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Characterization of an A3G-VifHIV-1-CRL5-CBFβ Structure Using a Cross-linking Mass Spectrometry Pipeline for Integrative Modeling of Host-Pathogen Complexes. Mol Cell Proteomics. 2021 Aug 11; 20:100132.
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. PMID: 34389466.
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Protein interaction landscapes revealed by advanced in vivo cross-linking-mass spectrometry. Proc Natl Acad Sci U S A. 2021 Aug 10; 118(32).
Wheat A, Yu C, Wang X, Burke AM, Chemmama IE, Kaake RM, Baker P, Rychnovsky SD, Yang J, Huang L. PMID: 34349018.
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Proteomic Approaches to Study SARS-CoV-2 Biology and COVID-19 Pathology. J Proteome Res. 2021 02 05; 20(2):1133-1152.
Haas P, Muralidharan M, Krogan NJ, Kaake RM, Hüttenhain R. PMID: 33464917.
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1 Fields:
Translation:
HumansCellsPHPublic Health
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Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science. 2020 12 04; 370(6521).
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, QCRG Structural Biology Consortium , Hodder AJ, Shun-Shion AS, Williams DM, White KM, Rosales R, Kehrer T, Miorin L, Moreno E, Patel AH, Rihn S, Khalid MM, Vallejo-Gracia A, Fozouni P, Simoneau CR, Roth TL, Wu D, Karim MA, Ghoussaini M, Dunham I, Berardi F, Weigang S, Chazal M, Park J, Logue J, McGrath M, Weston S, Haupt R, Hastie CJ, Elliott M, Brown F, Burness KA, Reid E, Dorward M, Johnson C, Wilkinson SG, Geyer A, Giesel DM, Baillie C, Raggett S, Leech H, Toth R, Goodman N, Keough KC, Lind AL, Zoonomia Consortium , Klesh RJ, Hemphill KR, Carlson-Stevermer J, Oki J, Holden K, Maures T, Pollard KS, Sali A, Agard DA, Cheng Y, Fraser JS, Frost A, Jura N, Kortemme T, Manglik A, Southworth DR, Stroud RM, Alessi DR, Davies P, Frieman MB, Ideker T, Abate C, Jouvenet N, Kochs G, Shoichet B, Ott M, Palmarini M, Shokat KM, García-Sastre A, Rassen JA, Grosse R, Rosenberg OS, Verba KA, Basler CF, Vignuzzi M, Peden AA, Beltrao P, Krogan NJ. PMID: 33060197.
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86 Fields:
Translation:
HumansCells
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Structural basis of CD4 downregulation by HIV-1 Nef. Nat Struct Mol Biol. 2020 09; 27(9):822-828.
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. PMID: 32719457.
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PubMed Mentions:
10 Fields:
Translation:
HumansCells
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The Global Phosphorylation Landscape of SARS-CoV-2 Infection. Cell. 2020 08 06; 182(3):685-712.e19.
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. PMID: 32645325.
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Hybrid Gene Origination Creates Human-Virus Chimeric Proteins during Infection. Cell. 2020 06 25; 181(7):1502-1517.e23.
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. PMID: 32559462.
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PubMed Mentions:
9 Fields:
Translation:
HumansAnimalsCells
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A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. 2020 07; 583(7816):459-468.
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. PMID: 32353859.
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A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing. bioRxiv. 2020 Mar 22.
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. PMID: 32511329.
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A systems approach to infectious disease. Nat Rev Genet. 2020 06; 21(6):339-354.
Eckhardt M, Hultquist JF, Kaake RM, Hüttenhain R, Krogan NJ. PMID: 32060427.
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PubMed Mentions:
20 Fields:
Translation:
Humans
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Abstract 934: Physical and Genetic Interaction Analyses in Human Pluripotent Stem Cell-Derived Cardiomyocytes to Study Protein Quality Control Disease in the Heart. Circulation Research. 2019 Aug 2; 125(Suppl_1).
Juan A Perez-Bermejo, Luke M Judge, Kenneth Wu, Christina L Jensen, Robyn M Kaake, Danielle Swaney, Po-Lin So, Nevan J Krogan, Bruce R Conklin. .
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Protein Interaction Mapping Identifies RBBP6 as a Negative Regulator of Ebola Virus Replication. Cell. 2018 12 13; 175(7):1917-1930.e13.
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. PMID: 30550789.
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PubMed Mentions:
31 Fields:
Translation:
HumansCells
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EpCAM homo-oligomerization is not the basis for its role in cell-cell adhesion. Sci Rep. 2018 09 05; 8(1):13269.
Gaber A, Kim SJ, Kaake RM, Bencina M, Krogan N, Šali A, Pavšic M, Lenarcic B. PMID: 30185875.
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PubMed Mentions:
15 Fields:
Translation:
HumansAnimalsCells
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A BAG3 chaperone complex maintains cardiomyocyte function during proteotoxic stress. JCI Insight. 2017 Jul 20; 2(14).
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. PMID: 28724793.
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PubMed Mentions:
28 Fields:
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The RNA Exosome Syncs IAV-RNAPII Transcription to Promote Viral Ribogenesis and Infectivity. Cell. 2017 05 04; 169(4):679-692.e14.
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. PMID: 28475896.
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PubMed Mentions:
23 Fields:
Translation:
HumansAnimalsCells
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Ty3 Retrotransposon Hijacks Mating Yeast RNA Processing Bodies to Infect New Genomes. PLoS Genet. 2015; 11(9):e1005528.
