Danielle Swaney, PhD
Associate Professor
Bioengineering
School of Pharmacy

My lab at UCSF is encompassed within the larger lab of Nevan Krogan. This provides scientists the best of both worlds - access to big-lab support and resources, but with strong small-lab mentorship. Additionally, I manage the proteomics facility at both the UCSF Weill Institute for Neurosciences, and at the Gladstone Institutes, where I am a visiting scientist.

• CRISPR screens in iPSC-derived neurons reveal principles of tau proteostasis.
  Cell 2026 Samelson AJ, Ariqat N, McKetney J, Rohanitazangi G, Parra Bravo C, Bose RS, Travaglini KJ, Lam VL, Goodness D, Ta T, Dixon G, Marzette E, Jin J, Tian R, Tse E, Abskharon R, Pan HS, Carroll EC, …
• Multicohort assessment of plasma metabolic signatures of tuberculosis disease in children: a retrospective cross-sectional study.
  Scientific reports 2026 Nellis MM, Luiz J, Jaganath D, Mousavian Z, Nkereuwem E, Wambi P, Calderon R, Paradkar M, Castro R, Nerurkar R, Franke MF, Kinikar A, Wobudeya E, Zar HJ, Jones DP, Segal M, Sigal G, Swaney DL, …
• Extracellular matrix proteolysis maintains synapse plasticity during brain development.
  Nature neuroscience 2025 Nakajo H, Cao R, Mula SA, McKetney J, Silva NJ, Li KH, Chalkley RJ, Randolph LK, Shah M, Rose IVL, Kampmann M, Swaney DL, Kirst C, Molofsky AV
• The Mac1 ADP-ribosylhydrolase is a therapeutic target for SARS-CoV-2.
  eLife 2025 Rahul K Suryawanshi, Priyadarshini Jaishankar, Galen J Correy, Moira M Rachman, Patrick C O'Leary, Taha Y Taha, Yusuke Matsui, Francisco J Zapatero-Belinchón, Maria McCavitt-Malvido, Yagmur U Doruk, …
• The Mac1 ADP-ribosylhydrolase is a therapeutic target for SARS-CoV-2.
  eLife 2025 Suryawanshi RK, Jaishankar P, Correy GJ, Rachman MM, O'Leary PC, Taha TY, Matsui Y, Zapatero-Belinchón FJ, McCavitt-Malvido M, Doruk YU, Stevens MGV, Diolaiti ME, Jogalekar MP, Chen H, Richards AL, …
• Lysosomal proteomics reveals mechanisms of neuronal APOE4-associated lysosomal dysfunction.
  Autophagy 2025 Krogsaeter EK, McKetney J, Valiente-Banuet L, Marquez A, Willis A, Cakir Z, Stevenson E, Jang GM, Rao A, Li E, Zhou A, Attili A, Chang TS, Kampmann M, Huang Y, Krogan NJ, Swaney DL
• Mycobacterium tuberculosis triggers reduced inflammatory cytokine responses and virulence in mice lacking Tax1bp1.
  PLoS pathogens 2025 Chin J, Abeydeera N, Repasy T, Rivera-Lugo R, Mitchell G, Nguyen VQ, Zheng W, Richards A, Stevenson E, Swaney DL, Krogan NJ, Ernst JD, Cox JS, Budzik JM
• Selective RNA sequestration in biomolecular condensates directs cell fate transitions.
  Nature biotechnology 2025 Pessina P, Nevo M, Shi J, Kodali S, Casas E, Cui Y, Richards AL, Park EJ, Chen X, Levin-Ferreyra F, Rivera Tostado A, Stevenson E, Krogan NJ, Swaney DL, Ying Q, Chen Q, Brumbaugh J, Di Stefano B
• The Mac1 ADP-ribosylhydrolase is a Therapeutic Target for SARS-CoV-2.
  bioRxiv : the preprint server for biology 2025 Suryawanshi RK, Jaishankar P, Correy GJ, Rachman MM, O'Leary PC, Taha TY, Matsui Y, Zapatero-Belinchón FJ, McCavitt-Malvido M, Doruk YU, Stevens MGV, Diolaiti ME, Jogalekar MP, Chen H, Richards AL, …
• Integrative multi-omics analysis in vivo identifies influenza virus host factors.
  iScience 2025 Shriver LP, Polacco BJ, Eckhardt M, Chang MW, Martínez-Romero C, Adkins-Travis K, Cahalane C, Haas K, Stein DA, Fourati S, Martin-Sancho L, Metreveli G, Johnson JR, Muñoz-Moreno R, Newton BW, Kaake RM…
• Coupled equilibria of dimerization and lipid binding modulate SARS Cov 2 Orf9b interactions and interferon response.
  eLife 2025 CJ San Felipe, Jyoti Batra, Monita Muralidharan, Shivali Malpotra, Durga Anand, Rachel Bauer, Kliment A Verba, Danielle L Swaney, Nevan J Krogan, Michael Grabe, James S Fraser
• Coupled equilibria of dimerization and lipid binding modulate SARS Cov 2 Orf9b interactions and interferon response.
