Publications

2025

907 Midkine suppresses interferon-driven antigen presentation and dendritic-cell activation in neuroendocrine tumors
Wang J, Perry C, Frey A, Fei Y, Costa P, Ghadermarzi S, Levine D, Ishizuka J. 907 Midkine suppresses interferon-driven antigen presentation and dendritic-cell activation in neuroendocrine tumors. 2025, a1027-a1027. DOI: 10.1136/jitc-2025-sitc2025.0907.
Peer-Reviewed Original Research
Concepts
TDP-43 loss brings RNA to a twist ending.
Yang S, Lei Z, Guo JU. TDP-43 loss brings RNA to a twist ending. Nat Neurosci 2025, 28: 2176-2177. PMID: 41120749, DOI: 10.1038/s41593-025-02065-3.
Peer-Reviewed Original Research
Myeloid cells mediate interferon-driven resistance to immunotherapy in advanced renal cell carcinoma
Bi K, Kashima S, Camp S, Meli K, Saad E, Titchen B, Labaki C, Bakouny Z, Pimenta E, Park J, Shannon E, Fu J, Xirenayi S, Horst J, Lum L, Ishizuka J, Choueiri T, Braun D, Van Allen E. Myeloid cells mediate interferon-driven resistance to immunotherapy in advanced renal cell carcinoma. Immunity 2025, 58: 2814-2829.e9. PMID: 41175876, PMCID: PMC12616721, DOI: 10.1016/j.immuni.2025.10.013.
Peer-Reviewed Original Research
MeSH Keywords and Concepts
Linker histone regulates the myeloid versus lymphoid bifurcation of multipotent hematopoietic stem and progenitors
Karatepe K, de Faria B, Zhang J, Chen X, Pinto H, Fyodorov D, Sefik E, Willcockson M, Flavell R, Skoultchi A, Guo S. Linker histone regulates the myeloid versus lymphoid bifurcation of multipotent hematopoietic stem and progenitors. Proceedings Of The National Academy Of Sciences Of The United States Of America 2025, 122: e2509412122. PMID: 41118213, PMCID: PMC12582276, DOI: 10.1073/pnas.2509412122.
Peer-Reviewed Original Research
MeSH Keywords and Concepts
Enhanced RNA quality control maintains long-term regenerative ability in planarians
Zelko M, Li D, Parambil S, Poulet A, Verdesca A, Mazeika K, Dasgupta K, van Wolfswinkel J. Enhanced RNA quality control maintains long-term regenerative ability in planarians. Development 2025, 152: dev204762. PMID: 40955864, PMCID: PMC12579931, DOI: 10.1242/dev.204762.
Peer-Reviewed Original Research
Concepts
Long noncoding RNA-dependent control of Myc transcriptional bursting
Li Q, Dilsavor C, Gahramanov V, Floyd E, Ding J, Glynn J, Chiotakakos I, Olivero C, Zamudio J, Dimitrova N. Long noncoding RNA-dependent control of Myc transcriptional bursting. Cell Reports 2025, 44: 116439. PMID: 41105511, PMCID: PMC12606467, DOI: 10.1016/j.celrep.2025.116439.
Peer-Reviewed Original Research
MeSH Keywords and Concepts
Digital breast tomosynthesis and breast cancer detection in older women: Smaller tumors and more invasive lobular carcinomas.
Huang S, Westvold S, Soulos P, Winer E, Lewin J, Lustberg M, Zhan H, Richman I, Robinson T, Dinan M. Digital breast tomosynthesis and breast cancer detection in older women: Smaller tumors and more invasive lobular carcinomas. JCO Oncology Practice 2025, 21: 285-285. DOI: 10.1200/op.2025.21.10_suppl.285.
Peer-Reviewed Original Research
Concepts
Sequencing-free whole-genome spatial transcriptomics at single-molecule resolution.
Cheng Y, Dang S, Zhang Y, Chen Y, Yu R, Liu M, Jin S, Han A, Katz S, Wang S. Sequencing-free whole-genome spatial transcriptomics at single-molecule resolution. Cell 2025 PMID: 41038164, DOI: 10.1016/j.cell.2025.09.006.
Peer-Reviewed Original Research
Collagen Post-Translational Modifications Are Altered in Idiopathic Pulmonary Fibrosis, Including within Extracellular Matrix Receptor Binding Motifs.
Merl-Pham J, Rothkirch Née Knüppel L, Binzenhöfer L, Hennen E, Kaminski N, Hatz R, Behr J, Hauck S, Hilgendorff A, Eickelberg O, Staab-Weijnitz C. Collagen Post-Translational Modifications Are Altered in Idiopathic Pulmonary Fibrosis, Including within Extracellular Matrix Receptor Binding Motifs. American Journal Of Respiratory And Critical Care Medicine 2025, 211: 1889-1892. PMID: 40845301, DOI: 10.1164/rccm.202505-1276rl.
