Publications

2012

Differential network biology.
Ideker T and Krogan NJ.
Molecular Systems Biology, in press.

2011

Vif hijacks CBFB to degrade APOBEC3G and promote HIV-1 infection.
Jäger S, Kim DY, Hultquist JF, Shindo K, Larue RS, Kwon E, Li M, Anderson BD, Yen L, Stanley D, Mahon C, Kane J, Franks-Skiba K, Cimermancic P, Burlingame A, Sali A, Craik CS, Harris RS, Gross JD, Krogan NJ.
Nature. 2011 Dec 21. doi: 10.1038/nature10693. [Epub ahead of print]
PMID: 22190037

Global landscape of HIV-human protein complexes.
Jäger S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K, Hernandez H, Jang GM, Roth SL, Akiva E, Marlett J, Stephens M, D'Orso I, Fernandes J, Fahey M, Mahon C, O'Donoghue AJ, Todorovic A, Morris JH, Maltby DA, Alber T, Cagney G, Bushman FD, Young JA, Chanda SK, Sundquist WI, Kortemme T, Hernandez RD, Craik CS, Burlingame A, Sali A, Frankel AD, Krogan NJ.
Nature. 2011 Dec 21. doi: 10.1038/nature10719. [Epub ahead of print]
PMID: 22190034

First-In-Class Small Molecule Inhibitors of the Single-strand DNA Cytosine Deaminase APOBEC3G.
Li M, Shandilya S, Carpenter M, Rathore A, Brown W, Perkins A, Harki DA, Solberg J, Hook D, Pandey KK, Parniak MA, Johnson J, Krogan NJ, Somasundaran M, Ali A, Schiffer CA, Harris R.
ACS Chem Biol. 2011 Dec 19. [Epub ahead of print].
PMID: 22181350

Host cell interactome of HIV-1 Rev includes RNA helicases involved in multiple facets of virus production.
Naji S, Ambrus G, Cimermancic P, Reyes JR, Johnson JR, Filbrandt R, Huber MD, Vesely P, Krogan NJ, Yates JR, Saphire AC, Gerace L.
Mol Cell Proteomics. 2011 Dec 15. [Epub ahead of print]
PMID: 22174317

RNA polymerase ii CTD phosphorylation regulates stability of the SET2 methyltransferase and histone H3 DI- and trimethylation at lysine 36.
Fuchs SM, Kizer KO, Braberg H, Krogan NJ, Strahl BD.
J Biol Chem. 2011 Dec 7. [Epub ahead of print].
PMID: 22157004

Eisosome proteins assemble into a membrane scaffold.
Karotki L, Huiskonen JT, Stefan CJ, Ziólkowska NE, Roth R, Surma MA, Krogan NJ, Emr SD, Heuser J, Grünewald K, Walther TC.
J Cell Biol. 2011 Nov 28;195(5):889-902.
PMID: 22123866

Imputing and predicting quantitative genetic interactions in epistatic MAPs.
Ryan C, Cagney G, Krogan NJ, Cunningham P, Greene D.
Methods Mol Biol. 2011;781:353-61.
PMID: 21877290

Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs.
Casey F, Krogan N, Shields DC, Cagney G.
BMC Syst Biol. 2011 Aug 22;5:133.
PMCID: PMC3176491

Key Functional Regions in the Histone Variant H2A.Z C-Terminal Docking Domain.
Wang AY, Aristizabal MJ, Ryan C, Krogan NJ, Kobor MS.
Mol Cell Biol. 2011 Jul 25.
PMID: 21791612

GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data.
Fahey ME, Bennett MJ, Mahon C, Jaeger S, Pache L, Kumar D, Shapiro A, Rao K, Chanda SK, Craik CS, Frankel AD, Krogan NJ.
BMC Bioinformatics. 2011 Jul 22;12(1):298. [Epub ahead of print]
PMCID: PMC3213248

Site-specific acetylation mark on an essential chromatin-remodeling complex promotes resistance to replication stress.
Charles GM, Chen C, Shih SC, Collins SR, Beltrao P, Zhang X, Sharma T, Tan S, Burlingame AL, Krogan NJ, Madhani HD, Narlikar GJ.
Proc Natl Acad Sci U S A. 2011 Jun 28;108(26):10620-5. Epub 2011 Jun 14.
PMCID: PMC3127919

Improved functional overview of protein complexes using inferred epistatic relationships.
Ryan C, Greene D, Guénolé A, van Attikum H, Krogan NJ, Cunningham P, Cagney G.
BMC Syst Biol. 2011 May 23;5(1):80.
PMCID: PMC3117733

