Nevan Krogan, PhD

QBI Director and Professor
Bioengineering
+1 415 476-2980

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.

Publications: 

SARS-CoV-2 evolution balances conflicting roles of N protein phosphorylation.

PLoS pathogens

Syed AM, Ciling A, Chen IP, Carlson CR, Adly AN, Martin HS, Taha TY, Khalid MM, Price N, Bouhaddou M, Ummadi MR, Moen JM, Krogan NJ, Morgan DO, Ott M, Doudna JA

A Perturbation Cell Atlas of Human Induced Pluripotent Stem Cells.

bioRxiv : the preprint server for biology

Nourreddine S, Doctor Y, Dailamy A, Forget A, Lee YH, Chinn B, Khaliq H, Polacco B, Muralidharan M, Pan E, Zhang Y, Sigaeva A, Hansen JN, Gao J, Parker JA, Obernier K, Clark T, Chen JY, Metallo C, Lundberg E, Ideker T, Krogan N, Mali P

Protocol for mapping differential protein-protein interaction networks using affinity purification-mass spectrometry.

STAR protocols

Kaushal P, Ummadi MR, Jang GM, Delgado Y, Makanani SK, Alba K, Winters DM, Blanc SF, Xu J, Polacco B, Zhou Y, Stevenson E, Eckhardt M, Zuliani-Alvarez L, Kaake R, Swaney DL, Krogan NJ, Bouhaddou M

Institutional Conversion to Energy-Efficient Ultra-Low Freezers Decreases Carbon Footprint and Reduces Energy Costs.

Biopreservation and biobanking

Shehu D, Kim MO, Rosendo J, Krogan N, Morgan DO, Guglielmo BJ

EGFR and EGFRvIII coopt host defense pathways, promoting progression in glioblastoma.

Neuro-oncology

An Z, Fan QW, Wang L, Yoda H, Barata MJ, Jimenez-Morales D, Phillips JJ, Swaney DL, Stevenson E, Lee E, Krogan N, Weiss WA

MerlinS13 phosphorylation regulates meningioma Wnt signaling and magnetic resonance imaging features.

Nature communications

Eaton CD, Avalos L, Liu SJ, Chen Z, Zakimi N, Casey-Clyde T, Bisignano P, Lucas CG, Stevenson E, Choudhury A, Vasudevan HN, Magill ST, Young JS, Krogan NJ, Villanueva-Meyer JE, Swaney DL, Raleigh DR

The Mac1 ADP-ribosylhydrolase is a Therapeutic Target for SARS-CoV-2.

bioRxiv : the preprint server for biology

Suryawanshi RK, Jaishankar P, Correy GJ, Rachman MM, O'Leary PC, Taha TY, Zapatero-Belinchón FJ, McCavitt-Malvido M, Doruk YU, Stevens MGV, Diolati ME, Jogalekar MP, Richards AL, Montano M, Rosecrans J, Matthay M, Togo T, Gonciarz RL, Gopalkrishnan S, Neitz RJ, Krogan NJ, Swaney DL, Shoichet BK, Ott M, Renslo AR, Ashworth A, Fraser JS

Fibrin drives thromboinflammation and neuropathology in COVID-19.

Nature

Ryu JK, Yan Z, Montano M, Sozmen EG, Dixit K, Suryawanshi RK, Matsui Y, Helmy E, Kaushal P, Makanani SK, Deerinck TJ, Meyer-Franke A, Rios Coronado PE, Trevino TN, Shin MG, Tognatta R, Liu Y, Schuck R, Le L, Miyajima H, Mendiola AS, Arun N, Guo B, Taha TY, Agrawal A, MacDonald E, Aries O, Yan A, Weaver O, Petersen MA, Meza Acevedo R, Alzamora MDPS, Thomas R, Traglia M, Kouznetsova VL, Tsigelny IF, Pico AR, Red-Horse K, Ellisman MH, Krogan NJ, Bouhaddou M, Ott M, Greene WC, Akassoglou K

Interactome of the HIV-1 proteome and human host RNA.

EMBO reports

Schynkel T, Snippenberg WV, Verniers K, Jang GM, Krogan NJ, Mestdagh P, Vandekerckhove L, Trypsteen W

A proximity proteomics pipeline with improved reproducibility and throughput.

Molecular systems biology

Zhong X, Li Q, Polacco BJ, Patil T, Marley A, Foussard H, Khare P, Vartak R, Xu J, DiBerto JF, Roth BL, Eckhardt M, von Zastrow M, Krogan NJ, Hüttenhain R

Targeting a lineage-specific PI3Kɣ-Akt signaling module in acute myeloid leukemia using a heterobifunctional degrader molecule.

Nature Cancer

Kelly LM, Rutter JC, Lin KH, Ling F, Duchmann M, Latour E, Arang N, Pasquer H, Ho Nhat D, Charles J, Killarney ST, Ang HX, Namor F, Culeux C, Lombard B, Loew D, Swaney DL, Krogan NJ, Brunel L, Carretero É, Verdié P, Amblard M, Fodil S, Huynh T, Sebert M, Adès L, Raffoux E, Fenouille N, Itzykson R, Lobry C, Benajiba L, Forget A, Martin AR, Wood KC, Puissant A

The Chlamydia trachomatis Inc Tri1 interacts with TRAF7 to displace native TRAF7 interacting partners.

Microbiology spectrum

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

Predicted mechanistic impacts of human protein missense variants.

bioRxiv : the preprint server for biology

Jänes J, Müller M, Selvaraj S, Manoel D, Stephenson J, Gonçalves C, Lafita A, Polacco B, Obernier K, Alasoo K, Lemos MC, Krogan N, Martin M, Saraiva LR, Burke D, Beltrao P

Cell Maps for Artificial Intelligence: AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines.

bioRxiv : the preprint server for biology

Clark T, Mohan J, Schaffer L, Obernier K, Al Manir S, Churas CP, Dailamy A, Doctor Y, Forget A, Hansen JN, Hu M, Lenkiewicz J, Levinson MA, Marquez C, Nourreddine S, Niestroy J, Pratt D, Qian G, Thaker S, Bélisle-Pipon JC, Brandt C, Chen J, Ding Y, Fodeh S, Krogan N, Lundberg E, Mali P, Payne-Foster P, Ratcliffe S, Ravitsky V, Sali A, Schulz W, Ideker T

Mapping Differential Protein-Protein Interaction Networks using Affinity Purification Mass Spectrometry.

ArXiv

Kaushal P, Ummadi MR, Jang GM, Delgado Y, Makanani SK, Blanc SF, Winters DM, Xu J, Polacco B, Zhou Y, Stevenson E, Eckhardt M, Zuliani-Alvarez L, Kaake R, Swaney DL, Krogan N, Bouhaddou M

A proximity proteomics pipeline with improved reproducibility and throughput.

bioRxiv : the preprint server for biology

Zhong X, Li Q, Polacco BJ, Patil T, Marley A, Foussard H, Khare P, Vartak R, Xu J, DiBerto JF, Roth BL, Eckhardt M, Zastrow MV, Krogan NJ, Hüttenhain R

Global mapping of the Chlamydia trachomatis conventional secreted effector - host interactome reveals CebN interacts with nucleoporins and Rae1 to impede STAT1 nuclear translocation.

bioRxiv : the preprint server for biology

Steiert B, Andersen SE, McCaslin PN, Elwell CA, Faris R, Tijerina X, Smith P, Eldridge Q, Imai BS, Arrington JV, Yau PM, Mirrashidi KM, Johnson JR, Verschueren E, Von Dollen J, Jang GM, Krogan NJ, Engel JN, Weber MM

ATG7(2) Interacts With Metabolic Proteins and Regulates Central Energy Metabolism.

Traffic (Copenhagen, Denmark)

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

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

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

CRISPR-Cas9 screen of E3 ubiquitin ligases identifies TRAF2 and UHRF1 as regulators of HIV latency in primary human T cells.

mBio

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, Eckhardt M, Hultquist JF, Marson A, Kaake RM, Krogan NJ

Spatial control of sensory adaptation modulates mechanosensing in Pseudomonas aeruginosa.

bioRxiv : the preprint server for biology

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

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

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, Khare P, Drake S, Drury V, Burke DF, Gonzalez S, Alkhairy S, Thomas R, Lam S, Morris M, Bader E, Seyler M, Baum T, Krasnoff R, Wang S, Pham P, Arbalaez J, Pratt D, Chag S, Mahmood N, Rolland T, Bourgeron T, Finkbeiner S, Swaney DL, Bandyopadhay S, Ideker T, Beltrao P, Willsey HR, Obernier K, Nowakowski TJ, Hüttenhain R, State MW, Willsey AJ, Krogan NJ

Protein interaction map of APOBEC3 enzyme family reveals deamination-independent role in cellular function.

bioRxiv : the preprint server for biology

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

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 KJ, Stevenson E, Chen KH, Lien BV, Wu D, Braunstein SE, Sneed PK, Magill ST, Lim D, McDermott MW, Berger MS, Perry A, Krogan NJ, Hansen MR, Spitzer MH, Gilbert L, Theodosopoulos PV, Raleigh DR

Cross-family small GTPase ubiquitination by the intracellular pathogen Legionella pneumophila.

Molecular biology of the cell

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

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

Hepatitis C virus infects and perturbs liver stem cells.

mBio

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, McDevitt TC, Yosef N, Ott M

De novo protein identification in mammalian sperm using in situ cryoelectron tomography and AlphaFold2 docking.

Cell

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

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

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, Srivastava D

High-throughput chemogenetic drug screening reveals PKC-RhoA/PKN as a targetable signaling vulnerability in GNAQ-driven uveal melanoma.

Cell reports. Medicine

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 S, Pachter JA, Aplin AE, Alessi DR, Thomas CJ, Gutkind JS

Lysosomal proteomics reveals mechanisms of neuronal apoE4associated lysosomal dysfunction.

bioRxiv : the preprint server for biology

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

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, Braberg H, Zhou Y, Metreveli G, Harjai B, Tummino TA, Melnyk JE, Soucheray M, Batra J, Pache L, Martin-Sancho L, Carlson-Stevermer J, Jureka AS, Basler CF, Shokat KM, Shoichet BK, Shriver LP, Johnson JR, Shaw ML, Chanda SK, Roden DM, Carter TC, Kottyan LC, Chisholm RL, Pacheco JA, Smith ME, Schrodi SJ, Albrecht RA, Vignuzzi M, Zuliani-Alvarez L, Swaney DL, Eckhardt M, Wolinsky SM, White KM, Hultquist JF, Kaake RM, García-Sastre A, Krogan NJ

Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis.

