Publications

2025

A ribosome-bound pseudoknot in the HCV coding region stimulates viral growth by tuning viral translation
Wan H, Jang H, Xu L, Abdallah K, Gilbert W, Pyle A. A ribosome-bound pseudoknot in the HCV coding region stimulates viral growth by tuning viral translation. Cell Reports 2025, 45: 116739. PMID: 41422509, DOI: 10.1016/j.celrep.2025.116739.
Peer-Reviewed Original Research
Concepts
MTHFR allele and one-carbon metabolic profile predict severity of COVID-19
Petrova B, Syphurs C, Culhane A, Chen J, Chen E, Cotsapas C, Esserman D, Montgomery R, Kleinstein S, Smolen K, Mendez K, Network I, Lasky-Su J, Steen H, Levy O, Diray-Arce J, Kanarek N. MTHFR allele and one-carbon metabolic profile predict severity of COVID-19. Proceedings Of The National Academy Of Sciences Of The United States Of America 2025, 122: e2509118122. PMID: 41410771, DOI: 10.1073/pnas.2509118122.
Peer-Reviewed Original Research
MeSH Keywords and Concepts
Unravelling the Immunological Enigma of Sickle Cell Disease: Current Understanding and Future Directions
Jamwal S, Calhoun C, Mohanty S, Montgomery R, Krishnamurti L, Shaw A, Yildirim I. Unravelling the Immunological Enigma of Sickle Cell Disease: Current Understanding and Future Directions. Immunology 2025 PMID: 41387179, DOI: 10.1111/imm.70080.
Peer-Reviewed Original Research
Concepts
Emicizumab for preventing intracranial hemorrhage in infants with severe hemophilia A: a cost-effectiveness analysis
Glaeser-Khan S, Ito S, Sra M, Richmond R, Bona R, Krumholz H, Croteau S, Cuker A, Goshua G. Emicizumab for preventing intracranial hemorrhage in infants with severe hemophilia A: a cost-effectiveness analysis. Blood Advances 2025, 9: 6237-6245. PMID: 40795232, PMCID: PMC12744270, DOI: 10.1182/bloodadvances.2025016822.
Peer-Reviewed Original Research
Concepts
Barriers perpetuating the lack of casualty data from neglected conflict settings
Wild H, Ratnayake A, Sanou S, Nacanabo Y, Asgedom A, Lawan K, Cheran A, Rogers S, Ko A, Meda N, Wren S. Barriers perpetuating the lack of casualty data from neglected conflict settings. British Journal Of Surgery 2025, 112: xv58-xv59. PMID: 41369649, DOI: 10.1093/bjs/znaf223.
Peer-Reviewed Original Research
Integrative single-cell RNA and ATAC sequencing reveals the impact of chronic cigarette smoking on lung epithelial responses to influenza and hyperoxia
Cha P, Zou Z, Nouws J, Brewster R, Dela Cruz C, Sharma L, Yan X, Sauler M. Integrative single-cell RNA and ATAC sequencing reveals the impact of chronic cigarette smoking on lung epithelial responses to influenza and hyperoxia. Respiratory Research 2025 PMID: 41366391, DOI: 10.1186/s12931-025-03393-5.
Peer-Reviewed Original Research
Concepts
Pre-existing and early cellular immune factors correlate with functionally complete protection against primary controlled human SARS-CoV-2 infection
Wagstaffe H, Thwaites R, Sidhu J, Lindeboom R, Kretschmer L, Worlock K, Dratva L, Huang A, Ascough S, Papargyris L, McKendry R, Collins A, Xu J, Lemm N, Killingley B, Kalinova M, Mann A, Catchpole A, Swadling L, Tsang J, Maini M, Noursadeghi M, Nikolić M, Teichmann S, Openshaw P, Chiu C. Pre-existing and early cellular immune factors correlate with functionally complete protection against primary controlled human SARS-CoV-2 infection. Nature Communications 2025 PMID: 41354730, DOI: 10.1038/s41467-025-67017-8.
Peer-Reviewed Original Research
Concepts
Epidemiology and severity risk factors of dengue virus infection during the 2023-2024 outbreak in Colombia
Torres-Hernández D, Grubaugh N, Murillo-Ortiz M, Hurtado I, Hill V, Breban M, Gómez-Zambrano M, López P, Cantor E, Dávalos D, López-Medina E. Epidemiology and severity risk factors of dengue virus infection during the 2023-2024 outbreak in Colombia. PLOS Neglected Tropical Diseases 2025, 19: e0013115. PMID: 41348908, PMCID: PMC12694831, DOI: 10.1371/journal.pntd.0013115.
