Mehdi Bouhaddou

Title(s)Assistant Professor, MIMG
SchoolMedicine
ORCID ORCID Icon0000-0002-9526-1427 Additional info
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    University of California, San Francisco, San FranciscoPostdoctoral Fellow02/2023Proteomics and Virology
    Icahn School of Medicine at Mount Sinai, New YorkPhD05/2018Math Modeling of Cancer Signaling Dynamics
    University of California, Berkeley, BerkeleyB.A.05/2010Cognitive Science

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    Dr. Mehdi Bouhaddou is an Assistant Professor in the Department of Microbiology, Immunology, and Molecular Genetics (MIMG) and co-affiliated with the Institute for Quantitative and Computational Biosciences (QCBio). Dr. Bouhaddou directs a Quantitative Systems Biology lab that studies how protein-protein interactions and post-translational modifications impact signaling networks, from systems-level features to basic mechanisms.

    The lab is half “wet” and half “dry”, cultivating an interactive exchange between experimental and computational workflows. Experimentally, we focus on global mass spectrometry proteomics, affinity purification mass spectrometry (APMS), cell culture-based virology, genetic perturbation screens, pharmacology, and molecular biology. Computationally, we specialize in bioinformatics, network modeling, and ordinary differential equation (ODE) modeling.

    Major projects in the lab include proteomics and mechanistic studies into (1) virus exchange with host post-translational modification signaling networks (herpesviruses, HIV, SARS-CoV-2, and alphaviruses), (2) co-morbidities in people living with HIV (PLWH) including peripheral neuropathy and cervical cancer, and (3) coral reef bleaching and coral-symbiont interactions. We are an extremely collaborative group, continually seeking new biological areas in which to apply our methodology. The lab owns and manages a Bruker timsTOF HT mass spectrometry instrument for proteomics analysis, a BSL-2 lab space, and computational resources.

    Dr. Mehdi Bouhaddou performed his postdoctoral training with Dr. Nevan J. Krogan at UC San Francisco (UCSF) in virology, mass spectrometry proteomics, bioinformatics, and network modeling receiving F32 (NCI) and K99 (NIAID) awards. He developed virus-host interaction networks for SARS-CoV-2 and other coronaviruses, and systematically compared the molecular response to emerging SARS-CoV-2 variants to pinpoint variant-specific mechanisms of pathogenesis. Prior to his postdoc, Dr Bouhaddou developed ordinary differential equation (ODE) mathematical models at Roche and during his PhD in Biomedical Sciences with Dr. Marc Birtwistle at the Icahn School of Medicine at Mount Sinai. Dr. Bouhaddou received his Bachelor’s degree from UC Berkeley in Cognitive Neuroscience.

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. SARS-CoV-2 evolution balances conflicting roles of N protein phosphorylation. PLoS Pathog. 2024 Nov 21; 20(11):e1012741. 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. PMID: 39571001.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    2. Protocol for mapping differential protein-protein interaction networks using affinity purification-mass spectrometry. STAR Protoc. 2024 Nov 02; 5(4):103286. 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. PMID: 39488835.
      View in: PubMed   Mentions:    Fields:    
    3. Interaction of chikungunya virus glycoproteins with macrophage factors controls virion production. EMBO J. 2024 Oct; 43(20):4625-4655. Yao Z, Ramachandran S, Huang S, Kim E, Jami-Alahmadi Y, Kaushal P, Bouhaddou M, Wohlschlegel JA, Li MM. PMID: 39261662; PMCID: PMC11480453.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    4. Fibrin drives thromboinflammation and neuropathology in COVID-19. Nature. 2024 Sep; 633(8031):905-913. 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. PMID: 39198643; PMCID: PMC11424477.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    5. PhosNetVis: a web-based tool for fast kinase-substrate enrichment analysis and interactive 2D/3D network visualizations of phosphoproteomics data. ArXiv. 2024 Jul 04. Rawal O, Turhan B, Peradejordi IF, Chandrasekar S, Kalayci S, Gnjatic S, Johnson J, Bouhaddou M, Gümüs ZH. PMID: 39010877; PMCID: PMC11247916.
      View in: PubMed   Mentions:
    6. Mapping Differential Protein-Protein Interaction Networks using Affinity Purification Mass Spectrometry. ArXiv. 2024 May 15. 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. PMID: 38800652; PMCID: PMC11118664.