SNX27 mediates retromer tubule entry and endosome-to-plasma membrane trafficking of signalling receptors.
Temkin P, Lauffer B, Jäger S, Cimermancic P, Krogan NJ, von Zastrow M.
Nat Cell Biol. 2011 Jun;13(6):717-23. Epub 2011 May 22.
PMCID: PMC3113693

Yeast SREBP cleavage activation requires the Golgi Dsc E3 ligase complex.
Stewart EV, Nwosu CC, Tong Z, Roguev A, Cummins TD, Kim DU, Hayles J, Park HO, Hoe KL, Powell DW, Krogan NJ, Espenshade PJ.
Molecular Cell. 2011 42:160-171.
PMID: 21504829

Phenotypic landscape of a bacterial cell.
Nichols RJ, Sen S, Choo YJ, Beltrao P, Zietek M, Chaba R, Lee S, Kazmierczak KM, Lee KJ, Wong A, Shales M, Lovett S, Winkler ME, Krogan NJ, Typas A, Gross CA.
Cell. 2011 Jan 7;144(1):143-56. Epub 2010 Dec 23.
PMID: 21185072

2010

Cross-species chemogenomic profiling identifies evolutionarily conserved drug mode of action.
Kapitzky L, Beltrao P, Berens T, Gassner N, Zhou C, Wuster A, Wu J, Babu M, Elledge SJ, Toczyski D, Lokey RS, Krogan NJ.
Molecular Systems Biology. 2010, 6: 451.
PMCID: PMC3018166

Functional overlap and regulatory links shape genetic interactions between signaling pathways.
van Wageningen S, Kemmeren P, Lijnzaad P, Margaritis T, Benschop JJ, de Castro IJ, van Leenen D, Groot Koerkamp MJ, Ko CW, Miles AJ, Barbers N, Brok MO, Lenstra TL, Fiedler D, Fokkens L, Aldecoa R, Apweiler E, Taliadouous V, Sameith K, van de Pasch LAL, van Hooff SR, Bakker LV, Krogan NJ, Snel B, Holstege FCP.
Cell. 2010;143: 991-1004.
PMCID: PMC3073509

Rewiring of genetic networks in response to DNA damage.
Bandyopadhyay S, Mehta M, Kuo D, Sung MK, Chuang R, Jaehnig E, Bodenmiller B, Licon K, Copeland W, Shales M, Fiedler D, Dutkowski J, Guenole A, van Attikum H, Shokat KM, Kolodner RD, Huh WH, Aebersold R, Keogh MC, Krogan NJ*, Ideker T*. (*co-corresponding)
Science. 2010;330: 1385-1389.
PMCID: PMC3006187

Epistatic relationships reveal the functional organization of the yeast transcriptional apparatus.
Zheng J, Benschop JJ, Shales M, Kemmeren P, Greenblatt J, Cagney G, Holstege F, Li H, Krogan NJ.
Mol Syst Biol. 2010 Oct 5;6:420.
PMCID: PMC2990640

Individual lysine acetylations on the N-terminus of S. Cerevisiae H2A.Z are highly but not differentially regulated.
Mehta M, Braberg H, Wang S, Lozsa A, Shales M, Solache A, Krogan NJ, Keogh MC.
J Biol Chem. 2010 Dec 17;285(51):39855-65. Epub 2010 Oct 14.
PMCID: PMC3000967

Quantitative genetic interaction mapping using the E-MAP approach.
Collins SR, Roguev A, Krogan NJ.
Methods Enzymol. 2010;470:205-31.
PMCID: PMC2957675

Purification and characterization of HIV-human protein complexes.
Jager S, Gulbahce N, Kane J, He N, Chou S, D'Orso I, Fernandes J, Jang G, Frankel AD, Alber T, Zhou Q, Krogan NJ.
Methods. 2011 Jan;53(1):13-9. Epub 2010 Aug 12.
PMCID: PMC3076283

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 8;6:377.
PMCID: PMC2913282

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.
PMCID: PMC3073498

Quantitative genetic interactions reveal layers of biological modularity.
Beltrao P, Cagney G, Krogan NJ.
Cell. 2010 May 28;141(5):739-45.
PMCID: PMC2946632

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.
PMCID: PMC3085314

The next frontier of systems biology: higher-order and interspecies interactions.
Fischbach MA, Krogan NJ.
Genome Biol. 2010;11(5):208.
PMID: 20441613

Polycomb-like 2 associates with PRC2 and is required for mouse embryonic stem cell commitment.
Walker E, Chang WY, Hunkapiller J, Cagney G, Garcha K, Torchia J, Krogan NJ, Reiter J, Stanford WL.
Cell Stem Cell. 2010; 6(2):153-66.
PMCID: PMC2849004