Peer-Reviewed Original Research
MeSH Keywords and Concepts
AI immunologists are here: Are they ready for prime time?
Kim J, Huang A, Tsang J. AI immunologists are here: Are they ready for prime time? Science Immunology 2025, 10: eaea8735. PMID: 41348863, DOI: 10.1126/sciimmunol.aea8735.
Peer-Reviewed Original Research
MeSH Keywords and Concepts
The lingering shadow of epidemics: post-acute sequelae across history
Miller C, Moen J, Iwasaki A. The lingering shadow of epidemics: post-acute sequelae across history. Trends In Immunology 2025 PMID: 41350176, DOI: 10.1016/j.it.2025.10.010.
Peer-Reviewed Original Research
Concepts
Dysregulated alveolar type 2 epithelial cell proteostasis promotes fibrogenic macrophage migration inhibitory factor–CD74 signaling
Kim S, Nouws J, Ruwisch J, Woodard G, Cooley J, Khoury J, Sun H, Doherty E, Piecychna M, Manning E, Kang M, Bruscia E, Wei H, Zhang Y, Yarovinsky T, Hwa J, Zacharias W, Ingram J, Lee C, Elias J, Kaminski N, Redente E, Herzog E, Prasse A, Bucala R, Sauler M. Dysregulated alveolar type 2 epithelial cell proteostasis promotes fibrogenic macrophage migration inhibitory factor–CD74 signaling. Science Translational Medicine 2025, 17: eadr2277. PMID: 41337540, DOI: 10.1126/scitranslmed.adr2277.
Peer-Reviewed Original Research
MeSH Keywords and Concepts
Matrix Stiffness Directs Early Injury and Ketogenesis Programs to Prime Kidney Repair
Gui Y, Wang Y, Li W, Liu J, Zheng K, Li J, Shaffer H, Jones C, Mallari S, Yu Y, Liu S, Liu Y, Zhou D. Matrix Stiffness Directs Early Injury and Ketogenesis Programs to Prime Kidney Repair. Journal Of The American Society Of Nephrology 2025 DOI: 10.1681/asn.0000000967.
Peer-Reviewed Original Research
Concepts
Leading Cause of Death and Life Expectancy Among US Superagers
Shah R, Arun A, Chen J, Fallon C, Krumholz H. Leading Cause of Death and Life Expectancy Among US Superagers. Journal Of The American Geriatrics Society 2025 PMID: 41329524, DOI: 10.1111/jgs.70232.
Peer-Reviewed Original Research
Network-based hierarchical heterogeneity analysis and applications to cancer omics data
Wang R, Zhang S, Ma S. Network-based hierarchical heterogeneity analysis and applications to cancer omics data. Science China Mathematics 2025, 1-14. DOI: 10.1007/s11425-024-2435-2.
Peer-Reviewed Original Research
Concepts
The impact of large-scale release of Wolbachia mosquitoes on dengue incidence in Campo Grande, Brazil: an ecological study
de Morais Batista F, Carcamo P, Nelson E, da Silva Neto A, Tsuha D, Lahdo V, dos Santos V, Ribeiro G, da Silva Lopes R, Amadeu P, Blanco M, da Costa T, de Melo Chalegre K, Riback T, da Silva C, Ranzani O, Cummings D, Andrews J, Ko A, Hitchings M, Anders K, Moreira L, Gonçalves C, Croda J. The impact of large-scale release of Wolbachia mosquitoes on dengue incidence in Campo Grande, Brazil: an ecological study. The Lancet Regional Health - Americas 2025, 54: 101327. PMID: 41438239, PMCID: PMC12719740, DOI: 10.1016/j.lana.2025.101327.
Peer-Reviewed Original Research
Concepts
Rapid Metagenomic Sequencing of Bronchoalveolar Lavage Fluid for Diagnosis of Infection in Patients With Hematologic Malignancies and Pulmonary Complications
Hensley M, Sayed K, Haidar G, Wang X, Benos P, Ito S, Im A, Geramita E, Shlomchik W, Methé B, Dela Cruz C, Morris A, Kitsios G. Rapid Metagenomic Sequencing of Bronchoalveolar Lavage Fluid for Diagnosis of Infection in Patients With Hematologic Malignancies and Pulmonary Complications. CHEST Pulmonary 2025, 3: 100173. DOI: 10.1016/j.chpulm.2025.100173.
Peer-Reviewed Original Research
Concepts
Joint identification of spatially variable genes via a network-assisted Bayesian regularization approach
Wu M, Li Y, Ma S, Wu M. Joint identification of spatially variable genes via a network-assisted Bayesian regularization approach. The Annals Of Applied Statistics 2025, 19: 2705-2723. DOI: 10.1214/25-aoas2097.