      View in: PubMed   Mentions:
    7. CRISPR-Cas9 screen of E3 ubiquitin ligases identifies TRAF2 and UHRF1 as regulators of HIV latency in primary human T cells. mBio. 2024 Apr 10; 15(4):e0222223. 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. PMID: 38411080; PMCID: PMC11005436.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    8. A foundational atlas of autism protein interactions reveals molecular convergence. bioRxiv. 2024 Feb 08. 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. PMID: 38076945; PMCID: PMC10705567.
      View in: PubMed   Mentions:
    9. Hyperphosphorylation of BCL-2 family proteins underlies functional resistance to venetoclax in lymphoid malignancies. J Clin Invest. 2023 11 15; 133(22). Chong SJF, Zhu F, Dashevsky O, Mizuno R, Lai JX, Hackett L, Ryan CE, Collins MC, Iorgulescu JB, Guièze R, Penailillo J, Carrasco R, Hwang YC, Muñoz DP, Bouhaddou M, Lim YC, Wu CJ, Allan JN, Furman RR, Goh BC, Pervaiz S, Coppé JP, Mitsiades CS, Davids MS. PMID: 37751299; PMCID: PMC10645378.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    10. Hepatitis C virus infects and perturbs liver stem cells. mBio. 2023 Dec 19; 14(6):e0131823. 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. PMID: 37938000; PMCID: PMC10746249.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    11. Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets. Nat Commun. 2023 09 27; 14(1):6030. 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. PMID: 37758692; PMCID: PMC10533562.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    12. SARS-CoV-2 variants evolve convergent strategies to remodel the host response. Cell. 2023 10 12; 186(21):4597-4614.e26. 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. PMID: 37738970; PMCID: PMC10604369.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansCellsPHPublic Health
    13. Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis. Cell Host Microbe. 2023 10 11; 31(10):1668-1684.e12. 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. PMID: 37738983; PMCID: PMC10750313.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansCells
    14. Network modeling suggests HIV infection phenocopies PI3K-AKT pathway mutations to enhance HPV-associated cervical cancer. Mol Omics. 2023 08 14; 19(7):538-551. Olwal CO, Fabius JM, Zuliani-Alvarez L, Eckhardt M, Kyei GB, Quashie PK, Krogan NJ, Bouhaddou M, Bediako Y. PMID: 37204043; PMCID: PMC10524288.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    15. Defining blood-induced microglia functions in neurodegeneration through multiomic profiling. Nat Immunol. 2023 07; 24(7):1173-1187. 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. PMID: 37291385; PMCID: PMC10307624.
      View in: PubMed   Mentions: 29     Fields:    Translation:AnimalsCells
    16. Current proteomics methods applicable to dissecting the DNA damage response. NAR Cancer. 2023 Jun; 5(2):zcad020. Muralidharan M, Krogan NJ, Bouhaddou M, Kim M. PMID: 37213254; PMCID: PMC10198729.
      View in: PubMed   Mentions: 1  
    17. Oncogenic PKA signaling increases c-MYC protein expression through multiple targetable mechanisms. Elife. 2023 01 24; 12. 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. PMID: 36692000; PMCID: PMC9925115.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    18. How can systems approaches help us understand and treat infectious disease? Cell Syst. 2022 12 21; 13(12):945-949. Kuchina A, Yang J, Aldridge B, Janes KA, Subramanian N, Krogan NJ, Bouhaddou M, Einav S, Papin J, Germain RN. PMID: 36549272.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    19. Network inference from perturbation time course data. NPJ Syst Biol Appl. 2022 11 01; 8(1):42. Sarmah D, Smith GR, Bouhaddou M, Stern AD, Erskine J, Birtwistle MR. PMID: 36316338; PMCID: PMC9622863.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    20. A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling. Nat Commun. 2022 06 21; 13(1):3555. Erdem C, Mutsuddy A, Bensman EM, Dodd WB, Saint-Antoine MM, Bouhaddou M, Blake RC, Gross SM, Heiser LM, Feltus FA, Birtwistle MR. PMID: 35729113; PMCID: PMC9213456.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    21. A functional map of HIV-host interactions in primary human T cells. Nat Commun. 2022 04 01; 13(1):1752. 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. PMID: 35365639; PMCID: PMC8976027.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansCells
    22. Publisher Correction: Evolution of enhanced innate immune evasion by SARS-CoV-2. Nature. 2022 Apr; 604(7905):E14. 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. PMID: 35332335; PMCID: PMC8944406.
