Selected Publications
On the cover: Cryptococcus neoformans is a deadly fungal pathogen whose intracellular lifestyle is important for virulence. In this issue, perform a global phosphoproteomic analysis of the host response to C. neoformans infection and identify numerous and diverse host proteins that are phosphorylated following fungal ingestion by macrophages. Among these, phosphorylation and activation of components of the host autophagy initiation complex confer susceptibility to fungal internalization and intracellular replication. The cover image presents an artistic rendition of a host cell internalizing C. neoformans with recruitment of host autophagy initiation proteins to the phagocytic cup. Art by Paul de Figueiredo.
Dai J, Huang C, Zhang, H, Samuel R, Li Y, Jayaraman A, de Figueiredo P, Han A
A microfluidic dielectrophoretic method enables on-demand spatial arrangement of bacteria-encapsulated agarose gel microparticles
In press
Yang J-M, Ren Y, Kumar A, Xiong X, et al.
NAC1 Modulates Autoimmunity by Suppressing Regulatory T Cell- Mediated Tolerance
2022 June 29. doi: 10.1126/sciadv.abo0183. PMID: 35767626
Han Z, Huang C, Li Y, Gupte R, et al.
FIDELITY: A Quality Control System for Droplet Microfluidics
2022 July 8. doi: 10.1126/sciadv.abc9108. PMID: 35857442
Willis JA, Cheburkanov V, Chen S, Soares JM, Kassab G, Blanco KC, Bagnato VS, de Figueiredo P, Yakovlev VV
Breaking down antibiotic resistance in methicillin-resistant Staphylococcus aureus: combining antimicrobial photodynamic and antibiotic treatments
2022 August 29. doi: 10.1073/pnas.2208378119. PMID: 36037346
Wells KM, He K, Pandey A, Cabello A, Zhang D, Yang J, Gomez G, Liu Y, Chang H, Li X, Zhang H, Feng X, da Costa LF, Metz R, Johnson CD, Martin CL, Skrobarczyk J, Berghman LR, Patrick KL, Leibowitz J, Ficht A, Sze S-H, Song J, Qian X, Qin Q-M, Ficht TA, de Figueiredo P
Brucella Activates the Host RIDD Pathway to Subvert BLOS1-Directed Immune Defense
2022 May 19. doi: 10.7554/eLife.73625. PMID: 35587649
Yang J, Eslami M, Chen YP, Das M, Zhang D, Chen S, Roberts AJ, Weston M, Volkova A, Faghihi K, Moore RK, Alaniz RC, Wattam AR, Dickerman A, Cucinell C, Kendziorski J, Coburn S, Paterson H, Obanor O, Maples J, Servetas S, Dootz J, Qin QM, Samuel JE, Han A, van Schaik EJ, de Figueiredo P.
Phenotype-Based Threat Assessment
2022 Apr 5. doi: 10.1073/pnas.2112886119. PMID: 35363569.
Guo F, Das JK, Kobayashi KS, Qin Q-M, Ficht TA, Alaniz RC, Song J, De Figueiredo P
Live Attenuated Bacterium Limits Cancer Resistance to CAR-T Therapy by Remodeling the Tumor Microenvironment
Journal for Immunotherapy of Cancer
2022 Jan 10. doi: 10.1136/jitc-2021-003760. PMID: 34987022.
Yoo J-S, Sasaki M, Cho SX, Kasuga Y, Zhu B, Ouda R, Orba Y, de Figueiredo P, Sawa H, Kobayashi KS
SARS-CoV-2 Inhibits Induction of the MHC Class I Pathway by Targeting the STAT1-IRF1-NLRC5 Axis
2021 Nov 15. doi: 10.1038/s41467-021-26910-8. PMID: 34782627.
Chen S, Zhang D, Roberts A-J, Lu H-C, Cannon CL, Qin Q-M, de Figueiredo P
Host Protease Activity on Bacterial Pathogens Promotes Complement and Antibiotic-Directed Killing
2021 Nov 18. doi: 10.3390/pathogens10111506. PMID: 34832660.
Yang J, Qin Q-M, Van Schaik E, Samuel JE, de Figueiredo P
Automated, High-Throughput Detection of Bacterial Adherence to Host Cells
2021 Sep 17. doi: 10.3791/62764. PMID: 34605819.
Ding S, Yang J, Feng X, Pandey A, Barhoumi R, Zhang D, Bell SL, Liu Y, Fachini da Costa L, Rice-Ficht A, Watson RO, Patrick KL, Qin Q-M, Ficht TA, de Figueiredo P
Interactions Between Fungal Hyaluronic Acid and Host CD44 Promote Internalization by Recruiting Host Autophagy Proteins to Forming Phagosomes
2021 Feb 12. doi:10.1016/j.isci.2021.102192. PMID: 33718841.
Wippold JA, Wang H, Tingling J, Leibowitz JL, de Figueiredo P, Han A
PRESCIENT: Platform for the Rapid Evaluation of Antibody Success Using Integrated Microfluidics Enabled Technology
2020 Mar 20. doi: 10.1039/c9lc01165j. PMID: 32196032.
Dadaneh SZ, de Figueiredo P, Sze S-H, Zhou M, Qian X
Bayesian Gamma-Negative Binomial Modeling of Single-Cell RNA Sequencing Data.