  eLife 2025 San Felipe CJ, Batra J, Muralidharan M, Malpotra S, Anand D, Bauer R, Verba KA, Swaney DL, Krogan NJ, Grabe M, Fraser JS
• Multi-omic phenotyping of iPSC-derived neurons harboring the MAPT V337M mutation reveals tau hypophosphorylation and perturbed axon morphology pathways.
  bioRxiv : the preprint server for biology 2025 Mohl GA, Dixon G, Marzette E, McKetney J, Samelson AJ, Serras CP, Jin J, Ariqat N, Li A, Boggess SC, Swaney DL, Kampmann M
• Anti-restriction functions of injected phage proteins revealed by peeling back layers of bacterial immunity.
  Nature communications 2025 Silas S, Carion H, Makarova KS, Sanchez Godinez D, Haniyur S, Volino L, Yee WX, Fossati A, Swaney D, Bocek M, Koonin EV, Bondy-Denomy J
• Coupled equilibria of dimerization and lipid binding modulate SARS Cov 2 Orf9b interactions and interferon response.
  bioRxiv : the preprint server for biology 2025 Felipe CS, Batra J, Muralidharaan M, Malpotra S, Anand D, Bauer R, Verba KA, Swaney DL, Krogan NJ, Grabe M, Fraser JS
• Multicohort assessment of plasma metabolic signatures of tuberculosis disease in children.
  Research square 2025 Nellis MM, Luiz J, Jaganath D, Mousavian Z, Nkereuwem E, Wambi P, Calderon R, Paradkar M, Castro R, Nerurkar R, Franke MF, Kinikar A, Wobudeya E, Zar HJ, Segal M, Sigal G, Swaney DL, Cattamanchi A, …
• 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, …
• Plasma proteomics for biomarker discovery in childhood tuberculosis.
  Nature communications 2025 Fossati A, Wambi P, Jaganath D, Calderon R, Castro R, Mohapatra A, McKetney J, Luiz J, Nerurkar R, Nkereuwem E, Franke MF, Mousavian Z, Collins JM, Sigal GB, Segal MR, Kampman B, Wobudeya E, …
• Programmable translational inhibition by a molecular glue-oligonucleotide conjugate.
  bioRxiv : the preprint server for biology 2025 Wang S, Kovalski JR, Zapatero-Belinchón FJ, Bennett M, Kuzuoglu-Öztürk D, Li Q, Stevenson E, Liu J, Krogan NJ, Ott M, Swaney DL, Ruggero D, Lou K, Shokat KM
• 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…
• Selective RNA sequestration in biomolecular condensates directs cell fate transitions.
  bioRxiv : the preprint server for biology 2025 Pessina P, Nevo M, Shi J, Kodali S, Casas E, Cui Y, Richards AL, Park EJ, Chen X, Levin-Ferreyra F, Stevenson E, Krogan NJ, Swaney DL, Ying Q, Chen Q, Brumbaugh J, Di Stefano B
• Structure-based discovery of highly bioavailable, covalent, broad-spectrum coronavirus MPro inhibitors with potent in vivo efficacy.
  Science advances 2025 Detomasi TC, Degotte G, Huang S, Suryawanshi RK, Diallo A, Lizzadro L, Zapatero-Belinchón FJ, Taha TY, Li J, Richards AL, Hantz ER, Alam Z, Montano M, McCavitt-Malvido M, Gumpena R, Partridge JR, …
• The Chlamydia effector Dre1 binds dynactin to reposition host organelles during infection.
  Cell reports 2025 Sherry J, Pawar KI, Dolat L, Smith E, Chang IC, Pha K, Kaake R, Swaney DL, Herrera C, McMahon E, Bastidas RJ, Johnson JR, Valdivia RH, Krogan NJ, Elwell CA, Verba K, Engel JN
• Enhanced RNA replication and pathogenesis in recent SARS-CoV-2 variants harboring the L260F mutation in NSP6.
  PLoS pathogens 2025 Taha TY, Ezzatpour S, Hayashi JM, Ye C, Zapatero-Belinchón FJ, Rosecrans JA, Kimmerly GR, Chen IP, Walcott K, Kurianowicz A, Jorgens DM, Chaplin NR, Choi A, Buchholz DW, Sahler J, Hilt ZT, Imbiakha B,…
• Integrated multi-omic characterizations of the synapse reveal RNA processing factors and ubiquitin ligases associated with neurodevelopmental disorders.
