Nevan Krogan, PhD
Professor
Cellular Molecular Pharmacology
School of Medicine
Dr. Krogan was born and raised in Regina, Saskatchewan, Canada, obtained his undergraduate degree from the University of Regina and his PhD from the University of Toronto. Dr. Krogan’s lab at UCSF focuses on developing and applying quantitative, systematic proteomic and genetic approaches to study complex biological and biomedical problems. At present time, the Krogan group is focused on studying cancer, infectious disease and psychiatric disorders.
Awards
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- Elected to EMBO, European Molecular Biology Organization, 2022
- France Legion of Honor, President of the French Republic, 2021
- Highly Cited Researchers 2020 - ranked in top 1% of citations for field and year, Clarivate Web of Science, 2020
- Excellence in Research Award, Laboratory of Genomics Research, 2020
- The Roddenberry Prize, Roddenberry Foundation, 2017
- Blavatnik Scholar, Blavatnik Foundation, 2015-2016
- Top 40 Under 40, Cell, 2014
- Distinguished Alumni Award, University of Regina, 2012
- Keck Distinguished Young Scholar, W. M. Keck Foundation, 2009-2014
- Searle Scholar, Searle Foundation, 2009-2012
- Top 25 authors of high-impact papers in molecular biology and genetics from 2002 to 2006, Sciencewatch.com, 2008
- L. W. Macpherson Microbiology Award, University of Toronto, 2005
- Hannah Farkas-Himsley and Alexander Memorial Award, University of Toronto, 2004
- CIHR Doctoral Fellowship, Canadian Institute of Health Research, 2001-2004
- PGS-B Award, Natural Sciences and Engineering Research Council, 1999-2001
- Merit Award, Society of Chemical Industry, 1997
- Studentship, Canadian Cancer Society, 1995-1996
Education & Training
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- PhD Medical Genetics University of Toronto 06/2006
- MSc Biology University of Regina 08/1999
- BSc (Hons) Biochemistry University of Regina 05/1997
Websites
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- @@kroganlab?lang=en on Twitter (twitter.com)
- Krogan Lab at UCSF (kroganlab.ucsf.edu)
- Host Pathogen Map Initiative (hpmi.ucsf.edu)
- Quantitative Biosciences Institue (qbi.ucsf.edu)
- Cancer Cell Map Initiative (ccmi.org)
- HARC Center (harc.ucsf.edu)
- Psychiatric Cell Map Initiative (pcmi.ucsf.edu)
Grants and Projects
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- The Cancer Cell Map Initiative v2.0, NIH, 2022-2027
- HARC: HIV accessory and regulatory complexes, NIH, 2022-2027
- Host Pathogen Variation & TB Pathogenesis, NIH, 2021-2026
- Building an Interpretable Genomic Translator Using Maps of Cell Architecture, NIH, 2022-2025
- QCRG Pandemic Response Program, NIH, 2022-2025
- Childhood ?Omics? and Mycobacterium tuberculosis-derived BiOsignatures (COMBO) for TB diagnosis in high HIV prevalence settings, NIH, 2020-2025
- Combinatorial Regulation of Gene Networks During Cardiac Development and Disease, NIH, 2019-2024
- Proteomic and Genetic Approaches Defining Apolipoprotein E4 Neuropathologic Mechanisms, NIH, 2019-2024
- Novel VP30-host Interactions that Negatively Regulate Ebola Virus Infection, NIH, 2019-2024
- The Psychiatric Cell Map Initiative: Connecting Genomics, Subcellular Networks, and Higher Order Phenotypes, NIH, 2018-2023
- Fluomics: The Next Generation, NIH, 2018-2022
- HARC Center: HIV Accessory and Regulatory Complexes, NIH, 2007-2022
- HARC Center: HIV Accessory and Regulatory Complexes, NIH, 2007-2022
- HPMI: Host Pathogen Mapping Initiative, NIH, 2018-2022
- Research Center for Cancer Systems Biology: Cancer Cell Map Initiative, NIH, 2017-2022
- CasCUT&RUN: An in vivo method to analyze locus-specific protein complexes driving transcription of target genes in cancer, NIH, 2019-2022
- Linking tau proteostasis with neuronal activity in FTD, NIH, 2016-2021
- Intracellular pathogens and innate immunity, NIH, 2004-2021
- Discovery of novel, ubiquitin-regulated mechanisms of TB control by macrophages, NIH, 2015-2021
- Decoding the Chlamydia inclusion membrane protein-host protein interactome, NIH, 2015-2020
- Dengue Human Immunology Project Consortium (DHIPC), NIH, 2015-2020
- Exploring Design Principles of Cellular Control Circuits, NIH, 2010-2019
- Physical and Genetic Interaction Landscape of the Tyrosine Kinome, NIH, 2014-2019
- Comparative Analysis of Genetic Interaction Networks, NIH, 2008-2019
- Transcriptional Networks During Cardiac Differentiation, NIH, 2007-2018
- Multiscale analysis of influenza host-pathogen interactions: Fluomics, NIH, 2013-2018
- Proteomics Analysis of Host-Pathogen Interactions in Histoplasma, NIH, 2015-2017
- Protein homeostasis mechanisms underlying enterovirus replication and evolution, NIH, 2011-2016
- Integrating computation and genetics to quantify specificity in protein networks, NIH, 2011-2016
- Global innate immune responses to HIV-1 infection, NIH, 2010-2015
- Bio-Organic Biomedical Mass Spectrometry Resource, NIH, 1982-2015
- Genetic Analysis of the Nucleosome and RNA Polymerase II: A Systems Approach, NIH, 2008-2014
- Global Genetic Interaction Profiling in Prokaryotes, NIH, 2008-2012
Publications (413)
Top publication keywords:
Epistasis, GeneticGenes, FungalGene Regulatory NetworksSchizosaccharomycesGenetics, MicrobialSystems BiologyHistonesSaccharomyces cerevisiae ProteinsHost-Pathogen InteractionsProtein Interaction MapsGene Expression Regulation, Fungalvif Gene Products, Human Immunodeficiency VirusUbiquitin-Protein LigasesSaccharomyces cerevisiaeProtein Interaction Mapping
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A protein network map of head and neck cancer reveals PIK3CA mutant drug sensitivity.
Science (New York, N.Y.) 2021 Swaney DL, Ramms DJ, Wang Z, Park J, Goto Y, Soucheray M, Bhola N, Kim K, Zheng F, Zeng Y, McGregor M, Herrington KA, O'Keefe R, Jin N, VanLandingham NK, Foussard H, Von Dollen J, Bouhaddou M, Jimenez… -
Protein Interaction Mapping Identifies RBBP6 as a Negative Regulator of Ebola Virus Replication.
Cell 2018 Batra J, Hultquist JF, Liu D, Shtanko O, Von Dollen J, Satkamp L, Jang GM, Luthra P, Schwarz TM, Small GI, Arnett E, Anantpadma M, Reyes A, Leung DW, Kaake R, Haas P, Schmidt CB, Schlesinger LS, … -
ATG7(2) Interacts With Metabolic Proteins and Regulates Central Energy Metabolism.
Traffic (Copenhagen, Denmark) 2024 Ostacolo K, López García de Lomana A, Larat C, Hjaltalin V, Holm KY, Hlynsdóttir SS, Soucheray M, Sooman L, Rolfsson O, Krogan NJ, Steingrimsson E, Swaney DL, Ogmundsdottir MH -
Protein interaction map of APOBEC3 enzyme family reveals deamination-independent role in cellular function.
Molecular & cellular proteomics : MCP 2024 Jang GM, Annan Sudarsan AK, Shayeganmehr A, Prando Munhoz E, Lao R, Gaba A, Granadillo Rodríguez M, Love RP, Polacco BJ, Zhou Y, Krogan NJ, Kaake RM, Chelico L -
Profiling the proximal proteome of the activated μ-opioid receptor.
Nature chemical biology 2024 Polacco BJ, Lobingier BT, Blythe EE, Abreu N, Khare P, Howard MK, Gonzalez-Hernandez AJ, Xu J, Li Q, Novy B, Naing ZZC, Shoichet BK, Coyote-Maestas W, Levitz J, Krogan NJ, Von Zastrow M, Hüttenhain R
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CRISPR-Cas9 screen of E3 ubiquitin ligases identifies TRAF2 and UHRF1 as regulators of HIV latency in primary human T cells.
mBio 2024 Rathore U, Haas P, Easwar Kumar V, Hiatt J, Haas KM, Bouhaddou M, Swaney DL, Stevenson E, Zuliani-Alvarez L, McGregor MJ, Turner-Groth A, Ochieng' Olwal C, Bediako Y, Braberg H, Soucheray M, Ott M, … -
Spatial control of sensory adaptation modulates mechanosensing in Pseudomonas aeruginosa.
bioRxiv : the preprint server for biology 2024 Patino R, Kühn MJ, Macmillan H, Inclan YF, Chavez I, Von Dollen J, Johnson JR, Swaney DL, Krogan NJ, Persat A, Engel JN -
The Chlamydia trachomatis Inc Tri1 interacts with TRAF7 to displace native TRAF7 interacting partners.
bioRxiv : the preprint server for biology 2024 Herrera CM, McMahon E, Swaney DL, Sherry J, Pha K, Adams-Boone K, Johnson JR, Krogan NJ, Stevers M, Solomon D, Elwell C, Engel J -
A foundational atlas of autism protein interactions reveals molecular convergence.
bioRxiv : the preprint server for biology 2024 Wang B, Vartak R, Zaltsman Y, Naing ZZC, Hennick KM, Polacco BJ, Bashir A, Eckhardt M, Bouhaddou M, Xu J, Sun N, Lasser MC, Zhou Y, McKetney J, Guiley KZ, Chan U, Kaye JA, Chadha N, Cakir M, Gordon M,… -
Protein interaction map of APOBEC3 enzyme family reveals deamination-independent role in cellular function.
bioRxiv : the preprint server for biology 2024 Jang GM, Sudarsan AKA, Shayeganmehr A, Munhoz EP, Lao R, Gaba A, Rodríguez MG, Love RP, Polacco BJ, Zhou Y, Krogan NJ, Kaake RM, Chelico L -
Epigenetic reprogramming shapes the cellular landscape of schwannoma.
Nature communications 2024 Liu SJ, Casey-Clyde T, Cho NW, Swinderman J, Pekmezci M, Dougherty MC, Foster K, Chen WC, Villanueva-Meyer JE, Swaney DL, Vasudevan HN, Choudhury A, Pak J, Breshears JD, Lang UE, Eaton CD, Hiam-Galvez… -
Cross-family small GTPase ubiquitination by the intracellular pathogen Legionella pneumophila.
Molecular biology of the cell 2023 Steinbach A, Bhadkamkar V, Jimenez-Morales D, Stevenson E, Jang GM, Krogan NJ, Swaney DL, Mukherjee S -
Molecular determinants of the crosstalk between endosomal microautophagy and chaperone-mediated autophagy.
Cell reports 2023 Krause GJ, Kirchner P, Stiller B, Morozova K, Diaz A, Chen KH, Krogan NJ, Agullo-Pascual E, Clement CC, Lindenau K, Swaney DL, Dilipkumar S, Bravo-Cordero JJ, Santambrogio L, Cuervo AM -
A foundational atlas of autism protein interactions reveals molecular convergence
BioRxiv 2023 Wang B, Vartak R, Zaltsman Y, Naing ZZC, Hennick KM, Polacco BJ, Bashir A, Eckhardt M, Bouhaddou M, Xu J, Sun N, Lasser M, Zhou Y, Guiley KZ, Chan U, Kaye JA, Khare P, Drake S, Drury V, Burke DF, … -
Hepatitis C virus infects and perturbs liver stem cells.
mBio 2023 Meyers NL, Ashuach T, Lyons DE, Khalid MM, Simoneau CR, Erickson AL, Bouhaddou M, Nguyen TT, Kumar GR, Taha TY, Natarajan V, Baron JL, Neff N, Zanini F, Mahmoudi T, Quake SR, Krogan NJ, Cooper S, … -
De novo protein identification in mammalian sperm using in situ cryoelectron tomography and AlphaFold2 docking.