Peer-Reviewed Original Research
Concepts
The asymmetric opening of HIV-1 Env by a potent CD4 mimetic enables anti-coreceptor binding site antibodies to mediate ADCC
Richard J, Grunst M, Niu L, Díaz-Salinas M, Zhu L, Tolbert W, Marchitto L, Zhou F, Bourassa C, Kim H, Boodapati S, Yang D, Chiu T, Chen H, Benlarbi M, Beaudoin-Bussières G, Gottumukkala S, Li W, Dionne K, Bélanger É, Chatterjee D, Medjahed H, Hendrickson W, Sodroski J, Lang Z, Morton A, Huang R, Matthies D, Smith A, Kumar P, Mothes W, Munro J, Pazgier M, Finzi A. The asymmetric opening of HIV-1 Env by a potent CD4 mimetic enables anti-coreceptor binding site antibodies to mediate ADCC. Nature Communications 2025, 16: 10419. PMID: 41326374, PMCID: PMC12669584, DOI: 10.1038/s41467-025-65866-x.
Peer-Reviewed Original Research
MeSH Keywords and Concepts
Conditional Graphical Models With A Hierarchical Sparse Estimation
Li R, Zhang Q, Ma S. Conditional Graphical Models With A Hierarchical Sparse Estimation. Statistics And Computing 2025, 36: 30. DOI: 10.1007/s11222-025-10783-8.
Peer-Reviewed Original Research
Concepts
A Phase 1 Double-Blinded Trial to Evaluate Safety, Immunogenicity, and Dosing of Measles-Vectored Chikungunya Virus Vaccine (MV-CHIK) in Healthy Adults
Winokur P, Hegmann T, Sahly H, Anderson E, Wagner N, Kaufman T, Keitel W, Atmar R, Yi J, Yildirim I, Kao C, Peters E, Stephens K, Rostad C, Dempsey W, Shahamatdar V, Beresney T, Tomashek K. A Phase 1 Double-Blinded Trial to Evaluate Safety, Immunogenicity, and Dosing of Measles-Vectored Chikungunya Virus Vaccine (MV-CHIK) in Healthy Adults. Journal Of Infectious Diseases 2025, jiaf571. PMID: 41313671, DOI: 10.1093/infdis/jiaf571.
Peer-Reviewed Original Research
Concepts
Zika Virus Neutralizing Antibody Responses Elicited by Vaccination or Infection
Galindo C, Ling Y, Kpamegan E, Nascimento E, Perez-Guzman E, Ticona J, Chan K, Castanha P, Buddhari D, Farmer A, Fernandez S, Baldwin W, Kaiser M, Fernandes J, Zahralban-Steele M, Brinkman A, Rindfleisch T, Moss K, Rouphael N, Sahly H, Marques E, Ko A, Acosta C. Zika Virus Neutralizing Antibody Responses Elicited by Vaccination or Infection. Open Forum Infectious Diseases 2025, 12: ofaf707. PMID: 41346444, PMCID: PMC12673849, DOI: 10.1093/ofid/ofaf707.
Peer-Reviewed Original Research
Concepts
Validation of polyester nasal swabs for post-mortem SARS-CoV-2 diagnosis in Karachi, Pakistan: a prospective surveillance analysis
Allana R, Aziz F, Belgaumi S, Kabir F, Yildirim I, Hotwani A, Malik F, Aguolu O, Muneer S, Ahsan N, Hasan Z, Omer S, Kazi A. Validation of polyester nasal swabs for post-mortem SARS-CoV-2 diagnosis in Karachi, Pakistan: a prospective surveillance analysis. Journal Of Global Health 2025, 15: 04288. PMID: 41264556, PMCID: PMC12634021, DOI: 10.7189/jogh.15.04288.
Peer-Reviewed Original Research
MeSH Keywords and Concepts
Editorial: The heme oxygenase system in immunity
Costa D, Bruscia E, Willis D. Editorial: The heme oxygenase system in immunity. Frontiers In Immunology 2025, 16: 1740080. PMID: 41346632, PMCID: PMC12672320, DOI: 10.3389/fimmu.2025.1740080.
Peer-Reviewed Original Research
Sequential class switching generates antigen-specific gut IgA from IgG1 B cells
Siniscalco E, Meng H, Gabernet G, Pacheco G, Saghaei S, Ramirez S, Hills L, Faraji F, Chen S, Yin X, Dien C, Hoyt L, Liu E, Barrett A, Briggs N, Williams A, Shukla V, Crotty S, Wesemann D, Kleinstein S, Craft J, Eisenbarth S. Sequential class switching generates antigen-specific gut IgA from IgG1 B cells. Immunity 2025, 58: 3075-3093.e6. PMID: 41253159, DOI: 10.1016/j.immuni.2025.10.022.
Peer-Reviewed Original Research
This study investigates how gut-specific IgA antibodies are generated from IgG1 B cells through sequential class switching, highlighting a crucial mechanism for designing effective mucosal vaccines.
Full Summary

