Publications

2025

Cutaneous lupus features specialized stromal niches and altered retroelement expression
Gehlhausen J, Kong Y, Baker E, Ramachandran S, Koumpouras F, Ko C, Vesely M, Little A, Damsky W, King B, Iwasaki A. Cutaneous lupus features specialized stromal niches and altered retroelement expression. Journal Of Investigative Dermatology 2025 PMID: 40409678, DOI: 10.1016/j.jid.2025.04.033.
Peer-Reviewed Original Research
Concepts
Cerebrospinal fluid immune phenotyping reveals distinct immunotypes of myalgic encephalomyelitis/chronic fatigue syndrome.
Bastos V, Greene K, Tabachnikova A, Bhattacharjee B, Sjögren P, Bertilson B, Reifert J, Zhang M, Kamath K, Shon J, Gehlhausen J, Guan L, VanElzakker M, Proal A, Bragée B, Iwasaki A. Cerebrospinal fluid immune phenotyping reveals distinct immunotypes of myalgic encephalomyelitis/chronic fatigue syndrome. The Journal Of Immunology 2025 PMID: 40373264, DOI: 10.1093/jimmun/vkaf087.
Peer-Reviewed Original Research
Concepts
Mucosal unadjuvanted booster vaccines elicit local IgA responses by conversion of pre-existing immunity in mice
Kwon D, Mao T, Israelow B, Santos Guedes de Sá K, Dong H, Iwasaki A. Mucosal unadjuvanted booster vaccines elicit local IgA responses by conversion of pre-existing immunity in mice. Nature Immunology 2025, 26: 908-919. PMID: 40360777, DOI: 10.1038/s41590-025-02156-0.
Peer-Reviewed Original Research
Concepts
Impact of COVID-19 vaccination on symptoms and immune phenotypes in vaccine-naïve individuals with Long COVID
Grady C, Bhattacharjee B, Silva J, Jaycox J, Lee L, Silva Monteiro V, Sawano M, Massey D, Caraballo C, Gehlhausen J, Tabachnikova A, Mao T, Lucas C, Peña-Hernandez M, Xu L, Tzeng T, Takahashi T, Herrin J, Güthe D, Akrami A, Assaf G, Davis H, Harris K, McCorkell L, Schulz W, Griffin D, Wei H, Ring A, Guan L, Dela Cruz C, Krumholz H, Iwasaki A. Impact of COVID-19 vaccination on symptoms and immune phenotypes in vaccine-naïve individuals with Long COVID. Communications Medicine 2025, 5: 163. PMID: 40346201, PMCID: PMC12064684, DOI: 10.1038/s43856-025-00829-3.
Peer-Reviewed Original Research
Concepts
Generative AI Models for Developing Neuroimaging Markers of Psychiatric Disorders
Abdallah C, van Dijk D. Generative AI Models for Developing Neuroimaging Markers of Psychiatric Disorders. Biological Psychiatry 2025 PMID: 40348311, DOI: 10.1016/j.biopsych.2025.05.002.
Peer-Reviewed Original Research
Understanding and Reducing Cardiopulmonary Sequelae Associated With Chronic Hypoxia
Manning E, Ramachandra A, Sharma P, Nikola F, De Man R, Doddaballapur P, Raredon M, Szafron J, Baernthaler T, Justet A, Akingbesote N, Perry R, Adams T, Cavinato C, Yan X, Tellides G, Kaminski N, Humphrey J. Understanding and Reducing Cardiopulmonary Sequelae Associated With Chronic Hypoxia. American Journal Of Respiratory And Critical Care Medicine 2025, 211: a3336-a3336. DOI: 10.1164/ajrccm.2025.211.abstracts.a3336.
Peer-Reviewed Original Research
The Potential Role of miR205 and miR205HG in Pulmonary Fibrosis
Anderson S, Johad K, Ahangari F, Justet A, Adams T, Yan X, Kaminski N. The Potential Role of miR205 and miR205HG in Pulmonary Fibrosis. American Journal Of Respiratory And Critical Care Medicine 2025, 211: a4662-a4662. DOI: 10.1164/ajrccm.2025.211.abstracts.a4662.
