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    Nevan Krogan, PhD

    SchoolUCSF School of Medicine
    DepartmentCellular Molecular Pharmacology
    Address1700 4th Street
    San Francisco CA 94158
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      Collapse Biography 
      Collapse Awards and Honors
      University of Regina2012Distinguished Alumni Award
      Searle Foundation2009 - 2012Searle Scholar
      W. M. Keck Foundation2009 - 2014Keck Distinguished Young Scholar
      Sciencewatch.com2008Top 25 authors of high-impact papers in molecular biology and genetics from 2002 to 2006
      University of Toronto2005L. W. Macpherson Microbiology Award
      University of Toronto2004Hannah Farkas-Himsley and Alexander Memorial Award
      Canadian Institute of Health Research2001 - 2004CIHR Doctoral Fellowship
      Natural Sciences and Engineering Research Council 1999 - 2001PGS-B Award
      Society of Chemical Industry 1997Merit Award
      Canadian Cancer Society 1995 - 1996Studentship

      Collapse Overview 
      Collapse Overview
      Dr. Krogan was born and raised in Regina, Saskatchewan, Canada and obtained his undergraduate degree from the University of Regina. As a graduate student at the University of Toronto, Dr. Krogan led a project that systematically identified protein complexes in the model organism, Saccharomyces cerevisiae, through an affinity tagging-purification/mass spectrometry strategy. This work led to the characterization of 547 complexes, comprising over 4000 proteins, and represents the most comprehensive protein-protein interaction map to date in any organism. To complement this physical interaction data, Dr. Krogan developed an approach, termed E-MAP (or epistatic miniarray profile), which allows for high-throughput generation and quantitative analysis of genetic interaction data. Dr. Krogan’s lab at UCSF focuses on applying these global proteomic and genomic approaches to formulate hypotheses about various biological processes, including transcriptional regulation, DNA repair/ replication and RNA processing. His lab at UCSF is now developing and applying methodologies to create genetic and physical interactions between pathogenic organisms, including HIV, Mtb, and Dengue, and their hosts, which is providing insight into the human pathways and complexes that are being hijacked during the course of infection.

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      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Johnson JR, Santos SD, Johnson T, Pieper U, Strumillo M, Wagih O, Sali A, Krogan NJ, Beltrao P. Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes. PLoS Comput Biol. 2015 Aug; 11(8):e1004362.
        View in: PubMed
      2. 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. Centriolar satellites assemble centrosomal microcephaly proteins to recruit CDK2 and promote centriole duplication. Elife. 2015; 4.
        View in: PubMed
      3. Mark KG, Meza-Gutierrez F, Johnson JR, Newton BW, Krogan NJ, Toczyski DP. Prb1 Protease Activity Is Required for Its Recognition by the F-Box Protein Saf1. Biochemistry. 2015 Jul 28; 54(29):4423-6.
        View in: PubMed
      4. 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. Global Mapping of the Inc-Human Interactome Reveals that Retromer Restricts Chlamydia Infection. Cell Host Microbe. 2015 Jul 8; 18(1):109-21.
        View in: PubMed
      5. Krogan NJ, Lippman S, Agard DA, Ashworth A, Ideker T. The cancer cell map initiative: defining the hallmark networks of cancer. Mol Cell. 2015 May 21; 58(4):690-8.
        View in: PubMed
      6. 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. Lineage-Specific Viral Hijacking of Non-canonical E3 Ubiquitin Ligase Cofactors in the Evolution of Vif Anti-APOBEC3 Activity. Cell Rep. 2015 May 26; 11(8):1236-50.
        View in: PubMed
      7. 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. Spindle Checkpoint Factors Bub1 and Bub2 Promote DNA Double-Strand Break Repair by Nonhomologous End Joining. Mol Cell Biol. 2015 Jul 15; 35(14):2448-63.
        View in: PubMed
      8. Martin H, Shales M, Fernandez-Piñar P, Wei P, Molina M, Fiedler D, Shokat KM, Beltrao P, Lim W, Krogan NJ. Differential genetic interactions of yeast stress response MAPK pathways. Mol Syst Biol. 2015; 11(4):800.
        View in: PubMed
      9. 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. Pharmacological dimerization and activation of the exchange factor eIF2B antagonizes the integrated stress response. Elife. 2015; 4.
        View in: PubMed
      10. 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. NF-?B-Activating Complex Engaged in Response to EGFR Oncogene Inhibition Drives Tumor Cell Survival and Residual Disease in Lung Cancer. Cell Rep. 2015 Apr 7; 11(1):98-110.
        View in: PubMed
      11. Patrick KL, Ryan CJ, Xu J, Lipp JJ, Nissen KE, Roguev A, Shales M, Krogan NJ, Guthrie C. Genetic Interaction Mapping Reveals a Role for the SWI/SNF Nucleosome Remodeler in Spliceosome Activation in Fission Yeast. PLoS Genet. 2015 Feb; 11(3):e1005074.
        View in: PubMed
      12. Sánchez A, Roguev A, Krogan NJ, Russell P. Genetic Interaction Landscape Reveals Critical Requirements for Schizosaccharomyces pombe Brc1 in DNA Damage Response Mutants. G3 (Bethesda). 2015; 5(5):953-62.