  Cell systems 2025 Mei Y, Gosztyla ML, Tan X, Dozier LE, Wilkinson B, McKetney J, Lee J, Chen M, Tsai D, Kopalle H, Gritsenko MA, Hartel N, Graham NA, Flores I, Gilmore-Hall SK, Xu S, Marquez CA, Liu SN, Fong D, Chen J,…
• Lysosomal proteomics reveals mechanisms of neuronal apoE4-associated lysosomal dysfunction.
  bioRxiv : the preprint server for biology 2025 Krogsaeter EK, McKetney J, Valiente-Banuet L, Marquez A, Willis A, Cakir Z, Stevenson E, Jang GM, Rao A, Li E, Zhou A, Attili A, Chang TS, Kampmann M, Huang Y, Krogan NJ, Swaney DL
• Extracellular matrix proteolysis maintains synapse plasticity during brain development.
  bioRxiv : the preprint server for biology 2025 Nakajo H, Cao R, Mula SA, McKetney J, Silva NJ, Shah M, Rose IVL, Kampmann M, Swaney DL, Kirst C, Molofsky AV
• 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 …
• EGFR and EGFRvIII coopt host defense pathways promoting progression in glioblastoma.
  Neuro-oncology 2025 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
• Malaria exposure remodels the plasma proteome of Ghanaian children.
  BMC infectious diseases 2025 Mohammed AM, Olwal CO, Fossati A, Nyakoe NK, Fabius JM, Gordon M, Polacco BJ, Swaney DL, Awandare GA, Krogan NJ, Bouhaddou M, Bediako Y
• BPS2025 - A matter of perspective: Integrative ensemble modeling of viral proteins.
  Biophysical Journal 2025 Kenneth Huang, Monita Muralidharan, Amy Diallo, Yulia Gutierrez, Robyn Kaake, Kliment A. Verba, Danielle Swaney, Nevan Krogan, Ignacia Echeverria, Andrej Sali
• Tax1bp1 enhances bacterial virulence and promotes inflammatory responses during Mycobacterium tuberculosis infection of alveolar macrophages.
  bioRxiv : the preprint server for biology 2024 Chin J, Abeydeera N, Repasy T, Rivera-Lugo R, Mitchell G, Nguyen VQ, Zheng W, Richards A, Swaney DL, Krogan NJ, Ernst JD, Cox JS, Budzik JM
• Central control of dynamic gene circuits governs T cell rest and activation.
  Nature 2024 Arce MM, Umhoefer JM, Arang N, Kasinathan S, Freimer JW, Steinhart Z, Shen H, Pham MTN, Ota M, Wadhera A, Dajani R, Dorovskyi D, Chen YY, Liu Q, Zhou Y, Swaney DL, Obernier K, Shy BR, Carnevale J, …
• CRISPR screens in iPSC-derived neurons reveal principles of tau proteostasis.
  bioRxiv : the preprint server for biology 2024 Samelson AJ, Ariqat N, McKetney J, Rohanitazangi G, Bravo CP, Bose R, Travaglini KJ, Lam VL, Goodness D, Dixon G, Marzette E, Jin J, Tian R, Tse E, Abskharon R, Pan H, Carroll EC, Lawrence RE, …
• 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
• MerlinS13 phosphorylation regulates meningioma Wnt signaling and magnetic resonance imaging features.
  Nature communications 2024 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
• Multiscale photocatalytic proximity labeling reveals cell surface neighbors on and between cells.
  Science (New York, N.Y.) 2024 Lin Z, Schaefer K, Lui I, Yao Z, Fossati A, Swaney DL, Palar A, Sali A, Wells JA
• Characterization of a lipid-based jumbo phage compartment as a hub for early phage infection.
  Cell host & microbe 2024 Mozumdar D, Fossati A, Stevenson E, Guan J, Nieweglowska E, Rao S, Agard D, Swaney DL, Bondy-Denomy J
• Targeting a lineage-specific PI3Kɣ-Akt signaling module in acute myeloid leukemia using a heterobifunctional degrader molecule.
  Nature cancer 2024 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, …
• The Chlamydia trachomatis Inc Tri1 interacts with TRAF7 to displace native TRAF7 interacting partners.
  Microbiology spectrum 2024 Herrera CM, McMahon E, Swaney DL, Sherry J, Pha K, Adams-Boone K, Johnson JR, Krogan NJ, Stevers M, Solomon D, Elwell C, Engel J
• 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
• ATG7(2) Interacts With Metabolic Proteins and Regulates Central Energy Metabolism.
  Traffic (Copenhagen, Denmark) 2024 Ostacolo K, López García de Lomana A, Larat C, Hjaltalin V, Holm KY, Hlynsdóttir SS, Soucheray M, Sooman L, Rolfsson O, Krogan NJ, Steingrimsson E, Swaney DL, Ogmundsdottir MH
• CRISPR-Cas9 screen of E3 ubiquitin ligases identifies TRAF2 and UHRF1 as regulators of HIV latency in primary human T cells.
  mBio 2024 Rathore U, Haas P, Easwar Kumar V, Hiatt J, Haas KM, Bouhaddou M, Swaney DL, Stevenson E, Zuliani-Alvarez L, McGregor MJ, Turner-Groth A, Ochieng' Olwal C, Bediako Y, Braberg H, Soucheray M, Ott M, …
• Spatial control of sensory adaptation modulates mechanosensing in Pseudomonas aeruginosa.