Cell host & microbe

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, Pisanelli G, Richardson RB, Veit EC, Fabius JM, Soucheray M, Polacco BJ, Ak B, Marin A, Evans MJ, Swaney DL, Gonzalez-Reiche AS, Sordillo EM, van Bakel H, Simon V, Zuliani-Alvarez L, Fontoura BMA, Rosenberg BR, Krogan NJ, Martinez-Sobrido L, García-Sastre A, Miorin L

SARS-CoV-2 variants evolve convergent strategies to remodel the host response.

Cell

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, Furnon W, De Lorenzo G, Cowton V, Syed AM, Ciling A, Deutsch N, Pirak D, Dowgier G, Mesner D, Turner JL, McGovern BL, Rodriguez ML, Leiva-Rebollo R, Dunham AS, Zhong X, Eckhardt M, Fossati A, Liotta NF, Kehrer T, Cupic A, Rutkowska M, Mena I, Aslam S, Hoffert A, Foussard H, Olwal CO, Huang W, Zwaka T, Pham J, Lyons M, Donohue L, Griffin A, Nugent R, Holden K, Deans R, Aviles P, Lopez-Martin JA, Jimeno JM, Obernier K, Fabius JM, Soucheray M, Hüttenhain R, Jungreis I, Kellis M, Echeverria I, Verba K, Bonfanti P, Beltrao P, Sharan R, Doudna JA, Martinez-Sobrido L, Patel AH, Palmarini M, Miorin L, White K, Swaney DL, Garcia-Sastre A, Jolly C, Zuliani-Alvarez L, Towers GJ, Krogan NJ

A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication in vivo.

PLoS pathogens

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, Ott M

Next-generation proteomics for quantitative Jumbophage-bacteria interaction mapping.

Nature communications

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

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

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

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

Functional analysis of a common BAG3 allele associated with protection from heart failure.

Nature Cardiovascular Research

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 PL, 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

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, Penn BH, Cox JS

Structural insights into regulation of the PEAK3 pseudokinase scaffold by 14-3-3.

Nature communications

Torosyan H, Paul MD, Forget A, Lo M, Diwanji D, Pawlowski K, Krogan NJ, Jura N, Verba KA

Defining blood-induced microglia functions in neurodegeneration through multiomic profiling.

Nature immunology

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 AR, Ryu JK, Krogan NJ, Akassoglou K

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

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, Gamarnik AV

A multi-scale map of protein assemblies in the DNA damage response.

Cell systems

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

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

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

Quantitative Proteomic Analysis Reveals apoE4-Dependent Phosphorylation of the Actin-Regulating Protein VASP.

Molecular & cellular proteomics : MCP

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

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

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

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

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

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 N, Gordan JD

Nuclear accumulation of host transcripts during Zika Virus Infection.

PLoS pathogens

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

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, Krasilnikov M, Krogan NJ, Langelier C, Lee E, Li LM, Licht D, Lien K, Lyons Z, Mboowa G, Mwebaza I, Mwesigwa S, Nalwadda G, Nichols R, Penaranda ME, Petnic S, Phelps M, Popper SJ, Rape M, Reingold A, Robbins R, Rosenberg OS, Savage DF, Schildhauer S, Settles ML, Sserwadda I, Stanley S, Tato CM, Tsitsiklis A, Van Dis E, Vanaerschot M, Vinden J, Cox JS, Joloba ML, Schaletzky J

How can systems approaches help us understand and treat infectious disease?

Cell systems

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

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

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

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 MR, Pisanelli G, Richardson RB, Veit EC, Fabius JM, Soucheray M, Polacco BJ, Evans MJ, Swaney DL, Gonzalez-Reiche AS, Sordillo EM, van Bakel H, Simon V, Zuliani-Alvarez L, Fontoura BMA, Rosenberg BR, Krogan NJ, Martinez-Sobrido L, García-Sastre A, Miorin L

EPCO-01. EPIGENETIC REPROGRAMMING SHAPES THE MOLECULAR AND CELLULAR LANDSCAPE OF SCHWANNOMA.

Neuro-oncology

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, Jonathan Breshears, Erica Stevenson, Kuei-Ho Chen, Brian Lien, David Wu, Ursula Lang, Stephen Magill, Daniel Lim, Michael McDermott, Mitchel S Berger, Arie Perry, Nevan J Krogan, Matthew Spitzer, Luke Gilbert, Philip Theodospoulos, David Raleigh

Resistance to ATR Inhibitors Is Mediated by Loss of the Nonsense-Mediated Decay Factor UPF2.

Cancer research

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

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

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, Rehwinkel J, Cooper-Knock J

Reduced endosomal microautophagy activity in aging associates with enhanced exocyst-mediated protein secretion.

Aging cell

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, Sidoli S, Bravo-Cordero JJ, Kampmann M, Cuervo AM

SIRT5 is a proviral factor that interacts with SARS-CoV-2 Nsp14 protein.

PLoS pathogens

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

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, Roth BL

CCL2: a Chemokine Potentially Promoting Early Seeding of the Latent HIV Reservoir.

mBio

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

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

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

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

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 Bemmel JG, Hüttenhain R, Vedantham V, Conklin BR, Black BL, Bruneau BG, Steinmetz L, Krogan NJ, Pollard KS, Srivastava D

A Whole-Genome CRISPR Screen Identifies AHR Loss as a Mechanism of Resistance to a PARP7 Inhibitor.

Molecular cancer therapeutics

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

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, Krogan N, Fujimori DG, Ott M

DLX1 and the NuRD complex cooperate in enhancer decommissioning and transcriptional repression.

Development (Cambridge, England)

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

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, Qiu Z, Martin MV, Susko MS, Braunstein SE, Bush NAO, Schulte JD, Butowski N, Sneed PK, Berger MS, Krogan NJ, Perry A, Phillips JJ, Solomon DA, Costello JF, McDermott MW, Rich JN, Raleigh DR

Global post-translational modification profiling of HIV-1-infected cells reveals mechanisms of host cellular pathway remodeling.

Cell reports

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, Fregoso OI, Young JAT, Krogan NJ

Integrative structure determination of histones H3 and H4 using genetic interactions.

The FEBS journal

Echeverria I, Braberg H, Krogan NJ, Sali A

A functional map of HIV-host interactions in primary human T cells.

Nature communications

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, Doudna JA, May AP, Marson A, Krogan NJ

Publisher Correction: Evolution of enhanced innate immune evasion by SARS-CoV-2.

Nature

Thorne LG, Bouhaddou M, Reuschl AK, Zuliani-Alvarez L, Polacco B, Pelin A, Batra J, Whelan MVX, Hosmillo M, Fossati A, Ragazzini R, Jungreis I, Ummadi M, Rojc A, Turner J, Bischof ML, Obernier K, Braberg H, Soucheray M, Richards A, Chen KH, Harjai B, Memon D, Hiatt J, Rosales R, McGovern BL, Jahun A, Fabius JM, White K, Goodfellow IG, Takeuchi Y, Bonfanti P, Shokat K, Jura N, Verba K, Noursadeghi M, Beltrao P, Kellis M, Swaney DL, García-Sastre A, Jolly C, Towers GJ, Krogan NJ

The E3 ligase TRIM1 ubiquitinates LRRK2 and controls its localization, degradation, and toxicity.

The Journal of cell biology

Stormo AED, Shavarebi F, FitzGibbon M, Earley EM, Ahrendt H, Lum LS, Verschueren E, Swaney DL, Skibinski G, Ravisankar A, van Haren J, Davis EJ, Johnson JR, Von Dollen J, Balen C, Porath J, Crosio C, Mirescu C, Iaccarino C, Dauer WT, Nichols RJ, Wittmann T, Cox TC, Finkbeiner S, Krogan NJ, Oakes SA, Hiniker A

The RNA helicase DHX16 recognizes specific viral RNA to trigger RIG-I-dependent innate antiviral immunity.

Cell reports

Hage A, Bharaj P, van Tol S, Giraldo MI, Gonzalez-Orozco M, Valerdi KM, Warren AN, Aguilera-Aguirre L, Xie X, Widen SG, Moulton HM, Lee B, Johnson JR, Krogan NJ, García-Sastre A, Shi PY, Freiberg AN, Rajsbaum R

Low expression of EXOSC2 protects against clinical COVID-19 and impedes SARS-CoV-2 replication.

bioRxiv : the preprint server for biology

Moll T, Odon V, Harvey C, Collins MO, Peden A, Franklin J, Graves E, Marshall JNG, Souza CDS, Zhang S, Azzouz M, Gordon D, Krogan N, Ferraiuolo L, Snyder MP, Shaw PJ, Rehwinkel J, Cooper-Knock J

Leveraging modeling and simulation to optimize the therapeutic window for epigenetic modifier drugs.

Pharmacology & therapeutics

Walz AC, Van De Vyver AJ, Yu L, Birtwistle MR, Krogan NJ, Bouhaddou M

Transcription factor protein interactomes reveal genetic determinants in heart disease.

Cell

Gonzalez-Teran B, Pittman M, Felix F, Thomas R, Richmond-Buccola D, Hüttenhain R, Choudhary K, Moroni E, Costa MW, Huang Y, Padmanabhan A, Alexanian M, Lee CY, Maven BEJ, Samse-Knapp K, Morton SU, McGregor M, Gifford CA, Seidman JG, Seidman CE, Gelb BD, Colombo G, Conklin BR, Black BL, Bruneau BG, Krogan NJ, Pollard KS, Srivastava D

Brahma safeguards canalization of cardiac mesoderm differentiation.