Cell 2023 Chen Z, Shiozaki M, Haas KM, Skinner WM, Zhao S, Guo C, Polacco BJ, Yu Z, Krogan NJ, Lishko PV, Kaake RM, Vale RD, Agard DA -
A Legionella toxin exhibits tRNA mimicry and glycosyl transferase activity to target the translation machinery and trigger a ribotoxic stress response.
Nature cell biology 2023 Subramanian A, Wang L, Moss T, Voorhies M, Sangwan S, Stevenson E, Pulido EH, Kwok S, Chalkley RJ, Li KH, Krogan NJ, Swaney DL, Burlingame AL, Floor SN, Sil A, Walter P, Mukherjee S -
The multi-lineage transcription factor ISL1 controls cardiomyocyte cell fate through interaction with NKX2.5.
Stem cell reports 2023 Maven BEJ, Gifford CA, Weilert M, Gonzalez-Teran B, Hüttenhain R, Pelonero A, Ivey KN, Samse-Knapp K, Kwong W, Gordon D, McGregor M, Nishino T, Okorie E, Rossman S, Costa MW, Krogan NJ, Zeitlinger J, … -
High-throughput chemogenetic drug screening reveals PKC-RhoA/PKN as a targetable signaling vulnerability in GNAQ-driven uveal melanoma.
Cell reports. Medicine 2023 Arang N, Lubrano S, Ceribelli M, Rigiracciolo DC, Saddawi-Konefka R, Faraji F, Ramirez SI, Kim D, Tosto FA, Stevenson E, Zhou Y, Wang Z, Bogomolovas J, Molinolo AA, Swaney DL, Krogan NJ, Yang J, Coma … -
Lysosomal proteomics reveals mechanisms of neuronal apoE4associated lysosomal dysfunction.
bioRxiv : the preprint server for biology 2023 Krogsaeter EK, McKetney J, Marquez A, Cakir Z, Stevenson E, Jang GM, Rao A, Zhou A, Huang Y, Krogan NJ, Swaney DL -
Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets.
Nature communications 2023 Haas KM, McGregor MJ, Bouhaddou M, Polacco BJ, Kim EY, Nguyen TT, Newton BW, Urbanowski M, Kim H, Williams MAP, Rezelj VV, Hardy A, Fossati A, Stevenson EJ, Sukerman E, Kim T, Penugonda S, Moreno E, … -
Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis.
Cell host & microbe 2023 Kehrer T, Cupic A, Ye C, Yildiz S, Bouhaddou M, Crossland NA, Barrall EA, Cohen P, Tseng A, Çagatay T, Rathnasinghe R, Flores D, Jangra S, Alam F, Mena I, Aslam S, Saqi A, Rutkowska M, Ummadi MR, … -
SARS-CoV-2 variants evolve convergent strategies to remodel the host response.
Cell 2023 Bouhaddou M, Reuschl AK, Polacco BJ, Thorne LG, Ummadi MR, Ye C, Rosales R, Pelin A, Batra J, Jang GM, Xu J, Moen JM, Richards AL, Zhou Y, Harjai B, Stevenson E, Rojc A, Ragazzini R, Whelan MVX, … -
A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication in vivo.
PLoS pathogens 2023 Taha TY, Suryawanshi RK, Chen IP, Correy GJ, McCavitt-Malvido M, O'Leary PC, Jogalekar MP, Diolaiti ME, Kimmerly GR, Tsou CL, Gascon R, Montano M, Martinez-Sobrido L, Krogan NJ, Ashworth A, Fraser JS,… -
Next-generation proteomics for quantitative Jumbophage-bacteria interaction mapping.
Nature communications 2023 Fossati A, Mozumdar D, Kokontis C, Mèndez-Moran M, Nieweglowska E, Pelin A, Li Y, Guo B, Krogan NJ, Agard DA, Bondy-Denomy J, Swaney DL -
Network modeling suggests HIV infection phenocopies PI3K-AKT pathway mutations to enhance HPV-associated cervical cancer.
Molecular omics 2023 Olwal CO, Fabius JM, Zuliani-Alvarez L, Eckhardt M, Kyei GB, Quashie PK, Krogan NJ, Bouhaddou M, Bediako Y -
Cross-family small GTPase ubiquitination by the intracellular pathogen Legionella pneumophila.
bioRxiv : the preprint server for biology 2023 Steinbach AM, Bhadkamkar VL, Jimenez-Morales D, Stevenson E, Jang GM, Krogan NJ, Swaney DL, Mukherjee S -
Functional analysis of a common BAG3 allele associated with protection from heart failure
Nature Cardiovascular Research 2023 Perez-Bermejo JA, Judge LM, Jensen CL, Wu K, Watry HL, Truong A, Ho JJ, Carter M, Runyon WV, Kaake RM, Pulido EH, Mandegar MA, Swaney DL, So P-L, Krogan NJ & Conklin BR -
Deficiency in Galectin-3, -8, and -9 impairs immunity to chronic Mycobacterium tuberculosis infection but not acute infection with multiple intracellular pathogens.
PLoS pathogens 2023 Morrison HM, Craft J, Rivera-Lugo R, Johnson JR, Golovkine GR, Bell SL, Dodd CE, Van Dis E, Beatty WL, Margolis SR, Repasy T, Shaker I, Lee AY, Vance RE, Stanley SA, Watson RO, Krogan NJ, Portnoy DA, … -
Structural insights into regulation of the PEAK3 pseudokinase scaffold by 14-3-3.
Nature communications 2023 Torosyan H, Paul MD, Forget A, Lo M, Diwanji D, Pawlowski K, Krogan NJ, Jura N, Verba KA -
Lessons learned for pandemic preparedness: A collaborative network is imperative.
Cell host & microbe 2023 Fabius JM, Krogan NJ -
Defining blood-induced microglia functions in neurodegeneration through multiomic profiling.
Nature immunology 2023 Mendiola AS, Yan Z, Dixit K, Johnson JR, Bouhaddou M, Meyer-Franke A, Shin MG, Yong Y, Agrawal A, MacDonald E, Muthukumar G, Pearce C, Arun N, Cabriga B, Meza-Acevedo R, Alzamora MDPS, Zamvil SS, Pico… -
Dengue virus NS5 degrades ERC1 during infection to antagonize NF-kB activation.
Proceedings of the National Academy of Sciences of the United States of America 2023 Gonzalez Lopez Ledesma MM, Costa Navarro G, Pallares HM, Paletta A, De Maio F, Iglesias NG, Gebhard L, Oviedo Rouco S, Ojeda DS, de Borba L, Giraldo M, Rajsbaum R, Ceballos A, Krogan NJ, Shah PS, … -
A multi-scale map of protein assemblies in the DNA damage response.
Cell systems 2023 Kratz A, Kim M, Kelly MR, Zheng F, Koczor CA, Li J, Ono K, Qin Y, Churas C, Chen J, Pillich RT, Park J, Modak M, Collier R, Licon K, Pratt D, Sobol RW, Krogan NJ, Ideker T -
Current proteomics methods applicable to dissecting the DNA damage response.
NAR cancer 2023 Muralidharan M, Krogan NJ, Bouhaddou M, Kim M -
A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication and pathogenesis in vivo.
bioRxiv : the preprint server for biology 2023 Taha TY, Suryawanshi RK, Chen IP, Correy GJ, O'Leary PC, Jogalekar MP, McCavitt-Malvido M, Diolaiti ME, Kimmerly GR, Tsou CL, Martinez-Sobrido L, Krogan NJ, Ashworth A, Fraser JS, Ott M -
An automated proximity proteomics pipeline for subcellular proteome and protein interaction mapping.
bioRxiv : the preprint server for biology 2023 Zhong X, Li Q, Polacco BJ, Patil T, DiBerto JF, Vartak R, Xu J, Marley A, Foussard H, Roth BL, Eckhardt M, Von Zastrow M, Krogan NJ, Hüttenhain R -
Quantitative Proteomic Analysis Reveals apoE4-Dependent Phosphorylation of the Actin-Regulating Protein VASP.
Molecular & cellular proteomics : MCP 2023 Cakir Z, Lord SJ, Zhou Y, Jang GM, Polacco BJ, Eckhardt M, Jimenez-Morales D, Newton BW, Orr AL, Johnson JR, da Cruz A, Mullins RD, Krogan NJ, Mahley RW, Swaney DL -
MerlinS13 phosphorylation controls meningioma Wnt signaling and magnetic resonance imaging features.
Research square 2023 Eaton C, Avalos L, Liu SJ, Casey-Clyde T, Bisignano P, Lucas CH, Stevenson E, Choudhury A, Vasudevan H, Magill S, Krogan N, Villanueva-Meyer J, Swaney D, Raleigh D -
Next-generation interaction proteomics for quantitative Jumbophage-bacteria interaction mapping.
bioRxiv : the preprint server for biology 2023 Fossati A, Mozumdar D, Kokontis C, Mèndez-Moran M, Nieweglowska E, Pelin A, Li Y, Guo B, Krogan NJ, Agard DA, Bondy-Denomy J, Swaney DL -
Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13.
Nature structural & molecular biology 2023 Kim SK, Dickinson MS, Finer-Moore J, Guan Z, Kaake RM, Echeverria I, Chen J, Pulido EH, Sali A, Krogan NJ, Rosenberg OS, Stroud RM -
Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13.
bioRxiv : the preprint server for biology 2023 Kim SK, Dickinson MS, Finer-Moore J, Guan Z, Kaake RM, Echeverria I, Chen J, Pulido EH, Sali A, Krogan NJ, Rosenberg OS, Stroud RM -
Oncogenic PKA signaling increases c-MYC protein expression through multiple targetable mechanisms.
eLife 2023 Chan GKL, Maisel S, Hwang YC, Pascual BC, Wolber RRB, Vu P, Patra KC, Bouhaddou M, Kenerson HL, Lim HC, Long D, Yeung RS, Sethupathy P, Swaney DL, Krogan NJ, Turnham RE, Riehle KJ, Scott JD, Bardeesy … -
Nuclear accumulation of host transcripts during Zika Virus Infection.
PLoS pathogens 2023 Leon KE, Khalid MM, Flynn RA, Fontaine KA, Nguyen TT, Kumar GR, Simoneau CR, Tomar S, Jimenez-Morales D, Dunlap M, Kaye J, Shah PS, Finkbeiner S, Krogan NJ, Bertozzi C, Carette JE, Ott M -
Workshop-based learning and networking: a scalable model for research capacity strengthening in low- and middle-income countries.
Global health action 2022 Perier C, Nasinghe E, Charles I, Ssetaba LJ, Ahyong V, Bangs D, Beatty PR, Czudnochowski N, Diallo A, Dugan E, Fabius JM, Fong Baker H, Gardner J, Isaacs S, Joanah B, Kalantar K, Kateete D, Knight M, … -
How can systems approaches help us understand and treat infectious disease?
Cell systems 2022 Kuchina A, Yang J, Aldridge B, Janes KA, Subramanian N, Krogan NJ, Bouhaddou M, Einav S, Papin J, Germain RN -
Quantitative proteomic analysis reveals apoE4-dependent phosphorylation of the actin regulating protein VASP.
Alzheimer's & Dementia 2022 Zeynep Cakir, Benjamin Polacco, Nevan J Krogan, Robert W Mahley, Danielle L Swaney -
Abstract B016: Inhibition of KRASG12C in colon cancer illustrates a link between beta-catenin, WNK, and the GID complex.
Cancer Research 2022 Kasturi Nayak, Yeonjoo Hwang, LeeAnn Wang, Danielle L. Swaney, Nevan J. Krogan, John D. Gordan -
Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis.
bioRxiv : the preprint server for biology 2022 Kehrer T, Cupic A, Ye C, Yildiz S, Bouhhadou M, Crossland NA, Barrall E, Cohen P, Tseng A, Çagatay T, Rathnasinghe R, Flores D, Jangra S, Alam F, Mena N, Aslam S, Saqi A, Marin A, Rutkowska M, Ummadi … -
EPCO-01. EPIGENETIC REPROGRAMMING SHAPES THE MOLECULAR AND CELLULAR LANDSCAPE OF SCHWANNOMA.