  bioRxiv : the preprint server for biology 2024 Patino R, Kühn MJ, Macmillan H, Inclan YF, Chavez I, Von Dollen J, Johnson JR, Swaney DL, Krogan NJ, Persat A, Engel JN
• The Chlamydia trachomatis Inc Tri1 interacts with TRAF7 to displace native TRAF7 interacting partners.
  bioRxiv : the preprint server for biology 2024 Herrera CM, McMahon E, Swaney DL, Sherry J, Pha K, Adams-Boone K, Johnson JR, Krogan NJ, Stevers M, Solomon D, Elwell C, Engel J
• A foundational atlas of autism protein interactions reveals molecular convergence.
  bioRxiv : the preprint server for biology 2024 Wang B, Vartak R, Zaltsman Y, Naing ZZC, Hennick KM, Polacco BJ, Bashir A, Eckhardt M, Bouhaddou M, Xu J, Sun N, Lasser MC, Zhou Y, McKetney J, Guiley KZ, Chan U, Kaye JA, Chadha N, Cakir M, Gordon M,…
• Epigenetic reprogramming shapes the cellular landscape of schwannoma.
  Nature communications 2024 Liu SJ, Casey-Clyde T, Cho NW, Swinderman J, Pekmezci M, Dougherty MC, Foster K, Chen WC, Villanueva-Meyer JE, Swaney DL, Vasudevan HN, Choudhury A, Pak J, Breshears JD, Lang UE, Eaton CD, Hiam-Galvez…
• Cross-family small GTPase ubiquitination by the intracellular pathogen Legionella pneumophila.
  Molecular biology of the cell 2023 Steinbach A, Bhadkamkar V, Jimenez-Morales D, Stevenson E, Jang GM, Krogan NJ, Swaney DL, Mukherjee S
• In vivo protein turnover rates in varying oxygen tensions nominate MYBBP1A as a mediator of the hyperoxia response.
  Science advances 2023 Chen X, Haribowo AG, Baik AH, Fossati A, Stevenson E, Chen YR, Reyes NS, Peng T, Matthay MA, Traglia M, Pico AR, Jarosz DF, Buchwalter A, Ghaemmaghami S, Swaney DL, Jain IH
• Molecular determinants of the crosstalk between endosomal microautophagy and chaperone-mediated autophagy.
  Cell reports 2023 Krause GJ, Kirchner P, Stiller B, Morozova K, Diaz A, Chen KH, Krogan NJ, Agullo-Pascual E, Clement CC, Lindenau K, Swaney DL, Dilipkumar S, Bravo-Cordero JJ, Santambrogio L, Cuervo AM
• Multi-scale photocatalytic proximity labeling reveals cell surface neighbors on and between cells.
  bioRxiv : the preprint server for biology 2023 Lin Z, Schaefer K, Lui I, Yao Z, Fossati A, Swaney DL, Palar A, Sali A, Wells JA
• A Legionella toxin exhibits tRNA mimicry and glycosyl transferase activity to target the translation machinery and trigger a ribotoxic stress response.
  Nature cell biology 2023 Subramanian A, Wang L, Moss T, Voorhies M, Sangwan S, Stevenson E, Pulido EH, Kwok S, Chalkley RJ, Li KH, Krogan NJ, Swaney DL, Burlingame AL, Floor SN, Sil A, Walter P, Mukherjee S
• High-throughput chemogenetic drug screening reveals PKC-RhoA/PKN as a targetable signaling vulnerability in GNAQ-driven uveal melanoma.
  Cell reports. Medicine 2023 Arang N, Lubrano S, Ceribelli M, Rigiracciolo DC, Saddawi-Konefka R, Faraji F, Ramirez SI, Kim D, Tosto FA, Stevenson E, Zhou Y, Wang Z, Bogomolovas J, Molinolo AA, Swaney DL, Krogan NJ, Yang J, Coma …
• Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets.
  Nature communications 2023 Haas KM, McGregor MJ, Bouhaddou M, Polacco BJ, Kim EY, Nguyen TT, Newton BW, Urbanowski M, Kim H, Williams MAP, Rezelj VV, Hardy A, Fossati A, Stevenson EJ, Sukerman E, Kim T, Penugonda S, Moreno E, …
• Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis.
  Cell host & microbe 2023 Kehrer T, Cupic A, Ye C, Yildiz S, Bouhaddou M, Crossland NA, Barrall EA, Cohen P, Tseng A, Çagatay T, Rathnasinghe R, Flores D, Jangra S, Alam F, Mena I, Aslam S, Saqi A, Rutkowska M, Ummadi MR, …
• SARS-CoV-2 variants evolve convergent strategies to remodel the host response.