Nature

Hota SK, Rao KS, Blair AP, Khalilimeybodi A, Hu KM, Thomas R, So K, Kameswaran V, Xu J, Polacco BJ, Desai RV, Chatterjee N, Hsu A, Muncie JM, Blotnick AM, Winchester SAB, Weinberger LS, Hüttenhain R, Kathiriya IS, Krogan NJ, Saucerman JJ, Bruneau BG

Mutations in SARS-CoV-2 variants of concern link to increased spike cleavage and virus transmission.

Cell host & microbe

Escalera A, Gonzalez-Reiche AS, Aslam S, Mena I, Laporte M, Pearl RL, Fossati A, Rathnasinghe R, Alshammary H, van de Guchte A, Farrugia K, Qin Y, Bouhaddou M, Kehrer T, Zuliani-Alvarez L, Meekins DA, Balaraman V, McDowell C, Richt JA, Bajic G, Sordillo EM, Dejosez M, Zwaka TP, Krogan NJ, Simon V, Albrecht RA, van Bakel H, García-Sastre A, Aydillo T

Tau interactome maps synaptic and mitochondrial processes associated with neurodegeneration.

Cell

Tracy TE, Madero-Pérez J, Swaney DL, Chang TS, Moritz M, Konrad C, Ward ME, Stevenson E, Hüttenhain R, Kauwe G, Mercedes M, Sweetland-Martin L, Chen X, Mok SA, Wong MY, Telpoukhovskaia M, Min SW, Wang C, Sohn PD, Martin J, Zhou Y, Luo W, Trojanowski JQ, Lee VMY, Gong S, Manfredi G, Coppola G, Krogan NJ, Geschwind DH, Gan L

From systems to structure - using genetic data to model protein structures.

Nature reviews. Genetics

Braberg H, Echeverria I, Kaake RM, Sali A, Krogan NJ

Preclinical and randomized phase I studies of plitidepsin in adults hospitalized with COVID-19.

Life science alliance

Varona JF, Landete P, Lopez-Martin JA, Estrada V, Paredes R, Guisado-Vasco P, Fernandez de Orueta L, Torralba M, Fortun J, Vates R, Barberan J, Clotet B, Ancochea J, Carnevali D, Cabello N, Porras L, Gijon P, Monereo A, Abad D, Zuñiga S, Sola I, Rodon J, Vergara-Alert J, Izquierdo-Useros N, Fudio S, Pontes MJ, de Rivas B, Giron de Velasco P, Nieto A, Gomez J, Aviles P, Lubomirov R, Belgrano A, Sopesen B, White KM, Rosales R, Yildiz S, Reuschl AK, Thorne LG, Jolly C, Towers GJ, Zuliani-Alvarez L, Bouhaddou M, Obernier K, McGovern BL, Rodriguez ML, Enjuanes L, Fernandez-Sousa JM, Krogan NJ, Jimeno JM, Garcia-Sastre A

Comparative Analysis of T-Cell Spatial Proteomics and the Influence of HIV Expression.

Molecular & cellular proteomics : MCP

Oom AL, Stoneham CA, Lewinski MK, Richards A, Wozniak JM, Shams-Ud-Doha K, Gonzalez DJ, Krogan NJ, Guatelli J

SIRT5 is a proviral factor that interacts with SARS-CoV-2 Nsp14 protein.

bioRxiv : the preprint server for biology

Walter M, Chen IP, Vallejo-Gracia A, Kim IJ, Bielska O, Lam VL, Hayashi JM, Cruz A, Shah S, Gross JD, Krogan NJ, Schilling B, Ott M, Verdin E

Evolution of enhanced innate immune evasion by SARS-CoV-2.

Nature

Thorne LG, Bouhaddou M, Reuschl AK, Zuliani-Alvarez L, Polacco B, Pelin A, Batra J, Whelan MVX, Hosmillo M, Fossati A, Ragazzini R, Jungreis I, Ummadi M, Rojc A, Turner J, Bischof ML, Obernier K, Braberg H, Soucheray M, Richards A, Chen KH, Harjai B, Memon D, Hiatt J, Rosales R, McGovern BL, Jahun A, Fabius JM, White K, Goodfellow IG, Takeuchi Y, Bonfanti P, Shokat K, Jura N, Verba K, Noursadeghi M, Beltrao P, Kellis M, Swaney DL, García-Sastre A, Jolly C, Towers GJ, Krogan NJ

Therapeutic implications of activating noncanonical PIK3CA mutations in head and neck squamous cell carcinoma.

The Journal of clinical investigation

Jin N, Keam B, Cho J, Lee MJ, Kim HR, Torosyan H, Jura N, Ng PK, Mills GB, Li H, Zeng Y, Barbash Z, Tarcic G, Kang H, Bauman JE, Kim MO, VanLandingham NK, Swaney DL, Krogan NJ, Johnson DE, Grandis JR

Viral E Protein Neutralizes BET Protein-Mediated Post-Entry Antagonism of SARS-CoV-2.

bioRxiv : the preprint server for biology

Chen IP, Longbotham JE, McMahon S, Suryawanshi RK, Carlson-Stevermer J, Gupta M, Zhang MY, Soveg FW, Hayashi JM, Taha TY, Lam VL, Li Y, Yu Z, Titus EW, Diallo A, Oki J, Holden K, QCRG Structural Biology Consortium, Krogan N, Galonic Fujimori D, Ott M

Caveolin-1 and Sox-2 are predictive biomarkers of cetuximab response in head and neck cancer.

JCI insight

Bouhaddou M, Lee RH, Li H, Bhola NE, O'Keefe RA, Naser M, Zhu TR, Nwachuku K, Duvvuri U, Olshen AB, Roy R, Hechmer A, Bolen J, Keysar SB, Jimeno A, Mills GB, Vandenberg S, Swaney DL, Johnson DE, Krogan NJ, Grandis JR

Systems-level effects of allosteric perturbations to a model molecular switch.

Nature

Perica T, Mathy CJP, Xu J, Jang G?, Zhang Y, Kaake R, Ollikainen N, Braberg H, Swaney DL, Lambright DG, Kelly MJS, Krogan NJ, Kortemme T

A protein interaction landscape of breast cancer.

Science (New York, N.Y.)

Kim M, Park J, Bouhaddou M, Kim K, Rojc A, Modak M, Soucheray M, McGregor MJ, O'Leary P, Wolf D, Stevenson E, Foo TK, Mitchell D, Herrington KA, Muñoz DP, Tutuncuoglu B, Chen KH, Zheng F, Kreisberg JF, Diolaiti ME, Gordan JD, Coppé JP, Swaney DL, Xia B, van 't Veer L, Ashworth A, Ideker T, Krogan NJ

A protein network map of head and neck cancer reveals PIK3CA mutant drug sensitivity.

Science (New York, N.Y.)

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-Morales D, Obernier K, Kreisberg JF, Kim M, Johnson DE, Jura N, Grandis JR, Gutkind JS, Ideker T, Krogan NJ

Interpretation of cancer mutations using a multiscale map of protein systems.

Science (New York, N.Y.)

Zheng F, Kelly MR, Ramms DJ, Heintschel ML, Tao K, Tutuncuoglu B, Lee JJ, Ono K, Foussard H, Chen M, Herrington KA, Silva E, Liu SN, Chen J, Churas C, Wilson N, Kratz A, Pillich RT, Patel DN, Park J, Kuenzi B, Yu MK, Licon K, Pratt D, Kreisberg JF, Kim M, Swaney DL, Nan X, Fraley SI, Gutkind JS, Krogan NJ, Ideker T

Restriction factor compendium for influenza A virus reveals a mechanism for evasion of autophagy.

Nature microbiology

Martin-Sancho L, Tripathi S, Rodriguez-Frandsen A, Pache L, Sanchez-Aparicio M, McGregor MJ, Haas KM, Swaney DL, Nguyen TT, Mamede JI, Churas C, Pratt D, Rosenthal SB, Riva L, Nguyen C, Beltran-Raygoza N, Soonthornvacharin S, Wang G, Jimenez-Morales D, De Jesus PD, Moulton HM, Stein DA, Chang MW, Benner C, Ideker T, Albrecht RA, Hultquist JF, Krogan NJ, García-Sastre A, Chanda SK

Brown adipocyte ATF4 activation improves thermoregulation and systemic metabolism.

Cell reports

Paulo E, Zhang Y, Masand R, Huynh TL, Seo Y, Swaney DL, Soucheray M, Stevenson E, Jimenez-Morales D, Krogan NJ, Wang B

An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia.

Current biology : CB

Souilmi Y, Lauterbur ME, Tobler R, Huber CD, Johar AS, Moradi SV, Johnston WA, Krogan NJ, Alexandrov K, Enard D

Characterization of an A3G-VifHIV-1-CRL5-CBFβ Structure Using a Cross-linking Mass Spectrometry Pipeline for Integrative Modeling of Host-Pathogen Complexes.

Molecular & cellular proteomics : MCP

Kaake RM, Echeverria I, Kim SJ, Von Dollen J, Chesarino NM, Feng Y, Yu C, Ta H, Chelico L, Huang L, Gross J, Sali A, Krogan NJ

Non-canonical proline-tyrosine interactions with multiple host proteins regulate Ebola virus infection.

The EMBO journal

Batra J, Mori H, Small GI, Anantpadma M, Shtanko O, Mishra N, Zhang M, Liu D, Williams CG, Biedenkopf N, Becker S, Gross ML, Leung DW, Davey RA, Amarasinghe GK, Krogan NJ, Basler CF

A ciliopathy complex builds distal appendages to initiate ciliogenesis.

The Journal of cell biology

Kumar D, Rains A, Herranz-Pérez V, Lu Q, Shi X, Swaney DL, Stevenson E, Krogan NJ, Huang B, Westlake C, Garcia-Verdugo JM, Yoder BK, Reiter JF

An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia.

Current biology : CB

Souilmi Y, Lauterbur ME, Tobler R, Huber CD, Johar AS, Moradi SV, Johnston WA, Krogan NJ, Alexandrov K, Enard D

Drug-induced phospholipidosis confounds drug repurposing for SARS-CoV-2.

Science (New York, N.Y.)

