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.

Plocica J, Guo F, Das JK, Kobayashi KS, Ficht TA, Alaniz RC, Song J, de Figueiredo P

Engineering live attenuated vaccines: Old dogs learning new tricks

Journal of Translational Autoimmunity

2023 March 26. doi: 10.1016/j.jtauto.2023.100198.

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

Analytical Chemistry

2022 September 27. doi: 10.1021/acs.analchem.2c02724. PMID:36108268

Yang J-M, Ren Y, Kumar A, Xiong X, et al.

NAC1 Modulates Autoimmunity by Suppressing Regulatory T Cell- Mediated Tolerance

Science Advances

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

Science Advances

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

Proc. Natl Acad. Sci. USA.

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

Proc Natl Acad Sci USA

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

Nature Communications

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

Lab Chip

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.

BMC Genomics

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

Cell Systems

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

Nature Plants

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

Cell Host & Microbe

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

PLoS Pathogens

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

PLoS Pathogens

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

PLoS Pathogens

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

Trends in Biotechnology

2013 Feb 28. doi: 10.1016/j.tibtech.2012.12.002. PMID: 23453527.

Criscitiello M and de Figueiredo P

Fifty Shades of Immune Defense

PLoS Pathogens

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

PLoS Pathogens

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

PLoS Pathogens

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

PLoS Pathogens

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

PLoS Pathogens

2008 July 25. doi: 10.1371/journal.ppat.1000110. PMID: 1865462.