  Cell 2023 Bouhaddou M, Reuschl AK, Polacco BJ, Thorne LG, Ummadi MR, Ye C, Rosales R, Pelin A, Batra J, Jang GM, Xu J, Moen JM, Richards AL, Zhou Y, Harjai B, Stevenson E, Rojc A, Ragazzini R, Whelan MVX, …
• Next-generation proteomics for quantitative Jumbophage-bacteria interaction mapping.
  Nature communications 2023 Fossati A, Mozumdar D, Kokontis C, Mèndez-Moran M, Nieweglowska E, Pelin A, Li Y, Guo B, Krogan NJ, Agard DA, Bondy-Denomy J, Swaney DL
• The microenvironment dictates glycocalyx construction and immune surveillance.
  Research square 2023 Tharp KM, Park S, Timblin GA, Richards AL, Berg JA, Twells NM, Riley NM, Peltan EL, Shon DJ, Stevenson E, Tsui K, Palomba F, Lefebvre AEYT, Soens RW, Ayad NME, Hoeve-Scott JT, Healy K, Digman M, …
• Cross-family small GTPase ubiquitination by the intracellular pathogen Legionella pneumophila.
  bioRxiv : the preprint server for biology 2023 Steinbach AM, Bhadkamkar VL, Jimenez-Morales D, Stevenson E, Jang GM, Krogan NJ, Swaney DL, Mukherjee S
• Functional analysis of a common BAG3 allele associated with protection from heart failure.
  Nature cardiovascular research 2023 Perez-Bermejo JA, Judge LM, Jensen CL, Wu K, Watry HL, Truong A, Ho JJ, Carter M, Runyon WV, Kaake RM, Pulido EH, Mandegar MA, Swaney DL, So PL, Krogan NJ, Conklin BR
• Deep learning from harmonized peptide libraries enables retention time prediction of diverse post translational modifications.
  bioRxiv : the preprint server for biology 2023 Wilburn DB, Shannon AE, Spicer V, Richards AL, Yeung D, Swaney DL, Krokhin OV, Searle BC
• Quantitative Proteomic Analysis Reveals apoE4-Dependent Phosphorylation of the Actin-Regulating Protein VASP.
  Molecular & cellular proteomics : MCP 2023 Cakir Z, Lord SJ, Zhou Y, Jang GM, Polacco BJ, Eckhardt M, Jimenez-Morales D, Newton BW, Orr AL, Johnson JR, da Cruz A, Mullins RD, Krogan NJ, Mahley RW, Swaney DL
• MerlinS13 phosphorylation controls meningioma Wnt signaling and magnetic resonance imaging features.
  Research square 2023 Eaton C, Avalos L, Liu SJ, Casey-Clyde T, Bisignano P, Lucas CH, Stevenson E, Choudhury A, Vasudevan H, Magill S, Krogan N, Villanueva-Meyer J, Swaney D, Raleigh D
• Next-generation interaction proteomics for quantitative Jumbophage-bacteria interaction mapping.
  bioRxiv : the preprint server for biology 2023 Fossati A, Mozumdar D, Kokontis C, Mèndez-Moran M, Nieweglowska E, Pelin A, Li Y, Guo B, Krogan NJ, Agard DA, Bondy-Denomy J, Swaney DL
• Oncogenic PKA signaling increases c-MYC protein expression through multiple targetable mechanisms.
  eLife 2023 Chan GKL, Maisel S, Hwang YC, Pascual BC, Wolber RRB, Vu P, Patra KC, Bouhaddou M, Kenerson HL, Lim HC, Long D, Yeung RS, Sethupathy P, Swaney DL, Krogan NJ, Turnham RE, Riehle KJ, Scott JD, Bardeesy …
• Quantitative proteomic analysis reveals apoE4-dependent phosphorylation of the actin regulating protein VASP.
  Alzheimer's & Dementia 2022 Zeynep Cakir, Benjamin Polacco, Nevan J Krogan, Robert W Mahley, Danielle L Swaney
• Abstract B016: Inhibition of KRASG12C in colon cancer illustrates a link between beta-catenin, WNK, and the GID complex.
  Cancer Research 2022 Kasturi Nayak, Yeonjoo Hwang, LeeAnn Wang, Danielle L. Swaney, Nevan J. Krogan, John D. Gordan
• Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis.
  bioRxiv : the preprint server for biology 2022 Kehrer T, Cupic A, Ye C, Yildiz S, Bouhhadou M, Crossland NA, Barrall E, Cohen P, Tseng A, Çagatay T, Rathnasinghe R, Flores D, Jangra S, Alam F, Mena N, Aslam S, Saqi A, Marin A, Rutkowska M, Ummadi …
• CSIG-37. MERLIN S13 DEPHOSPHORYLATION DRIVES MENINGIOMA WNT SIGNALLING AND CELL PROLIFERATION.
  Neuro-Oncology 2022 Charlotte Eaton, S John Liu, Calixto-Hope Lucas, Tim Casey-Clyde, Abrar Choudhury, Vikas Daggubati, Harish Vasudevan, Danielle Swaney, David Raleigh
• EPCO-01. EPIGENETIC REPROGRAMMING SHAPES THE MOLECULAR AND CELLULAR LANDSCAPE OF SCHWANNOMA.