Tummino TA, Rezelj VV, Fischer B, Fischer A, O'Meara MJ, Monel B, Vallet T, White KM, Zhang Z, Alon A, Schadt H, O'Donnell HR, Lyu J, Rosales R, McGovern BL, Rathnasinghe R, Jangra S, Schotsaert M, Galarneau JR, Krogan NJ, Urban L, Shokat KM, Kruse AC, García-Sastre A, Schwartz O, Moretti F, Vignuzzi M, Pognan F, Shoichet BK

Endosomal cAMP production broadly impacts the cellular phosphoproteome.

The Journal of biological chemistry

Tsvetanova NG, Trester-Zedlitz M, Newton BW, Peng GE, Johnson JR, Jimenez-Morales D, Kurland AP, Krogan NJ, von Zastrow M

Evolution of enhanced innate immune evasion by the SARS-CoV-2 B.1.1.7 UK variant.

bioRxiv : the preprint server for biology

Thorne LG, Bouhaddou M, Reuschl AK, Zuliani-Alvarez L, Polacco B, Pelin A, Batra J, Whelan MVX, Ummadi M, Rojc A, Turner J, Obernier K, Braberg H, Soucheray M, Richards A, Chen KH, Harjai B, Memon D, Hosmillo M, Hiatt J, Jahun A, Goodfellow IG, Fabius JM, Shokat K, Jura N, Verba K, Noursadeghi M, Beltrao P, Swaney DL, Garcia-Sastre A, Jolly C, Towers GJ, Krogan NJ

Plitidepsin has a positive therapeutic index in adult patients with COVID-19 requiring hospitalization.

medRxiv : the preprint server for health sciences

Varona JF, Landete P, Lopez-Martin JA, Estrada V, Paredes R, Guisado-Vasco P, de Orueta LF, Torralba M, Fortún J, Vates R, Barberán J, Clotet B, Ancochea J, Carnevali D, Cabello N, Porras L, Gijón P, Monereo A, Abad D, Zúñiga S, Sola I, Rodon J, Izquierdo-Useros N, Fudio S, Pontes MJ, de Rivas B, Girón de Velasco P, Sopesén B, Nieto A, Gómez J, Avilés P, Lubomirov R, White KM, Rosales R, Yildiz S, Reuschl AK, Thorne LG, Jolly C, Towers GJ, Zuliani-Alvarez L, Bouhaddou M, Obernier K, Enjuanes L, Fernández-Sousa JM, Plitidepsin – COVID - 19 Study Group, Krogan NJ, Jimeno JM, García-Sastre A

Adhesion-mediated mechanosignaling forces mitohormesis.

Cell metabolism

Tharp KM, Higuchi-Sanabria R, Timblin GA, Ford B, Garzon-Coral C, Schneider C, Muncie JM, Stashko C, Daniele JR, Moore AS, Frankino PA, Homentcovschi S, Manoli SS, Shao H, Richards AL, Chen KH, Hoeve JT, Ku GM, Hellerstein M, Nomura DK, Saijo K, Gestwicki J, Dunn AR, Krogan NJ, Swaney DL, Dillin A, Weaver VM

Chemical-genetic interrogation of RNA polymerase mutants reveals structure-function relationships and physiological tradeoffs.

Molecular cell

Shiver AL, Osadnik H, Peters JM, Mooney RA, Wu PI, Henry KK, Braberg H, Krogan NJ, Hu JC, Landick R, Huang KC, Gross CA

CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.

Research square

Gupta M, Azumaya CM, Moritz M, Pourmal S, Diallo A, Merz GE, Jang G, Bouhaddou M, Fossati A, Brilot AF, Diwanji D, Hernandez E, Herrera N, Kratochvil HT, Lam VL, Li F, Li Y, Nguyen HC, Nowotny C, Owens TW, Peters JK, Rizo AN, Schulze-Gahmen U, Smith AM, Young ID, Yu Z, Asarnow D, Billesbølle C, Campbell MG, Chen J, Chen KH, Chio US, Dickinson MS, Doan L, Jin M, Kim K, Li J, Li YL, Linossi E, Liu Y, Lo M, Lopez J, Lopez KE, Mancino A, Moss FR, Paul MD, Pawar KI, Pelin A, Pospiech TH, Puchades C, Remesh SG, Safari M, Schaefer K, Sun M, Tabios MC, Thwin AC, Titus EW, Trenker R, Tse E, Tsui TKM, Wang F, Zhang K, Zhang Y, Zhao J, Zhou F, Zhou Y, Zuliani-Alvarez L, QCRG Structural Biology Consortium, Agard DA, Cheng Y, Fraser JS, Jura N, Kortemme T, Manglik A, Southworth DR, Stroud RM, Swaney DL, Krogan NJ, Frost A, Rosenberg OS, Verba KA

CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.

bioRxiv : the preprint server for biology

Gupta M, Azumaya CM, Moritz M, Pourmal S, Diallo A, Merz GE, Jang G, Bouhaddou M, Fossati A, Brilot AF, Diwanji D, Hernandez E, Herrera N, Kratochvil HT, Lam VL, Li F, Li Y, Nguyen HC, Nowotny C, Owens TW, Peters JK, Rizo AN, Schulze-Gahmen U, Smith AM, Young ID, Yu Z, Asarnow D, Billesbølle C, Campbell MG, Chen J, Chen KH, Chio US, Dickinson MS, Doan L, Jin M, Kim K, Li J, Li YL, Linossi E, Liu Y, Lo M, Lopez J, Lopez KE, Mancino A, Moss FR, Paul MD, Pawar KI, Pelin A, Pospiech TH, Puchades C, Remesh SG, Safari M, Schaefer K, Sun M, Tabios MC, Thwin AC, Titus EW, Trenker R, Tse E, Tsui TKM, Wang F, Zhang K, Zhang Y, Zhao J, Zhou F, Zhou Y, Zuliani-Alvarez L, QCRG Structural Biology Consortium, Agard DA, Cheng Y, Fraser JS, Jura N, Kortemme T, Manglik A, Southworth DR, Stroud RM, Swaney DL, Krogan NJ, Frost A, Rosenberg OS, Verba KA

Efficient generation of isogenic primary human myeloid cells using CRISPR-Cas9 ribonucleoproteins.

Cell reports

Hiatt J, Cavero DA, McGregor MJ, Zheng W, Budzik JM, Roth TL, Haas KM, Wu D, Rathore U, Meyer-Franke A, Bouzidi MS, Shifrut E, Lee Y, Kumar VE, Dang EV, Gordon DE, Wojcechowskyj JA, Hultquist JF, Fontaine KA, Pillai SK, Cox JS, Ernst JD, Krogan NJ, Marson A

Chaperone-mediated autophagy prevents collapse of the neuronal metastable proteome.

Cell

Bourdenx M, Martín-Segura A, Scrivo A, Rodriguez-Navarro JA, Kaushik S, Tasset I, Diaz A, Storm NJ, Xin Q, Juste YR, Stevenson E, Luengo E, Clement CC, Choi SJ, Krogan NJ, Mosharov EV, Santambrogio L, Grueninger F, Collin L, Swaney DL, Sulzer D, Gavathiotis E, Cuervo AM

Smoothened transduces Hedgehog signals via activity-dependent sequestration of PKA catalytic subunits.

PLoS biology

Arveseth CD, Happ JT, Hedeen DS, Zhu JF, Capener JL, Klatt Shaw D, Deshpande I, Liang J, Xu J, Stubben SL, Nelson IB, Walker MF, Kawakami K, Inoue A, Krogan NJ, Grunwald DJ, Hüttenhain R, Manglik A, Myers BR

The AMBRA1 E3 ligase adaptor regulates the stability of cyclin D.

Nature

Chaikovsky AC, Li C, Jeng EE, Loebell S, Lee MC, Murray CW, Cheng R, Demeter J, Swaney DL, Chen SH, Newton BW, Johnson JR, Drainas AP, Shue YT, Seoane JA, Srinivasan P, He A, Yoshida A, Hipkins SQ, McCrea E, Poltorack CD, Krogan NJ, Diehl JA, Kong C, Jackson PK, Curtis C, Petrov DA, Bassik MC, Winslow MM, Sage J

Phospholipidosis is a shared mechanism underlying the in vitro antiviral activity of many repurposed drugs against SARS-CoV-2.

bioRxiv : the preprint server for biology

Tummino TA, Rezelj VV, Fischer B, Fischer A, O'Meara MJ, Monel B, Vallet T, Zhang Z, Alon A, O'Donnell HR, Lyu J, Schadt H, White KM, Krogan NJ, Urban L, Shokat KM, Kruse AC, García-Sastre A, Schwartz O, Moretti F, Vignuzzi M, Pognan F, Shoichet BK

Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution.

Virology

Jungreis I, Nelson CW, Ardern Z, Finkel Y, Krogan NJ, Sato K, Ziebuhr J, Stern-Ginossar N, Pavesi A, Firth AE, Gorbalenya AE, Kellis M

Host-directed therapies against early-lineage SARS-CoV-2 retain efficacy against B.1.1.7 variant.

bioRxiv : the preprint server for biology

Reuschl AK, Thorne LG, Zuliani-Alvarez L, Bouhaddou M, Obernier K, Hiatt J, Soucheray M, Turner J, Fabius JM, Nguyen GT, Swaney DL, Rosales R, White KM, Avilés P, Kirby IT, Melnyk JE, Shi Y, Zhang Z, Shokat KM, García-Sastre A, Jolly C, Towers GJ, Krogan NJ

Evaluating a New Class of AKT/mTOR Activators for HIV Latency Reversing Activity Ex Vivo and In Vivo.

Journal of virology

Gramatica A, Schwarzer R, Brantley W, Varco-Merth B, Sperber HS, Hull PA, Montano M, Migueles SA, Rosenthal D, Hogan LE, Johnson JR, Packard TA, Grimmett ZW, Herzig E, Besnard E, Nekorchuk M, Hsiao F, Deeks SG, Snape M, Kiernan B, Roan NR, Lifson JD, Estes JD, Picker LJ, Verdin E, Krogan NJ, Henrich TJ, Connors M, Ott M, Pillai SK, Okoye AA, Greene WC

SUMO is a pervasive regulator of meiosis.

eLife

Bhagwat NR, Owens SN, Ito M, Boinapalli JV, Poa P, Ditzel A, Kopparapu S, Mahalawat M, Davies OR, Collins SR, Johnson JR, Krogan NJ, Hunter N

Plitidepsin has potent preclinical efficacy against SARS-CoV-2 by targeting the host protein eEF1A.