Neuro-Oncology 2022 S John Liu, Tim Casey-Clyde, Jason Swinderman, Nam Woo Cho, Harish Vasudevan, Kyla Foster, Melike Pekmezci, William Chen, Javier Villanueva-Meyer, Kamir J Hiam-Galvez, Danielle Swaney, Abrar Choudhury… -
Resistance to ATR Inhibitors Is Mediated by Loss of the Nonsense-Mediated Decay Factor UPF2.
Cancer research 2022 O'Leary PC, Chen H, Doruk YU, Williamson T, Polacco B, McNeal AS, Shenoy T, Kale N, Carnevale J, Stevenson E, Quigley DA, Chou J, Feng FY, Swaney DL, Krogan NJ, Kim M, Diolaiti ME, Ashworth A -
A balancing act: interactions within NuA4/TIP60 regulate picNuA4 function in Saccharomyces cerevisiae and humans.
Genetics 2022 Lu PYT, Kirlin AC, Aristizabal MJ, Brewis HT, Lévesque N, Setiaputra DT, Avvakumov N, Benschop JJ, Groot Koerkamp M, Holstege FCP, Krogan NJ, Yip CK, Côté J, Kobor MS -
Low expression of EXOSC2 protects against clinical COVID-19 and impedes SARS-CoV-2 replication.
Life science alliance 2022 Moll T, Odon V, Harvey C, Collins MO, Peden A, Franklin J, Graves E, Marshall JN, Dos Santos Souza C, Zhang S, Castelli L, Hautbergue G, Azzouz M, Gordon D, Krogan N, Ferraiuolo L, Snyder MP, Shaw PJ,… -
Reduced endosomal microautophagy activity in aging associates with enhanced exocyst-mediated protein secretion.
Aging cell 2022 Krause GJ, Diaz A, Jafari M, Khawaja RR, Agullo-Pascual E, Santiago-Fernández O, Richards AL, Chen KH, Dmitriev P, Sun Y, See SK, Abdelmohsen K, Mazan-Mamczarz K, Krogan NJ, Gorospe M, Swaney DL, … -
SIRT5 is a proviral factor that interacts with SARS-CoV-2 Nsp14 protein.
PLoS pathogens 2022 Walter M, Chen IP, Vallejo-Gracia A, Kim IJ, Bielska O, Lam VL, Hayashi JM, Cruz A, Shah S, Soveg FW, Gross JD, Krogan NJ, Jerome KR, Schilling B, Ott M, Verdin E -
Signaling snapshots of a serotonin receptor activated by the prototypical psychedelic LSD.
Neuron 2022 Cao C, Barros-Álvarez X, Zhang S, Kim K, Dämgen MA, Panova O, Suomivuori CM, Fay JF, Zhong X, Krumm BE, Gumpper RH, Seven AB, Robertson MJ, Krogan NJ, Hüttenhain R, Nichols DE, Dror RO, Skiniotis G, … -
CCL2: a Chemokine Potentially Promoting Early Seeding of the Latent HIV Reservoir.
mBio 2022 Packard TA, Schwarzer R, Herzig E, Rao D, Luo X, Egedal JH, Hsiao F, Widera M, Hultquist JF, Grimmett ZW, Messer RJ, Krogan NJ, Deeks SG, Roan NR, Dittmer U, Hasenkrug KJ, Greene WC -
Structure-function analysis of enterovirus protease 2A in complex with its essential host factor SETD3.
Nature communications 2022 Peters CE, Schulze-Gahmen U, Eckhardt M, Jang GM, Xu J, Pulido EH, Bardine C, Craik CS, Ott M, Gozani O, Verba KA, Hüttenhain R, Carette JE, Krogan NJ -
Correction: Cross-talk Signaling between HER3 and HPV16 E6 and E7 Mediates Resistance to PI3K Inhibitors in Head and Neck Cancer.
Cancer research 2022 Brand TM, Hartmann S, Bhola NE, Li H, Zeng Y, O'Keefe RA, Ranall MV, Bandyopadhyay S, Soucheray M, Krogan NJ, Kemp C, Duvvuri U, LaVallee T, Johnson DE, Ozbun MA, Bauman JE, Grandis JR -
Editor's Note: Cross-talk Signaling between HER3 and HPV16 E6 and E7 Mediates Resistance to PI3K Inhibitors in Head and Neck Cancer.
Cancer research 2022 Brand TM, Hartmann S, Bhola NE, Li H, Zeng Y, O'Keefe RA, Ranall MV, Bandyopadhyay S, Soucheray M, Krogan NJ, Kemp C, Duvvuri U, LaVallee T, Johnson DE, Ozbun MA, Bauman JE, Grandis JR -
Transcription Factor GATA4 Regulates Cell Type-Specific Splicing Through Direct Interaction With RNA in Human Induced Pluripotent Stem Cell-Derived Cardiac Progenitors.
Circulation 2022 Zhu L, Choudhary K, Gonzalez-Teran B, Ang YS, Thomas R, Stone NR, Liu L, Zhou P, Zhu C, Ruan H, Huang Y, Jin S, Pelonero A, Koback F, Padmanabhan A, Sadagopan N, Hsu A, Costa MW, Gifford CA, van … -
A Whole-Genome CRISPR Screen Identifies AHR Loss as a Mechanism of Resistance to a PARP7 Inhibitor.
Molecular cancer therapeutics 2022 Chen H, Diolaiti ME, O'Leary PC, Rojc A, Krogan NJ, Kim M, Ashworth A -
Viral E protein neutralizes BET protein-mediated post-entry antagonism of SARS-CoV-2.
Cell reports 2022 Chen IP, Longbotham JE, McMahon S, Suryawanshi RK, Khalid MM, Taha TY, Tabata T, Hayashi JM, Soveg FW, Carlson-Stevermer J, Gupta M, Zhang MY, Lam VL, Li Y, Yu Z, Titus EW, Diallo A, Oki J, Holden K, … -
DLX1 and the NuRD complex cooperate in enhancer decommissioning and transcriptional repression.
Development (Cambridge, England) 2022 Price JD, Lindtner S, Ypsilanti A, Binyameen F, Johnson JR, Newton BW, Krogan NJ, Rubenstein JLR -
Meningioma DNA methylation groups identify biological drivers and therapeutic vulnerabilities.
Nature genetics 2022 Choudhury A, Magill ST, Eaton CD, Prager BC, Chen WC, Cady MA, Seo K, Lucas CG, Casey-Clyde TJ, Vasudevan HN, Liu SJ, Villanueva-Meyer JE, Lam TC, Pu JK, Li LF, Leung GK, Swaney DL, Zhang MY, Chan JW,… -
Global post-translational modification profiling of HIV-1-infected cells reveals mechanisms of host cellular pathway remodeling.
Cell reports 2022 Johnson JR, Crosby DC, Hultquist JF, Kurland AP, Adhikary P, Li D, Marlett J, Swann J, Hüttenhain R, Verschueren E, Johnson TL, Newton BW, Shales M, Simon VA, Beltrao P, Frankel AD, Marson A, Cox JS, … -
Integrative structure determination of histones H3 and H4 using genetic interactions.
The FEBS journal 2022 Echeverria I, Braberg H, Krogan NJ, Sali A -
A functional map of HIV-host interactions in primary human T cells.
Nature communications 2022 Hiatt J, Hultquist JF, McGregor MJ, Bouhaddou M, Leenay RT, Simons LM, Young JM, Haas P, Roth TL, Tobin V, Wojcechowskyj JA, Woo JM, Rathore U, Cavero DA, Shifrut E, Nguyen TT, Haas KM, Malik HS, … -
Publisher Correction: Evolution of enhanced innate immune evasion by SARS-CoV-2.
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Cell 2019 Stanley SY, Borges AL, Chen KH, Swaney DL, Krogan NJ, Bondy-Denomy J, Davidson AR -
Synthetic Essentiality of Metabolic Regulator PDHK1 in PTEN-Deficient Cells and Cancers.
Cell reports 2019 Chatterjee N, Pazarentzos E, Mayekar MK, Gui P, Allegakoen DV, Hrustanovic G, Olivas V, Lin L, Verschueren E, Johnson JR, Hofree M, Yan JJ, Newton BW, Dollen JV, Earnshaw CH, Flanagan J, Chan E, … -
Large dataset enables prediction of repair after CRISPR-Cas9 editing in primary T cells.
Nature biotechnology 2019 Leenay RT, Aghazadeh A, Hiatt J, Tse D, Roth TL, Apathy R, Shifrut E, Hultquist JF, Krogan N, Wu Z, Cirolia G, Canaj H, Leonetti MD, Marson A, May AP, Zou J -
PEAK3/C19orf35 pseudokinase, a new NFK3 kinase family member, inhibits CrkII through dimerization.
Proceedings of the National Academy of Sciences of the United States of America 2019 Lopez ML, Lo M, Kung JE, Dudkiewicz M, Jang GM, Von Dollen J, Johnson JR, Krogan NJ, Pawlowski K, Jura N -
Mapping the protein-protein and genetic interactions of cancer to guide precision medicine.
Current opinion in genetics & development 2019 Bouhaddou M, Eckhardt M, Chi Naing ZZ, Kim M, Ideker T, Krogan NJ -
Dynamic BAF chromatin remodeling complex subunit inclusion promotes temporally distinct gene expression programs in cardiogenesis.
Development (Cambridge, England) 2019 Hota SK, Johnson JR, Verschueren E, Thomas R, Blotnick AM, Zhu Y, Sun X, Pennacchio LA, Krogan NJ, Bruneau BG -
ARIH2 Is a Vif-Dependent Regulator of CUL5-Mediated APOBEC3G Degradation in HIV Infection.
Cell host & microbe 2019 Hüttenhain R, Xu J, Burton LA, Gordon DE, Hultquist JF, Johnson JR, Satkamp L, Hiatt J, Rhee DY, Baek K, Crosby DC, Frankel AD, Marson A, Harper JW, Alpi AF, Schulman BA, Gross JD, Krogan NJ -
Two Accessory Proteins Govern MmpL3 Mycolic Acid Transport in Mycobacteria.
mBio 2019 Fay A, Czudnochowski N, Rock JM, Johnson JR, Krogan NJ, Rosenberg O, Glickman MS -
Heart failure drug proscillaridin A targets MYC overexpressing leukemia through global loss of lysine acetylation.
Journal of experimental & clinical cancer research : CR 2019 Da Costa EM, Armaos G, McInnes G, Beaudry A, Moquin-Beaudry G, Bertrand-Lehouillier V, Caron M, Richer C, St-Onge P, Johnson JR, Krogan N, Sai Y, Downey M, Rafei M, Boileau M, Eppert K, Flores-Díaz E,… -
Chaperone-mediated reflux of secretory proteins to the cytosol during endoplasmic reticulum stress.
Proceedings of the National Academy of Sciences of the United States of America 2019 Igbaria A, Merksamer PI, Trusina A, Tilahun F, Johnson JR, Brandman O, Krogan NJ, Weissman JS, Papa FR -
Crosstalk between RNA Pol II C-Terminal Domain Acetylation and Phosphorylation via RPRD Proteins.
Molecular cell 2019 Ali I, Ruiz DG, Ni Z, Johnson JR, Zhang H, Li PC, Khalid MM, Conrad RJ, Guo X, Min J, Greenblatt J, Jacobson M, Krogan NJ, Ott M -
SIRT3 controls brown fat thermogenesis by deacetylation regulation of pathways upstream of UCP1.
Molecular metabolism 2019 Sebaa R, Johnson J, Pileggi C, Norgren M, Xuan J, Sai Y, Tong Q, Krystkowiak I, Bondy-Chorney E, Davey NE, Krogan N, Downey M, Harper ME -
Identification of antiviral roles for the exon-junction complex and nonsense-mediated decay in flaviviral infection.
Nature microbiology 2019 Li M, Johnson JR, Truong B, Kim G, Weinbren N, Dittmar M, Shah PS, Von Dollen J, Newton BW, Jang GM, Krogan NJ, Cherry S, Ramage H -
CRISPR-Cas9 genome engineering of primary CD4+ T cells for the interrogation of HIV-host factor interactions.