  Neuro-Oncology 2022 S John Liu, Tim Casey-Clyde, Jason Swinderman, Nam Woo Cho, Harish Vasudevan, Kyla Foster, Melike Pekmezci, William Chen, Javier Villanueva-Meyer, Kamir J Hiam-Galvez, Danielle Swaney, Abrar Choudhury…
• Resistance to ATR Inhibitors Is Mediated by Loss of the Nonsense-Mediated Decay Factor UPF2.
  Cancer research 2022 O'Leary PC, Chen H, Doruk YU, Williamson T, Polacco B, McNeal AS, Shenoy T, Kale N, Carnevale J, Stevenson E, Quigley DA, Chou J, Feng FY, Swaney DL, Krogan NJ, Kim M, Diolaiti ME, Ashworth A
• Reduced endosomal microautophagy activity in aging associates with enhanced exocyst-mediated protein secretion.
  Aging cell 2022 Krause GJ, Diaz A, Jafari M, Khawaja RR, Agullo-Pascual E, Santiago-Fernández O, Richards AL, Chen KH, Dmitriev P, Sun Y, See SK, Abdelmohsen K, Mazan-Mamczarz K, Krogan NJ, Gorospe M, Swaney DL, …
• Meningioma DNA methylation groups identify biological drivers and therapeutic vulnerabilities.
  Nature genetics 2022 Choudhury A, Magill ST, Eaton CD, Prager BC, Chen WC, Cady MA, Seo K, Lucas CG, Casey-Clyde TJ, Vasudevan HN, Liu SJ, Villanueva-Meyer JE, Lam TC, Pu JK, Li LF, Leung GK, Swaney DL, Zhang MY, Chan JW,…
• The E3 ligase TRIM1 ubiquitinates LRRK2 and controls its localization, degradation, and toxicity.
  The Journal of cell biology 2022 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, …
• Data-Independent Acquisition Protease-Multiplexing Enables Increased Proteome Sequence Coverage Across Multiple Fragmentation Modes.
  Journal of proteome research 2022 Richards AL, Chen KH, Wilburn DB, Stevenson E, Polacco BJ, Searle BC, Swaney DL
• Tau interactome maps synaptic and mitochondrial processes associated with neurodegeneration.
  Cell 2022 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…
• Evolution of enhanced innate immune evasion by SARS-CoV-2.
  Nature 2021 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, …
• Therapeutic implications of activating noncanonical PIK3CA mutations in head and neck squamous cell carcinoma.
  The Journal of clinical investigation 2021 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
• Caveolin-1 and Sox-2 are predictive biomarkers of cetuximab response in head and neck cancer.
  JCI insight 2021 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, …
• Systems-level effects of allosteric perturbations to a model molecular switch.
  Nature 2021 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.) 2021 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…
• Interpretation of cancer mutations using a multiscale map of protein systems.
  Science (New York, N.Y.) 2021 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, …
• Restriction factor compendium for influenza A virus reveals a mechanism for evasion of autophagy.
  Nature microbiology 2021 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-…
• Brown adipocyte ATF4 activation improves thermoregulation and systemic metabolism.
  Cell reports 2021 Paulo E, Zhang Y, Masand R, Huynh TL, Seo Y, Swaney DL, Soucheray M, Stevenson E, Jimenez-Morales D, Krogan NJ, Wang B
• Toward Comprehensive Plasma Proteomics by Orthogonal Protease Digestion.
  Journal of proteome research 2021 Fossati A, Richards AL, Chen KH, Jaganath D, Cattamanchi A, Ernst JD, Swaney DL
• A ciliopathy complex builds distal appendages to initiate ciliogenesis.
  The Journal of cell biology 2021 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
• Adhesion-mediated mechanosignaling forces mitohormesis.
  Cell metabolism 2021 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 …
• Chaperone-mediated autophagy prevents collapse of the neuronal metastable proteome.
  Cell 2021 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,…
• The AMBRA1 E3 ligase adaptor regulates the stability of cyclin D.
  Nature 2021 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, …
• CIDer: A Statistical Framework for Interpreting Differences in CID and HCD Fragmentation.
  Journal of proteome research 2021 Wilburn DB, Richards AL, Swaney DL, Searle BC
• An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike.
  Science (New York, N.Y.) 2020 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,…
• 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 Global Phosphorylation Landscape of SARS-CoV-2 Infection.
  Cell 2020 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…
• The kinase Isr1 negatively regulates hexosamine biosynthesis in S. cerevisiae.
  PLoS genetics 2020 Alme EB, Stevenson E, Krogan NJ, Swaney DL, Toczyski DP
• Unbiased Proteomic Profiling Uncovers a Targetable GNAS/PKA/PP2A Axis in Small Cell Lung Cancer Stem Cells.