Science (New York, N.Y.)

White KM, Rosales R, Yildiz S, Kehrer T, Miorin L, Moreno E, Jangra S, Uccellini MB, Rathnasinghe R, Coughlan L, Martinez-Romero C, Batra J, Rojc A, Bouhaddou M, Fabius JM, Obernier K, Dejosez M, Guillén MJ, Losada A, Avilés P, Schotsaert M, Zwaka T, Vignuzzi M, Shokat KM, Krogan NJ, García-Sastre A

Proteomic Approaches to Study SARS-CoV-2 Biology and COVID-19 Pathology.

Journal of proteome research

Haas P, Muralidharan M, Krogan NJ, Kaake RM, Hüttenhain R

Mass spectrometry-based protein-protein interaction networks for the study of human diseases.

Molecular systems biology

Richards AL, Eckhardt M, Krogan NJ

Genetic interaction mapping informs integrative structure determination of protein complexes.

Science (New York, N.Y.)

Braberg H, Echeverria I, Bohn S, Cimermancic P, Shiver A, Alexander R, Xu J, Shales M, Dronamraju R, Jiang S, Dwivedi G, Bogdanoff D, Chaung KK, Hüttenhain R, Wang S, Mavor D, Pellarin R, Schneidman D, Bader JS, Fraser JS, Morris J, Haber JE, Strahl BD, Gross CA, Dai J, Boeke JD, Sali A, Krogan NJ

Genetic Screens Identify Host Factors for SARS-CoV-2 and Common Cold Coronaviruses.

Cell

Wang R, Simoneau CR, Kulsuptrakul J, Bouhaddou M, Travisano KA, Hayashi JM, Carlson-Stevermer J, Zengel JR, Richards CM, Fozouni P, Oki J, Rodriguez L, Joehnk B, Walcott K, Holden K, Sil A, Carette JE, Krogan NJ, Ott M, Puschnik AS

An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike.

Science (New York, N.Y.)

Schoof M, Faust B, Saunders RA, Sangwan S, Rezelj V, Hoppe N, Boone M, Billesbølle CB, Puchades C, Azumaya CM, Kratochvil HT, Zimanyi M, Deshpande I, Liang J, Dickinson S, Nguyen HC, Chio CM, Merz GE, Thompson MC, Diwanji D, Schaefer K, Anand AA, Dobzinski N, Zha BS, Simoneau CR, Leon K, White KM, Chio US, Gupta M, Jin M, Li F, Liu Y, Zhang K, Bulkley D, Sun M, Smith AM, Rizo AN, Moss F, Brilot AF, Pourmal S, Trenker R, Pospiech T, Gupta S, Barsi-Rhyne B, Belyy V, Barile-Hill AW, Nock S, Liu Y, Krogan NJ, Ralston CY, Swaney DL, García-Sastre A, Ott M, Vignuzzi M, QCRG Structural Biology Consortium, Walter P, Manglik A

SARS-CoV-2 Orf6 hijacks Nup98 to block STAT nuclear import and antagonize interferon signaling.

Proceedings of the National Academy of Sciences of the United States of America

Miorin L, Kehrer T, Sanchez-Aparicio MT, Zhang K, Cohen P, Patel RS, Cupic A, Makio T, Mei M, Moreno E, Danziger O, White KM, Rathnasinghe R, Uccellini M, Gao S, Aydillo T, Mena I, Yin X, Martin-Sancho L, Krogan NJ, Chanda SK, Schotsaert M, Wozniak RW, Ren Y, Rosenberg BR, Fontoura BMA, García-Sastre A

Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.

Science (New York, N.Y.)

Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM, Weckstein AR, Owens TW, Gupta M, Pourmal S, Titus EW, Cakir M, Soucheray M, McGregor M, Cakir Z, Jang G, O'Meara MJ, Tummino TA, Zhang Z, Foussard H, Rojc A, Zhou Y, Kuchenov D, Hüttenhain R, Xu J, Eckhardt M, Swaney DL, Fabius JM, Ummadi M, Tutuncuoglu B, Rathore U, Modak M, Haas P, Haas KM, Naing ZZC, Pulido EH, Shi Y, Barrio-Hernandez I, Memon D, Petsalaki E, Dunham A, Marrero MC, Burke D, Koh C, Vallet T, Silvas JA, Azumaya CM, Billesbølle C, Brilot AF, Campbell MG, Diallo A, Dickinson MS, Diwanji D, Herrera N, Hoppe N, Kratochvil HT, Liu Y, Merz GE, Moritz M, Nguyen HC, Nowotny C, Puchades C, Rizo AN, Schulze-Gahmen U, Smith AM, Sun M, Young ID, Zhao J, Asarnow D, Biel J, Bowen A, Braxton JR, Chen J, Chio CM, Chio US, Deshpande I, Doan L, Faust B, Flores S, Jin M, Kim K, Lam VL, Li F, Li J, Li YL, Li Y, Liu X, Lo M, Lopez KE, Melo AA, Moss FR, Nguyen P, Paulino J, Pawar KI, Peters JK, Pospiech TH, Safari M, Sangwan S, Schaefer K, Thomas PV, Thwin AC, Trenker R, Tse E, Tsui TKM, Wang F, Whitis N, Yu Z, Zhang K, Zhang Y, Zhou F, Saltzberg D

Functional genomic screens identify human host factors for SARS-CoV-2 and common cold coronaviruses.

bioRxiv : the preprint server for biology

Wang R, Simoneau CR, Kulsuptrakul J, Bouhaddou M, Travisano K, Hayashi JM, Carlson-Stevermer J, Oki J, Holden K, Krogan NJ, Ott M, Puschnik AS

The E3 Ubiquitin-Protein Ligase Cullin 3 Regulates HIV-1 Transcription.

Cells

Langer S, Yin X, Diaz A, Portillo AJ, Gordon DE, Rogers UH, Marlett JM, Krogan NJ, Young JAT, Pache L, Chanda SK

Evaluation of SARS-CoV-2 serology assays reveals a range of test performance.

Nature biotechnology

Whitman JD, Hiatt J, Mowery CT, Shy BR, Yu R, Yamamoto TN, Rathore U, Goldgof GM, Whitty C, Woo JM, Gallman AE, Miller TE, Levine AG, Nguyen DN, Bapat SP, Balcerek J, Bylsma SA, Lyons AM, Li S, Wong AW, Gillis-Buck EM, Steinhart ZB, Lee Y, Apathy R, Lipke MJ, Smith JA, Zheng T, Boothby IC, Isaza E, Chan J, Acenas DD, Lee J, Macrae TA, Kyaw TS, Wu D, Ng DL, Gu W, York VA, Eskandarian HA, Callaway PC, Warrier L, Moreno ME, Levan J, Torres L, Farrington LA, Loudermilk RP, Koshal K, Zorn KC, Garcia-Beltran WF, Yang D, Astudillo MG, Bernstein BE, Gelfand JA, Ryan ET, Charles RC, Iafrate AJ, Lennerz JK, Miller S, Chiu CY, Stramer SL, Wilson MR, Manglik A, Ye CJ, Krogan NJ, Anderson MS, Cyster JG, Ernst JD, Wu AHB, Lynch KL, Bern C, Hsu PD, Marson A

SARS-CoV-2 ORF9c Is a Membrane-Associated Protein that Suppresses Antiviral Responses in Cells.

bioRxiv : the preprint server for biology

Dominguez Andres A, Feng Y, Campos AR, Yin J, Yang CC, James B, Murad R, Kim H, Deshpande AJ, Gordon DE, Krogan N, Pippa R, Ronai ZA

An ultra-potent synthetic nanobody neutralizes SARS-CoV-2 by locking Spike into an inactive conformation.

bioRxiv : the preprint server for biology

Schoof M, Faust B, Saunders RA, Sangwan S, Rezelj V, Hoppe N, Boone M, Billesbølle CB, Puchades C, Azumaya CM, Kratochvil HT, Zimanyi M, Deshpande I, Liang J, Dickinson S, Nguyen HC, Chio CM, Merz GE, Thompson MC, Diwanji D, Schaefer K, Anand AA, Dobzinski N, Zha BS, Simoneau CR, Leon K, White KM, Chio US, Gupta M, Jin M, Li F, Liu Y, Zhang K, Bulkley D, Sun M, Smith AM, Rizo AN, Moss F, Brilot AF, Pourmal S, Trenker R, Pospiech T, Gupta S, Barsi-Rhyne B, Belyy V, Barile-Hill AW, Nock S, Liu Y, Krogan NJ, Ralston CY, Swaney DL, García-Sastre A, Ott M, Vignuzzi M, QCRG Structural Biology Consortium, Walter P, Manglik A

Structural basis of CD4 downregulation by HIV-1 Nef.

Nature structural & molecular biology

Kwon Y, Kaake RM, Echeverria I, Suarez M, Karimian Shamsabadi M, Stoneham C, Ramirez PW, Kress J, Singh R, Sali A, Krogan N, Guatelli J, Jia X

Envelope protein ubiquitination drives entry and pathogenesis of Zika virus.

Nature

Giraldo MI, Xia H, Aguilera-Aguirre L, Hage A, van Tol S, Shan C, Xie X, Sturdevant GL, Robertson SJ, McNally KL, Meade-White K, Azar SR, Rossi SL, Maury W, Woodson M, Ramage H, Johnson JR, Krogan NJ, Morais MC, Best SM, Shi PY, Rajsbaum R

Correction: Thioredoxin-related protein 32 is an arsenite-regulated thiol reductase of the proteasome 19 S particle.

The Journal of biological chemistry

Wiseman RL, Chin KT, Haynes CM, Stanhill A, Xu CF, Roguev A, Krogan NJ, Neubert TA, Ron D

The Global Phosphorylation Landscape of SARS-CoV-2 Infection.

