Manon Eckhardt, PhD
Sr. Manager, Sci. Publications
Quantitative_Bioscience_Ins
School of Pharmacy

Education & Training

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• Postdoctoral Scholar Systems Biology / Protein-Protein Interactions Gladstone Institutes, San Francisco 2018
• Postdoctoral Scholar Systems Biology / Protein-Protein Interactions University of California, San Francisco 2016
• Postdoctoral Scholar Department of Virology University Hospital Heidelberg, Germany 2011
• Ph.D. Faculty of Biosciences University of Heidelberg, Germany 2010
• Diplom (M.Sc.) Biochemistry / Biophysical Chemistry / Cell Biology J.W. Goethe University Frankfurt, Germany 2004

Publications (29)

Top publication keywords:
Drug RepositioningSystems BiologyMolecular ProbesCommunicable DiseasesHost-Pathogen InteractionsProtein Interaction MapsPapillomavirus InfectionsMass SpectrometryChromatography, AffinityProtein Interaction Mappinggag Gene Products, Human Immunodeficiency VirusVirus InternalizationPapillomaviridaeProteomicsCarcinogenesis

• Coronavirus protein interaction mapping in bat and human cells identifies molecular and genetic switches for immune evasion and replication.
  bioRxiv : the preprint server for biology 2025 Batra J, Rutkowska M, Zhou Y, Ye C, Adavikolanu R, Young JM, Anand D, Verma S, Gordon M, Malpotra S, Cupic A, Kehrer T, Moen JM, Winters DM, Rojc A, Mena I, Aslam S, Martinez-Romero C, Conde Viñas I, …
• Paracrine Signals from HIV-1 Infected Immune Cells Reprogram Cervical Cancer Pathways.
  bioRxiv : the preprint server for biology 2025 Olwal CO, Rathore U, Makanani S, Kaushal P, Ashley IA, Ummadi MR, Appiah V, Zune ALD, Blanc S, Winters D, Delgado Y, Muthoka K, Fabius JM, Eckhardt M, Kaake RM, Su M, Fregoso OI, Hultquist JF, Orang'o…
• Affinity Purification Mass Spectrometry on the Orbitrap-Astral Mass Spectrometer Enables High-Throughput Protein-Protein Interaction Mapping.
  Journal of proteome research 2025 Serrano LR, Pelin A, Arrey TN, Damoc NE, Richards AL, Zhou Y, Lancaster NM, Peters-Clarke TM, Pashkova A, Jang GM, Eckhardt M, Quarmby ST, Zeller M, Hermanson D, Stewart H, Hock C, Makarov A, …
• HBV Remodels PP2A Complexes to Rewire Kinase Signaling in Hepatocellular Carcinoma.
  Cancer research 2025 Turnham RE, Pitea A, Jang GM, Xu Z, Lim HC, Choi AL, Von Dollen J, Levin RS, Webber JT, McCarthy E, Hu J, Li X, Che L, Singh A, Yoon A, Chan GKL, Kelley RK, Swaney DL, Zhang W, Bandyopadhyay S, Theis …
• Protocol for mapping differential protein-protein interaction networks using affinity purification-mass spectrometry.
  STAR protocols 2024 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

