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Best practices for cysteine analysis.
Choudhury FK, DeNicola GM. Choudhury FK, et al. Ferroptosis Oxid Stress. 2026;2:202508. doi: 10.70401/fos.2025.0010. Epub 2025 Dec 31. Ferroptosis Oxid Stress. 2026. PMID: 41736907 Free PMC article.
TAp73 mediates anti-tumor immunity through regulation of lipid metabolism in the lung tumor microenvironment.
Ackerman HD, Rubio VY, Davis AJ, Lockhart JH, Hackel N, Jimenez RV, Sierra-Mondragon RA, Baldwin JR, Carr C, Reiser M, Napoli M, Yu X, Cheng CH, Stewart PA, Acevedo-Acevedo S, Checker R, Grammatikakis I, Su X, Wu Y, Gould T, Bailey A, Robinson LA, Haura EB, Koomen JM, Rodriguez PC, Flores ER. Ackerman HD, et al. bioRxiv [Preprint]. 2025 Nov 24:2025.11.21.689807. doi: 10.1101/2025.11.21.689807. bioRxiv. 2025. PMID: 41383778 Free PMC article. Preprint.
A machine learning framework for classifying lipids in untargeted metabolomics using mass-to-charge ratios and retention times.
Colin-Leitzinger C, Mekonnen YA, Narvaez-Bandera I, Rubio VY, Ercan D, Welsh EA, Darville LNF, Liu M, Ackerman HD, Avila-Pacheco J, Clish CB, Hicks K, Koomen JM, Gillis N, Fridley BL, Flores ER, Zeleznik OA, Stewart PA. Colin-Leitzinger C, et al. Metabolomics. 2025 Oct 18;21(6):151. doi: 10.1007/s11306-025-02343-y. Metabolomics. 2025. PMID: 41109916 Free PMC article.
Lymphoma accelerates T cell and tissue aging.
Hesterberg RS, Davis JT, Handoo KJ, Elmarsafawi AG, Augello AC, Cheng CH, Atkins R, Lee DH, Yang C, Yao J, Patel KR, Mediavilla-Varela M, Pinilla-Ibarz J, Soto-Palma C, Locke FL, Song X, Wang X, Berglund AE, Rodriguez PC, Knittel G, Flümann R, Reinhardt HC, Shaw TI, Yu X, Niedernhofer LJ, Cleveland JL. Hesterberg RS, et al. Cancer Cell. 2025 Oct 13;43(10):1917-1936.e8. doi: 10.1016/j.ccell.2025.07.023. Epub 2025 Aug 21. Cancer Cell. 2025. PMID: 40845845 Free PMC article.
CAR T cell-driven induction of iNOS in tumor-associated macrophages promotes CAR T cell resistance in B cell lymphoma.
Davila M, Lee SB, Kang YP, Boucher J, Mandula J, Roselli E, Chang D, Jimenez R, Kotani H, Reid K, Vazquez-Martinez J, Beatty N, Goala P, Sierra-Mondragon R, Liu M, Koomen J, Nguyen J, Hussaini M, Shaw T, Wang X, Faramand R, Jain M, Locke F, Rodriguez P, Sailer C, McSain S, Hamid S, Tariq M, Wang J, Abraham-Miranda J. Davila M, et al. Res Sq [Preprint]. 2025 Mar 31:rs.3.rs-3481746. doi: 10.21203/rs.3.rs-3481746/v1. Res Sq. 2025. PMID: 40235478 Free PMC article. Preprint.
Differential Infiltration of Key Immune T-Cell Populations Across Malignancies Varying by Immunogenic Potential and the Likelihood of Response to Immunotherapy.
Eljilany I, Coleman S, Tan AC, McCarter MD, Carpten J, Colman H, Naqash AR, Puzanov I, Arnold SM, Churchman ML, Spakowicz D, Salhia B, Marin J, Ganesan S, Ratan A, Shriver C, Hwu P, Dalton WS, Weiner GJ, Conejo-Garcia JR, Rodriguez P, Tarhini AA. Eljilany I, et al. Cells. 2024 Dec 3;13(23):1993. doi: 10.3390/cells13231993. Cells. 2024. PMID: 39682743 Free PMC article.
iModMix: Integrative Module Analysis for Multi-omics Data.
Narváez-Bandera I, Lui A, Mekonnen YA, Rubio V, Sulman N, Wilson C, Ackerman HD, Ospina OE, Gonzalez-Calderon G, Flores E, Li Q, Chen A, Fridley B, Stewart P. Narváez-Bandera I, et al. bioRxiv [Preprint]. 2025 May 14:2024.11.12.623208. doi: 10.1101/2024.11.12.623208. bioRxiv. 2025. Update in: Bioinformatics. 2026 Feb 3;42(2):btag030. doi: 10.1093/bioinformatics/btag030. PMID: 39605665 Free PMC article. Updated. Preprint.
Oncolytic immunotherapy with nivolumab in muscle-invasive bladder cancer: a phase 1b trial.
Li R, Villa NY, Yu X, Johnson JO, Borjas G, Dhillon J, Moran-Segura CM, Kim Y, Francis N, Dorman D, Powers JJ, Sexton WJ, Spiess PE, Poch MA, Zemp L, Gilbert SM, Zhang J, Pow-Sang JM, Anderson ARA, Li T, Wang X, Grass GD, Burke JM, Dinney CPN, Rodriguez PC, Jain RK, Mulé JJ, Conejo-Garcia JR. Li R, et al. Nat Med. 2025 Jan;31(1):176-188. doi: 10.1038/s41591-024-03324-9. Epub 2024 Nov 9. Nat Med. 2025. PMID: 39521884 Free PMC article. Clinical Trial.
