblatt JF et al..  2005.  Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile.. Cell. 123(3):507-19.
Keogh M-C, Kurdistani SK, Morris SA, Ahn SHoon, Podolny V, Collins SR, Schuldiner M, Chin K, Punna T, Thompson NJ et al..  2005.  Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex.. Cell. 123(4):593-605.
Prather D, Krogan NJ, Emili A, Greenblatt JF, Winston F.  2005.  Identification and characterization of Elf1, a conserved transcription elongation factor in Saccharomyces cerevisiae.. Mol Cell Biol. 25(22):10122-35.
Savchenko A, Krogan NJ, Cort JR, Evdokimova E, Lew JM, Yee AA, Sánchez-Pulido L, Andrade MA, Bochkarev A, Watson JD et al..  2005.  The Shwachman-Bodian-Diamond syndrome protein family is involved in RNA metabolism.. J Biol Chem. 280(19):19213-20.
Zhao R, Davey M, Hsu Y-C, Kaplanek P, Tong A, Parsons AB, Krogan NJ, Cagney G, Mai D, Greenblatt J et al..  2005.  Navigating the chaperone network: an integrative map of physical and genetic interactions mediated by the hsp90 chaperone.. Cell. 120(5):715-27.
Hoang T, Peng W-T, Vanrobays E, Krogan NJ, Hiley S, Beyer AL, Osheim YN, Greenblatt J, Hughes TR, Lafontaine DLJ.  2005.  Esf2p, a U3-associated factor required for small-subunit processome assembly and compaction.. Mol Cell Biol. 25(13):5523-34.
Xiao T, Kao C-F, Krogan NJ, Sun Z-W, Greenblatt JF, Osley MAnn, Strahl BD.  2005.  Histone H2B ubiquitylation is associated with elongating RNA polymerase II.. Mol Cell Biol. 25(2):637-51.
Butland G, Peregrín-Alvarez JManuel, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan NJ et al..  2005.  Interaction network containing conserved and essential protein complexes in Escherichia coli.. Nature. 433(7025):531-7.
Emre NCTolga, Ingvarsdottir K, Wyce A, Wood A, Krogan NJ, Henry KW, Li K, Marmorstein R, Greenblatt JF, Shilatifard A et al..  2005.  Maintenance of low histone ubiquitylation by Ubp10 correlates with telomere-proximal Sir2 association and gene silencing.. Mol Cell. 17(4):585-94.
Kong SE, Kobor MS, Krogan NJ, Somesh BP, T Søgaard MM, Greenblatt JF, Svejstrup JQ.  2005.  Interaction of Fcp1 phosphatase with elongating RNA polymerase II holoenzyme, enzymatic mechanism of action, and genetic interaction with elongator.. J Biol Chem. 280(6):4299-306.
Ingvarsdottir K, Krogan NJ, Emre NCTolga, Wyce A, Thompson NJ, Emili A, Hughes TR, Greenblatt JF, Berger SL.  2005.  H2B ubiquitin protease Ubp8 and Sgf11 constitute a discrete functional module within the Saccharomyces cerevisiae SAGA complex.. Mol Cell Biol. 25(3):1162-72.
R Laribee N, Krogan NJ, Xiao T, Shibata Y, Hughes TR, Greenblatt JF, Strahl BD.  2005.  BUR kinase selectively regulates H3 K4 trimethylation and H2B ubiquitylation through recruitment of the PAF elongation complex.. Curr Biol. 15(16):1487-93.
Krogan NJ, Baetz K, Keogh M-C, Datta N, Sawa C, C Y Kwok T, Thompson NJ, Davey MG, Pootoolal J, Hughes TR et al..  2004.  Regulation of chromosome stability by the histone H2A variant Htz1, the Swr1 chromatin remodeling complex, and the histone acetyltransferase NuA4.. Proc Natl Acad Sci U S A. 101(37):13513-8.
Kim M, Krogan NJ, Vasiljeva L, Rando OJ, Nedea E, Greenblatt JF, Buratowski S.  2004.  The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II.. Nature. 432(7016):517-22.
Sawa C, Nedea E, Krogan NJ, Wada T, Handa H, Greenblatt J, Buratowski S.  2004.  Bromodomain factor 1 (Bdf1) is phosphorylated by protein kinase CK2.. Mol Cell Biol. 24(11):4734-42.
Mnaimneh S, Davierwala AP, Haynes J, Moffat J, Peng W-T, Zhang W, Yang X, Pootoolal J, Chua G, Lopez A et al..  2004.  Exploration of essential gene functions via titratable promoter alleles.. Cell. 118(1):31-44.