        View in: PubMed
      13. Verschueren E, Von Dollen J, Cimermancic P, Gulbahce N, Sali A, Krogan NJ. Scoring Large-Scale Affinity Purification Mass Spectrometry Datasets with MiST. Curr Protoc Bioinformatics. 2015; 49:8.19.1-8.19.16.
        View in: PubMed
      14. DePaula-Silva AB, Cassiday PA, Chumley J, Bosque A, Monteiro-Filho CM, Mahon CS, Cone KR, Krogan N, Elde NC, Planelles V. Determinants for degradation of SAMHD1, Mus81 and induction of G2 arrest in HIV-1 Vpr and SIVagm Vpr. Virology. 2015 Mar; 477:10-7.
        View in: PubMed
      15. Ramage HR, Kumar GR, Verschueren E, Johnson JR, Von Dollen J, Johnson T, Newton B, Shah P, Horner J, Krogan NJ, Ott M. A combined proteomics/genomics approach links hepatitis C virus infection with nonsense-mediated mRNA decay. Mol Cell. 2015 Jan 22; 57(2):329-40.
        View in: PubMed
      16. 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. Global mapping of herpesvirus-host protein complexes reveals a transcription strategy for late genes. Mol Cell. 2015 Jan 22; 57(2):349-60.
        View in: PubMed
      17. Martins MM, Zhou AY, Corella A, Horiuchi D, Yau C, Rakshandehroo 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. Linking Tumor Mutations to Drug Responses via a Quantitative Chemical-Genetic Interaction Map. Cancer Discov. 2015 Feb; 5(2):154-67.
        View in: PubMed
      18. Lin C, Yao E, Wang K, Nozawa Y, Shimizu H, Johnson JR, Chen JN, Krogan NJ, Chuang PT. Regulation of Sufu activity by p66ß and Mycbp provides new insight into vertebrate Hedgehog signaling. Genes Dev. 2014 Nov 15; 28(22):2547-63.
        View in: PubMed PMC4233246
      19. Eifler TT, Shao W, Bartholomeeusen K, Fujinaga K, Jäger S, Johnson JR, Luo Z, Krogan NJ, Peterlin BM. Cyclin-Dependent Kinase 12 Increases 3' End Processing of Growth Factor-Induced c-FOS Transcripts. Mol Cell Biol. 2015 Jan 15; 35(2):468-78.
        View in: PubMed
      20. Downey M, Johnson JR, Davey NE, Newton BW, Johnson TL, Galaang S, Seller CA, Krogan N, Toczyski DP. Acetylome profiling reveals overlap in the regulation of diverse processes by sirtuins, gcn5, and esa1. Mol Cell Proteomics. 2015 Jan; 14(1):162-76.
        View in: PubMed
      21. Mahon C, Krogan NJ, Craik CS, Pick E. Cullin E3 ligases and their rewiring by viral factors. Biomolecules. 2014; 4(4):897-930.
        View in: PubMed
      22. Tosti E, Katakowski JA, Schaetzlein S, Kim HS, Ryan CJ, Shales M, Roguev A, Krogan NJ, Palliser D, Keogh MC, Edelmann W. Evolutionarily conserved genetic interactions with budding and fission yeast MutS identify orthologous relationships in mismatch repair-deficient cancer cells. Genome Med. 2014; 6(9):68.
        View in: PubMed PMC4189729
      23. Braberg H, Alexander R, Shales M, Xu J, Franks-Skiba KE, Wu Q, Haber JE, Krogan NJ. Quantitative analysis of triple-mutant genetic interactions. Nat Protoc. 2014 Aug; 9(8):1867-81.
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      24. Anver S, Roguev A, Zofall M, Krogan NJ, Grewal SI, Harmer SL. Yeast X-chromosome-associated protein 5 (Xap5) functions with H2A.Z to suppress aberrant transcripts. EMBO Rep. 2014 Aug; 15(8):894-902.
        View in: PubMed PMC4197047
      25. Braberg H, Moehle EA, Shales M, Guthrie C, Krogan NJ. 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. Bioessays. 2014 Jul; 36(7):706-13.
        View in: PubMed
      26. Moehle EA, Braberg H, Krogan NJ, Guthrie C. Adventures in time and space: splicing efficiency and RNA polymerase II elongation rate. RNA Biol. 2014 Apr; 11(4):313-9.
        View in: PubMed PMC4075515
      27. Leung GP, Aristizabal MJ, Krogan NJ, Kobor MS. Conditional genetic interactions of RTT107, SLX4, and HRQ1 reveal dynamic networks upon DNA damage in S. cerevisiae. G3 (Bethesda). 2014 Jun; 4(6):1059-69.
        View in: PubMed PMC4065249
      28. 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. Identification of a BET family bromodomain/casein kinase II/TAF-containing complex as a regulator of mitotic condensin function. Cell Rep. 2014 Mar 13; 6(5):892-905.