HIV Nef is secreted in exosomes and triggers apoptosis in bystander CD4+ cells.
Lenassi M, Cagney G, Maofu L, Vaupotic T, Cheng Y, Krogan NJ, Plemenitas A, Matija Peterlin B.
Traffic. 2010 Jan;11(1):110-22.
PMID: 19912576

2009

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;5(12):e1000782.
PMCID: PMC2788232

Towards accurate imputation of quantitative genetic interactions.
Ulitsky I, Krogan NJ, Shamir R.
Genome Biol. 2009;10(12):R140.
PMCID: PMC2812947

From information to knowledge: new technologies for defining gene function.
Collins SR, Weissman JS, Krogan NJ.
Nat Methods. 2009 Oct;6(10):721-23.
PMCID: PMC3066030

A systematic analysis of genetic, physical and functional interactions involving Cwc21, the yeast ortholog of the human spliceosomal protein SRm300.
Khanna M, Van Bakel H, Tang X, Calarco J, Babek T, Guo G, Emili A, Greenblatt J, Hughes TR, Krogan NJ, Blencowe BJ.
RNA. 2009 Dec;15(12):2174-85.
PMCID: PMC2779666

An acetylated form of histone H2A.Z regulates chromosome architecture in Schizosaccharomyces pombe.
Kim HS, Vanoosthuye V, Fillingham J, Roguev A, Wattnv S, Kislinger T, Treye A, Carpenter LR, Bennett CS, Emili A, Greenblatt JF, Hardwick KG, Krogan NJ, Bahler J, Keogh MC.
Nat Struct Mol Biol. 2009 Dec;16(12):1286-93.
PMCID: PMC2788674

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.
PMCID: PMC2691599

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.
PMCID: PMC2710862

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.
PMID: 19521826

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.
PMCID: PMC2682202

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 May 26. [Epub ahead of print]
PMCID: PMC2715805

Thioredoxin related protein 32 is an arsenite-regulated thiol reductase of the proteasome 19S particle.
Wiseman RL, Chin KT, Haynes CM, Stanhill A, Xu CF, Roguev A, Krogan NJ, Neubert TA, Ron D.
J. Biol. Chem. 2009 doi:10.1074/jbc.M109.002121.
PMCID: PMC2685704

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 6;136(5):952-63.
PMCID: PMC2957675

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. Epub 2009 Jan 30.
PMCID: PMC2627940

A complex-based reconstruction of the S. cerevisiae interactome.
Wang H, Kakaradov B, Collins SR, Karotki L, Fiedler D, Shales M, Shokat KM, Walther T, Krogan NJ, Koller D.
Mol Cell Proteomics. 2009 Jan 27. [Epub ahead of print]
PMCID: PMC2690481

2008

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 5;32(5):735-46.
PMCID: PMC2644724

A single SR-like protein, Npl3, promotes pre-mRNA splicing in budding yeast.
Kress TL, Krogan NJ, Guthrie C.
Mol Cell. 2008 Dec 5;32(5):727-34.
PMCID: PMC2677966

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.
PMCID: PMC2614481

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.
PMID: 18948542

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 S, Qu H, Shales M, Park H, Hayles J, Hoe K, Kim D, Ideker T, Grewal S, Weissman J, Krogan NJ.
Science. 2008 Oct 17;322(5900):405-10.
PMCID: PMC2753251

Optimal stepwise experimental design for pairwise functional interaction studies.
Casey FP, Cagney G, Krogan NJ, Shields DC.
Bioinformatics. 2008 Dec 1;24(23):2733-9. Epub 2008 Sep 18.
PMID: 18805797

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.
PMCID: PMC2700713

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.
PMCID: PMC2756093

Ensemble non-negative matrix factorization methods for clustering protein-protein interactions.
Greene D, Cagney G, Krogan N, Cunningham P.
Bioinformatics. 2008 Aug 1;24(15):1722-8.
PMID: 18556670

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.
PMCID: PMC2447148

BAC to the future: functional genomics in mammals.
Roguev A, Krogan NJ.
Nat Methods. 2008 May;5(5):409-15.
PMID: 18446155

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.
PMCID: PMC2289880

2007

Association with the origin recognition complex suggests a novel role for histone acetyltransferase Hat1p/Hat2p.
Suter B, Pogouste O, Guo X, Krogan N, Lewis P, Greenblatt JF, Rine J, Emili A.
BMC Biology. 2007;5:38.
PMCID: PMC2140264