Peer-Reviewed Original Research
The PPFE Cell Atlas - The Discovery of the Usual Fibrotic Niche at the Edge of Pleuro-Parenchymal Fibroelastotic Remodeling Surprises as an Immune Cell Driven Phenomenon
Ruwisch J, Cazes A, leiber L, Borie R, Leonhard C, Mal H, Langer L, de Montpréville V, Kamp J, Greer M, Wrede C, Hegermann J, Artysh N, Gottlieb J, Seeliger B, Bernaudin J, Knudsen L, Mordant P, Neubert L, Crestani B, Prasse A, Kaminski N, Justet A, Schupp J. The PPFE Cell Atlas - The Discovery of the Usual Fibrotic Niche at the Edge of Pleuro-Parenchymal Fibroelastotic Remodeling Surprises as an Immune Cell Driven Phenomenon. American Journal Of Respiratory And Critical Care Medicine 2025, 211: a5272-a5272. DOI: 10.1164/ajrccm.2025.211.abstracts.a5272.
Peer-Reviewed Original Research
Concepts
Early IPF Is Characterized by a Dramatic Shift of the Epithelial and Endothelial Populations Within the Alveolar Niche
Justet A, Adams T, Khoury J, Balayev A, Abu Hussein N, Schupp J, Zhao A, Manning E, Ahangari F, Yan X, Ravaglia C, Tomassetti S, Poletti V, Kaminski N. Early IPF Is Characterized by a Dramatic Shift of the Epithelial and Endothelial Populations Within the Alveolar Niche. American Journal Of Respiratory And Critical Care Medicine 2025, 211: a7109-a7109. DOI: 10.1164/ajrccm.2025.211.abstracts.a7109.
Peer-Reviewed Original Research
The Potential Role of GPR87 in the Development of Pulmonary Fibrosis
Khoury J, Ahangari F, Justet A, Adams T, Manning E, Mcdonough J, Anderson S, Nekola F, Beermann M, Bauer Y, Gomez J, Kaminski N. The Potential Role of GPR87 in the Development of Pulmonary Fibrosis. American Journal Of Respiratory And Critical Care Medicine 2025, 211: a7110-a7110. DOI: 10.1164/ajrccm.2025.211.abstracts.a7110.
Peer-Reviewed Original Research
Emerging roles of transcriptional condensates as temporal signal integrators
Meyer K, Huang B, Weiner O. Emerging roles of transcriptional condensates as temporal signal integrators. Nature Reviews Genetics 2025, 1-12. PMID: 40240649, DOI: 10.1038/s41576-025-00837-y.
Peer-Reviewed Original Research
Concepts
Natural killer cells’ functional impairment drives the immune escape of pre-malignant clones in early-stage myelodysplastic syndromes
Rodriguez-Sevilla J, Ganan-Gomez I, Kumar B, Thongon N, Ma F, Chien K, Kim Y, Yang H, Loghavi S, Tan R, Adema V, Li Z, Tanaka T, Uryu H, Kanagal-Shamanna R, Al-Atrash G, Bejar R, Banerjee P, Lynn Cha S, Montalban-Bravo G, Dougherty M, Fernandez Laurita M, Wheeler N, Jia B, Papapetrou E, Izzo F, Dueñas D, McAllen S, Gu Y, Todisco G, Ficara F, Della Porta M, Jain A, Takahashi K, Clise-Dwyer K, Halene S, Bertilaccio M, Garcia-Manero G, Daher M, Colla S. Natural killer cells’ functional impairment drives the immune escape of pre-malignant clones in early-stage myelodysplastic syndromes. Nature Communications 2025, 16: 3450. PMID: 40216768, DOI: 10.1038/s41467-025-58662-0.
Peer-Reviewed Original Research
MeSH Keywords and Concepts
Clinical characteristics and outcomes of disseminated intravascular coagulation in patients with severe fever with thrombocytopenia syndrome
Zhang Z, Hu X, Du Q, Mo P, Chen X, Luo M, Jiang Q, Deng L, Xiong Y. Clinical characteristics and outcomes of disseminated intravascular coagulation in patients with severe fever with thrombocytopenia syndrome. BMC Infectious Diseases 2025, 25: 508. PMID: 40217170, DOI: 10.1186/s12879-025-10900-y.