Peer-Reviewed Original Research
Concepts
Codanin-1, defective in congenital dyserythropoietic anemia I (CDA-I), regulates erythroid differentiation
Bosques L, Modepalli S, Nagarajan A, Tang C, Martínez-Morilla S, Rahman N, Mehta S, Krause D, Tamary H, Gallagher P, Hattangadi S, Kupfer G. Codanin-1, defective in congenital dyserythropoietic anemia I (CDA-I), regulates erythroid differentiation. Annals Of Hematology 2025, 1-15. PMID: 41028447, DOI: 10.1007/s00277-025-06540-6.
Peer-Reviewed Original Research
Concepts
Targeting an essential viral oncoprotein with an IL-7-enhanced mRNA vaccine induces durable immunity to Merkel cell carcinoma
Frey A, Clulo K, Fei Y, Dumit T, Scallo F, Williams J, Chang E, Perry C, Wirth L, Jacobs D, Braun D, Bosenberg M, Tran T, Clune J, Kluger H, Olino K, Ishizuka J. Targeting an essential viral oncoprotein with an IL-7-enhanced mRNA vaccine induces durable immunity to Merkel cell carcinoma. Cell Reports 2025, 44: 116359. PMID: 41042672, DOI: 10.1016/j.celrep.2025.116359.
Peer-Reviewed Original Research
Concepts
Genotype‐by‐sex interaction analyses for alcohol use disorder across biobanks
Zhou H, Wang L, Mao Z, Deans P, Kember R, Chen Q, Zakiniaeiz Y, Kohler R, Peltier M, Verplaetse T, Program V, Potenza M, Brennand K, Justice A, Kranzler H, Gelernter J, McKee S. Genotype‐by‐sex interaction analyses for alcohol use disorder across biobanks. Alcohol Clinical And Experimental Research 2025 PMID: 41017299, DOI: 10.1111/acer.70173.
Peer-Reviewed Original Research
Concepts
Transcriptional regulation of thorn tip sclerification in plants
Ren J, Duan Y, Li R, Zhang X, Shi Y, Zhou S, Xie K, Wu X, Irish V, Deng X, Zhang F, Guo W. Transcriptional regulation of thorn tip sclerification in plants. Proceedings Of The National Academy Of Sciences Of The United States Of America 2025, 122: e2510775122. PMID: 40986360, DOI: 10.1073/pnas.2510775122.
Peer-Reviewed Original Research
MeSH Keywords and Concepts
hiPSC‐Derived Astrocytes From Individuals With Schizophrenia Induce a Dystrophic Phenotype in Microglial‐Like Cells
Cardozo P, Lee C, Lacerda J, Fahel J, Trindade P, Vitória G, Chicaybam L, Cordeiro R, de Faria I, Silva N, Todjro Y, do P. Maciel J, Bonamino M, Vieira L, Cruz B, Nicolato R, Brennand K, Rehen S, Ribeiro F. hiPSC‐Derived Astrocytes From Individuals With Schizophrenia Induce a Dystrophic Phenotype in Microglial‐Like Cells. Glia 2025 PMID: 40970468, DOI: 10.1002/glia.70085.
Peer-Reviewed Original Research
Concepts
Enhancing RNA base editing on mammalian transcripts with small nuclear RNAs
Smargon A, Pant D, Gomberg T, Fagre C, Glynne S, Nguyen J, Naritomi J, Gilbert W, Yeo G. Enhancing RNA base editing on mammalian transcripts with small nuclear RNAs. Nature Chemical Biology 2025, 1-9. PMID: 40968292, DOI: 10.1038/s41589-025-02026-8.
Peer-Reviewed Original Research
Concepts
Risks of AI scientists: prioritizing safeguarding over autonomy
Tang X, Jin Q, Zhu K, Yuan T, Zhang Y, Zhou W, Qu M, Zhao Y, Tang J, Zhang Z, Cohan A, Greenbaum D, Lu Z, Gerstein M. Risks of AI scientists: prioritizing safeguarding over autonomy. Nature Communications 2025, 16: 8317. PMID: 40968279, PMCID: PMC12446425, DOI: 10.1038/s41467-025-63913-1.
Peer-Reviewed Original Research
MeSH Keywords and Concepts
Network-based drug repurposing for psychiatric disorders using single-cell genomics
Gupta C, Kalafut N, Clarke D, Choi J, Arachchilage K, Khullar S, Xia Y, Zhou X, Dursun C, Gerstein M, Wang D. Network-based drug repurposing for psychiatric disorders using single-cell genomics. Cell Genomics 2025, 101003. PMID: 40972584, DOI: 10.1016/j.xgen.2025.101003.
Peer-Reviewed Original Research
Concepts
Sclerotic GVHD and Scleroderma Share Dysregulated Gene Expression that is Ameliorated by EREG Therapeutic Antibody
Newton N, Agrawal K, Odell A, Tracy T, Hackett C, Eldrup A, Whitfield M, Martyanov V, Girardi M, Sefik E, Flavell R, Odell I. Sclerotic GVHD and Scleroderma Share Dysregulated Gene Expression that is Ameliorated by EREG Therapeutic Antibody. Blood 2025 PMID: 40961242, DOI: 10.1182/blood.2025029836.