Cell

Bouhaddou M, Memon D, Meyer B, White KM, Rezelj VV, Correa Marrero M, Polacco BJ, Melnyk JE, Ulferts S, Kaake RM, Batra J, Richards AL, Stevenson E, Gordon DE, Rojc A, Obernier K, Fabius JM, Soucheray M, Miorin L, Moreno E, Koh C, Tran QD, Hardy A, Robinot R, Vallet T, Nilsson-Payant BE, Hernandez-Armenta C, Dunham A, Weigang S, Knerr J, Modak M, Quintero D, Zhou Y, Dugourd A, Valdeolivas A, Patil T, Li Q, Hüttenhain R, Cakir M, Muralidharan M, Kim M, Jang G, Tutuncuoglu B, Hiatt J, Guo JZ, Xu J, Bouhaddou S, Mathy CJP, Gaulton A, Manners EJ, Félix E, Shi Y, Goff M, Lim JK, McBride T, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, De Wit E, Leach AR, Kortemme T, Shoichet B, Ott M, Saez-Rodriguez J, tenOever BR, Mullins RD, Fischer ER, Kochs G, Grosse R, García-Sastre A, Vignuzzi M, Johnson JR, Shokat KM, Swaney DL, Beltrao P, Krogan NJ

The kinase Isr1 negatively regulates hexosamine biosynthesis in S. cerevisiae.

PLoS genetics

Alme EB, Stevenson E, Krogan NJ, Swaney DL, Toczyski DP

Hybrid Gene Origination Creates Human-Virus Chimeric Proteins during Infection.

Cell

Ho JSY, Angel M, Ma Y, Sloan E, Wang G, Martinez-Romero C, Alenquer M, Roudko V, Chung L, Zheng S, Chang M, Fstkchyan Y, Clohisey S, Dinan AM, Gibbs J, Gifford R, Shen R, Gu Q, Irigoyen N, Campisi L, Huang C, Zhao N, Jones JD, van Knippenberg I, Zhu Z, Moshkina N, Meyer L, Noel J, Peralta Z, Rezelj V, Kaake R, Rosenberg B, Wang B, Wei J, Paessler S, Wise HM, Johnson J, Vannini A, Amorim MJ, Baillie JK, Miraldi ER, Benner C, Brierley I, Digard P, Luksza M, Firth AE, Krogan N, Greenbaum BD, MacLeod MK, van Bakel H, Garcìa-Sastre A, Yewdell JW, Hutchinson E, Marazzi I

Unbiased Proteomic Profiling Uncovers a Targetable GNAS/PKA/PP2A Axis in Small Cell Lung Cancer Stem Cells.

Cancer cell

Coles GL, Cristea S, Webber JT, Levin RS, Moss SM, He A, Sangodkar J, Hwang YC, Arand J, Drainas AP, Mooney NA, Demeter J, Spradlin JN, Mauch B, Le V, Shue YT, Ko JH, Lee MC, Kong C, Nomura DK, Ohlmeyer M, Swaney DL, Krogan NJ, Jackson PK, Narla G, Gordan JD, Shokat KM, Sage J

The Landscape of Human Cancer Proteins Targeted by SARS-CoV-2.

Cancer discovery

Tutuncuoglu B, Cakir M, Batra J, Bouhaddou M, Eckhardt M, Gordon DE, Krogan NJ

Test performance evaluation of SARS-CoV-2 serological assays.

medRxiv : the preprint server for health sciences

Whitman JD, Hiatt J, Mowery CT, Shy BR, Yu R, Yamamoto TN, Rathore U, Goldgof GM, Whitty C, Woo JM, Gallman AE, Miller TE, Levine AG, Nguyen DN, Bapat SP, Balcerek J, Bylsma SA, Lyons AM, Li S, Wong AW, Gillis-Buck EM, Steinhart ZB, Lee Y, Apathy R, Lipke MJ, Smith JA, Zheng T, Boothby IC, Isaza E, Chan J, Acenas DD, Lee J, Macrae TA, Kyaw TS, Wu D, Ng DL, Gu W, York VA, Eskandarian HA, Callaway PC, Warrier L, Moreno ME, Levan J, Torres L, Farrington LA, Loudermilk R, Koshal K, Zorn KC, Garcia-Beltran WF, Yang D, Astudillo MG, Bernstein BE, Gelfand JA, Ryan ET, Charles RC, Iafrate AJ, Lennerz JK, Miller S, Chiu CY, Stramer SL, Wilson MR, Manglik A, Ye CJ, Krogan NJ, Anderson MS, Cyster JG, Ernst JD, Wu AHB, Lynch KL, Bern C, Hsu PD, Marson A

mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1.

Nature communications

Du Y, Hultquist JF, Zhou Q, Olson A, Tseng Y, Zhang TH, Hong M, Tang K, Chen L, Meng X, McGregor MJ, Dai L, Gong D, Martin-Sancho L, Chanda S, Li X, Bensenger S, Krogan NJ, Sun R

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.

Nature

Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Meyer B, Roesch F, Vallet T, Mac Kain A, Miorin L, Moreno E, Naing ZZC, Zhou Y, Peng S, Shi Y, Zhang Z, Shen W, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Lyu J, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Rakesh R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Liboy-Lugo J, Lin Y, Huang XP, Liu Y, Wankowicz SA, Bohn M, Safari M, Ugur FS, Koh C, Savar NS, Tran QD, Shengjuler D, Fletcher SJ, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, Sharp PP, Wenzell NA, Kuzuoglu-Ozturk D, Wang HY, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Stroud RM, Frankel AD, Rosenberg OS, Verba KA, Agard DA, Ott M, Emerman M, Jura N, von Zastrow M, Verdin E, Ashworth A, Schwartz O, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor SN, Fraser JS, Gross JD, Sali A, Roth BL, Ruggero D, Taunton J, Kortemme T, Beltrao P, Vignuzzi M, García-Sastre A, Shokat KM, Shoichet BK, Krogan NJ

A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing.

bioRxiv : the preprint server for biology

Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O'Meara MJ, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Naing ZZC, Zhou Y, Peng S, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Shen W, Shi Y, Zhang Z, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Ramachandran R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Lin Y, Wankowicz SA, Bohn M, Trenker R, Young JM, Cavero D, Hiatt J, Roth T, Rathore U, Subramanian A, Noack J, Hubert M, Roesch F, Vallet T, Meyer B, White KM, Miorin L, Agard D, Emerman M, Ruggero D, García-Sastre A, Jura N, von Zastrow M, Taunton J, Schwartz O, Vignuzzi M, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor S, Fraser JS, Gross J, Sali A, Kortemme T, Beltrao P, Shokat K, Shoichet BK, Krogan NJ

Cyclophilin A Prevents HIV-1 Restriction in Lymphocytes by Blocking Human TRIM5α Binding to the Viral Core.

Cell reports

Selyutina A, Persaud M, Simons LM, Bulnes-Ramos A, Buffone C, Martinez-Lopez A, Scoca V, Di Nunzio F, Hiatt J, Marson A, Krogan NJ, Hultquist JF, Diaz-Griffero F

A Quantitative Genetic Interaction Map of HIV Infection.

Molecular cell

Gordon DE, Watson A, Roguev A, Zheng S, Jang GM, Kane J, Xu J, Guo JZ, Stevenson E, Swaney DL, Franks-Skiba K, Verschueren E, Shales M, Crosby DC, Frankel AD, Marson A, Marazzi I, Cagney G, Krogan NJ

A systems approach to infectious disease.

Nature reviews. Genetics

Eckhardt M, Hultquist JF, Kaake RM, Hüttenhain R, Krogan NJ

Dynamic post-translational modification profiling of Mycobacterium tuberculosis-infected primary macrophages.

eLife

Budzik JM, Swaney DL, Jimenez-Morales D, Johnson JR, Garelis NE, Repasy T, Roberts AW, Popov LM, Parry TJ, Pratt D, Ideker T, Krogan NJ, Cox JS

Splicing Defects of the Profilin Gene Alter Actin Dynamics in an S. pombe SMN Mutant.

iScience

Antoine M, Patrick KL, Soret J, Duc P, Rage F, Cacciottolo R, Nissen KE, Cauchi RJ, Krogan NJ, Guthrie C, Gachet Y, Bordonné R

The functional landscape of the human phosphoproteome.

Nature biotechnology

Ochoa D, Jarnuczak AF, Viéitez C, Gehre M, Soucheray M, Mateus A, Kleefeldt AA, Hill A, Garcia-Alonso L, Stein F, Krogan NJ, Savitski MM, Swaney DL, Vizcaíno JA, Noh KM, Beltrao P

Mutations in ANKLE2, a ZIKA Virus Target, Disrupt an Asymmetric Cell Division Pathway in Drosophila Neuroblasts to Cause Microcephaly.

Developmental cell

Link N, Chung H, Jolly A, Withers M, Tepe B, Arenkiel BR, Shah PS, Krogan NJ, Aydin H, Geckinli BB, Tos T, Isikay S, Tuysuz B, Mochida GH, Thomas AX, Clark RD, Mirzaa GM, Lupski JR, Bellen HJ

UNC93B1 recruits syntenin-1 to dampen TLR7 signalling and prevent autoimmunity.

Nature

Majer O, Liu B, Kreuk LSM, Krogan N, Barton GM

Systematic Identification of Host Cell Regulators of Legionella pneumophila Pathogenesis Using a Genome-wide CRISPR Screen.

Cell host & microbe

Jeng EE, Bhadkamkar V, Ibe NU, Gause H, Jiang L, Chan J, Jian R, Jimenez-Morales D, Stevenson E, Krogan NJ, Swaney DL, Snyder MP, Mukherjee S, Bassik MC

Enterovirus pathogenesis requires the host methyltransferase SETD3.

Nature microbiology

Diep J, Ooi YS, Wilkinson AW, Peters CE, Foy E, Johnson JR, Zengel J, Ding S, Weng KF, Laufman O, Jang G, Xu J, Young T, Verschueren E, Kobluk KJ, Elias JE, Sarnow P, Greenberg HB, Hüttenhain R, Nagamine CM, Andino R, Krogan NJ, Gozani O, Carette JE

Regulation of Skn7-dependent, oxidative stress-induced genes by the RNA polymerase II-CTD phosphatase, Fcp1, and Mediator kinase subunit, Cdk8, in yeast.