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• A proximity proteomics pipeline with improved reproducibility and throughput.
  Molecular systems biology 2024 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
• Mapping Differential Protein-Protein Interaction Networks using Affinity Purification Mass Spectrometry.
  ArXiv 2024 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 2024 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
• CRISPR-Cas9 screen of E3 ubiquitin ligases identifies TRAF2 and UHRF1 as regulators of HIV latency in primary human T cells.
  mBio 2024 Rathore U, Haas P, Easwar Kumar V, Hiatt J, Haas KM, Bouhaddou M, Swaney DL, Stevenson E, Zuliani-Alvarez L, McGregor MJ, Turner-Groth A, Ochieng' Olwal C, Bediako Y, Braberg H, Soucheray M, Ott M, …
• A foundational atlas of autism protein interactions reveals molecular convergence.
  bioRxiv : the preprint server for biology 2024 Wang B, Vartak R, Zaltsman Y, Naing ZZC, Hennick KM, Polacco BJ, Bashir A, Eckhardt M, Bouhaddou M, Xu J, Sun N, Lasser MC, Zhou Y, McKetney J, Guiley KZ, Chan U, Kaye JA, Chadha N, Cakir M, Gordon M,…
• Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets.
  Nature communications 2023 Haas KM, McGregor MJ, Bouhaddou M, Polacco BJ, Kim EY, Nguyen TT, Newton BW, Urbanowski M, Kim H, Williams MAP, Rezelj VV, Hardy A, Fossati A, Stevenson EJ, Sukerman E, Kim T, Penugonda S, Moreno E, …
• SARS-CoV-2 variants evolve convergent strategies to remodel the host response.
  Cell 2023 Bouhaddou M, Reuschl AK, Polacco BJ, Thorne LG, Ummadi MR, Ye C, Rosales R, Pelin A, Batra J, Jang GM, Xu J, Moen JM, Richards AL, Zhou Y, Harjai B, Stevenson E, Rojc A, Ragazzini R, Whelan MVX, …
• Network modeling suggests HIV infection phenocopies PI3K-AKT pathway mutations to enhance HPV-associated cervical cancer.
  Molecular omics 2023 Olwal CO, Fabius JM, Zuliani-Alvarez L, Eckhardt M, Kyei GB, Quashie PK, Krogan NJ, Bouhaddou M, Bediako Y
• Quantitative Proteomic Analysis Reveals apoE4-Dependent Phosphorylation of the Actin-Regulating Protein VASP.
  Molecular & cellular proteomics : MCP 2023 Cakir Z, Lord SJ, Zhou Y, Jang GM, Polacco BJ, Eckhardt M, Jimenez-Morales D, Newton BW, Orr AL, Johnson JR, da Cruz A, Mullins RD, Krogan NJ, Mahley RW, Swaney DL
• Structure-function analysis of enterovirus protease 2A in complex with its essential host factor SETD3.
  Nature communications 2022 Peters CE, Schulze-Gahmen U, Eckhardt M, Jang GM, Xu J, Pulido EH, Bardine C, Craik CS, Ott M, Gozani O, Verba KA, Hüttenhain R, Carette JE, Krogan NJ
• Mass spectrometry-based protein-protein interaction networks for the study of human diseases.
  Molecular systems biology 2021 Richards AL, Eckhardt M, Krogan NJ
• Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.
  Science (New York, N.Y.) 2020 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…
• The Landscape of Human Cancer Proteins Targeted by SARS-CoV-2.
  Cancer discovery 2020 Tutuncuoglu B, Cakir M, Batra J, Bouhaddou M, Eckhardt M, Gordon DE, Krogan NJ
• A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.
  Nature 2020 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, …
• A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing.
  bioRxiv : the preprint server for biology 2020 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, …
• A systems approach to infectious disease.
  Nature reviews. Genetics 2020 Eckhardt M, Hultquist JF, Kaake RM, Hüttenhain R, Krogan NJ
• Mapping the protein-protein and genetic interactions of cancer to guide precision medicine.
  Current opinion in genetics & development 2019 Bouhaddou M, Eckhardt M, Chi Naing ZZ, Kim M, Ideker T, Krogan NJ
• Multiple Routes to Oncogenesis Are Promoted by the Human Papillomavirus-Host Protein Network.
  Cancer discovery 2018 Eckhardt M, Zhang W, Gross AM, Von Dollen J, Johnson JR, Franks-Skiba KE, Swaney DL, Johnson TL, Jang GM, Shah PS, Brand TM, Archambault J, Kreisberg JF, Grandis JR, Ideker T, Krogan NJ
• Comparative mapping of host-pathogen protein-protein interactions.
  Current opinion in microbiology 2015 Shah PS, Wojcechowskyj JA, Eckhardt M, Krogan NJ
• HIV-1 entry in SupT1-R5, CEM-ss, and primary CD4+ T cells occurs at the plasma membrane and does not require endocytosis.
  Journal of virology 2014 Herold N, Anders-Ößwein M, Glass B, Eckhardt M, Müller B, Kräusslich HG
• An expanded model of HIV cell entry phenotype based on multi-parameter single-cell data.
  Retrovirology 2012 Bozek K, Eckhardt M, Sierra S, Anders M, Kaiser R, Kräusslich HG, Müller B, Lengauer T
• Escape from R-peptide deletion in a γ-retrovirus.
  Virology 2011 Schneider IC, Eckhardt M, Brynza J, Collins MK, Cichutek K, Buchholz CJ
• A SNAP-tagged derivative of HIV-1--a versatile tool to study virus-cell interactions.
  PloS one 2011 Eckhardt M, Anders M, Muranyi W, Heilemann M, Krijnse-Locker J, Müller B
• CD317/tetherin is enriched in the HIV-1 envelope and downregulated from the plasma membrane upon virus infection.
  Journal of virology 2010 Habermann A, Krijnse-Locker J, Oberwinkler H, Eckhardt M, Homann S, Andrew A, Strebel K, Kräusslich HG