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      29. Kriegenburg F, Jakopec V, Poulsen EG, Nielsen SV, Roguev A, Krogan N, Gordon C, Fleig U, Hartmann-Petersen R. A chaperone-assisted degradation pathway targets kinetochore proteins to ensure genome stability. PLoS Genet. 2014 Jan; 10(1):e1004140.
        View in: PubMed PMC3907333
      30. Martín GM, King DA, Green EM, Garcia-Nieto PE, Alexander R, Collins SR, Krogan NJ, Gozani OP, Morrison AJ. Set5 and Set1 cooperate to repress gene expression at telomeres and retrotransposons. Epigenetics. 2014 Apr; 9(4):513-22.
        View in: PubMed PMC4121362
      31. Kabeche R, Roguev A, Krogan NJ, Moseley JB. A Pil1-Sle1-Syj1-Tax4 functional pathway links eisosomes with PI(4,5)P2 regulation. J Cell Sci. 2014 Mar 15; 127(Pt 6):1318-26.
        View in: PubMed PMC3953819
      32. Lu H, Li Z, Xue Y, Schulze-Gahmen U, Johnson JR, Krogan NJ, Alber T, Zhou Q. 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. 2014 Jan 7; 111(1):E15-24.
        View in: PubMed PMC3890890
      33. Beltrao P, Bork P, Krogan NJ, van Noort V. Evolution and functional cross-talk of protein post-translational modifications. Mol Syst Biol. 2013; 9:714.
        View in: PubMed PMC4019982
      34. Kliegman JI, Fiedler D, Ryan CJ, Xu YF, Su XY, Thomas D, Caccese MC, Cheng A, Shales M, Rabinowitz JD, Krogan NJ, Shokat KM. Chemical genetics of rapamycin-insensitive TORC2 in S. cerevisiae. Cell Rep. 2013 Dec 26; 5(6):1725-36.
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      35. Monroe KM, Yang Z, Johnson JR, Geng X, Doitsh G, Krogan NJ, Greene WC. IFI16 DNA sensor is required for death of lymphoid CD4 T cells abortively infected with HIV. Science. 2014 Jan 24; 343(6169):428-32.
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      36. Ryan CJ, Cimermancic P, Szpiech ZA, Sali A, Hernandez RD, Krogan NJ. High-resolution network biology: connecting sequence with function. Nat Rev Genet. 2013 Dec; 14(12):865-79.
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      37. Millán-Zambrano G, Rodríguez-Gil A, Peñate X, de Miguel-Jiménez L, Morillo-Huesca M, Krogan N, Chávez S. The prefoldin complex regulates chromatin dynamics during transcription elongation. PLoS Genet. 2013; 9(9):e1003776.
        View in: PubMed PMC3777993
      38. Aristizabal MJ, Negri GL, Benschop JJ, Holstege FC, Krogan NJ, Kobor MS. High-throughput genetic and gene expression analysis of the RNAPII-CTD reveals unexpected connections to SRB10/CDK8. PLoS Genet. 2013 Aug; 9(8):e1003758.
        View in: PubMed PMC3757075
      39. 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. From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II. Cell. 2013 Aug 15; 154(4):775-88.
        View in: PubMed
      40. 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. A lipid E-MAP identifies Ubx2 as a critical regulator of lipid saturation and lipid bilayer stress. Mol Cell. 2013 Aug 22; 51(4):519-30.
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      41. Swaney DL, Beltrao P, Starita L, Guo A, Rush J, Fields S, Krogan NJ, Villén J. Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation. Nat Methods. 2013 Jul; 10(7):676-82.
        View in: PubMed
      42. 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. Systematic triple-mutant analysis uncovers functional connectivity between pathways involved in chromosome regulation. Cell Rep. 2013 Jun 27; 3(6):2168-78.
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      43. Bushman FD, Barton S, Bailey A, Greig C, Malani N, Bandyopadhyay S, Young J, Chanda S, Krogan N. Bringing it all together: big data and HIV research. AIDS. 2013 Mar 13; 27(5):835-8.
        View in: PubMed
      44. Schulze-Gahmen U, Upton H, Birnberg A, Bao K, Chou S, Krogan NJ, Zhou Q, Alber T. The AFF4 scaffold binds human P-TEFb adjacent to HIV Tat. Elife. 2013; 2:e00327.
        View in: PubMed PMC3589825
      45. Roguev A, Talbot D, Negri GL, Shales M, Cagney G, Bandyopadhyay S, Panning B, Krogan NJ. Quantitative genetic-interaction mapping in mammalian cells. Nat Methods. 2013 May; 10(5):432-7.
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      46. Fraser JS, Gross JD, Krogan NJ. From systems to structure: bridging networks and mechanism. Mol Cell. 2013 Jan 24; 49(2):222-31.
        View in: PubMed
      47. Kim DY, Kwon E, Hartley PD, Crosby DC, Mann S, Krogan NJ, Gross JD. CBFß stabilizes HIV Vif to counteract APOBEC3 at the expense of RUNX1 target gene expression. Mol Cell. 2013 Feb 21; 49(4):632-44.