The Journal of biological chemistry

Aristizabal MJ, Dever K, Negri GL, Shen M, Hawe N, Benschop JJ, Holstege FCP, Krogan NJ, Sadowski I, Kobor MS

Anti-CRISPR-Associated Proteins Are Crucial Repressors of Anti-CRISPR Transcription.

Cell

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

Chatterjee N, Pazarentzos E, Mayekar MK, Gui P, Allegakoen DV, Hrustanovic G, Olivas V, Lin L, Verschueren E, Johnson JR, Hofree M, Yan JJ, Newton BW, Dollen JV, Earnshaw CH, Flanagan J, Chan E, Asthana S, Ideker T, Wu W, Suzuki J, Barad BA, Kirichok Y, Fraser JS, Weiss WA, Krogan NJ, Tulpule A, Sabnis AJ, Bivona TG

Large dataset enables prediction of repair after CRISPR-Cas9 editing in primary T cells.

Nature biotechnology

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

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

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)

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

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

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

Da Costa EM, Armaos G, McInnes G, Beaudry A, Moquin-Beaudry G, Bertrand-Lehouillier V, Caron M, Richer C, St-Onge P, Johnson JR, Krogan N, Sai Y, Downey M, Rafei M, Boileau M, Eppert K, Flores-Díaz E, Haman A, Hoang T, Sinnett D, Beauséjour C, McGraw S, Raynal NJ

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

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

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

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

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

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

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

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

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

Shah PS, Link N, Jang GM, Sharp PP, Zhu T, Swaney DL, Johnson JR, Von Dollen J, Ramage HR, Satkamp L, Newton B, Hüttenhain R, Petit MJ, Baum T, Everitt A, Laufman O, Tassetto M, Shales M, Stevenson E, Iglesias GN, Shokat L, Tripathi S, Balasubramaniam V, Webb LG, Aguirre S, Willsey AJ, Garcia-Sastre A, Pollard KS, Cherry S, Gamarnik AV, Marazzi I, Taunton J, Fernandez-Sesma A, Bellen HJ, Andino R, Krogan NJ

Protein Interaction Mapping Identifies RBBP6 as a Negative Regulator of Ebola Virus Replication.

Cell

Batra J, Hultquist JF, Liu D, Shtanko O, Von Dollen J, Satkamp L, Jang GM, Luthra P, Schwarz TM, Small GI, Arnett E, Anantpadma M, Reyes A, Leung DW, Kaake R, Haas P, Schmidt CB, Schlesinger LS, LaCount DJ, Davey RA, Amarasinghe GK, Basler CF, Krogan NJ

Virus and host interactions critical for filoviral RNA synthesis as therapeutic targets.

Antiviral research

Basler CF, Krogan NJ, Leung DW, Amarasinghe GK

The Yeast DNA Damage Checkpoint Kinase Rad53 Targets the Exoribonuclease, Xrn1.

G3 (Bethesda, Md.)

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

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

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

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

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

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 V, Prinjha RK, Tarakhovsky A, Squatrito M, Pinto D, Allette K, Byun M, Smith ML, Sebra R, Guccione E, Tumpey T, Krogan N, Greenbaum B, van Bakel H, García-Sastre A, Marazzi I

CRL4AMBRA1 targets Elongin C for ubiquitination and degradation to modulate CRL5 signaling.

The EMBO journal

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

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

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, Portnoy DA, Hernandez R, Coscoy L, Cox JS, Krogan NJ

Quantitative Yeast Genetic Interaction Profiling of Bacterial Effector Proteins Uncovers a Role for the Human Retromer in Salmonella Infection.

Cell systems

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

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, Shoichet B, von Zastrow M, Mucke L, Finkbeiner S, Gan L, Sestan N, Ward ME, Huttenhain R, Nowakowski TJ, Bellen HJ, Frank LM, Khokha MK, Lifton RP, Kampmann M, Ideker T, State MW, Krogan NJ

Sympathetic inputs regulate adaptive thermogenesis in brown adipose tissue through cAMP-Salt inducible kinase axis.

Scientific reports

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

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

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

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

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

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

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, Jewett MC, Kelleher NL, Kiessling LL, Krogan NJ, Larsen MR, Loo JA, Ogorzalek Loo RR, Lundberg E, MacCoss MJ, Mallick P, Mootha VK, Mrksich M, Muir TW, Patrie SM, Pesavento JJ, Pitteri SJ, Rodriguez H, Saghatelian A, Sandoval W, Schlüter H, Sechi S, Slavoff SA, Smith LM, Snyder MP, Thomas PM, Uhlén M, Van Eyk JE, Vidal M, Walt DR, White FM, Williams ER, Wohlschlager T, Wysocki VH, Yates NA, Young NL, Zhang B

Cross-talk Signaling between HER3 and HPV16 E6 and E7 Mediates Resistance to PI3K Inhibitors in Head and Neck Cancer.

Cancer research

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 Score (S-Score) Calculation, Clustering, and Visualization of Genetic Interaction Profiles for Yeast.

Cold Spring Harbor protocols

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

Roguev A, Ryan CJ, Hartsuiker E, Krogan NJ

SMARCA2-regulated host cell factors are required for MxA restriction of influenza A viruses.

Scientific reports

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

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

Roguev A, Xu J, Krogan NJ

Transformation of Schizosaccharomyces pombe in a 96-Well Format.

Cold Spring Harbor protocols

Roguev A, Xu J, Krogan NJ

Evolutionary Proteomics Uncovers Ancient Associations of Cilia with Signaling Pathways.

Developmental cell

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

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

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, Bird TD, Raskind WH, Schwake M, Duvet S, Foulquier F, Matthijs G, Marquardt T, Simons M

Protein Moonlighting Revealed by Noncatalytic Phenotypes of Yeast Enzymes.

Genetics

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

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

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

Gong D, Dai X, Xiao Y, Du Y, Chapa TJ, Johnson JR, Li X, Krogan NJ, Deng H, Wu TT, Sun R

SMYD2-Mediated Histone Methylation Contributes to HIV-1 Latency.

Cell host & microbe

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

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

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, Byun M, Basu U, García-Sastre A, Krogan N, van Bakel H, Marazzi I

An Approach to Spatiotemporally Resolve Protein Interaction Networks in Living Cells.

Cell

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

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

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

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, Qi L, Ideker T, Mali P

Chlamydia interfere with an interaction between the mannose-6-phosphate receptor and sorting nexins to counteract host restriction.

eLife

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

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 R, Krogan NJ, García-Sastre A, Yoh SM, Chanda SK

Suppression of C9orf72 RNA repeat-induced neurotoxicity by the ALS-associated RNA-binding protein Zfp106.

eLife

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

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

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, Walker BD

The mTOR Complex Controls HIV Latency.

Cell host & microbe

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 JS, Verdin E

G Protein-Coupled Receptor Endocytosis Confers Uniformity in Responses to Chemically Distinct Ligands.

Molecular pharmacology

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

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

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

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

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

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

Shiver AL, Osadnik H, Kritikos G, Li B, Krogan N, Typas A, Gross CA

Non-degradative Ubiquitination of Protein Kinases.

PLoS computational biology

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

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

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

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, Weissman JS, Qi LS, So PL, Conklin BR

Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems.

Cell systems

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

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, Metreveli G, Gamarnik AV, García-Sastre A, Greenbaum B, Simon V, Fernandez-Sesma A, Krogan NJ, Mulder LCF, van Bakel H, Tortorella D, Taunton J, Palese P, Marazzi I

Meta- and Orthogonal Integration of Influenza "OMICs" Data Defines a Role for UBR4 in Virus Budding.

Cell host & microbe

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, Brass A, Elledge S, White M, Shapira S, Hacohen N, Karlas A, Meyer TF, Shales M, Gatorano A, Johnson JR, Jang G, Johnson T, Verschueren E, Sanders D, Krogan N, Shaw M, König R, Stertz S, García-Sastre A, Chanda SK

CDK11 in TREX/THOC Regulates HIV mRNA 3' End Processing.

Cell host & microbe

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

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

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, Verdin E, Gan L

Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes.

PLoS computational biology

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

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

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

Shah PS, Wojcechowskyj JA, Eckhardt M, Krogan NJ

Prb1 Protease Activity Is Required for Its Recognition by the F-Box Protein Saf1.

Biochemistry

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

Mirrashidi KM, Elwell CA, Verschueren E, Johnson JR, Frando A, Von Dollen J, Rosenberg O, Gulbahce N, Jang G, Johnson T, Jäger S, Gopalakrishnan AM, Sherry J, Dunn JD, Olive A, Penn B, Shales M, Cox JS, Starnbach MN, Derre I, Valdivia R, Krogan NJ, Engel J

The cancer cell map initiative: defining the hallmark networks of cancer.

Molecular cell

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

Kane JR, Stanley DJ, Hultquist JF, Johnson JR, Mietrach N, Binning JM, Jónsson SR, Barelier S, Newton BW, Johnson TL, Franks-Skiba KE, Li M, Brown WL, Gunnarsson HI, Adalbjornsdóttir A, Fraser JS, Harris RS, Andrésdóttir V, Gross JD, Krogan NJ

Spindle Checkpoint Factors Bub1 and Bub2 Promote DNA Double-Strand Break Repair by Nonhomologous End Joining.

Molecular and cellular biology

Jessulat M, Malty RH, Nguyen-Tran DH, Deineko V, Aoki H, Vlasblom J, Omidi K, Jin K, Minic Z, Hooshyar M, Burnside D, Samanfar B, Phanse S, Freywald T, Prasad B, Zhang Z, Vizeacoumar F, Krogan NJ, Freywald A, Golshani A, Babu M

Differential genetic interactions of yeast stress response MAPK pathways.

Molecular systems biology

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

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

Blakely CM, Pazarentzos E, Olivas V, Asthana S, Yan JJ, Tan I, Hrustanovic G, Chan E, Lin L, Neel DS, Newton W, Bobb KL, Fouts TR, Meshulam J, Gubens MA, Jablons DM, Johnson JR, Bandyopadhyay S, Krogan NJ, Bivona TG

Genetic interaction mapping reveals a role for the SWI/SNF nucleosome remodeler in spliceosome activation in fission yeast.