Peer-Reviewed Original Research
Concepts
Humanization of CD47 enables development of functional human neutrophils via postirradiation remodeling of the bone marrow.
Sefik E, Philbrick W, Zhang F, Agrawal K, Van Lee B, Sam J, Karatepe K, Zheng Y, Liang K, Peng S, Mirza H, Rangavajhula A, Simon P, Arun N, Babu P, Eynon E, Chiorazzi M, Shan L, Halene S, Luo H, Rongvaux A, Kluger Y, Flavell R. Humanization of CD47 enables development of functional human neutrophils via postirradiation remodeling of the bone marrow. Proceedings Of The National Academy Of Sciences Of The United States Of America 2025, 122: e2426546122. PMID: 40956886, PMCID: PMC12478129, DOI: 10.1073/pnas.2426546122.
Peer-Reviewed Original Research
MeSH Keywords and Concepts
Impaired hematopoiesis and embryonic lethality at midgestation of mice lacking both lipid transfer proteins VPS13A and VPS13C
Xu P, Mancuso R, Leonzino M, Zeiss C, Krause D, De Camilli P. Impaired hematopoiesis and embryonic lethality at midgestation of mice lacking both lipid transfer proteins VPS13A and VPS13C. PLOS Biology 2025, 23: e3003393. PMID: 40956846, PMCID: PMC12463328, DOI: 10.1371/journal.pbio.3003393.
Peer-Reviewed Original Research
MeSH Keywords and Concepts
Regulatory genome annotation
Kumar S, Gerstein M. Regulatory genome annotation. Nature Reviews Genetics 2025, 26: 661-662. PMID: 40957943, DOI: 10.1038/s41576-025-00885-4.
Peer-Reviewed Original Research
Concepts
Advancing biological understanding of cellular senescence with computational multiomics
Li S, Agudelo Garcia P, Aliferis C, Becich M, Calyeca J, Cosgrove B, Elisseeff J, Farzad N, Fertig E, Glass C, Gu L, Hu Q, Ji Z, Königshoff M, LeBrasseur N, Li D, Ma A, Ma Q, Menon V, Mitchell J, Mora A, Nagaraj S, Nelson A, Niedernhofer L, Rojas M, Taha H, Wang J, Wang S, Wu P, Xie J, Xu M, Yu M, Zhang X, Zhao Y, Adams P, Aguayo-Mazzucato C, Baker D, Benz C, Bernlohr D, Bueno M, Chen J, Childs B, Chuang J, Chung D, Dileepan M, Ding L, Dong M, Duncan F, Enninful A, Flynn W, Franco A, Furman D, Garovic V, Halene S, Herman A, Hertzel A, Iwasaki K, Jeon H, Kang J, Karmakar S, Kirkland J, Korstanje R, Kummerfeld E, Lee J, Liu Y, Lu Y, Lugo-Martinez J, Martini H, Melov S, Musi N, Passos J, Peters S, Rahman I, Ramasamy R, Rindone A, Robbins P, Robson P, Rodriguez-Lopez J, Rosas L, Rosenthal N, Schafer M, Schilling B, Schmidt E, Schneider K, Sengupta K, Shu J, So P, Sun L, Tchkonia T, Teneche M, Vanegas N, Wang J, Xie J, Yin S, Zhang K, Zhu Q, Fan R. Advancing biological understanding of cellular senescence with computational multiomics. Nature Genetics 2025, 1-14. PMID: 40954249, DOI: 10.1038/s41588-025-02314-y.
Peer-Reviewed Original Research
Concepts
Hypoxia Induces Immunosuppression by Silencing STING in Cancer.
Lu Y, Yurkevicz A, Liu Y, Glazer P. Hypoxia Induces Immunosuppression by Silencing STING in Cancer. Cancer Research 2025 PMID: 40939188, DOI: 10.1158/0008-5472.can-24-2038.
Peer-Reviewed Original Research
Concepts
Prognostic Biomarkers for Idiopathic Pulmonary Fibrosis: Findings from ISABELA Clinical Trials
Randall M, Andersen C, Brown K, de Bernard S, Ford P, Kaminski N, Kreuter M, Lim S, Maher T, Prasad N, Prasse A, Pujuguet P, Teneggi V, van den Blink B, Wain L, Watkins T, Wuyts W, Bauer Y. Prognostic Biomarkers for Idiopathic Pulmonary Fibrosis: Findings from ISABELA Clinical Trials. ERJ Open Research 2025, 00893-2025. DOI: 10.1183/23120541.00893-2025.
Peer-Reviewed Original Research
Concepts
Label-Efficient Deep Color Deconvolution of Brightfield Multiplex IHC Images
Abousamra S, Fassler D, Gupta R, Kurc T, Escobar-Hoyos L, Samaras D, Shroyer K, Saltz J, Chen C. Label-Efficient Deep Color Deconvolution of Brightfield Multiplex IHC Images. IEEE Transactions On Medical Imaging 2025, PP: 1-1. PMID: 40932806, DOI: 10.1109/tmi.2025.3609245.
Peer-Reviewed Original Research
Concepts

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