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. Epub 2007 Sep 23.
PMID: 17893680

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.
PMID: 17693258

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. 2007 Aug;153(Pt 8):2472-82.
PMID: 17660412

H2B ubquitylation acts as a barrier to Ctk1 nucleosomal recruitment prior to removal by SALSA-associated Ubp8.
Wyce A, Whelan KA, Xiao T, Walter W, Hughes TR, Krogan NJ, Strahl BD, Berger SL.
Mol Cell. 2007 Jul 20;27(2):275-88.
PMID: 17643376

Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast.
Gupta R, Kus B, Fladd C, Wasmuth J, Tonikian R, Sindhu D, Krogan NJ, Parkinson J, Rotin D.
Mol Syst Biol. 2007;3:116. Epub 2007 Jun 5.
PMCID: PMC1911201

SIN-fully silent. HDAC complexes in S. pombe.
Roguev A, Krogan NJ.
Nat Struct Mol Biol. 2007 May;14(5):358-9.
PMID: 17473877

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. Epub 2007 Mar 27.
PMCID: PMC1847942

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 USA. 2007 Apr 3;104(14):5836-41. Epub 2007 Mar 26.
PMCID: PMC1851578

Towards 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. Epub 2007 Jan 2.
PMID: 17200106

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 Feb 21.
PMID: 17314980

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.
PMID: 16983699

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. Epub 2006 Nov 6.
PMCID: PMC1800795

2006

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.
PMID: 17101447

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.
PMCID: PMC1794544

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. Review.
PMID: 16936829

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.
PMCID: PMC1557541

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.
PMCID: PMC1779568

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. Epub 2006 Jan 17.
PMCID: PMC1681477

Signals and systems.
Krogan NJ, Hughes TR.
Genome Biol. 2006;7(4):313. Epub 2006 Apr 25. No abstract available.
PMCID: PMC1557984

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, Peregrin-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.
PMID: 16554755

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.
PMID: 16564010

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.
PMCID: PMC1413285

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. Epub 2005 Nov 20.
PMID: 16299494

2005

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.
PMID: 16286008

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 4;123(3):507-19.
PMID: 16269340

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.
PMCID: PMC1280281

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.
PMID: 16040246

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.
PMCID: PMC1156982

The Shwachman-Bodian-Diamond syndrome protein family is involved in RNA metabolism.
Savchenko A, Krogan N, Cort JR, Evdokimova E, Lew JM, Yee AA, Sanchez-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. Epub 2005 Feb 8.
PMID: 15701634

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.
PMID: 15766533

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.
PMID: 15721261

Interaction network containing conserved and essential protein complexes in Escherichia coli.
Butland G, Peregrin-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 3;433(7025):531-7.
PMID: 15690043

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, Sogaard TM, Greenblatt JF, Svejstrup JQ.
J Biol Chem. 2005 Feb 11;280(6):4299-306. Epub 2004 Nov 24.
PMID: 15563457

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.
PMCID: PMC544016

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.
PMCID: PMC543430

2004

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.
PMID: 15610744

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.
PMID: 15607974

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. Epub 2004 Dec 6.
PMCID: PMC549719

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. Erratum in: Nature. 2005 Feb 10;433(7026):661.
PMID: 15565157

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. Epub 2004 Sep 7. Erratum in: Proc Natl Acad Sci U S A. 2006 Apr 18;103(16):6410.
PMCID: PMC518788

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 9;118(1):31-44.
PMID: 15242642

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.
PMCID: PMC416403

ESF1 is required for 18S rRNA synthesis in Saccharomyces cerevisiae.
Peng WT, Krogan NJ, Richards DP, Greenblatt JF, Hughes TR.
Nucleic Acids Res. 2004 Mar 31;32(6):1993-9. Print 2004.
PMCID: PMC390369

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.
PMID: 15044080

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, Menard 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 6;303(5659):808-13.
PMID: 14764870

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.
PMCID: PMC321452

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.
PMID: 14759368

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. Epub 2004 Jan 22.
PMCID: PMC1271760

2003

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.
PMID: 14690608

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.
PMID: 14564010

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.
PMID: 12837249

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.
PMCID: PMC427527

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.
PMID: 12667454

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.
PMID: 12535539

2002

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.
PMCID: PMC139818

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. Epub 2002 Jan 22.
PMID: 11805083

2001

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.
PMCID: PMC99985

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 USA. 2001 Nov 6;98(23):12902-7. Epub 2001 Oct 30. Erratum in: Proc Natl Acad Sci U S A 2001 Dec 18;98(26):15393-4.
PMCID: PMC60797

1998

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.
PMCID: PMC107662