  Cancer cell 2020 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, …
• 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 Quantitative Genetic Interaction Map of HIV Infection.
  Molecular cell 2020 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
• Dynamic post-translational modification profiling of Mycobacterium tuberculosis-infected primary macrophages.
  eLife 2020 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
• The functional landscape of the human phosphoproteome.
  Nature biotechnology 2019 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
• Systematic Identification of Host Cell Regulators of Legionella pneumophila Pathogenesis Using a Genome-wide CRISPR Screen.
  Cell host & microbe 2019 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
• Anti-CRISPR-Associated Proteins Are Crucial Repressors of Anti-CRISPR Transcription.
  Cell 2019 Stanley SY, Borges AL, Chen KH, Swaney DL, Krogan NJ, Bondy-Denomy J, Davidson AR
• KRASG12C inhibition produces a driver-limited state revealing collateral dependencies.
  Science signaling 2019 Lou K, Steri V, Ge AY, Hwang YC, Yogodzinski CH, Shkedi AR, Choi ALM, Mitchell DC, Swaney DL, Hann B, Gordan JD, Shokat KM, Gilbert LA
• Abstract P6-06-01: Analyzing the physical and functional protein interaction landscape of breast cancer.
  Poster Session Abstracts 2019 M Kim, K Kim, B Tutuncuoglu, M Soucheray, D Swaney, F Zheng, J Park, P O'Leary, J-P Coppé, L van 't Veer, A Ashworth, T Ideker, N Krogan
• Neuronal Apolipoprotein E4 Expression Results in Proteome-Wide Alterations and Compromises Bioenergetic Capacity by Disrupting Mitochondrial Function.
  Journal of Alzheimer's disease : JAD 2019 Orr AL, Kim C, Jimenez-Morales D, Newton BW, Johnson JR, Krogan NJ, Swaney DL, Mahley RW
• TCO, a Putative Transcriptional Regulator in Arabidopsis, Is a Target of the Protein Kinase CK2.
  International journal of molecular sciences 2018 Weinman LM, Running KLD, Carey NS, Stevenson EJ, Swaney DL, Chow BY, Krogan NJ, Krogan NT
• Comparative Flavivirus-Host Protein Interaction Mapping Reveals Mechanisms of Dengue and Zika Virus Pathogenesis.
  Cell 2018 Shah PS, Link N, Jang GM, Sharp PP, Zhu T, Swaney DL, Johnson JR, Von Dollen J, Ramage HR, Satkamp L, Newton B, Hüttenhain R, Petit MJ, Baum T, Everitt A, Laufman O, Tassetto M, Shales M, Stevenson E,…
• 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
• Abstract B45: Studying the interactome of breast cancer: The cancer cell map initiative.
  Validation of Driver Mutations 2018 Minkyu Kim, Kyumin Kim, Margaret Soucheray, Danielle Swaney, Nevan Krogan
• Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance.
  Biology open 2018 Mavor D, Barlow KA, Asarnow D, Birman Y, Britain D, Chen W, Green EM, Kenner LR, Mensa B, Morinishi LS, Nelson CA, Poss EM, Suresh P, Tian R, Arhar T, Ary BE, Bauer DP, Bergman ID, Brunetti RM, Chio …
• Sympathetic inputs regulate adaptive thermogenesis in brown adipose tissue through cAMP-Salt inducible kinase axis.
  Scientific reports 2018 Paulo E, Wu D, Wang Y, Zhang Y, Wu Y, Swaney DL, Soucheray M, Jimenez-Morales D, Chawla A, Krogan NJ, Wang B
• Proteome Imbalance of Mitochondrial Electron Transport Chain in Brown Adipocytes Leads to Metabolic Benefits.
  Cell metabolism 2018 Masand R, Paulo E, Wu D, Wang Y, Swaney DL, Jimenez-Morales D, Krogan NJ, Wang B
• Abstract PR04: HER3 crosstalk with HPV16-E6E7 is a feedback resistance mechanism to PI3K-targeted therapies in head and neck cancer.
  Viral Cancers HPV/EBV 2017 Toni M. Brand, Stefan Hartmann, Neil E. Bhola, Hua Li, Yan Zeng, Rachel O'Keefe, Max V. Ranall, Sourav Bandyopadhyay, Margaret Soucheray, Danielle L. Swaney, Nevan Krogan, Carolyn Kemp, Umamaheswar …
• Abstract P1-05-31: Studying the interactome of breast cancer: The cancer cell map initiative.
  Poster Session Abstracts 2017 M Kim, K Kim, M Soucheray, D Swaney, N Krogan
• Evolution of protein phosphorylation across 18 fungal species.
  Science (New York, N.Y.) 2016 Studer RA, Rodriguez-Mias RA, Haas KM, Hsu JI, Viéitez C, Solé C, Swaney DL, Stanford LB, Liachko I, Böttcher R, Dunham MJ, de Nadal E, Posas F, Beltrao P, Villén J
• Enrichment of Modified Peptides via Immunoaffinity Precipitation with Modification-Specific Antibodies.