      View in: PubMed   Mentions: 2     Fields:    
    23. Leveraging modeling and simulation to optimize the therapeutic window for epigenetic modifier drugs. Pharmacol Ther. 2022 07; 235:108162. Walz AC, Van De Vyver AJ, Yu L, Birtwistle MR, Krogan NJ, Bouhaddou M. PMID: 35189161; PMCID: PMC9292061.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    24. Mutations in SARS-CoV-2 variants of concern link to increased spike cleavage and virus transmission. Cell Host Microbe. 2022 03 09; 30(3):373-387.e7. 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. PMID: 35150638; PMCID: PMC8776496.
      View in: PubMed   Mentions: 101     Fields:    Translation:HumansCells
    25. Preclinical and randomized phase I studies of plitidepsin in adults hospitalized with COVID-19. Life Sci Alliance. 2022 04; 5(4). 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. PMID: 35012962; PMCID: PMC8761492.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansCellsCTClinical Trials
    26. Evolution of enhanced innate immune evasion by SARS-CoV-2. Nature. 2022 02; 602(7897):487-495. 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. PMID: 34942634; PMCID: PMC8850198.
      View in: PubMed   Mentions: 186     Fields:    Translation:HumansCells
    27. Caveolin-1 and Sox-2 are predictive biomarkers of cetuximab response in head and neck cancer. JCI Insight. 2021 10 22; 6(20). 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. PMID: 34546978; PMCID: PMC8564908.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimals
    28. A protein network map of head and neck cancer reveals PIK3CA mutant drug sensitivity. Science. 2021 Oct; 374(6563):eabf2911. 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. PMID: 34591642; PMCID: PMC9005332.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansAnimalsCells
    29. A protein interaction landscape of breast cancer. Science. 2021 Oct; 374(6563):eabf3066. 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. PMID: 34591612; PMCID: PMC9040556.
      View in: PubMed   Mentions: 50     Fields:    Translation:HumansCells
    30. Evolution of enhanced innate immune evasion by the SARS-CoV-2 B.1.1.7 UK variant. bioRxiv. 2021 Jun 07. 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. PMID: 34127972; PMCID: PMC8202424.
      View in: PubMed   Mentions: 8  
    31. Plitidepsin has a positive therapeutic index in adult patients with COVID-19 requiring hospitalization. medRxiv. 2021 May 25. 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. PMID: 34075384; PMCID: PMC8168388.
      View in: PubMed   Mentions:
    32. CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes. Res Sq. 2021 May 19. 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. PMID: 34031651; PMCID: PMC8142659.
      View in: PubMed   Mentions: 2  
    33. CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes. bioRxiv. 2021 May 11. 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. PMID: 34013269; PMCID: PMC8132225.
      View in: PubMed   Mentions: 4  
    34. Host-directed therapies against early-lineage SARS-CoV-2 retain efficacy against B.1.1.7 variant. bioRxiv. 2021 Feb 04. 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. PMID: 33501437; PMCID: PMC7836107.
      View in: PubMed   Mentions: 2  
    35. Plitidepsin has potent preclinical efficacy against SARS-CoV-2 by targeting the host protein eEF1A. Science. 2021 02 26; 371(6532):926-931. 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. PMID: 33495306; PMCID: PMC7963220.
      View in: PubMed   Mentions: 164     Fields:    Translation:HumansAnimalsCells
    36. Genetic Screens Identify Host Factors for SARS-CoV-2 and Common Cold Coronaviruses. Cell. 2021 01 07; 184(1):106-119.e14. 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. PMID: 33333024; PMCID: PMC7723770.
      View in: PubMed   Mentions: 243     Fields:    Translation:HumansAnimalsCells
    37. 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, et al. PMID: 33060197; PMCID: PMC7808408.
      View in: PubMed   Mentions: 382     Fields:    Translation:HumansCells
    38. Functional genomic screens identify human host factors for SARS-CoV-2 and common cold coronaviruses. bioRxiv. 2020 Sep 24. 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. PMID: 32995787; PMCID: PMC7523113.
      View in: PubMed   Mentions: 1  
    39. 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; PMCID: PMC7321036.
      View in: PubMed   Mentions: 553     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    40. The Landscape of Human Cancer Proteins Targeted by SARS-CoV-2. Cancer Discov. 2020 07; 10(7):916-921. Tutuncuoglu B, Cakir M, Batra J, Bouhaddou M, Eckhardt M, Gordon DE, Krogan NJ. PMID: 32444466; PMCID: PMC7357668.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansCellsPHPublic Health
    41. 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; PMCID: PMC7431030.