        View in: PubMed
      48. Albin JS, Anderson JS, Johnson JR, Harjes E, Matsuo H, Krogan NJ, Harris RS. Dispersed sites of HIV Vif-dependent polyubiquitination in the DNA deaminase APOBEC3F. J Mol Biol. 2013 Apr 12; 425(7):1172-82.
        View in: PubMed
      49. Dutkowski J, Kramer M, Surma MA, Balakrishnan R, Cherry JM, Krogan NJ, Ideker T. A gene ontology inferred from molecular networks. Nat Biotechnol. 2013 Jan; 31(1):38-45.
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      50. Ryan CJ, Krogan NJ, Cunningham P, Cagney G. All or nothing: protein complexes flip essentiality between distantly related eukaryotes. Genome Biol Evol. 2013; 5(6):1049-59.
        View in: PubMed PMC3698920
      51. Guénolé A, Srivas R, Vreeken K, Wang ZZ, Wang S, Krogan NJ, Ideker T, van Attikum H. Dissection of DNA damage responses using multiconditional genetic interaction maps. Mol Cell. 2013 Jan 24; 49(2):346-58.
        View in: PubMed
      52. 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. Inhibition of a NEDD8 Cascade Restores Restriction of HIV by APOBEC3G. PLoS Pathog. 2012 Dec; 8(12):e1003085.
        View in: PubMed PMC3531493
      53. Chou S, Upton H, Bao K, Schulze-Gahmen U, Samelson AJ, He N, Nowak A, Lu H, Krogan NJ, Zhou Q, Alber T. HIV-1 Tat recruits transcription elongation factors dispersed along a flexible AFF4 scaffold. Proc Natl Acad Sci U S A. 2013 Jan 8; 110(2):E123-31.
        View in: PubMed PMC3545800
      54. Moehle EA, Ryan CJ, Krogan NJ, Kress TL, Guthrie C. The yeast SR-like protein Npl3 links chromatin modification to mRNA processing. PLoS Genet. 2012; 8(11):e1003101.
        View in: PubMed PMC3510044
      55. Armakola M, Higgins MJ, Figley MD, Barmada SJ, Scarborough EA, Diaz Z, Fang X, Shorter J, Krogan NJ, Finkbeiner S, Farese RV, Gitler AD. Inhibition of RNA lariat debranching enzyme suppresses TDP-43 toxicity in ALS disease models. Nat Genet. 2012 Dec; 44(12):1302-9.
        View in: PubMed
      56. Sánchez A, Sharma S, Rozenzhak S, Roguev A, Krogan NJ, Chabes A, Russell P. Replication fork collapse and genome instability in a deoxycytidylate deaminase mutant. Mol Cell Biol. 2012 Nov; 32(21):4445-54.
        View in: PubMed PMC3486156
      57. Beltrao P, Albanèse V, Kenner LR, Swaney DL, Burlingame A, Villén J, Lim WA, Fraser JS, Frydman J, Krogan NJ. Systematic functional prioritization of protein posttranslational modifications. Cell. 2012 Jul 20; 150(2):413-25.
        View in: PubMed
      58. Lu C, Luo Z, Jäger S, Krogan NJ, Peterlin BM. Moloney leukemia virus type 10 inhibits reverse transcription and retrotransposition of intracisternal a particles. J Virol. 2012 Oct; 86(19):10517-23.
        View in: PubMed PMC3457264
      59. 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. Hierarchical modularity and the evolution of genetic interactomes across species. Mol Cell. 2012 Jun 8; 46(5):691-704.
        View in: PubMed
      60. Hunkapiller J, Shen Y, Diaz A, Cagney G, McCleary D, Ramalho-Santos M, Krogan N, Ren B, Song JS, Reiter JF. Polycomb-like 3 promotes polycomb repressive complex 2 binding to CpG islands and embryonic stem cell self-renewal. PLoS Genet. 2012; 8(3):e1002576.
        View in: PubMed PMC3305387
      61. Ideker T, Krogan NJ. Differential network biology. Mol Syst Biol. 2012; 8:565.
        View in: PubMed PMC3296360
      62. 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. First-in-class small molecule inhibitors of the single-strand DNA cytosine deaminase APOBEC3G. ACS Chem Biol. 2012 Mar 16; 7(3):506-17.
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      63. Beltrao P, Ryan C, Krogan NJ. Comparative interaction networks: bridging genotype to phenotype. Adv Exp Med Biol. 2012; 751:139-56.
        View in: PubMed
      64. 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. Vif hijacks CBF-ß to degrade APOBEC3G and promote HIV-1 infection. Nature. 2012 Jan 19; 481(7381):371-5.
        View in: PubMed
      65. 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. Global landscape of HIV-human protein complexes. Nature. 2012 Jan 19; 481(7381):365-70.
        View in: PubMed
      66. Naji S, Ambrus G, Cimermancic P, Reyes JR, Johnson JR, Filbrandt R, Huber MD, Vesely P, Krogan NJ, Yates JR, Saphire AC, Gerace L. Host cell interactome of HIV-1 Rev includes RNA helicases involved in multiple facets of virus production. Mol Cell Proteomics. 2012 Apr; 11(4):M111.015313.