Nature protocols 2019 Hultquist JF, Hiatt J, Schumann K, McGregor MJ, Roth TL, Haas P, Doudna JA, Marson A, Krogan NJ -
Neuronal Apolipoprotein E4 Expression Results in Proteome-Wide Alterations and Compromises Bioenergetic Capacity by Disrupting Mitochondrial Function.
Journal of Alzheimer's disease : JAD 2019 Orr AL, Kim C, Jimenez-Morales D, Newton BW, Johnson JR, Krogan NJ, Swaney DL, Mahley RW -
TCO, a Putative Transcriptional Regulator in Arabidopsis, Is a Target of the Protein Kinase CK2.
International journal of molecular sciences 2018 Weinman LM, Running KLD, Carey NS, Stevenson EJ, Swaney DL, Chow BY, Krogan NJ, Krogan NT -
Genetic analysis reveals functions of atypical polyubiquitin chains.
eLife 2018 Meza Gutierrez F, Simsek D, Mizrak A, Deutschbauer A, Braberg H, Johnson J, Xu J, Shales M, Nguyen M, Tamse-Kuehn R, Palm C, Steinmetz LM, Krogan NJ, Toczyski DP -
Comparative Flavivirus-Host Protein Interaction Mapping Reveals Mechanisms of Dengue and Zika Virus Pathogenesis.
Cell 2018 Shah PS, Link N, Jang GM, Sharp PP, Zhu T, Swaney DL, Johnson JR, Von Dollen J, Ramage HR, Satkamp L, Newton B, Hüttenhain R, Petit MJ, Baum T, Everitt A, Laufman O, Tassetto M, Shales M, Stevenson E,… -
Virus and host interactions critical for filoviral RNA synthesis as therapeutic targets.
Antiviral research 2018 Basler CF, Krogan NJ, Leung DW, Amarasinghe GK -
The Yeast DNA Damage Checkpoint Kinase Rad53 Targets the Exoribonuclease, Xrn1.
G3 (Bethesda, Md.) 2018 Lao JP, Ulrich KM, Johnson JR, Newton BW, Vashisht AA, Wohlschlegel JA, Krogan NJ, Toczyski DP -
Proteasome lid bridges mitochondrial stress with Cdc53/Cullin1 NEDDylation status.
Redox biology 2018 Bramasole L, Sinha A, Gurevich S, Radzinski M, Klein Y, Panat N, Gefen E, Rinaldi T, Jimenez-Morales D, Johnson J, Krogan NJ, Reis N, Reichmann D, Glickman MH, Pick E -
The Cellular NMD Pathway Restricts Zika Virus Infection and Is Targeted by the Viral Capsid Protein.
mBio 2018 Fontaine KA, Leon KE, Khalid MM, Tomar S, Jimenez-Morales D, Dunlap M, Kaye JA, Shah PS, Finkbeiner S, Krogan NJ, Ott M -
Multiple Routes to Oncogenesis Are Promoted by the Human Papillomavirus-Host Protein Network.
Cancer discovery 2018 Eckhardt M, Zhang W, Gross AM, Von Dollen J, Johnson JR, Franks-Skiba KE, Swaney DL, Johnson TL, Jang GM, Shah PS, Brand TM, Archambault J, Kreisberg JF, Grandis JR, Ideker T, Krogan NJ -
EpCAM homo-oligomerization is not the basis for its role in cell-cell adhesion.
Scientific reports 2018 Gaber A, Kim SJ, Kaake RM, Bencina M, Krogan N, Šali A, Pavšic M, Lenarcic B -
Influenza virus infection causes global RNAPII termination defects.
Nature structural & molecular biology 2018 Zhao N, Sebastiano V, Moshkina N, Mena N, Hultquist J, Jimenez-Morales D, Ma Y, Rialdi A, Albrecht R, Fenouil R, Sánchez-Aparicio MT, Ayllon J, Ravisankar S, Haddad B, Ho JSY, Low D, Jin J, Yurchenko … -
CRL4AMBRA1 targets Elongin C for ubiquitination and degradation to modulate CRL5 signaling.
The EMBO journal 2018 Chen SH, Jang GM, Hüttenhain R, Gordon DE, Du D, Newton BW, Johnson JR, Hiatt J, Hultquist JF, Johnson TL, Liu YL, Burton LA, Ye J, Reichermeier KM, Stroud RM, Marson A, Debnath J, Gross JD, Krogan NJ -
Mycobacterial Mutagenesis and Drug Resistance Are Controlled by Phosphorylation- and Cardiolipin-Mediated Inhibition of the RecA Coprotease.
Molecular cell 2018 Wipperman MF, Heaton BE, Nautiyal A, Adefisayo O, Evans H, Gupta R, van Ditmarsch D, Soni R, Hendrickson R, Johnson J, Krogan N, Glickman MS -
An Mtb-Human Protein-Protein Interaction Map Identifies a Switch between Host Antiviral and Antibacterial Responses.
Molecular cell 2018 Penn BH, Netter Z, Johnson JR, Von Dollen J, Jang GM, Johnson T, Ohol YM, Maher C, Bell SL, Geiger K, Golovkine G, Du X, Choi A, Parry T, Mohapatra BC, Storck MD, Band H, Chen C, Jäger S, Shales M, … -
Quantitative Yeast Genetic Interaction Profiling of Bacterial Effector Proteins Uncovers a Role for the Human Retromer in Salmonella Infection.
Cell systems 2018 Patrick KL, Wojcechowskyj JA, Bell SL, Riba MN, Jing T, Talmage S, Xu P, Cabello AL, Xu J, Shales M, Jimenez-Morales D, Ficht TA, de Figueiredo P, Samuel JE, Li P, Krogan NJ, Watson RO -
The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders.
Cell 2018 Willsey AJ, Morris MT, Wang S, Willsey HR, Sun N, Teerikorpi N, Baum TB, Cagney G, Bender KJ, Desai TA, Srivastava D, Davis GW, Doudna J, Chang E, Sohal V, Lowenstein DH, Li H, Agard D, Keiser MJ, … -
Sympathetic inputs regulate adaptive thermogenesis in brown adipose tissue through cAMP-Salt inducible kinase axis.
Scientific reports 2018 Paulo E, Wu D, Wang Y, Zhang Y, Wu Y, Swaney DL, Soucheray M, Jimenez-Morales D, Chawla A, Krogan NJ, Wang B -
The HIV-1 Tat protein recruits a ubiquitin ligase to reorganize the 7SK snRNP for transcriptional activation.
eLife 2018 Faust TB, Li Y, Bacon CW, Jang GM, Weiss A, Jayaraman B, Newton BW, Krogan NJ, D'Orso I, Frankel AD -
Author Correction: SMARCA2-regulated host cell factors are required for MxA restriction of influenza A viruses.
Scientific reports 2018 Dornfeld D, Dudek AH, Vausselin T, Günther SC, Hultquist JF, Giese S, Khokhlova-Cubberley D, Chew YC, Pache L, Krogan NJ, Garcia-Sastre A, Schwemmle M, Shaw ML -
The H3K36me2 Methyltransferase Nsd1 Demarcates PRC2-Mediated H3K27me2 and H3K27me3 Domains in Embryonic Stem Cells.
Molecular cell 2018 Streubel G, Watson A, Jammula SG, Scelfo A, Fitzpatrick DJ, Oliviero G, McCole R, Conway E, Glancy E, Negri GL, Dillon E, Wynne K, Pasini D, Krogan NJ, Bracken AP, Cagney G -
SIRT1 Deacetylates Tau and Reduces Pathogenic Tau Spread in a Mouse Model of Tauopathy.
The Journal of neuroscience : the official journal of the Society for Neuroscience 2018 Min SW, Sohn PD, Li Y, Devidze N, Johnson JR, Krogan NJ, Masliah E, Mok SA, Gestwicki JE, Gan L -
Proteome Imbalance of Mitochondrial Electron Transport Chain in Brown Adipocytes Leads to Metabolic Benefits.
Cell metabolism 2018 Masand R, Paulo E, Wu D, Wang Y, Swaney DL, Jimenez-Morales D, Krogan NJ, Wang B -
How many human proteoforms are there?
Nature chemical biology 2018 Aebersold R, Agar JN, Amster IJ, Baker MS, Bertozzi CR, Boja ES, Costello CE, Cravatt BF, Fenselau C, Garcia BA, Ge Y, Gunawardena J, Hendrickson RC, Hergenrother PJ, Huber CG, Ivanov AR, Jensen ON, … -
Cross-talk Signaling between HER3 and HPV16 E6 and E7 Mediates Resistance to PI3K Inhibitors in Head and Neck Cancer.
Cancer research 2018 Brand TM, Hartmann S, Bhola NE, Li H, Zeng Y, O'Keefe RA, Ranall MV, Bandyopadhyay S, Soucheray M, Krogan NJ, Kemp C, Duvvuri U, LaVallee T, Johnson DE, Ozbun MA, Bauman JE, Grandis JR -
Genetic Interaction Mapping in Schizosaccharomyces pombe Using the Pombe Epistasis Mapper (PEM) System and a ROTOR HDA Colony Replicating Robot in a 1536 Array Format.
Cold Spring Harbor protocols 2018 Roguev A, Xu J, Krogan N -
Genetic Interaction Score (S-Score) Calculation, Clustering, and Visualization of Genetic Interaction Profiles for Yeast.
Cold Spring Harbor protocols 2018 Roguev A, Ryan CJ, Xu J, Colson I, Hartsuiker E, Krogan N -
High-Throughput Quantitative Genetic Interaction Mapping in the Fission Yeast Schizosaccharomyces pombe.
Cold Spring Harbor protocols 2018 Roguev A, Ryan CJ, Hartsuiker E, Krogan NJ -
SMARCA2-regulated host cell factors are required for MxA restriction of influenza A viruses.
Scientific reports 2018 Dornfeld D, Dudek AH, Vausselin T, Günther SC, Hultquist JF, Giese S, Khokhlova-Cubberley D, Chew YC, Pache L, Krogan NJ, Garcia-Sastre A, Schwemmle M, Shaw ML -
Fab-based inhibitors reveal ubiquitin independent functions for HIV Vif neutralization of APOBEC3 restriction factors.
PLoS pathogens 2018 Binning JM, Smith AM, Hultquist JF, Craik CS, Caretta Cartozo N, Campbell MG, Burton L, La Greca F, McGregor MJ, Ta HM, Bartholomeeusen K, Peterlin BM, Krogan NJ, Sevillano N, Cheng Y, Gross JD -
DNA Preparation from Schizosaccharomyces pombe.
Cold Spring Harbor protocols 2018 Roguev A, Xu J, Krogan NJ -
Transformation of Schizosaccharomyces pombe in a 96-Well Format.
Cold Spring Harbor protocols 2018 Roguev A, Xu J, Krogan NJ -
Evolutionary Proteomics Uncovers Ancient Associations of Cilia with Signaling Pathways.
Developmental cell 2017 Sigg MA, Menchen T, Lee C, Johnson J, Jungnickel MK, Choksi SP, Garcia G, Busengdal H, Dougherty GW, Pennekamp P, Werner C, Rentzsch F, Florman HM, Krogan N, Wallingford JB, Omran H, Reiter JF -
Metabolic reprogramming of human CD8+ memory T cells through loss of SIRT1.
The Journal of experimental medicine 2017 Jeng MY, Hull PA, Fei M, Kwon HS, Tsou CL, Kasler H, Ng CP, Gordon DE, Johnson J, Krogan N, Verdin E, Ott M -
Mutations in the X-linked ATP6AP2 cause a glycosylation disorder with autophagic defects.
The Journal of experimental medicine 2017 Rujano MA, Cannata Serio M, Panasyuk G, Péanne R, Reunert J, Rymen D, Hauser V, Park JH, Freisinger P, Souche E, Guida MC, Maier EM, Wada Y, Jäger S, Krogan NJ, Kretz O, Nobre S, Garcia P, Quelhas D, … -
Protein Moonlighting Revealed by Noncatalytic Phenotypes of Yeast Enzymes.