PLoS genetics

Patrick KL, Ryan CJ, Xu J, Lipp JJ, Nissen KE, Roguev A, Shales M, Krogan NJ, Guthrie C

Scoring Large-Scale Affinity Purification Mass Spectrometry Datasets with MiST.

Current protocols in bioinformatics

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

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

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

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

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 KM, McCormick F, Goga A, Bandyopadhyay S

Regulation of Sufu activity by p66β and Mycbp provides new insight into vertebrate Hedgehog signaling.

Genes & development

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

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

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

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

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

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

Anver S, Roguev A, Zofall M, Krogan NJ, Grewal SI, Harmer SL

Identification of a BET family bromodomain/casein kinase II/TAF-containing complex as a regulator of mitotic condensin function.

Cell reports

Kim HS, Mukhopadhyay R, Rothbart SB, Silva AC, Vanoosthuyse V, Radovani E, Kislinger T, Roguev A, Ryan CJ, Xu J, Jahari H, Hardwick KG, Greenblatt JF, Krogan NJ, Fillingham JS, Strahl BD, Bouhassira EE, Edelmann W, Keogh MC

A chaperone-assisted degradation pathway targets kinetochore proteins to ensure genome stability.

PLoS genetics

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

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

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

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

Beltrao P, Bork P, Krogan NJ, van Noort V

Chemical genetics of rapamycin-insensitive TORC2 in S. cerevisiae.

Cell reports

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.)

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

Ryan CJ, Cimermancic P, Szpiech ZA, Sali A, Hernandez RD, Krogan NJ

The prefoldin complex regulates chromatin dynamics during transcription elongation.

PLoS genetics

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

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

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

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

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

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)

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

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

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

Fraser JS, Gross JD, Krogan NJ

CBFβ stabilizes HIV Vif to counteract APOBEC3 at the expense of RUNX1 target gene expression.

Molecular cell

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

Albin JS, Anderson JS, Johnson JR, Harjes E, Matsuo H, Krogan NJ, Harris RS

A gene ontology inferred from molecular networks.

Nature biotechnology

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

Ryan CJ, Krogan NJ, Cunningham P, Cagney G

Dissection of DNA damage responses using multiconditional genetic interaction maps.

Molecular cell

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

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

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

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

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

Sánchez A, Sharma S, Rozenzhak S, Roguev A, Krogan NJ, Chabes A, Russell P

Systematic functional prioritization of protein posttranslational modifications.

Cell

Beltrao P, Albanèse V, Kenner LR, Swaney DL, Burlingame A, Villén J, Lim WA, Fraser JS, Frydman J, Krogan NJ

Hierarchical modularity and the evolution of genetic interactomes across species.

Molecular cell

Ryan CJ, Roguev A, Patrick K, Xu J, Jahari H, Tong Z, Beltrao P, Shales M, Qu H, Collins SR, Kliegman JI, Jiang L, Kuo D, Tosti E, Kim HS, Edelmann W, Keogh MC, Greene D, Tang C, Cunningham P, Shokat KM, Cagney G, Svensson JP, Guthrie C, Espenshade PJ, Ideker T, Krogan NJ

Polycomb-like 3 promotes polycomb repressive complex 2 binding to CpG islands and embryonic stem cell self-renewal.

PLoS genetics

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

Ideker T, Krogan NJ

First-in-class small molecule inhibitors of the single-strand DNA cytosine deaminase APOBEC3G.

ACS chemical biology

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

Beltrao P, Ryan C, Krogan NJ

Global landscape of HIV-human protein complexes.

Nature

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

Vif hijacks CBF-β to degrade APOBEC3G and promote HIV-1 infection.

Nature

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

Host cell interactome of HIV-1 Rev includes RNA helicases involved in multiple facets of virus production.

Molecular & cellular proteomics : MCP

Naji S, Ambrus G, Cimermancic P, Reyes JR, Johnson JR, Filbrandt R, Huber MD, Vesely P, Krogan NJ, Yates JR, Saphire AC, Gerace L

Eisosome proteins assemble into a membrane scaffold.

The Journal of cell biology

Karotki L, Huiskonen JT, Stefan CJ, Ziólkowska NE, Roth R, Surma MA, Krogan NJ, Emr SD, Heuser J, Grünewald K, Walther TC

Key functional regions in the histone variant H2A.Z C-terminal docking domain.

Molecular and cellular biology

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

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

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

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

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

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.)

Ryan C, Cagney G, Krogan N, Cunningham P, Greene D

Phenotypic landscape of a bacterial cell.

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

Cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action.

Molecular systems biology

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

van Wageningen S, Kemmeren P, Lijnzaad P, Margaritis T, Benschop JJ, de Castro IJ, van Leenen D, Groot Koerkamp MJ, Ko CW, Miles AJ, Brabers N, Brok MO, Lenstra TL, Fiedler D, Fokkens L, Aldecoa R, Apweiler E, Taliadouros V, Sameith K, van de Pasch LA, van Hooff SR, Bakker LV, Krogan NJ, Snel B, Holstege FC

Rewiring of genetic networks in response to DNA damage.

Science (New York, N.Y.)

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, Aebersold R, Keogh MC, Krogan NJ, Ideker T

Individual lysine acetylations on the N terminus of Saccharomyces cerevisiae H2A.Z are highly but not differentially regulated.

The Journal of biological chemistry

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

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.)

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

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

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 interaction mapping using the E-MAP approach.

Methods in enzymology

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

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)

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

Hannum G, Srivas R, Guénolé A, van Attikum H, Krogan NJ, Karp RM, Ideker T

Towards accurate imputation of quantitative genetic interactions.

Genome biology

Ulitsky I, Krogan NJ, Shamir R

An acetylated form of histone H2A.Z regulates chromosome architecture in Schizosaccharomyces pombe.

Nature structural & molecular biology

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

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.)

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

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

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

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

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

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

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

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

Wang H, Kakaradov B, Collins SR, Karotki L, Fiedler D, Shales M, Shokat KM, Walther TC, Krogan NJ, Koller D

A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing.

Molecular cell

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

Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment.

Genome biology

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.)

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.)

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)

Casey FP, Cagney G, Krogan NJ, Shields DC

High-throughput, quantitative analyses of genetic interactions in E. coli.

Nature methods

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

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)

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

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

Roguev A, Krogan NJ

Functional maps of protein complexes from quantitative genetic interaction data.

PLoS computational biology

Bandyopadhyay S, Kelley R, Krogan NJ, Ideker T

Association with the origin recognition complex suggests a novel role for histone acetyltransferase Hat1p/Hat2p.

BMC biology

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

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)

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

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

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

Roguev A, Krogan NJ

Backup without redundancy: genetic interactions reveal the cost of duplicate gene loss.

Molecular systems biology

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

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

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

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

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

Collins SR, Kemmeren P, Zhao XC, Greenblatt JF, Spencer F, Holstege FC, Weissman JS, Krogan NJ

The RNA polymerase II kinase Ctk1 regulates positioning of a 5' histone methylation boundary along genes.

Molecular and cellular biology

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

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

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

Krogan NJ, Hughes TR

A genome-wide screen identifies the evolutionarily conserved KEOPS complex as a telomere regulator.

Cell

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

Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrín-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete MM, Vlasblom J, Wu S, Orsi C, Collins SR, Chandran S, Haw R, Rilstone JJ, Gandi K, Thompson NJ, Musso G, St Onge P, Ghanny S, Lam MH, Butland G, Altaf-Ul AM, Kanaya S, Shilatifard A, O'Shea E, Weissman JS, Ingles CJ, Hughes TR, Parkinson J, Gerstein M, Wodak SJ, Emili A, Greenblatt JF

The Saccharomyces cerevisiae histone H2A variant Htz1 is acetylated by NuA4.

Genes & development

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

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

Collins SR, Schuldiner M, Krogan NJ, Weissman JS

Functional genomics of the yeast DNA-damage response.

Genome biology

Cagney G, Alvaro D, Reid RJ, Thorpe PH, Rothstein R, Krogan NJ

A phosphatase complex that dephosphorylates gammaH2AX regulates DNA damage checkpoint recovery.

Nature

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

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

Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile.

Cell

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

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

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

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

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

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

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

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

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

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

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

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

Zhang W, Morris QD, Chang R, Shai O, Bakowski MA, Mitsakakis N, Mohammad N, Robinson MD, Zirngibl R, Somogyi E, Laurin N, Eftekharpour E, Sat E, Grigull J, Pan Q, Peng WT, Krogan N, Greenblatt J, Fehlings M, van der Kooy D, Aubin J, Bruneau BG, Rossant J, Blencowe BJ, Frey BJ, Hughes TR

The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II.

Nature

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

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

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

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

Bromodomain factor 1 (Bdf1) is phosphorylated by protein kinase CK2.

Molecular and cellular biology

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

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

Peng WT, Krogan NJ, Richards DP, Greenblatt JF, Hughes TR

Global mapping of the yeast genetic interaction network.

Science (New York, N.Y.)

Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M, Chen Y, Cheng X, Chua G, Friesen H, Goldberg DS, Haynes J, Humphries C, He G, Hussein S, Ke L, Krogan N, Li Z, Levinson JN, Lu H, Ménard P, Munyana C, Parsons AB, Ryan O, Tonikian R, Roberts T, Sdicu AM, Shapiro J, Sheikh B, Suter B, Wong SL, Zhang LV, Zhu H, Burd CG, Munro S, Sander C, Rine J, Greenblatt J, Peter M, Bretscher A, Bell G, Roth FP, Brown GW, Andrews B, Bussey H, Boone C

High-definition macromolecular composition of yeast RNA-processing complexes.

Molecular cell

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

Transitions in RNA polymerase II elongation complexes at the 3' ends of genes.

The EMBO journal

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

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.)

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

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

Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II.

Molecular and cellular biology

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

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

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

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

Krogan NJ, Dover J, Khorrami S, Greenblatt JF, Schneider J, Johnston M, Shilatifard A

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

Miller T, Krogan NJ, Dover J, Erdjument-Bromage H, Tempst P, Johnston M, Greenblatt JF, Shilatifard A

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