        View in: PubMed PMC3322577
      67. Fuchs SM, Kizer KO, Braberg H, Krogan NJ, Strahl BD. RNA polymerase II carboxyl-terminal domain phosphorylation regulates protein stability of the Set2 methyltransferase and histone H3 di- and trimethylation at lysine 36. J Biol Chem. 2012 Jan 27; 287(5):3249-56.
        View in: PubMed PMC3270979
      68. Karotki L, Huiskonen JT, Stefan CJ, Ziólkowska NE, Roth R, Surma MA, Krogan NJ, Emr SD, Heuser J, Grünewald K, Walther TC. Eisosome proteins assemble into a membrane scaffold. J Cell Biol. 2011 Nov 28; 195(5):889-902.
        View in: PubMed PMC3257569
      69. Casey F, Krogan N, Shields DC, Cagney G. Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs. BMC Syst Biol. 2011; 5:133.
        View in: PubMed PMC3176491
      70. Wang AY, Aristizabal MJ, Ryan C, Krogan NJ, Kobor MS. Key functional regions in the histone variant H2A.Z C-terminal docking domain. Mol Cell Biol. 2011 Sep; 31(18):3871-84.
        View in: PubMed PMC3165728
      71. Fahey ME, Bennett MJ, Mahon C, Jäger S, Pache L, Kumar D, Shapiro A, Rao K, Chanda SK, Craik CS, Frankel AD, Krogan NJ. GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data. BMC Bioinformatics. 2011; 12:298.
        View in: PubMed PMC3213248
      72. Charles GM, Chen C, Shih SC, Collins SR, Beltrao P, Zhang X, Sharma T, Tan S, Burlingame AL, Krogan NJ, Madhani HD, Narlikar GJ. Site-specific acetylation mark on an essential chromatin-remodeling complex promotes resistance to replication stress. Proc Natl Acad Sci U S A. 2011 Jun 28; 108(26):10620-5.
        View in: PubMed PMC3127919
      73. Ryan C, Greene D, Guénolé A, van Attikum H, Krogan NJ, Cunningham P, Cagney G. Improved functional overview of protein complexes using inferred epistatic relationships. BMC Syst Biol. 2011; 5:80.
        View in: PubMed PMC3117733
      74. Temkin P, Lauffer B, Jäger S, Cimermancic P, Krogan NJ, von Zastrow M. SNX27 mediates retromer tubule entry and endosome-to-plasma membrane trafficking of signalling receptors. Nat Cell Biol. 2011 Jun; 13(6):715-21.
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      75. Stewart EV, Nwosu CC, Tong Z, Roguev A, Cummins TD, Kim DU, Hayles J, Park HO, Hoe KL, Powell DW, Krogan NJ, Espenshade PJ. Yeast SREBP cleavage activation requires the Golgi Dsc E3 ligase complex. Mol Cell. 2011 Apr 22; 42(2):160-71.
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      76. Ryan C, Cagney G, Krogan N, Cunningham P, Greene D. Imputing and predicting quantitative genetic interactions in epistatic MAPs. Methods Mol Biol. 2011; 781:353-61.
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      77. 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. Phenotypic landscape of a bacterial cell. Cell. 2011 Jan 7; 144(1):143-56.
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      78. Kapitzky L, Beltrao P, Berens TJ, Gassner N, Zhou C, Wüster A, Wu J, Babu MM, Elledge SJ, Toczyski D, Lokey RS, Krogan NJ. Cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action. Mol Syst Biol. 2010 Dec 21; 6:451.
        View in: PubMed PMC3018166
      79. 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. Functional overlap and regulatory links shape genetic interactions between signaling pathways. Cell. 2010 Dec 10; 143(6):991-1004.
        View in: PubMed
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      83. 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. Purification and characterization of HIV-human protein complexes. Methods. 2011 Jan; 53(1):13-9.
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      84. 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. A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers. Mol Syst Biol. 2010 Jun 8; 6:377.
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      87. He N, Liu M, Hsu J, Xue Y, Chou S, Burlingame A, Krogan NJ, Alber T, Zhou Q. HIV-1 Tat and host AFF4 recruit two transcription elongation factors into a bifunctional complex for coordinated activation of HIV-1 transcription. Mol Cell. 2010 May 14; 38(3):428-38.
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      91. Lenassi M, Cagney G, Liao M, Vaupotic T, Bartholomeeusen K, Cheng Y, Krogan NJ, Plemenitas A, Peterlin BM. HIV Nef is secreted in exosomes and triggers apoptosis in bystander CD4+ T cells. Traffic. 2010 Jan; 11(1):110-22.
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      92. Hannum G, Srivas R, Guénolé A, van Attikum H, Krogan NJ, Karp RM, Ideker T. Genome-wide association data reveal a global map of genetic interactions among protein complexes. PLoS Genet. 2009 Dec; 5(12):e1000782.
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      94. 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. An acetylated form of histone H2A.Z regulates chromosome architecture in Schizosaccharomyces pombe. Nat Struct Mol Biol. 2009 Dec; 16(12):1286-93.