Genetics 2017 Espinosa-Cantú A, Ascencio D, Herrera-Basurto S, Xu J, Roguev A, Krogan NJ, DeLuna A -
The Host E3-Ubiquitin Ligase TRIM6 Ubiquitinates the Ebola Virus VP35 Protein and Promotes Virus Replication.
Journal of virology 2017 Bharaj P, Atkins C, Luthra P, Giraldo MI, Dawes BE, Miorin L, Johnson JR, Krogan NJ, Basler CF, Freiberg AN, Rajsbaum R -
A BAG3 chaperone complex maintains cardiomyocyte function during proteotoxic stress.
JCI insight 2017 Judge LM, Perez-Bermejo JA, Truong A, Ribeiro AJ, Yoo JC, Jensen CL, Mandegar MA, Huebsch N, Kaake RM, So PL, Srivastava D, Pruitt BL, Krogan NJ, Conklin BR -
Virus-Like Vesicles of Kaposi's Sarcoma-Associated Herpesvirus Activate Lytic Replication by Triggering Differentiation Signaling.
Journal of virology 2017 Gong D, Dai X, Xiao Y, Du Y, Chapa TJ, Johnson JR, Li X, Krogan NJ, Deng H, Wu TT, Sun R -
The Tyrosine Kinase Inhibitor Gefitinib Restricts Mycobacterium tuberculosis Growth through Increased Lysosomal Biogenesis and Modulation of Cytokine Signaling.
ACS infectious diseases 2017 Sogi KM, Lien KA, Johnson JR, Krogan NJ, Stanley SA -
SMYD2-Mediated Histone Methylation Contributes to HIV-1 Latency.
Cell host & microbe 2017 Boehm D, Jeng M, Camus G, Gramatica A, Schwarzer R, Johnson JR, Hull PA, Montano M, Sakane N, Pagans S, Godin R, Deeks SG, Krogan NJ, Greene WC, Ott M -
Genetic interaction mapping in mammalian cells using CRISPR interference.
Nature methods 2017 Du D, Roguev A, Gordon DE, Chen M, Chen SH, Shales M, Shen JP, Ideker T, Mali P, Qi LS, Krogan NJ -
The RNA Exosome Syncs IAV-RNAPII Transcription to Promote Viral Ribogenesis and Infectivity.
Cell 2017 Rialdi A, Hultquist J, Jimenez-Morales D, Peralta Z, Campisi L, Fenouil R, Moshkina N, Wang ZZ, Laffleur B, Kaake RM, McGregor MJ, Haas K, Pefanis E, Albrecht RA, Pache L, Chanda S, Jen J, Ochando J, … -
An Approach to Spatiotemporally Resolve Protein Interaction Networks in Living Cells.
Cell 2017 Lobingier BT, Hüttenhain R, Eichel K, Miller KB, Ting AY, von Zastrow M, Krogan NJ -
The histone variant H2A.Z promotes splicing of weak introns.
Genes & development 2017 Nissen KE, Homer CM, Ryan CJ, Shales M, Krogan NJ, Patrick KL, Guthrie C -
PJA2 ubiquitinates the HIV-1 Tat protein with atypical chain linkages to activate viral transcription.
Scientific reports 2017 Faust TB, Li Y, Jang GM, Johnson JR, Yang S, Weiss A, Krogan NJ, Frankel AD -
Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions.
Nature methods 2017 Shen JP, Zhao D, Sasik R, Luebeck J, Birmingham A, Bojorquez-Gomez A, Licon K, Klepper K, Pekin D, Beckett AN, Sanchez KS, Thomas A, Kuo CC, Du D, Roguev A, Lewis NE, Chang AN, Kreisberg JF, Krogan N,… -
Chlamydia interfere with an interaction between the mannose-6-phosphate receptor and sorting nexins to counteract host restriction.
eLife 2017 Elwell CA, Czudnochowski N, von Dollen J, Johnson JR, Nakagawa R, Mirrashidi K, Krogan NJ, Engel JN, Rosenberg OS -
Systems-based analysis of RIG-I-dependent signalling identifies KHSRP as an inhibitor of RIG-I receptor activation.
Nature microbiology 2017 Soonthornvacharin S, Rodriguez-Frandsen A, Zhou Y, Galvez F, Huffmaster NJ, Tripathi S, Balasubramaniam VR, Inoue A, de Castro E, Moulton H, Stein DA, Sánchez-Aparicio MT, De Jesus PD, Nguyen Q, König… -
Suppression of C9orf72 RNA repeat-induced neurotoxicity by the ALS-associated RNA-binding protein Zfp106.
eLife 2017 Celona B, Dollen JV, Vatsavayai SC, Kashima R, Johnson JR, Tang AA, Hata A, Miller BL, Huang EJ, Krogan NJ, Seeley WW, Black BL -
Inhibition of CRISPR-Cas9 with Bacteriophage Proteins.
Cell 2016 Rauch BJ, Silvis MR, Hultquist JF, Waters CS, McGregor MJ, Krogan NJ, Bondy-Denomy J -
A genome-wide CRISPR screen identifies a restricted set of HIV host dependency factors.
Nature genetics 2016 Park RJ, Wang T, Koundakjian D, Hultquist JF, Lamothe-Molina P, Monel B, Schumann K, Yu H, Krupzcak KM, Garcia-Beltran W, Piechocka-Trocha A, Krogan NJ, Marson A, Sabatini DM, Lander ES, Hacohen N, … -
The mTOR Complex Controls HIV Latency.
Cell host & microbe 2016 Besnard E, Hakre S, Kampmann M, Lim HW, Hosmane NN, Martin A, Bassik MC, Verschueren E, Battivelli E, Chan J, Svensson JP, Gramatica A, Conrad RJ, Ott M, Greene WC, Krogan NJ, Siliciano RF, Weissman … -
G Protein-Coupled Receptor Endocytosis Confers Uniformity in Responses to Chemically Distinct Ligands.
Molecular pharmacology 2016 Tsvetanova NG, Trester-Zedlitz M, Newton BW, Riordan DP, Sundaram AB, Johnson JR, Krogan NJ, von Zastrow M -
A Herpesvirus Protein Selectively Inhibits Cellular mRNA Nuclear Export.
Cell host & microbe 2016 Gong D, Kim YH, Xiao Y, Du Y, Xie Y, Lee KK, Feng J, Farhat N, Zhao D, Shu S, Dai X, Chanda SK, Rana TM, Krogan NJ, Sun R, Wu TT -
Combined Action of Histone Reader Modules Regulates NuA4 Local Acetyltransferase Function but Not Its Recruitment on the Genome.
Molecular and cellular biology 2016 Steunou AL, Cramet M, Rossetto D, Aristizabal MJ, Lacoste N, Drouin S, Côté V, Paquet E, Utley RT, Krogan N, Robert F, Kobor MS, Côté J -
Microcephaly Proteins Wdr62 and Aspm Define a Mother Centriole Complex Regulating Centriole Biogenesis, Apical Complex, and Cell Fate.
Neuron 2016 Jayaraman D, Kodani A, Gonzalez DM, Mancias JD, Mochida GH, Vagnoni C, Johnson J, Krogan N, Harper JW, Reiter JF, Yu TW, Bae BI, Walsh CA -
A Cas9 Ribonucleoprotein Platform for Functional Genetic Studies of HIV-Host Interactions in Primary Human T Cells.
Cell reports 2016 Hultquist JF, Schumann K, Woo JM, Manganaro L, McGregor MJ, Doudna J, Simon V, Krogan NJ, Marson A -
The Dengue Virus NS5 Protein Intrudes in the Cellular Spliceosome and Modulates Splicing.
PLoS pathogens 2016 De Maio FA, Risso G, Iglesias NG, Shah P, Pozzi B, Gebhard LG, Mammi P, Mancini E, Yanovsky MJ, Andino R, Krogan N, Srebrow A, Gamarnik AV -
A Chemical-Genomic Screen of Neglected Antibiotics Reveals Illicit Transport of Kasugamycin and Blasticidin S.
PLoS genetics 2016 Shiver AL, Osadnik H, Kritikos G, Li B, Krogan N, Typas A, Gross CA -
Non-degradative Ubiquitination of Protein Kinases.
PLoS computational biology 2016 Ball KA, Johnson JR, Lewinski MK, Guatelli J, Verschueren E, Krogan NJ, Jacobson MP -
A scaffold protein connects type IV pili with the Chp chemosensory system to mediate activation of virulence signaling in Pseudomonas aeruginosa.
Molecular microbiology 2016 Inclan YF, Persat A, Greninger A, Von Dollen J, Johnson J, Krogan N, Gitai Z, Engel JN -
Nonsense-mediated decay regulates key components of homologous recombination.
Nucleic acids research 2016 Janke R, Kong J, Braberg H, Cantin G, Yates JR, Krogan NJ, Heyer WD -
CRISPR Interference Efficiently Induces Specific and Reversible Gene Silencing in Human iPSCs.
Cell stem cell 2016 Mandegar MA, Huebsch N, Frolov EB, Shin E, Truong A, Olvera MP, Chan AH, Miyaoka Y, Holmes K, Spencer CI, Judge LM, Gordon DE, Eskildsen TV, Villalta JE, Horlbeck MA, Gilbert LA, Krogan NJ, Sheikh SP,… -
Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems.
Cell systems 2016 Yu MK, Kramer M, Dutkowski J, Srivas R, Licon K, Kreisberg J, Ng CT, Krogan N, Sharan R, Ideker T -
Targeting Viral Proteostasis Limits Influenza Virus, HIV, and Dengue Virus Infection.
Immunity 2016 Heaton NS, Moshkina N, Fenouil R, Gardner TJ, Aguirre S, Shah PS, Zhao N, Manganaro L, Hultquist JF, Noel J, Sachs D, Hamilton J, Leon PE, Chawdury A, Tripathi S, Melegari C, Campisi L, Hai R, … -
Meta- and Orthogonal Integration of Influenza "OMICs" Data Defines a Role for UBR4 in Virus Budding.
Cell host & microbe 2015 Tripathi S, Pohl MO, Zhou Y, Rodriguez-Frandsen A, Wang G, Stein DA, Moulton HM, DeJesus P, Che J, Mulder LC, Yángüez E, Andenmatten D, Pache L, Manicassamy B, Albrecht RA, Gonzalez MG, Nguyen Q, … -
CDK11 in TREX/THOC Regulates HIV mRNA 3' End Processing.
Cell host & microbe 2015 Pak V, Eifler TT, Jäger S, Krogan NJ, Fujinaga K, Peterlin BM -
Discovery and functional characterization of a neomorphic PTEN mutation.
Proceedings of the National Academy of Sciences of the United States of America 2015 Costa HA, Leitner MG, Sos ML, Mavrantoni A, Rychkova A, Johnson JR, Newton BW, Yee MC, De La Vega FM, Ford JM, Krogan NJ, Shokat KM, Oliver D, Halaszovich CR, Bustamante CD -
Critical role of acetylation in tau-mediated neurodegeneration and cognitive deficits.
Nature medicine 2015 Min SW, Chen X, Tracy TE, Li Y, Zhou Y, Wang C, Shirakawa K, Minami SS, Defensor E, Mok SA, Sohn PD, Schilling B, Cong X, Ellerby L, Gibson BW, Johnson J, Krogan N, Shamloo M, Gestwicki J, Masliah E, … -
Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes.
PLoS computational biology 2015 Johnson JR, Santos SD, Johnson T, Pieper U, Strumillo M, Wagih O, Sali A, Krogan NJ, Beltrao P -
Systems Analyses Reveal Shared and Diverse Attributes of Oct4 Regulation in Pluripotent Cells.
Cell systems 2015 Ding L, Paszkowski-Rogacz M, Winzi M, Chakraborty D, Theis M, Singh S, Ciotta G, Poser I, Roguev A, Chu WK, Choudhary C, Mann M, Stewart AF, Krogan N, Buchholz F -
Centriolar satellites assemble centrosomal microcephaly proteins to recruit CDK2 and promote centriole duplication.
eLife 2015 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 -
Comparative mapping of host-pathogen protein-protein interactions.