Bilanchone V, Clemens K, Kaake R, Dawson AR, Matheos D, Nagashima K, Sitlani P, Patterson K, Chang I, Huang L, Sandmeyer S. PMID: 26421679.
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PubMed Mentions:
12 Fields:
Translation:
AnimalsCells
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Synthesis of two new enrichable and MS-cleavable cross-linkers to define protein-protein interactions by mass spectrometry. Org Biomol Chem. 2015 May 07; 13(17):5030-7.
Burke AM, Kandur W, Novitsky EJ, Kaake RM, Yu C, Kao A, Vellucci D, Huang L, Rychnovsky SD. PMID: 25823605.
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PubMed Mentions:
12 Fields:
Translation:
Cells
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A new in vivo cross-linking mass spectrometry platform to define protein-protein interactions in living cells. Mol Cell Proteomics. 2014 Dec; 13(12):3533-43.
Kaake RM, Wang X, Burke A, Yu C, Kandur W, Yang Y, Novtisky EJ, Second T, Duan J, Kao A, Guan S, Vellucci D, Rychnovsky SD, Huang L. PMID: 25253489.
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PubMed Mentions:
67 Fields:
Translation:
HumansAnimalsCells
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RNA binding and core complexes constitute the U-insertion/deletion editosome. Mol Cell Biol. 2014 Dec 01; 34(23):4329-42.
Aphasizheva I, Zhang L, Wang X, Kaake RM, Huang L, Monti S, Aphasizhev R. PMID: 25225332.
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PubMed Mentions:
39 Fields:
Translation:
AnimalsCells
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Characterizing the dynamics of proteasome complexes by proteomics approaches. Antioxid Redox Signal. 2014 Dec 10; 21(17):2444-56.
Kaake RM, Kao A, Yu C, Huang L. PMID: 24423446.
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PubMed Mentions:
3 Fields:
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Combining docking site and phosphosite predictions to find new substrates: identification of smoothelin-like-2 (SMTNL2) as a c-Jun N-terminal kinase (JNK) substrate. Cell Signal. 2013 Dec; 25(12):2518-29.
Gordon EA, Whisenant TC, Zeller M, Kaake RM, Gordon WM, Krotee P, Patel V, Huang L, Baldi P, Bardwell L. PMID: 23981301.
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PubMed Mentions:
10 Fields:
Translation:
HumansAnimalsCells
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Signal-induced disassembly of the SCF ubiquitin ligase complex by Cdc48/p97. Mol Cell. 2012 Oct 26; 48(2):288-97.
Yen JL, Flick K, Papagiannis CV, Mathur R, Tyrrell A, Ouni I, Kaake RM, Huang L, Kaiser P. PMID: 23000173.
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PubMed Mentions:
20 Fields:
Translation:
AnimalsCells
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Mapping the protein interaction network of the human COP9 signalosome complex using a label-free QTAX strategy. Mol Cell Proteomics. 2012 May; 11(5):138-47.
Fang L, Kaake RM, Patel VR, Yang Y, Baldi P, Huang L. PMID: 22474085.
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PubMed Mentions:
21 Fields:
Translation:
HumansCells
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Oxidative stress-mediated regulation of proteasome complexes. Mol Cell Proteomics. 2011 May; 10(5):R110.006924.
Aiken CT, Kaake RM, Wang X, Huang L. PMID: 21543789.
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PubMed Mentions:
121 Fields:
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HumansAnimalsCells
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Oxidative stress-mediated regulation of proteasome complexes. Molecular & Cellular Proteomics. 2011 Jan 31.
Charity T. Aiken, Robyn M. Kaake, Xiaorong Wang, Lan Huang. .
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Computational prediction and experimental verification of new MAP kinase docking sites and substrates including Gli transcription factors. PLoS Comput Biol. 2010 Aug 26; 6(8).
Whisenant TC, Ho DT, Benz RW, Rogers JS, Kaake RM, Gordon EA, Huang L, Baldi P, Bardwell L. PMID: 20865152.
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PubMed Mentions:
40 Fields:
Translation:
HumansCells
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Profiling of protein interaction networks of protein complexes using affinity purification and quantitative mass spectrometry. Mol Cell Proteomics. 2010 Aug; 9(8):1650-65.
Kaake RM, Wang X, Huang L. PMID: 20445003.
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PubMed Mentions:
36 Fields:
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Selective enrichment and identification of azide-tagged cross-linked peptides using chemical ligation and mass spectrometry. J Am Soc Mass Spectrom. 2010 Aug; 21(8):1432-45.
Vellucci D, Kao A, Kaake RM, Rychnovsky SD, Huang L. PMID: 20472459.
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PubMed Mentions:
18 Fields:
Translation:
Cells
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Characterization of cell cycle specific protein interaction networks of the yeast 26S proteasome complex by the QTAX strategy. J Proteome Res. 2010 Apr 05; 9(4):2016-29.
Kaake RM, Milenkovic T, Przulj N, Kaiser P, Huang L. PMID: 20170199.
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PubMed Mentions:
33 Fields:
Translation:
Animals
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Proteomics Analysis of the Drosophila CRAC Channel Complex in the Resting and Active State. Biophysical Journal. 2010 Jan 1; 98(3):97a.
Aubin Penna, Robyn Kaake, Olga Safrina, Luette Forrest, Andriy V. Yeromin, Peter Kaiser, Lan Huang, Michael D. Cahalan. .
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