2020 Sep 9. doi: 10.1186/s12864-020-06938-8. PMID: PMC7487589.
Patrick KL, Wojcechowskyj JA, Bell SL, Riba MN, Jing T, Talmage S, Xu P, Cabello AL, Xu J, Shales M, Jimenez-Morales D, Ficht TA, de Figueiredo P, Samuel JE, Li P, Krogan NJ, Watson RO
Quantitative Yeast Genetic Interaction Profiling of Bacterial Effector Proteins Uncovers a Role for the Human Retromer in Salmonella Infection
2018 Sep 26. doi: 10.1016/j.cels.2018.06.010. PMID: 30077634.
Pandey A, Lin F, Cabello AL, da Costa LF, Feng X, Feng HQ, Zhang MZ, Iwawaki T, Rice-Ficht A, Ficht TA, de Figueiredo P, Qin QM
Activation of Host IRE1α-Dependent Signaling Axis Contributes the Intracellular Parasitism of Brucella melitensis.
Frontiers in Cellular and Infection Biology
2018 Apr 20. doi: 10.3389/fcimb.2018.00103. PMID: 29732320.
Dickman M, Williams B, Li Y, de Figueiredo P, Wolpert T
Reassessing Plant Apoptosis
2017 Oct 16. doi: 10.1038/s41477-017-0045-1. PMID: 28947814.
Pandey A, Ding SL, Qin QM, Gupta R, Gomez G, Lin F, Feng X, Fachini da Costa L, Chaki SP, Katepalli M, Case ED, van Schaik EJ, Sidiq T, Khalaf O, Arenas A, Kobayashi KS, Samuel JE, Rivera GM, Alaniz RC, Sze SH, Qian X, Brown WJ, Rice-Ficht A, Russell WK, Ficht TA, de Figueiredo P
Global Reprogramming of Host Kinase Signaling in Response to Fungal Infection
2017 May 10. doi: 10.1016/j.chom.2017.04.008. PMID: 28494245
Mwangi W, de Figueiredo P, Criscitiello MF
One Health: Addressing Global Challenges at the Nexus of Human, Animal, and Environmental Health
2016 Sep 15. doi: 10.1371/journal.ppat.1005731. PMID: 27631500
Pandey A, Cabello A, Akoolo L, Rice-Ficht A, Arenas-Gamboa A, McMurray D, Ficht TA, de Figueiredo P
The Case for Live Attenuated Vaccines Against the Neglected Zoonotic Diseases Brucellosis and Bovine Tuberculosis
PLoS Neglected Tropical Diseases
2016 Aug 18. doi: 10.1371/journal.pntd.0004572. PMID: 27537413
Dickman MB and de Figueiredo P
Death Be Not Proud-Cell Death Control in Plant Fungal Interactions
2013 Sep 9. doi: 10.1371/journal.ppat.1003542. PMID: 24068920
Criscitiello MF, Dickman MB, Samuel JE, de Figueiredo P
Tripping on Acid: Trans-Kingdom Perspectives on Biological Acids in Immunity and Pathogenesis
2013 Jul 18. doi:10.1371/journal.ppat.1003402. PMID: 23874196
Han A, Hou H, Li L, Kim HS, de Figueiredo P
Microfabricated Devices in Microbial Bioenergy Sciences
2013 Feb 28. doi: 10.1016/j.tibtech.2012.12.002. PMID: 23453527.
Criscitiello M and de Figueiredo P
Fifty Shades of Immune Defense
2013 Feb 7. doi:10.1371/journal.ppat.1003110. PMID: 23408882.
Dickman MB and de Figueiredo P
Comparative Pathobiology of Pathogenic Fungi of Plants and Animals
2011 Dec 15. doi:10.1371/journal.ppat.1002324. PMID: 22194681.
Qin QM, Luo J, Lin X, Pei J, Li L, Ficht TA, de Figueiredo P
Functional Analysis of Host Factors That Mediate Cryptococcus neoformans Intracellular Trafficking
2011 Jun 16. doi: 10.1371/journal.ppat.1002078. PMID: 21698225.
Jupiter DC, Ficht TA, Samuel J, Qin QM, de Figueiredo P
DNA Watermarking of Infectious Agents: Progress and Prospects
2010 June 17. doi: 10.1371/journal.ppat.1000950. PMID: 20585560.
Qin QM, Pei J, Ancona V, Shaw BD, Ficht TA, de Figueiredo P
RNAi Screen of Endoplasmic Reticulum-Associated Host Factors Reveals a Role for IRE1a in Supporting Brucella Replication
2008 July 25. doi: 10.1371/journal.ppat.1000110. PMID: 1865462.
The de Figueiredo Lab 