Current opinion in microbiology 2015 Shah PS, Wojcechowskyj JA, Eckhardt M, Krogan NJ -
Prb1 Protease Activity Is Required for Its Recognition by the F-Box Protein Saf1.
Biochemistry 2015 Mark KG, Meza-Gutierrez F, Johnson JR, Newton BW, Krogan NJ, Toczyski DP -
Global Mapping of the Inc-Human Interactome Reveals that Retromer Restricts Chlamydia Infection.
Cell host & microbe 2015 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 … -
The cancer cell map initiative: defining the hallmark networks of cancer.
Molecular cell 2015 Krogan NJ, Lippman S, Agard DA, Ashworth A, Ideker T -
Lineage-Specific Viral Hijacking of Non-canonical E3 Ubiquitin Ligase Cofactors in the Evolution of Vif Anti-APOBEC3 Activity.
Cell reports 2015 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, … -
Spindle Checkpoint Factors Bub1 and Bub2 Promote DNA Double-Strand Break Repair by Nonhomologous End Joining.
Molecular and cellular biology 2015 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, … -
Differential genetic interactions of yeast stress response MAPK pathways.
Molecular systems biology 2015 Martin H, Shales M, Fernandez-Piñar P, Wei P, Molina M, Fiedler D, Shokat KM, Beltrao P, Lim W, Krogan NJ -
Pharmacological dimerization and activation of the exchange factor eIF2B antagonizes the integrated stress response.
eLife 2015 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 -
NF-κB-activating complex engaged in response to EGFR oncogene inhibition drives tumor cell survival and residual disease in lung cancer.
Cell reports 2015 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, … -
Genetic interaction mapping reveals a role for the SWI/SNF nucleosome remodeler in spliceosome activation in fission yeast.
PLoS genetics 2015 Patrick KL, Ryan CJ, Xu J, Lipp JJ, Nissen KE, Roguev A, Shales M, Krogan NJ, Guthrie C -
Genetic Interaction Landscape Reveals Critical Requirements for Schizosaccharomyces pombe Brc1 in DNA Damage Response Mutants.
G3 (Bethesda, Md.) 2015 Sánchez A, Roguev A, Krogan NJ, Russell P -
Scoring Large-Scale Affinity Purification Mass Spectrometry Datasets with MiST.
Current protocols in bioinformatics 2015 Verschueren E, Von Dollen J, Cimermancic P, Gulbahce N, Sali A, Krogan NJ -
A combined proteomics/genomics approach links hepatitis C virus infection with nonsense-mediated mRNA decay.
Molecular cell 2015 Ramage HR, Kumar GR, Verschueren E, Johnson JR, Von Dollen J, Johnson T, Newton B, Shah P, Horner J, Krogan NJ, Ott M -
Determinants for degradation of SAMHD1, Mus81 and induction of G2 arrest in HIV-1 Vpr and SIVagm Vpr.
Virology 2015 DePaula-Silva AB, Cassiday PA, Chumley J, Bosque A, Monteiro-Filho CMR, Mahon CS, Cone KR, Krogan N, Elde NC, Planelles V -
Global mapping of herpesvirus-host protein complexes reveals a transcription strategy for late genes.
Molecular cell 2014 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 -
Linking tumor mutations to drug responses via a quantitative chemical-genetic interaction map.
Cancer discovery 2014 Martins MM, Zhou AY, Corella A, Horiuchi D, Yau C, Rakhshandehroo T, Gordan JD, Levin RS, Johnson J, Jascur J, Shales M, Sorrentino A, Cheah J, Clemons PA, Shamji AF, Schreiber SL, Krogan NJ, Shokat … -
Regulation of Sufu activity by p66β and Mycbp provides new insight into vertebrate Hedgehog signaling.
Genes & development 2014 Lin C, Yao E, Wang K, Nozawa Y, Shimizu H, Johnson JR, Chen JN, Krogan NJ, Chuang PT -
Cyclin-dependent kinase 12 increases 3' end processing of growth factor-induced c-FOS transcripts.
Molecular and cellular biology 2014 Eifler TT, Shao W, Bartholomeeusen K, Fujinaga K, Jäger S, Johnson JR, Luo Z, Krogan NJ, Peterlin BM -
Acetylome profiling reveals overlap in the regulation of diverse processes by sirtuins, gcn5, and esa1.
Molecular & cellular proteomics : MCP 2014 Downey M, Johnson JR, Davey NE, Newton BW, Johnson TL, Galaang S, Seller CA, Krogan N, Toczyski DP -
Cullin E3 ligases and their rewiring by viral factors.
Biomolecules 2014 Mahon C, Krogan NJ, Craik CS, Pick E -
Evolutionarily conserved genetic interactions with budding and fission yeast MutS identify orthologous relationships in mismatch repair-deficient cancer cells.
Genome medicine 2014 Tosti E, Katakowski JA, Schaetzlein S, Kim HS, Ryan CJ, Shales M, Roguev A, Krogan NJ, Palliser D, Keogh MC, Edelmann W -
Quantitative analysis of triple-mutant genetic interactions.
Nature protocols 2014 Braberg H, Alexander R, Shales M, Xu J, Franks-Skiba KE, Wu Q, Haber JE, Krogan NJ -
Yeast X-chromosome-associated protein 5 (Xap5) functions with H2A.Z to suppress aberrant transcripts.
EMBO reports 2014 Anver S, Roguev A, Zofall M, Krogan NJ, Grewal SI, Harmer SL -
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 : news and reviews in molecular, cellular and developmental biology 2014 Braberg H, Moehle EA, Shales M, Guthrie C, Krogan NJ -
Adventures in time and space: splicing efficiency and RNA polymerase II elongation rate.
RNA biology 2014 Moehle EA, Braberg H, Krogan NJ, Guthrie C -
Conditional genetic interactions of RTT107, SLX4, and HRQ1 reveal dynamic networks upon DNA damage in S. cerevisiae.
G3 (Bethesda, Md.) 2014 Leung GP, Aristizabal MJ, Krogan NJ, Kobor MS -
Identification of a BET family bromodomain/casein kinase II/TAF-containing complex as a regulator of mitotic condensin function.
Cell reports 2014 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 … -
A chaperone-assisted degradation pathway targets kinetochore proteins to ensure genome stability.
PLoS genetics 2014 Kriegenburg F, Jakopec V, Poulsen EG, Nielsen SV, Roguev A, Krogan N, Gordon C, Fleig U, Hartmann-Petersen R -
Set5 and Set1 cooperate to repress gene expression at telomeres and retrotransposons.
Epigenetics 2014 Martín GM, King DA, Green EM, Garcia-Nieto PE, Alexander R, Collins SR, Krogan NJ, Gozani OP, Morrison AJ -
A Pil1-Sle1-Syj1-Tax4 functional pathway links eisosomes with PI(4,5)P2 regulation.
Journal of cell science 2014 Kabeche R, Roguev A, Krogan NJ, Moseley JB -
AFF1 is a ubiquitous P-TEFb partner to enable Tat extraction of P-TEFb from 7SK snRNP and formation of SECs for HIV transactivation.
Proceedings of the National Academy of Sciences of the United States of America 2013 Lu H, Li Z, Xue Y, Schulze-Gahmen U, Johnson JR, Krogan NJ, Alber T, Zhou Q -
Evolution and functional cross-talk of protein post-translational modifications.
Molecular systems biology 2013 Beltrao P, Bork P, Krogan NJ, van Noort V -
Chemical genetics of rapamycin-insensitive TORC2 in S. cerevisiae.
Cell reports 2013 Kliegman JI, Fiedler D, Ryan CJ, Xu YF, Su XY, Thomas D, Caccese MC, Cheng A, Shales M, Rabinowitz JD, Krogan NJ, Shokat KM -
IFI16 DNA sensor is required for death of lymphoid CD4 T cells abortively infected with HIV.
Science (New York, N.Y.) 2013 Monroe KM, Yang Z, Johnson JR, Geng X, Doitsh G, Krogan NJ, Greene WC -
High-resolution network biology: connecting sequence with function.
Nature reviews. Genetics 2013 Ryan CJ, Cimermancic P, Szpiech ZA, Sali A, Hernandez RD, Krogan NJ -
The prefoldin complex regulates chromatin dynamics during transcription elongation.
PLoS genetics 2013 Millán-Zambrano G, Rodríguez-Gil A, Peñate X, de Miguel-Jiménez L, Morillo-Huesca M, Krogan N, Chávez S -
High-throughput genetic and gene expression analysis of the RNAPII-CTD reveals unexpected connections to SRB10/CDK8.
PLoS genetics 2013 Aristizabal MJ, Negri GL, Benschop JJ, Holstege FC, Krogan NJ, Kobor MS -
From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II.
Cell 2013 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 -
A lipid E-MAP identifies Ubx2 as a critical regulator of lipid saturation and lipid bilayer stress.
Molecular cell 2013 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 -
Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.
Nature methods 2013 Swaney DL, Beltrao P, Starita L, Guo A, Rush J, Fields S, Krogan NJ, Villén J -
Systematic triple-mutant analysis uncovers functional connectivity between pathways involved in chromosome regulation.
Cell reports 2013 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 -
Bringing it all together: big data and HIV research.
AIDS (London, England) 2013 Bushman FD, Barton S, Bailey A, Greig C, Malani N, Bandyopadhyay S, Young J, Chanda S, Krogan N -
The AFF4 scaffold binds human P-TEFb adjacent to HIV Tat.
eLife 2013 Schulze-Gahmen U, Upton H, Birnberg A, Bao K, Chou S, Krogan NJ, Zhou Q, Alber T -
Quantitative genetic-interaction mapping in mammalian cells.
Nature methods 2013 Roguev A, Talbot D, Negri GL, Shales M, Cagney G, Bandyopadhyay S, Panning B, Krogan NJ -
From systems to structure: bridging networks and mechanism.
Molecular cell 2013 Fraser JS, Gross JD, Krogan NJ -
CBFβ stabilizes HIV Vif to counteract APOBEC3 at the expense of RUNX1 target gene expression.
Molecular cell 2013 Kim DY, Kwon E, Hartley PD, Crosby DC, Mann S, Krogan NJ, Gross JD -
Dispersed sites of HIV Vif-dependent polyubiquitination in the DNA deaminase APOBEC3F.
Journal of molecular biology 2013 Albin JS, Anderson JS, Johnson JR, Harjes E, Matsuo H, Krogan NJ, Harris RS -
A gene ontology inferred from molecular networks.
Nature biotechnology 2013 Dutkowski J, Kramer M, Surma MA, Balakrishnan R, Cherry JM, Krogan NJ, Ideker T -
All or nothing: protein complexes flip essentiality between distantly related eukaryotes.
Genome biology and evolution 2013 Ryan CJ, Krogan NJ, Cunningham P, Cagney G -
Dissection of DNA damage responses using multiconditional genetic interaction maps.
Molecular cell 2012 Guénolé A, Srivas R, Vreeken K, Wang ZZ, Wang S, Krogan NJ, Ideker T, van Attikum H -
Inhibition of a NEDD8 Cascade Restores Restriction of HIV by APOBEC3G.
PLoS pathogens 2012 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 -
HIV-1 Tat recruits transcription elongation factors dispersed along a flexible AFF4 scaffold.
Proceedings of the National Academy of Sciences of the United States of America 2012 Chou S, Upton H, Bao K, Schulze-Gahmen U, Samelson AJ, He N, Nowak A, Lu H, Krogan NJ, Zhou Q, Alber T -
The yeast SR-like protein Npl3 links chromatin modification to mRNA processing.
PLoS genetics 2012 Moehle EA, Ryan CJ, Krogan NJ, Kress TL, Guthrie C -
Inhibition of RNA lariat debranching enzyme suppresses TDP-43 toxicity in ALS disease models.
Nature genetics 2012 Armakola M, Higgins MJ, Figley MD, Barmada SJ, Scarborough EA, Diaz Z, Fang X, Shorter J, Krogan NJ, Finkbeiner S, Farese RV, Gitler AD -
Replication fork collapse and genome instability in a deoxycytidylate deaminase mutant.