Peer-Reviewed Original Research
MeSH Keywords and Concepts
Nirmatrelvir–ritonavir versus placebo–ritonavir in individuals with long COVID in the USA (PAX LC): a double-blind, randomised, placebo-controlled, phase 2, decentralised trial
Sawano M, Bhattacharjee B, Caraballo C, Khera R, Li S, Herrin J, Christian D, Coppi A, Warner F, Holub J, Henriquez Y, Johnson M, Goddard T, Rocco E, Hummel A, Mouslmani M, Hooper W, Putrino D, Carr K, Charnas L, De Jesus M, Nepert D, Abreu P, Ziegler F, Spertus J, Iwasaki A, Krumholz H. Nirmatrelvir–ritonavir versus placebo–ritonavir in individuals with long COVID in the USA (PAX LC): a double-blind, randomised, placebo-controlled, phase 2, decentralised trial. The Lancet Infectious Diseases 2025 PMID: 40188838, DOI: 10.1016/s1473-3099(25)00073-8.
Peer-Reviewed Original Research
Concepts
Quantum variational autoencoder utilizing regularized mixed-state latent representations
Wang G, Warrell J, Emani P, Gerstein M. Quantum variational autoencoder utilizing regularized mixed-state latent representations. Physical Review A 2025, 111: 042416. DOI: 10.1103/physreva.111.042416.
Peer-Reviewed Original Research
Concepts
Applying single cell profiling to assess drug anti fibrotic properties in the human precision cut lung slice model of fibrosis
Justet A, Mitash N, Pineda R, Adams T, Balayev A, Abu Hussein N, Ishizuka M, Kim H, Khoury J, Cala-García J, Ahangari F, Yan X, Kaminski N, Königshoff M. Applying single cell profiling to assess drug anti fibrotic properties in the human precision cut lung slice model of fibrosis. Revue Des Maladies Respiratoires 2025, 42: 223. DOI: 10.1016/j.rmr.2025.02.083.
Peer-Reviewed Original Research
Concepts
Reducing clinical trial eligibility barriers for patients with MDS: an icMDS position statement
Borate U, Pugh K, Waller A, Welkie R, Huang Y, Bewersdorf J, Stahl M, DeZern A, Platzbecker U, Sekeres M, Wei A, Buckstein R, Roboz G, Savona M, Loghavi S, Hasserjian R, Fenaux P, Sallman D, Hourigan C, Della Porta M, Nimer S, Little R, Santini V, Efficace F, Taylor J, Garcia-Manero G, Odenike O, Kim T, Halene S, Komrokji R, Griffiths E, Greenberg P, Xu M, Xie Z, Bejar R, Sanz G, Patnaik M, Figueroa M, Carraway H, Abdel-Wahab O, Starczynowski D, Padron E, Boultwood J, Gore S, Daver N, Churpek J, Majeti R, Bennett J, List A, Brunner A, Zeidan A. Reducing clinical trial eligibility barriers for patients with MDS: an icMDS position statement. Blood 2025, 145: 1369-1381. PMID: 40146152, DOI: 10.1182/blood.2023023717.
Peer-Reviewed Original Research
MeSH Keywords and Concepts
In the time of COVID-19: challenges, successes and lessons learned from studies in cancer patients
Mack P, Crawford J, Chang A, Yin A, Klein S, Shea P, Hirsch F, Zidar D, Simon V, Gleason C, McBride R, Cordon-Cardo C, VanOudenhove J, Halene S, Lee F, Mantis N, Kushi L, Weiskopf D, Merchant A, Reckamp K, Skarbinski J, Figueiredo J. In the time of COVID-19: challenges, successes and lessons learned from studies in cancer patients. Journal Of The National Cancer Institute 2025, djaf073. PMID: 40127178, DOI: 10.1093/jnci/djaf073.