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      95. Collins SR, Weissman JS, Krogan NJ. From information to knowledge: new technologies for defining gene function. Nat Methods. 2009 Oct; 6(10):721-23.
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      96. Khanna M, Van Bakel H, Tang X, Calarco JA, Babak T, Guo G, Emili A, Greenblatt JF, Hughes TR, Krogan NJ, Blencowe BJ. A systematic characterization of Cwc21, the yeast ortholog of the human spliceosomal protein SRm300. RNA. 2009 Dec; 15(12):2174-85.
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      97. Gong Y, Kakihara Y, Krogan N, Greenblatt J, Emili A, Zhang Z, Houry WA. An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell. Mol Syst Biol. 2009; 5:275.
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      99. 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. Host cell factors in HIV replication: meta-analysis of genome-wide studies. PLoS Pathog. 2009 May; 5(5):e1000437.
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      100. Selth LA, Lorch Y, Ocampo-Hafalla MT, Mitter R, Shales M, Krogan NJ, Kornberg RD, Svejstrup JQ. An rtt109-independent role for vps75 in transcription-associated nucleosome dynamics. Mol Cell Biol. 2009 Aug; 29(15):4220-34.
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      101. Wiseman RL, Chin KT, Haynes CM, Stanhill A, Xu CF, Roguev A, Krogan NJ, Neubert TA, Ron D. Thioredoxin-related Protein 32 is an arsenite-regulated Thiol Reductase of the proteasome 19 S particle. J Biol Chem. 2009 May 29; 284(22):15233-45.
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      105. Babu M, Krogan NJ, Awrey DE, Emili A, Greenblatt JF. Systematic characterization of the protein interaction network and protein complexes in Saccharomyces cerevisiae using tandem affinity purification and mass spectrometry. Methods Mol Biol. 2009; 548:187-207.
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      106. 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. A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing. Mol Cell. 2008 Dec 5; 32(5):735-46.
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      107. Kress TL, Krogan NJ, Guthrie C. A single SR-like protein, Npl3, promotes pre-mRNA splicing in budding yeast. Mol Cell. 2008 Dec 5; 32(5):727-34.
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      109. Nagai S, Dubrana K, Tsai-Pflugfelder M, Davidson MB, Roberts TM, Brown GW, Varela E, Hediger F, Gasser SM, Krogan NJ. Functional targeting of DNA damage to a nuclear pore-associated SUMO-dependent ubiquitin ligase. Science. 2008 Oct 24; 322(5901):597-602.
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      110. 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. Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. Science. 2008 Oct 17; 322(5900):405-10.
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      111. Casey FP, Cagney G, Krogan NJ, Shields DC. Optimal stepwise experimental design for pairwise functional interaction studies. Bioinformatics. 2008 Dec 1; 24(23):2733-9.
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      113. Breslow DK, Cameron DM, Collins SR, Schuldiner M, Stewart-Ornstein J, Newman HW, Braun S, Madhani HD, Krogan NJ, Weissman JS. A comprehensive strategy enabling high-resolution functional analysis of the yeast genome. Nat Methods. 2008 Aug; 5(8):711-8.
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      114. Greene D, Cagney G, Krogan N, Cunningham P. Ensemble non-negative matrix factorization methods for clustering protein-protein interactions. Bioinformatics. 2008 Aug 1; 24(15):1722-8.
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      115. Fillingham J, Recht J, Silva AC, Suter B, Emili A, Stagljar I, Krogan NJ, Allis CD, Keogh MC, Greenblatt JF. Chaperone control of the activity and specificity of the histone H3 acetyltransferase Rtt109. Mol Cell Biol. 2008 Jul; 28(13):4342-53.
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      121. Zaharik ML, Lamb SS, Baker KE, Krogan NJ, Neuhard J, Kelln RA. Mutations in yhiT enable utilization of exogenous pyrimidine intermediates in Salmonella enterica serovar Typhimurium. Microbiology. 2007 Aug; 153(Pt 8):2472-82.
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      122. Wyce A, Xiao T, Whelan KA, Kosman C, Walter W, Eick D, Hughes TR, Krogan NJ, Strahl BD, Berger SL. H2B ubiquitylation acts as a barrier to Ctk1 nucleosomal recruitment prior to removal by Ubp8 within a SAGA-related complex. Mol Cell. 2007 Jul 20; 27(2):275-88.
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      126. Laribee RN, Shibata Y, Mersman DP, Collins SR, Kemmeren P, Roguev A, Weissman JS, Briggs SD, Krogan NJ, Strahl BD. CCR4/NOT complex associates with the proteasome and regulates histone methylation. Proc Natl Acad Sci U S A. 2007 Apr 3; 104(14):5836-41.
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      127. 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. Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature. 2007 Apr 12; 446(7137):806-10.
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      128. 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. 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. 2007 Feb 15; 100(3):642-52.
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      129. Collins SR, Kemmeren P, Zhao XC, Greenblatt JF, Spencer F, Holstege FC, Weissman JS, Krogan NJ. Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol Cell Proteomics. 2007 Mar; 6(3):439-50.