Molecular and cellular biology 2012 Sánchez A, Sharma S, Rozenzhak S, Roguev A, Krogan NJ, Chabes A, Russell P -
Systematic functional prioritization of protein posttranslational modifications.
Cell 2012 Beltrao P, Albanèse V, Kenner LR, Swaney DL, Burlingame A, Villén J, Lim WA, Fraser JS, Frydman J, Krogan NJ -
Moloney leukemia virus type 10 inhibits reverse transcription and retrotransposition of intracisternal a particles.
Journal of virology 2012 Lu C, Luo Z, Jäger S, Krogan NJ, Peterlin BM -
Hierarchical modularity and the evolution of genetic interactomes across species.
Molecular cell 2012 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 … -
Polycomb-like 3 promotes polycomb repressive complex 2 binding to CpG islands and embryonic stem cell self-renewal.
PLoS genetics 2012 Hunkapiller J, Shen Y, Diaz A, Cagney G, McCleary D, Ramalho-Santos M, Krogan N, Ren B, Song JS, Reiter JF -
Differential network biology.
Molecular systems biology 2012 Ideker T, Krogan NJ -
First-in-class small molecule inhibitors of the single-strand DNA cytosine deaminase APOBEC3G.
ACS chemical biology 2012 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 -
Comparative interaction networks: bridging genotype to phenotype.
Advances in experimental medicine and biology 2012 Beltrao P, Ryan C, Krogan NJ -
Global landscape of HIV-human protein complexes.
Nature 2011 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… -
Vif hijacks CBF-β to degrade APOBEC3G and promote HIV-1 infection.
Nature 2011 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, … -
Host cell interactome of HIV-1 Rev includes RNA helicases involved in multiple facets of virus production.
Molecular & cellular proteomics : MCP 2011 Naji S, Ambrus G, Cimermancic P, Reyes JR, Johnson JR, Filbrandt R, Huber MD, Vesely P, Krogan NJ, Yates JR, Saphire AC, Gerace L -
RNA polymerase II carboxyl-terminal domain phosphorylation regulates protein stability of the Set2 methyltransferase and histone H3 di- and trimethylation at lysine 36.
The Journal of biological chemistry 2011 Fuchs SM, Kizer KO, Braberg H, Krogan NJ, Strahl BD -
Eisosome proteins assemble into a membrane scaffold.
The Journal of cell biology 2011 Karotki L, Huiskonen JT, Stefan CJ, Ziólkowska NE, Roth R, Surma MA, Krogan NJ, Emr SD, Heuser J, Grünewald K, Walther TC -
Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs.
BMC systems biology 2011 Casey F, Krogan N, Shields DC, Cagney G -
Key functional regions in the histone variant H2A.Z C-terminal docking domain.
Molecular and cellular biology 2011 Wang AY, Aristizabal MJ, Ryan C, Krogan NJ, Kobor MS -
GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data.
BMC bioinformatics 2011 Fahey ME, Bennett MJ, Mahon C, Jäger S, Pache L, Kumar D, Shapiro A, Rao K, Chanda SK, Craik CS, Frankel AD, Krogan NJ -
Site-specific acetylation mark on an essential chromatin-remodeling complex promotes resistance to replication stress.
Proceedings of the National Academy of Sciences of the United States of America 2011 Charles GM, Chen C, Shih SC, Collins SR, Beltrao P, Zhang X, Sharma T, Tan S, Burlingame AL, Krogan NJ, Madhani HD, Narlikar GJ -
Improved functional overview of protein complexes using inferred epistatic relationships.
BMC systems biology 2011 Ryan C, Greene D, Guénolé A, van Attikum H, Krogan NJ, Cunningham P, Cagney G -
SNX27 mediates retromer tubule entry and endosome-to-plasma membrane trafficking of signalling receptors.
Nature cell biology 2011 Temkin P, Lauffer B, Jäger S, Cimermancic P, Krogan NJ, von Zastrow M -
Yeast SREBP cleavage activation requires the Golgi Dsc E3 ligase complex.
Molecular cell 2011 Stewart EV, Nwosu CC, Tong Z, Roguev A, Cummins TD, Kim DU, Hayles J, Park HO, Hoe KL, Powell DW, Krogan NJ, Espenshade PJ -
Imputing and predicting quantitative genetic interactions in epistatic MAPs.
Methods in molecular biology (Clifton, N.J.) 2011 Ryan C, Cagney G, Krogan N, Cunningham P, Greene D -
Phenotypic landscape of a bacterial cell.
Cell 2010 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 -
Cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action.
Molecular systems biology 2010 Kapitzky L, Beltrao P, Berens TJ, Gassner N, Zhou C, Wüster A, Wu J, Babu MM, Elledge SJ, Toczyski D, Lokey RS, Krogan NJ -
Functional overlap and regulatory links shape genetic interactions between signaling pathways.
Cell 2010 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, … -
Rewiring of genetic networks in response to DNA damage.
Science (New York, N.Y.) 2010 Bandyopadhyay S, Mehta M, Kuo D, Sung MK, Chuang R, Jaehnig EJ, Bodenmiller B, Licon K, Copeland W, Shales M, Fiedler D, Dutkowski J, Guénolé A, van Attikum H, Shokat KM, Kolodner RD, Huh WK, … -
Individual lysine acetylations on the N terminus of Saccharomyces cerevisiae H2A.Z are highly but not differentially regulated.
The Journal of biological chemistry 2010 Mehta M, Braberg H, Wang S, Lozsa A, Shales M, Solache A, Krogan NJ, Keogh MC -
Epistatic relationships reveal the functional organization of yeast transcription factors.
Molecular systems biology 2010 Zheng J, Benschop JJ, Shales M, Kemmeren P, Greenblatt J, Cagney G, Holstege F, Li H, Krogan NJ -
Purification and characterization of HIV-human protein complexes.
Methods (San Diego, Calif.) 2010 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 -
A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers.
Molecular systems biology 2010 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 plasma-membrane E-MAP reveals links of the eisosome with sphingolipid metabolism and endosomal trafficking.
Nature structural & molecular biology 2010 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 -
Quantitative genetic interactions reveal biological modularity.
Cell 2010 Beltrao P, Cagney G, Krogan NJ -
HIV-1 Tat and host AFF4 recruit two transcription elongation factors into a bifunctional complex for coordinated activation of HIV-1 transcription.
Molecular cell 2010 He N, Liu M, Hsu J, Xue Y, Chou S, Burlingame A, Krogan NJ, Alber T, Zhou Q -
The next frontier of systems biology: higher-order and interspecies interactions.
Genome biology 2010 Fischbach MA, Krogan NJ -
Quantitative genetic interaction mapping using the E-MAP approach.
Methods in enzymology 2010 Collins SR, Roguev A, Krogan NJ -
Polycomb-like 2 associates with PRC2 and regulates transcriptional networks during mouse embryonic stem cell self-renewal and differentiation.
Cell stem cell 2010 Walker E, Chang WY, Hunkapiller J, Cagney G, Garcha K, Torchia J, Krogan NJ, Reiter JF, Stanford WL -
HIV Nef is secreted in exosomes and triggers apoptosis in bystander CD4+ T cells.
Traffic (Copenhagen, Denmark) 2010 Lenassi M, Cagney G, Liao M, Vaupotic T, Bartholomeeusen K, Cheng Y, Krogan NJ, Plemenitas A, Peterlin BM -
Genome-wide association data reveal a global map of genetic interactions among protein complexes.
PLoS genetics 2009 Hannum G, Srivas R, Guénolé A, van Attikum H, Krogan NJ, Karp RM, Ideker T -
Towards accurate imputation of quantitative genetic interactions.
Genome biology 2009 Ulitsky I, Krogan NJ, Shamir R -
An acetylated form of histone H2A.Z regulates chromosome architecture in Schizosaccharomyces pombe.
Nature structural & molecular biology 2009 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 -
From information to knowledge: new technologies for defining gene function.
Nature methods 2009 Collins SR, Weissman JS, Krogan NJ -
A systematic characterization of Cwc21, the yeast ortholog of the human spliceosomal protein SRm300.
RNA (New York, N.Y.) 2009 Khanna M, Van Bakel H, Tang X, Calarco JA, Babak T, Guo G, Emili A, Greenblatt JF, Hughes TR, Krogan NJ, Blencowe BJ -
An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell.
Molecular systems biology 2009 Gong Y, Kakihara Y, Krogan N, Greenblatt J, Emili A, Zhang Z, Houry WA -
Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species.
PLoS biology 2009 Beltrao P, Trinidad JC, Fiedler D, Roguev A, Lim WA, Shokat KM, Burlingame AL, Krogan NJ -
Host cell factors in HIV replication: meta-analysis of genome-wide studies.
PLoS pathogens 2009 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 -
An rtt109-independent role for vps75 in transcription-associated nucleosome dynamics.
Molecular and cellular biology 2009 Selth LA, Lorch Y, Ocampo-Hafalla MT, Mitter R, Shales M, Krogan NJ, Kornberg RD, Svejstrup JQ -
Thioredoxin-related Protein 32 is an arsenite-regulated Thiol Reductase of the proteasome 19 S particle.
The Journal of biological chemistry 2009 Wiseman RL, Chin KT, Haynes CM, Stanhill A, Xu CF, Roguev A, Krogan NJ, Neubert TA, Ron D -
Functional organization of the S. cerevisiae phosphorylation network.
Cell 2009 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 -
Learning a prior on regulatory potential from eQTL data.
PLoS genetics 2009 Lee SI, Dudley AM, Drubin D, Silver PA, Krogan NJ, Pe'er D, Koller D -
A complex-based reconstruction of the Saccharomyces cerevisiae interactome.
Molecular & cellular proteomics : MCP 2009 Wang H, Kakaradov B, Collins SR, Karotki L, Fiedler D, Shales M, Shokat KM, Walther TC, Krogan NJ, Koller D -
Systematic characterization of the protein interaction network and protein complexes in Saccharomyces cerevisiae using tandem affinity purification and mass spectrometry.
Methods in molecular biology (Clifton, N.J.) 2009 Babu M, Krogan NJ, Awrey DE, Emili A, Greenblatt JF -
A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing.
Molecular cell 2008 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 single SR-like protein, Npl3, promotes pre-mRNA splicing in budding yeast.
Molecular cell 2008 Kress TL, Krogan NJ, Guthrie C -
Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment.
Genome biology 2008 Shevchenko A, Roguev A, Schaft D, Buchanan L, Habermann B, Sakalar C, Thomas H, Krogan NJ, Shevchenko A, Stewart AF -
Functional targeting of DNA damage to a nuclear pore-associated SUMO-dependent ubiquitin ligase.
Science (New York, N.Y.) 2008 Nagai S, Dubrana K, Tsai-Pflugfelder M, Davidson MB, Roberts TM, Brown GW, Varela E, Hediger F, Gasser SM, Krogan NJ -
Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast.
Science (New York, N.Y.) 2008 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 -
Optimal stepwise experimental design for pairwise functional interaction studies.
Bioinformatics (Oxford, England) 2008 Casey FP, Cagney G, Krogan NJ, Shields DC -
High-throughput, quantitative analyses of genetic interactions in E. coli.
Nature methods 2008 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 -
A comprehensive strategy enabling high-resolution functional analysis of the yeast genome.
Nature methods 2008 Breslow DK, Cameron DM, Collins SR, Schuldiner M, Stewart-Ornstein J, Newman HW, Braun S, Madhani HD, Krogan NJ, Weissman JS -
Ensemble non-negative matrix factorization methods for clustering protein-protein interactions.
Bioinformatics (Oxford, England) 2008 Greene D, Cagney G, Krogan N, Cunningham P -
Chaperone control of the activity and specificity of the histone H3 acetyltransferase Rtt109.
Molecular and cellular biology 2008 Fillingham J, Recht J, Silva AC, Suter B, Emili A, Stagljar I, Krogan NJ, Allis CD, Keogh MC, Greenblatt JF -
BAC to the future: functional genomics in mammals.