Krogan NJ, Peng W-T, Cagney G, Robinson MD, Haw R, Zhong G, Guo X, Zhang X, Canadien V, Richards DP et al..  2004.  High-definition macromolecular composition of yeast RNA-processing complexes.. Mol Cell. 13(2):225-39.
Kim M, Ahn S-H, Krogan NJ, Greenblatt JF, Buratowski S.  2004.  Transitions in RNA polymerase II elongation complexes at the 3' ends of genes.. EMBO J. 23(2):354-64.
Tong AHin Yan, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M et al..  2004.  Global mapping of the yeast genetic interaction network.. Science. 303(5659):808-13.
Krogan NJ, H Y Lam M, Fillingham J, Keogh M-C, Gebbia M, Li J, Datta N, Cagney G, Buratowski S, Emili A et al..  2004.  Proteasome involvement in the repair of DNA double-strand breaks.. Mol Cell. 16(6):1027-34.
Morrison AJ, Highland J, Krogan NJ, Arbel-Eden A, Greenblatt JF, Haber JE, Shen X.  2004.  INO80 and gamma-H2AX interaction links ATP-dependent chromatin remodeling to DNA damage repair.. Cell. 119(6):767-75.
Golshani A, Krogan NJ, Xu J, Pacal M, Yang X-C, Ivanov I, Providenti MA, M Ganoza C, Ivanov IG, Abouhaidar MG.  2004.  Escherichia coli mRNAs with strong Shine/Dalgarno sequences also contain 5' end sequences complementary to domain # 17 on the 16S ribosomal RNA.. Biochem Biophys Res Commun. 316(4):978-83.
Zhang W, Morris QD, Chang R, Shai O, Bakowski MA, Mitsakakis N, Mohammad N, Robinson MD, Zirngibl R, Somogyi E et al..  2004.  The functional landscape of mouse gene expression.. J Biol. 3(5):21.
Peng W-T, Krogan NJ, Richards DP, Greenblatt JF, Hughes TR.  2004.  ESF1 is required for 18S rRNA synthesis in Saccharomyces cerevisiae.. Nucleic Acids Res. 32(6):1993-9.
Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M.  2003.  A Bayesian networks approach for predicting protein-protein interactions from genomic data.. Science. 302(5644):449-53.
Krogan NJ, Dover J, Wood A, Schneider J, Heidt J, Boateng MAnn, Dean K, Ryan OW, Golshani A, Johnston M et al..  2003.  The Paf1 complex is required for histone H3 methylation by COMPASS and Dot1p: linking transcriptional elongation to histone methylation.. Mol Cell. 11(3):721-9.
Peng WTao, Robinson MD, Mnaimneh S, Krogan NJ, Cagney G, Morris Q, Davierwala AP, Grigull J, Yang X, Zhang W et al..  2003.  A panoramic view of yeast noncoding RNA processing.. Cell. 113(7):919-33.
Krogan NJ, Kim M, Tong A, Golshani A, Cagney G, Canadien V, Richards DP, Beattie BK, Emili A, Boone C et al..  2003.  Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II.. Mol Cell Biol. 23(12):4207-18.
Wood A, Krogan NJ, Dover J, Schneider J, Heidt J, Boateng MAnn, Dean K, Golshani A, Zhang Y, Greenblatt JF et al..  2003.  Bre1, an E3 ubiquitin ligase required for recruitment and substrate selection of Rad6 at a promoter.. Mol Cell. 11(1):267-74.
Krogan NJ, Keogh M-C, Datta N, Sawa C, Ryan OW, Ding H, Haw RA, Pootoolal J, Tong A, Canadien V et al..  2003.  A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1.. Mol Cell. 12(6):1565-76.
Krogan NJ, Kim M, Ahn SHoon, Zhong G, Kobor MS, Cagney G, Emili A, Shilatifard A, Buratowski S, Greenblatt JF.  2002.  RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach.. Mol Cell Biol. 22(20):6979-92.
Krogan NJ, Dover J, Khorrami S, Greenblatt JF, Schneider J, Johnston M, Shilatifard A.  2002.  COMPASS, a histone H3 (Lysine 4) methyltransferase required for telomeric silencing of gene expression.. J Biol Chem. 277(13):10753-5.
Miller T, Krogan NJ, Dover J, Erdjument-Bromage H, Tempst P, Johnston M, Greenblatt JF, Shilatifard A.  2001.  COMPASS: a complex of proteins associated with a trithorax-related SET domain protein.. Proc Natl Acad Sci U S A. 98(23):12902-7.