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      131. Xiao T, Shibata Y, Rao B, Laribee RN, O'Rourke R, Buck MJ, Greenblatt JF, Krogan NJ, Lieb JD, Strahl BD. The RNA polymerase II kinase Ctk1 regulates positioning of a 5' histone methylation boundary along genes. Mol Cell Biol. 2007 Jan; 27(2):721-31.
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      132. Fillingham J, Keogh MC, Krogan NJ. GammaH2AX and its role in DNA double-strand break repair. Biochem Cell Biol. 2006 Aug; 84(4):568-77.
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      133. Pitre S, Dehne F, Chan A, Cheetham J, Duong A, Emili A, Gebbia M, Greenblatt J, Jessulat M, Krogan N, Luo X, Golshani A. PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs. BMC Bioinformatics. 2006; 7:365.
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      136. 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. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature. 2006 Mar 30; 440(7084):637-43.
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      137. Keogh MC, Mennella TA, Sawa C, Berthelet S, Krogan NJ, Wolek A, Podolny V, Carpenter LR, Greenblatt JF, Baetz K, Buratowski S. The Saccharomyces cerevisiae histone H2A variant Htz1 is acetylated by NuA4. Genes Dev. 2006 Mar 15; 20(6):660-5.
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      138. Maciag K, Altschuler SJ, Slack MD, Krogan NJ, Emili A, Greenblatt JF, Maniatis T, Wu LF. Systems-level analyses identify extensive coupling among gene expression machines. Mol Syst Biol. 2006; 2:2006.0003.
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      139. Cagney G, Alvaro D, Reid RJ, Thorpe PH, Rothstein R, Krogan NJ. Functional genomics of the yeast DNA-damage response. Genome Biol. 2006; 7(9):233.
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      142. 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. Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell. 2005 Nov 18; 123(4):593-605.
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      143. Schuldiner M, Collins SR, Thompson NJ, Denic V, Bhamidipati A, Punna T, Ihmels J, Andrews B, Boone C, Greenblatt JF, Weissman JS, Krogan NJ. Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. Cell. 2005 Nov 4; 123(3):507-19.
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      144. Prather D, Krogan NJ, Emili A, Greenblatt JF, Winston F. Identification and characterization of Elf1, a conserved transcription elongation factor in Saccharomyces cerevisiae. Mol Cell Biol. 2005 Nov; 25(22):10122-35.
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      145. Laribee RN, Krogan NJ, Xiao T, Shibata Y, Hughes TR, Greenblatt JF, Strahl BD. BUR kinase selectively regulates H3 K4 trimethylation and H2B ubiquitylation through recruitment of the PAF elongation complex. Curr Biol. 2005 Aug 23; 15(16):1487-93.
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      146. Hoang T, Peng WT, Vanrobays E, Krogan N, Hiley S, Beyer AL, Osheim YN, Greenblatt J, Hughes TR, Lafontaine DL. Esf2p, a U3-associated factor required for small-subunit processome assembly and compaction. Mol Cell Biol. 2005 Jul; 25(13):5523-34.
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      147. 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. Navigating the chaperone network: an integrative map of physical and genetic interactions mediated by the hsp90 chaperone. Cell. 2005 Mar 11; 120(5):715-27.
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      148. Emre NC, Ingvarsdottir K, Wyce A, Wood A, Krogan NJ, Henry KW, Li K, Marmorstein R, Greenblatt JF, Shilatifard A, Berger SL. Maintenance of low histone ubiquitylation by Ubp10 correlates with telomere-proximal Sir2 association and gene silencing. Mol Cell. 2005 Feb 18; 17(4):585-94.
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      149. 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. The Shwachman-Bodian-Diamond syndrome protein family is involved in RNA metabolism. J Biol Chem. 2005 May 13; 280(19):19213-20.
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      150. 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. Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature. 2005 Feb 3; 433(7025):531-7.
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      151. Ingvarsdottir K, Krogan NJ, Emre NC, Wyce A, Thompson NJ, Emili A, Hughes TR, Greenblatt JF, Berger SL. H2B ubiquitin protease Ubp8 and Sgf11 constitute a discrete functional module within the Saccharomyces cerevisiae SAGA complex. Mol Cell Biol. 2005 Feb; 25(3):1162-72.
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      152. Xiao T, Kao CF, Krogan NJ, Sun ZW, Greenblatt JF, Osley MA, Strahl BD. Histone H2B ubiquitylation is associated with elongating RNA polymerase II. Mol Cell Biol. 2005 Jan; 25(2):637-51.
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      153. Krogan NJ, Lam MH, Fillingham J, Keogh MC, Gebbia M, Li J, Datta N, Cagney G, Buratowski S, Emili A, Greenblatt JF. Proteasome involvement in the repair of DNA double-strand breaks. Mol Cell. 2004 Dec 22; 16(6):1027-34.
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      154. Morrison AJ, Highland J, Krogan NJ, Arbel-Eden A, Greenblatt JF, Haber JE, Shen X. INO80 and gamma-H2AX interaction links ATP-dependent chromatin remodeling to DNA damage repair. Cell. 2004 Dec 17; 119(6):767-75.