Peer-Reviewed Original Research
Concepts
Igniting Language Intelligence: The Hitchhiker's Guide from Chain-of-Thought Reasoning to Language Agents
Zhang Z, Yao Y, Zhang A, Tang X, Ma X, He Z, Wang Y, Gerstein M, Wang R, Liu G, Zhao H. Igniting Language Intelligence: The Hitchhiker's Guide from Chain-of-Thought Reasoning to Language Agents. ACM Computing Surveys 2025, 57: 1-39. DOI: 10.1145/3719341.
Peer-Reviewed Original Research
Concepts
Subcellular proteomics and iPSC modeling uncover reversible mechanisms of axonal pathology in Alzheimer’s disease
Cai Y, Kanyo J, Wilson R, Bathla S, Cardozo P, Tong L, Qin S, Fuentes L, Pinheiro-de-Sousa I, Huynh T, Sun L, Mansuri M, Tian Z, Gan H, Braker A, Trinh H, Huttner A, Lam T, Petsalaki E, Brennand K, Nairn A, Grutzendler J. Subcellular proteomics and iPSC modeling uncover reversible mechanisms of axonal pathology in Alzheimer’s disease. Nature Aging 2025, 5: 504-527. PMID: 40065072, PMCID: PMC11922768, DOI: 10.1038/s43587-025-00823-3.
Peer-Reviewed Original Research
MeSH Keywords and Concepts
Synthetic Genetic Elements Enable Rapid Characterization of Inorganic Carbon Uptake Systems in Cupriavidus necator H16
Nakamura A, Fulk E, Johnson C, Isaacs F. Synthetic Genetic Elements Enable Rapid Characterization of Inorganic Carbon Uptake Systems in Cupriavidus necator H16. ACS Synthetic Biology 2025, 14: 943-953. PMID: 40048245, DOI: 10.1021/acssynbio.4c00869.
Peer-Reviewed Original Research
MeSH Keywords and Concepts
Investigation of the protein corona and biodistribution profile of polymeric nanoparticles for intra-amniotic delivery
Lynn A, Shin K, Eaton D, Rose M, Zhang X, Ene M, Grundler J, Deschenes E, Rivero R, Bracaglia L, Glazer P, Stitelman D, Saltzman W. Investigation of the protein corona and biodistribution profile of polymeric nanoparticles for intra-amniotic delivery. Biomaterials 2025, 320: 123238. PMID: 40064138, DOI: 10.1016/j.biomaterials.2025.123238.
Peer-Reviewed Original Research
Concepts
Hypercholesterolemia-induced LXR signaling in smooth muscle cells contributes to vascular lesion remodeling and visceral function
Zhang H, de Urturi D, Fernández-Tussy P, Huang Y, Jovin D, Zhang X, Huang S, Lek M, da Silva Catarino J, Sternak M, Citrin K, Swirski F, Gustafsson J, Greif D, Esplugues E, Biwer L, Suárez Y, Fernández-Hernando C. Hypercholesterolemia-induced LXR signaling in smooth muscle cells contributes to vascular lesion remodeling and visceral function. Proceedings Of The National Academy Of Sciences Of The United States Of America 2025, 122: e2417512122. PMID: 40035761, PMCID: PMC11912459, DOI: 10.1073/pnas.2417512122.
Peer-Reviewed Original Research
MeSH Keywords and Concepts
Corrigendum to ‘Prospective solutions to ovarian reserve damage during the ovarian tissue cryopreservation and transplantation procedure’ [Fertility and Sterility 122 (2024) 565-573]
Mercier A, Johnson J, Kallen A. Corrigendum to ‘Prospective solutions to ovarian reserve damage during the ovarian tissue cryopreservation and transplantation procedure’ [Fertility and Sterility 122 (2024) 565-573]. Fertility And Sterility 2025 PMID: 40047740, DOI: 10.1016/j.fertnstert.2024.12.021.
Peer-Reviewed Original Research
Concepts
Implications of gene × environment interactions in post-traumatic stress disorder risk and treatment
Seah C, Sidamon-Eristoff A, Huckins L, Brennand K. Implications of gene × environment interactions in post-traumatic stress disorder risk and treatment. Journal Of Clinical Investigation 2025, 135: e185102. PMID: 40026250, PMCID: PMC11870735, DOI: 10.1172/jci185102.
Peer-Reviewed Original Research
MeSH Keywords and Concepts

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