See All Publications

Publications

2026

Hierarchical structure-guided high-dimensional multi-view clustering

2025

A ribosome-bound pseudoknot in the HCV coding region stimulates viral growth by tuning viral translation

MTHFR allele and one-carbon metabolic profile predict severity of COVID-19

Unravelling the Immunological Enigma of Sickle Cell Disease: Current Understanding and Future Directions

Emicizumab for preventing intracranial hemorrhage in infants with severe hemophilia A: a cost-effectiveness analysis

Barriers perpetuating the lack of casualty data from neglected conflict settings

Integrative single-cell RNA and ATAC sequencing reveals the impact of chronic cigarette smoking on lung epithelial responses to influenza and hyperoxia

Pre-existing and early cellular immune factors correlate with functionally complete protection against primary controlled human SARS-CoV-2 infection

Epidemiology and severity risk factors of dengue virus infection during the 2023-2024 outbreak in Colombia

AI immunologists are here: Are they ready for prime time?

The lingering shadow of epidemics: post-acute sequelae across history

Dysregulated alveolar type 2 epithelial cell proteostasis promotes fibrogenic macrophage migration inhibitory factor–CD74 signaling

Matrix Stiffness Directs Early Injury and Ketogenesis Programs to Prime Kidney Repair

Leading Cause of Death and Life Expectancy Among US Superagers

Network-based hierarchical heterogeneity analysis and applications to cancer omics data

The impact of large-scale release of Wolbachia mosquitoes on dengue incidence in Campo Grande, Brazil: an ecological study

Rapid Metagenomic Sequencing of Bronchoalveolar Lavage Fluid for Diagnosis of Infection in Patients With Hematologic Malignancies and Pulmonary Complications

Joint identification of spatially variable genes via a network-assisted Bayesian regularization approach

The asymmetric opening of HIV-1 Env by a potent CD4 mimetic enables anti-coreceptor binding site antibodies to mediate ADCC

Conditional Graphical Models With A Hierarchical Sparse Estimation

A Phase 1 Double-Blinded Trial to Evaluate Safety, Immunogenicity, and Dosing of Measles-Vectored Chikungunya Virus Vaccine (MV-CHIK) in Healthy Adults

Zika Virus Neutralizing Antibody Responses Elicited by Vaccination or Infection

Validation of polyester nasal swabs for post-mortem SARS-CoV-2 diagnosis in Karachi, Pakistan: a prospective surveillance analysis

Editorial: The heme oxygenase system in immunity

Sequential class switching generates antigen-specific gut IgA from IgG1 B cells