      View in: PubMed   Mentions: 2487     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    42. A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing. bioRxiv. 2020 Mar 27. Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O'Meara MJ, Guo JZ, Swaney DL, Tummino TA, Huettenhain 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, Liboy-Lugo J, Lin Y, Wankowicz SA, Bohn M, Sharp PP, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Roesch F, Vallet T, Meyer B, White KM, Miorin L, Rosenberg OS, Verba KA, Agard D, Ott M, Emerman M, Ruggero D, García-Sastre A, Jura N, von Zastrow M, Taunton J, Ashworth A, 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; PMCID: PMC7239059.
      View in: PubMed   Mentions: 6  
    43. Predicting In Vivo Efficacy from In Vitro Data: Quantitative Systems Pharmacology Modeling for an Epigenetic Modifier Drug in Cancer. Clin Transl Sci. 2020 03; 13(2):419-429. Bouhaddou M, Yu LJ, Lunardi S, Stamatelos SK, Mack F, Gallo JM, Birtwistle MR, Walz AC. PMID: 31729169; PMCID: PMC7070804.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    44. Mapping the protein-protein and genetic interactions of cancer to guide precision medicine. Curr Opin Genet Dev. 2019 02; 54:110-117. Bouhaddou M, Eckhardt M, Chi Naing ZZ, Kim M, Ideker T, Krogan NJ. PMID: 31288129; PMCID: PMC6746583.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    45. Fluorescence Multiplexing with Spectral Imaging and Combinatorics. ACS Comb Sci. 2018 11 12; 20(11):653-659. Holzapfel HY, Stern AD, Bouhaddou M, Anglin CM, Putur D, Comer S, Birtwistle MR. PMID: 30339749; PMCID: PMC9827428.
      View in: PubMed   Mentions: 9     Fields:    
    46. Validating Antibodies for Quantitative Western Blot Measurements with Microwestern Array. Sci Rep. 2018 07 27; 8(1):11329. Koch RJ, Barrette AM, Stern AD, Hu B, Bouhaddou M, Azeloglu EU, Iyengar R, Birtwistle MR. PMID: 30054510; PMCID: PMC6063895.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    47. A mechanistic pan-cancer pathway model informed by multi-omics data interprets stochastic cell fate responses to drugs and mitogens. PLoS Comput Biol. 2018 03; 14(3):e1005985. Bouhaddou M, Barrette AM, Stern AD, Koch RJ, DiStefano MS, Riesel EA, Santos LC, Tan AL, Mertz AE, Birtwistle MR. PMID: 29579036; PMCID: PMC5886578.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansCells
    48. Analysis of copy number loss of the ErbB4 receptor tyrosine kinase in glioblastoma. PLoS One. 2018; 13(1):e0190664. Jones DC, Scanteianu A, DiStefano M, Bouhaddou M, Birtwistle MR. PMID: 29342193; PMCID: PMC5771580.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    49. A Comparison of mRNA Sequencing with Random Primed and 3'-Directed Libraries. Sci Rep. 2017 11 07; 7(1):14626. Xiong Y, Soumillon M, Wu J, Hansen J, Hu B, van Hasselt JGC, Jayaraman G, Lim R, Bouhaddou M, Ornelas L, Bochicchio J, Lenaeus L, Stocksdale J, Shim J, Gomez E, Sareen D, Svendsen C, Thompson LM, Mahajan M, Iyengar R, Sobie EA, Azeloglu EU, Birtwistle MR. PMID: 29116112; PMCID: PMC5676863.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansCells
    50. Integrating Transcriptomic Data with Mechanistic Systems Pharmacology Models for Virtual Drug Combination Trials. ACS Chem Neurosci. 2018 01 17; 9(1):118-129. Barrette AM, Bouhaddou M, Birtwistle MR. PMID: 28950062; PMCID: PMC5771884.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    51. Drug response consistency in CCLE and CGP. Nature. 2016 11 30; 540(7631):E9-E10. Bouhaddou M, DiStefano MS, Riesel EA, Carrasco E, Holzapfel HY, Jones DC, Smith GR, Stern AD, Somani SS, Thompson TV, Birtwistle MR. PMID: 27905419; PMCID: PMC5554885.
      View in: PubMed   Mentions: 34     Fields:    
    52. Engineered Mammalian RNAi Can Elicit Antiviral Protection that Negates the Requirement for the Interferon Response. Cell Rep. 2015 Nov 17; 13(7):1456-1466. Benitez AA, Spanko LA, Bouhaddou M, Sachs D, tenOever BR. PMID: 26549455; PMCID: PMC4654977.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansAnimalsCells
    53. Dimerization-based control of cooperativity. Mol Biosyst. 2014 Jul; 10(7):1824-32. Bouhaddou M, Birtwistle MR. PMID: 24736836; PMCID: PMC4060435.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
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