Nature methods 2008 Roguev A, Krogan NJ -
Functional maps of protein complexes from quantitative genetic interaction data.
PLoS computational biology 2008 Bandyopadhyay S, Kelley R, Krogan NJ, Ideker T -
High-throughput genetic interaction mapping in the fission yeast Schizosaccharomyces pombe.
Nature methods 2007 Roguev A, Wiren M, Weissman JS, Krogan NJ -
Association with the origin recognition complex suggests a novel role for histone acetyltransferase Hat1p/Hat2p.
BMC biology 2007 Suter B, Pogoutse O, Guo X, Krogan N, Lewis P, Greenblatt JF, Rine J, Emili A -
Mec1/Tel1 phosphorylation of the INO80 chromatin remodeling complex influences DNA damage checkpoint responses.
Cell 2007 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 -
Mutations in yhiT enable utilization of exogenous pyrimidine intermediates in Salmonella enterica serovar Typhimurium.
Microbiology (Reading, England) 2007 Zaharik ML, Lamb SS, Baker KE, Krogan NJ, Neuhard J, Kelln RA -
H2B ubiquitylation acts as a barrier to Ctk1 nucleosomal recruitment prior to removal by Ubp8 within a SAGA-related complex.
Molecular cell 2007 Wyce A, Xiao T, Whelan KA, Kosman C, Walter W, Eick D, Hughes TR, Krogan NJ, Strahl BD, Berger SL -
Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast.
Molecular systems biology 2007 Gupta R, Kus B, Fladd C, Wasmuth J, Tonikian R, Sidhu S, Krogan NJ, Parkinson J, Rotin D -
SIN-fully silent: HDAC complexes in fission yeast.
Nature structural & molecular biology 2007 Roguev A, Krogan NJ -
Backup without redundancy: genetic interactions reveal the cost of duplicate gene loss.
Molecular systems biology 2007 Ihmels J, Collins SR, Schuldiner M, Krogan NJ, Weissman JS -
CCR4/NOT complex associates with the proteasome and regulates histone methylation.
Proceedings of the National Academy of Sciences of the United States of America 2007 Laribee RN, Shibata Y, Mersman DP, Collins SR, Kemmeren P, Roguev A, Weissman JS, Briggs SD, Krogan NJ, Strahl BD -
Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map.
Nature 2007 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… -
Investigating the in vivo activity of the DeaD protein using protein-protein interactions and the translational activity of structured chloramphenicol acetyltransferase mRNAs.
Journal of cellular biochemistry 2007 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 -
Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae.
Molecular & cellular proteomics : MCP 2007 Collins SR, Kemmeren P, Zhao XC, Greenblatt JF, Spencer F, Holstege FC, Weissman JS, Krogan NJ -
Quantitative genetic analysis in Saccharomyces cerevisiae using epistatic miniarray profiles (E-MAPs) and its application to chromatin functions.
Methods (San Diego, Calif.) 2006 Schuldiner M, Collins SR, Weissman JS, Krogan NJ -
The RNA polymerase II kinase Ctk1 regulates positioning of a 5' histone methylation boundary along genes.
Molecular and cellular biology 2006 Xiao T, Shibata Y, Rao B, Laribee RN, O'Rourke R, Buck MJ, Greenblatt JF, Krogan NJ, Lieb JD, Strahl BD -
GammaH2AX and its role in DNA double-strand break repair.
Biochemistry and cell biology = Biochimie et biologie cellulaire 2006 Fillingham J, Keogh MC, Krogan NJ -
PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs.
BMC bioinformatics 2006 Pitre S, Dehne F, Chan A, Cheetham J, Duong A, Emili A, Gebbia M, Greenblatt J, Jessulat M, Krogan N, Luo X, Golshani A -
Signals and systems.
Genome biology 2006 Krogan NJ, Hughes TR -
A genome-wide screen identifies the evolutionarily conserved KEOPS complex as a telomere regulator.
Cell 2006 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 -
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.
Nature 2006 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, … -
The Saccharomyces cerevisiae histone H2A variant Htz1 is acetylated by NuA4.
Genes & development 2006 Keogh MC, Mennella TA, Sawa C, Berthelet S, Krogan NJ, Wolek A, Podolny V, Carpenter LR, Greenblatt JF, Baetz K, Buratowski S -
Systems-level analyses identify extensive coupling among gene expression machines.
Molecular systems biology 2006 Maciag K, Altschuler SJ, Slack MD, Krogan NJ, Emili A, Greenblatt JF, Maniatis T, Wu LF -
A strategy for extracting and analyzing large-scale quantitative epistatic interaction data.
Genome biology 2006 Collins SR, Schuldiner M, Krogan NJ, Weissman JS -
Functional genomics of the yeast DNA-damage response.
Genome biology 2006 Cagney G, Alvaro D, Reid RJ, Thorpe PH, Rothstein R, Krogan NJ -
A phosphatase complex that dephosphorylates gammaH2AX regulates DNA damage checkpoint recovery.
Nature 2005 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 -
Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex.
Cell 2005 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, … -
Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile.
Cell 2005 Schuldiner M, Collins SR, Thompson NJ, Denic V, Bhamidipati A, Punna T, Ihmels J, Andrews B, Boone C, Greenblatt JF, Weissman JS, Krogan NJ -
Identification and characterization of Elf1, a conserved transcription elongation factor in Saccharomyces cerevisiae.
Molecular and cellular biology 2005 Prather D, Krogan NJ, Emili A, Greenblatt JF, Winston F -
BUR kinase selectively regulates H3 K4 trimethylation and H2B ubiquitylation through recruitment of the PAF elongation complex.
Current biology : CB 2005 Laribee RN, Krogan NJ, Xiao T, Shibata Y, Hughes TR, Greenblatt JF, Strahl BD -
Esf2p, a U3-associated factor required for small-subunit processome assembly and compaction.
Molecular and cellular biology 2005 Hoang T, Peng WT, Vanrobays E, Krogan N, Hiley S, Beyer AL, Osheim YN, Greenblatt J, Hughes TR, Lafontaine DL -
Navigating the chaperone network: an integrative map of physical and genetic interactions mediated by the hsp90 chaperone.
Cell 2005 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 -
Maintenance of low histone ubiquitylation by Ubp10 correlates with telomere-proximal Sir2 association and gene silencing.
Molecular cell 2005 Emre NC, Ingvarsdottir K, Wyce A, Wood A, Krogan NJ, Henry KW, Li K, Marmorstein R, Greenblatt JF, Shilatifard A, Berger SL -
The Shwachman-Bodian-Diamond syndrome protein family is involved in RNA metabolism.
The Journal of biological chemistry 2005 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 -
Interaction network containing conserved and essential protein complexes in Escherichia coli.
Nature 2005 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 -
H2B ubiquitin protease Ubp8 and Sgf11 constitute a discrete functional module within the Saccharomyces cerevisiae SAGA complex.
Molecular and cellular biology 2005 Ingvarsdottir K, Krogan NJ, Emre NC, Wyce A, Thompson NJ, Emili A, Hughes TR, Greenblatt JF, Berger SL -
Histone H2B ubiquitylation is associated with elongating RNA polymerase II.
Molecular and cellular biology 2005 Xiao T, Kao CF, Krogan NJ, Sun ZW, Greenblatt JF, Osley MA, Strahl BD -
Proteasome involvement in the repair of DNA double-strand breaks.
Molecular cell 2004 Krogan NJ, Lam MH, Fillingham J, Keogh MC, Gebbia M, Li J, Datta N, Cagney G, Buratowski S, Emili A, Greenblatt JF -
INO80 and gamma-H2AX interaction links ATP-dependent chromatin remodeling to DNA damage repair.
Cell 2004 Morrison AJ, Highland J, Krogan NJ, Arbel-Eden A, Greenblatt JF, Haber JE, Shen X -
The functional landscape of mouse gene expression.
Journal of biology 2004 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, … -
The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II.
Nature 2004 Kim M, Krogan NJ, Vasiljeva L, Rando OJ, Nedea E, Greenblatt JF, Buratowski S -
Interaction of Fcp1 phosphatase with elongating RNA polymerase II holoenzyme, enzymatic mechanism of action, and genetic interaction with elongator.
The Journal of biological chemistry 2004 Kong SE, Kobor MS, Krogan NJ, Somesh BP, Søgaard TM, Greenblatt JF, Svejstrup JQ -
Regulation of chromosome stability by the histone H2A variant Htz1, the Swr1 chromatin remodeling complex, and the histone acetyltransferase NuA4.
Proceedings of the National Academy of Sciences of the United States of America 2004 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 -
Exploration of essential gene functions via titratable promoter alleles.
Cell 2004 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, … -
Bromodomain factor 1 (Bdf1) is phosphorylated by protein kinase CK2.
Molecular and cellular biology 2004 Sawa C, Nedea E, Krogan N, Wada T, Handa H, Greenblatt J, Buratowski S -
Escherichia coli mRNAs with strong Shine/Dalgarno sequences also contain 5' end sequences complementary to domain # 17 on the 16S ribosomal RNA.
Biochemical and biophysical research communications 2004 Golshani A, Krogan NJ, Xu J, Pacal M, Yang XC, Ivanov I, Providenti MA, Ganoza MC, Ivanov IG, AbouHaidar MG -
ESF1 is required for 18S rRNA synthesis in Saccharomyces cerevisiae.
Nucleic acids research 2004 Peng WT, Krogan NJ, Richards DP, Greenblatt JF, Hughes TR -
Global mapping of the yeast genetic interaction network.
Science (New York, N.Y.) 2004 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, … -
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.
Molecular and cellular biology 2004 Baetz KK, Krogan NJ, Emili A, Greenblatt J, Hieter P -
High-definition macromolecular composition of yeast RNA-processing complexes.
Molecular cell 2004 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… -
Transitions in RNA polymerase II elongation complexes at the 3' ends of genes.
The EMBO journal 2004 Kim M, Ahn SH, Krogan NJ, Greenblatt JF, Buratowski S -
A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1.
Molecular cell 2003 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 Bayesian networks approach for predicting protein-protein interactions from genomic data.
Science (New York, N.Y.) 2003 Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M -
A panoramic view of yeast noncoding RNA processing.
Cell 2003 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, … -
Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II.
Molecular and cellular biology 2003 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 -
The Paf1 complex is required for histone H3 methylation by COMPASS and Dot1p: linking transcriptional elongation to histone methylation.
Molecular cell 2003 Krogan NJ, Dover J, Wood A, Schneider J, Heidt J, Boateng MA, Dean K, Ryan OW, Golshani A, Johnston M, Greenblatt JF, Shilatifard A -
Bre1, an E3 ubiquitin ligase required for recruitment and substrate selection of Rad6 at a promoter.
Molecular cell 2003 Wood A, Krogan NJ, Dover J, Schneider J, Heidt J, Boateng MA, Dean K, Golshani A, Zhang Y, Greenblatt JF, Johnston M, Shilatifard A -
RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach.
Molecular and cellular biology 2002 Krogan NJ, Kim M, Ahn SH, Zhong G, Kobor MS, Cagney G, Emili A, Shilatifard A, Buratowski S, Greenblatt JF -
COMPASS, a histone H3 (Lysine 4) methyltransferase required for telomeric silencing of gene expression.
The Journal of biological chemistry 2002 Krogan NJ, Dover J, Khorrami S, Greenblatt JF, Schneider J, Johnston M, Shilatifard A -
Characterization of a six-subunit holo-elongator complex required for the regulated expression of a group of genes in Saccharomyces cerevisiae.
Molecular and cellular biology 2001 Krogan NJ, Greenblatt JF -
COMPASS: a complex of proteins associated with a trithorax-related SET domain protein.
Proceedings of the National Academy of Sciences of the United States of America 2001 Miller T, Krogan NJ, Dover J, Erdjument-Bromage H, Tempst P, Johnston M, Greenblatt JF, Shilatifard A -
A combination of three mutations, dcd, pyrH, and cdd, establishes thymidine (Deoxyuridine) auxotrophy in thyA+ strains of Salmonella typhimurium.
Journal of bacteriology 1998 Krogan NJ, Zaharik ML, Neuhard J, Kelln RA