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      155. 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. The functional landscape of mouse gene expression. J Biol. 2004; 3(5):21.
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      156. Kim M, Krogan NJ, Vasiljeva L, Rando OJ, Nedea E, Greenblatt JF, Buratowski S. The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II. Nature. 2004 Nov 25; 432(7016):517-22.
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      157. Kong SE, Kobor MS, Krogan NJ, Somesh BP, Søgaard TM, Greenblatt JF, Svejstrup JQ. Interaction of Fcp1 phosphatase with elongating RNA polymerase II holoenzyme, enzymatic mechanism of action, and genetic interaction with elongator. J Biol Chem. 2005 Feb 11; 280(6):4299-306.
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      158. 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. 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. 2004 Sep 14; 101(37):13513-8.
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      159. 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. Exploration of essential gene functions via titratable promoter alleles. Cell. 2004 Jul 9; 118(1):31-44.
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      160. Sawa C, Nedea E, Krogan N, Wada T, Handa H, Greenblatt J, Buratowski S. Bromodomain factor 1 (Bdf1) is phosphorylated by protein kinase CK2. Mol Cell Biol. 2004 Jun; 24(11):4734-42.
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      161. Golshani A, Krogan NJ, Xu J, Pacal M, Yang XC, Ivanov I, Providenti MA, Ganoza MC, Ivanov IG, AbouHaidar MG. 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. 2004 Apr 16; 316(4):978-83.
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      162. Peng WT, Krogan NJ, Richards DP, Greenblatt JF, Hughes TR. ESF1 is required for 18S rRNA synthesis in Saccharomyces cerevisiae. Nucleic Acids Res. 2004; 32(6):1993-9.
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      163. 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. Global mapping of the yeast genetic interaction network. Science. 2004 Feb 6; 303(5659):808-13.
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      164. Baetz KK, Krogan NJ, Emili A, Greenblatt J, Hieter P. 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. Mol Cell Biol. 2004 Feb; 24(3):1232-44.
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      165. 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. High-definition macromolecular composition of yeast RNA-processing complexes. Mol Cell. 2004 Jan 30; 13(2):225-39.
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      166. Kim M, Ahn SH, Krogan NJ, Greenblatt JF, Buratowski S. Transitions in RNA polymerase II elongation complexes at the 3' ends of genes. EMBO J. 2004 Jan 28; 23(2):354-64.
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      167. 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. A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1. Mol Cell. 2003 Dec; 12(6):1565-76.
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      168. Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M. A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science. 2003 Oct 17; 302(5644):449-53.
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      169. 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. A panoramic view of yeast noncoding RNA processing. Cell. 2003 Jun 27; 113(7):919-33.
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      170. 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. Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Mol Cell Biol. 2003 Jun; 23(12):4207-18.
        View in: PubMed PMC427527
      171. Krogan NJ, Dover J, Wood A, Schneider J, Heidt J, Boateng MA, Dean K, Ryan OW, Golshani A, Johnston M, Greenblatt JF, Shilatifard A. The Paf1 complex is required for histone H3 methylation by COMPASS and Dot1p: linking transcriptional elongation to histone methylation. Mol Cell. 2003 Mar; 11(3):721-9.
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      172. Wood A, Krogan NJ, Dover J, Schneider J, Heidt J, Boateng MA, Dean K, Golshani A, Zhang Y, Greenblatt JF, Johnston M, Shilatifard A. Bre1, an E3 ubiquitin ligase required for recruitment and substrate selection of Rad6 at a promoter. Mol Cell. 2003 Jan; 11(1):267-74.
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      173. Krogan NJ, Kim M, Ahn SH, Zhong G, Kobor MS, Cagney G, Emili A, Shilatifard A, Buratowski S, Greenblatt JF. RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach. Mol Cell Biol. 2002 Oct; 22(20):6979-92.
        View in: PubMed PMC139818
      174. Krogan NJ, Dover J, Khorrami S, Greenblatt JF, Schneider J, Johnston M, Shilatifard A. COMPASS, a histone H3 (Lysine 4) methyltransferase required for telomeric silencing of gene expression. J Biol Chem. 2002 Mar 29; 277(13):10753-5.
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      175. Krogan NJ, Greenblatt JF. Characterization of a six-subunit holo-elongator complex required for the regulated expression of a group of genes in Saccharomyces cerevisiae. Mol Cell Biol. 2001 Dec; 21(23):8203-12.
        View in: PubMed PMC99985
      176. Miller T, Krogan NJ, Dover J, Erdjument-Bromage H, Tempst P, Johnston M, Greenblatt JF, Shilatifard A. COMPASS: a complex of proteins associated with a trithorax-related SET domain protein. Proc Natl Acad Sci U S A. 2001 Nov 6; 98(23):12902-7.
        View in: PubMed PMC60797
      177. Krogan NJ, Zaharik ML, Neuhard J, Kelln RA. A combination of three mutations, dcd, pyrH, and cdd, establishes thymidine (Deoxyuridine) auxotrophy in thyA+ strains of Salmonella typhimurium. J Bacteriol. 1998 Nov; 180(22):5891-5.
        View in: PubMed PMC107662
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