  Cold Spring Harbor protocols 2016 Swaney DL, Villén J
• Enrichment of Phosphopeptides via Immobilized Metal Affinity Chromatography.
  Cold Spring Harbor protocols 2016 Swaney DL, Villén J
• Proteomic Analysis of Protein Posttranslational Modifications by Mass Spectrometry.
  Cold Spring Harbor protocols 2016 Swaney DL, Villén J
• Phosphorylation of ubiquitin at Ser65 affects its polymerization, targets, and proteome-wide turnover.
  EMBO reports 2015 Swaney DL, Rodríguez-Mias RA, Villén J
• E2~Ub conjugates regulate the kinase activity of Shigella effector OspG during pathogenesis.
  The EMBO journal 2014 Pruneda JN, Smith FD, Daurie A, Swaney DL, Villén J, Scott JD, Stadnyk AW, Le Trong I, Stenkamp RE, Klevit RE, Rohde JR, Brzovic PS
• Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.
  Nature methods 2013 Swaney DL, Beltrao P, Starita L, Guo A, Rush J, Fields S, Krogan NJ, Villén J
• Correction to “Affinity-Based Probes Based on Type II Kinase Inhibitors”.
  Journal of the American Chemical Society 2013 Pratistha Ranjitkar, B. Gayani K. Perera, Danielle L. Swaney, Sanjay B. Hari, Eric T. Larson, Ratika Krishnamurty, Ethan A. Merritt, Judit Villén, Dustin J. Maly
• Affinity-based probes based on type II kinase inhibitors.
  Journal of the American Chemical Society 2012 Ranjitkar P, Perera BG, Swaney DL, Swaney DL, Hari SB, Larson ET, Krishnamurty R, Merritt EA, Villén J, Maly DJ
• Systematic functional prioritization of protein posttranslational modifications.
  Cell 2012 Beltrao P, Albanèse V, Kenner LR, Swaney DL, Burlingame A, Villén J, Lim WA, Fraser JS, Frydman J, Krogan NJ
• Proteomic and phosphoproteomic comparison of human ES and iPS cells.
  Nature methods 2011 Phanstiel DH, Brumbaugh J, Wenger CD, Tian S, Probasco MD, Bailey DJ, Swaney DL, Tervo MA, Bolin JM, Ruotti V, Stewart R, Thomson JA, Coon JJ
• Tra1 has specific regulatory roles, rather than global functions, within the SAGA co-activator complex.
  The EMBO journal 2011 Helmlinger D, Marguerat S, Villén J, Swaney DL, Gygi SP, Bähler J, Winston F
• Phosphoproteomics for the masses.
  ACS chemical biology 2010 Grimsrud PA, Swaney DL, Wenger CD, Beauchene NA, Coon JJ
• Large-scale phosphoprotein analysis in Medicago truncatula roots provides insight into in vivo kinase activity in legumes.
  Plant physiology 2009 Grimsrud PA, den Os D, Wenger CD, Swaney DL, Schwartz D, Sussman MR, Ané JM, Coon JJ
• Dual-pressure linear ion trap mass spectrometer improving the analysis of complex protein mixtures.
  Analytical chemistry 2009 Second TP, Blethrow JD, Schwartz JC, Merrihew GE, MacCoss MJ, Swaney DL, Russell JD, Coon JJ, Zabrouskov V
• A new probabilistic database search algorithm for ETD spectra.
  Journal of proteome research 2009 Sadygov RG, Good DM, Swaney DL, Coon JJ
• Toward defining the phosphoproteome of Xenopus laevis embryos.
  Developmental dynamics : an official publication of the American Association of Anatomists 2009 McGivern JV, Swaney DL, Coon JJ, Sheets MD
• Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry.
  Proceedings of the National Academy of Sciences of the United States of America 2009 Swaney DL, Wenger CD, Thomson JA, Coon JJ
• A proteomics grade electron transfer dissociation-enabled hybrid linear ion trap-orbitrap mass spectrometer.
  Journal of proteome research 2008 McAlister GC, Berggren WT, Griep-Raming J, Horning S, Makarov A, Phanstiel D, Stafford G, Swaney DL, Syka JE, Zabrouskov V, Coon JJ
• Tandem phosphorylation of Ser-911 and Thr-912 at the C terminus of yeast plasma membrane H+-ATPase leads to glucose-dependent activation.
  The Journal of biological chemistry 2007 Lecchi S, Nelson CJ, Allen KE, Swaney DL, Thompson KL, Coon JJ, Sussman MR, Slayman CW
• Probing the dynamics of O-GlcNAc glycosylation in the brain using quantitative proteomics.
  Nature chemical biology 2007 Khidekel N, Ficarro SB, Clark PM, Bryan MC, Swaney DL, Rexach JE, Sun YE, Coon JJ, Peters EC, Hsieh-Wilson LC