BatchFLEX: feature-level equalization of X-batch.
Davis JT, Obermayer AN, Soupir AC, Hesterberg RS, Duong T, Yang CY, Dao KP, Manley BJ, Grass GD, Avram D, Rodriguez PC, Fridley BL, Yu X, Teng M, Wang X, Shaw TI. Davis JT, et al. Bioinformatics. 2024 Oct 1;40(10):btae587. doi: 10.1093/bioinformatics/btae587. Bioinformatics. 2024. PMID: 39360977 Free PMC article.
Glucose-driven histone lactylation promotes the immunosuppressive activity of monocyte-derived macrophages in glioblastoma.
De Leo A, Ugolini A, Yu X, Scirocchi F, Scocozza D, Peixoto B, Pace A, D'Angelo L, Liu JKC, Etame AB, Rughetti A, Nuti M, Santoro A, Vogelbaum MA, Conejo-Garcia JR, Rodriguez PC, Veglia F. De Leo A, et al. Immunity. 2024 May 14;57(5):1105-1123.e8. doi: 10.1016/j.immuni.2024.04.006. Epub 2024 May 3. Immunity. 2024. PMID: 38703775 Free PMC article.
Jagged2 targeting in lung cancer activates anti-tumor immunity via Notch-induced functional reprogramming of tumor-associated macrophages.
Mandula JK, Sierra-Mondragon RA, Jimenez RV, Chang D, Mohamed E, Chang S, Vazquez-Martinez JA, Cao Y, Anadon CM, Lee SB, Das S, Rocha-Munguba L, Pham VM, Li R, Tarhini AA, Furqan M, Dalton W, Churchman M, Moran-Segura CM, Nguyen J, Perez B, Kojetin DJ, Obermayer A, Yu X, Chen A, Shaw TI, Conejo-Garcia JR, Rodriguez PC. Mandula JK, et al. Immunity. 2024 May 14;57(5):1124-1140.e9. doi: 10.1016/j.immuni.2024.03.020. Epub 2024 Apr 17. Immunity. 2024. PMID: 38636522 Free PMC article.
Baseline Serum Inflammatory Proteins Predict Poor CAR T Outcomes in Diffuse Large B-cell Lymphoma.
Faramand RG, Lee SB, Jain MD, Cao B, Wang X, Rejeski K, Subklewe M, Fahrmann JF, Saini NY, Hanash SM, Kang YP, Chang D, Rodriguez PC, Dean EA, Nishihori T, Shah BD, Lazaryan A, Chavez J, Khimani F, Pinilla-Ibarz JA, Dam M, Reid KM, Corallo SA, Menges M, Hidalgo Vargas M, Mandula JK, Holliday BA, Bachmeier CA, Speth K, Song Q, Mattie M, Locke FL, Davila ML. Faramand RG, et al. Blood Cancer Discov. 2024 Mar 1;5(2):106-113. doi: 10.1158/2643-3230.BCD-23-0056. Blood Cancer Discov. 2024. PMID: 38194367 Free PMC article.
Transgelin 2 guards T cell lipid metabolic programming and anti-tumor function.
Hwang SM, Awasthi D, Jeong J, Sandoval TA, Chae CS, Ramos Y, Tan C, Falco MM, McBain IT, Mishra B, Ivashkiv LB, Zamarin D, Cantillo E, Chapman-Davis E, Holcomb K, Morales DK, Rodriguez PC, Conejo-Garcia JR, Kaczocha M, Vähärautio A, Song M, Cubillos-Ruiz JR. Hwang SM, et al. Res Sq [Preprint]. 2023 Dec 14:rs.3.rs-3683989. doi: 10.21203/rs.3.rs-3683989/v1. Res Sq. 2023. Update in: Nature. 2024 Nov;635(8040):1010-1018. doi: 10.1038/s41586-024-08071-y. PMID: 38168227 Free PMC article. Updated. Preprint.
Enniatin A inhibits the chaperone Hsp90 and unleashes the immune system against triple-negative breast cancer.
Eisa NH, Crowley VM, Elahi A, Kommalapati VK, Serwetnyk MA, Llbiyi T, Lu S, Kainth K, Jilani Y, Marasco D, El Andaloussi A, Lee S, Tsai FTF, Rodriguez PC, Munn D, Celis E, Korkaya H, Debbab A, Blagg B, Chadli A. Eisa NH, et al. iScience. 2023 Oct 24;26(12):108308. doi: 10.1016/j.isci.2023.108308. eCollection 2023 Dec 15. iScience. 2023. PMID: 38025772 Free PMC article.
Targeting intracellular oncoproteins with dimeric IgA promotes expulsion from the cytoplasm and immune-mediated control of epithelial cancers.
Biswas S, Mandal G, Anadon CM, Chaurio RA, Lopez-Bailon LU, Nagy MZ, Mine JA, Hänggi K, Sprenger KB, Innamarato P, Harro CM, Powers JJ, Johnson J, Fang B, Eysha M, Nan X, Li R, Perez BA, Curiel TJ, Yu X, Rodriguez PC, Conejo-Garcia JR. Biswas S, et al. Immunity. 2023 Nov 14;56(11):2570-2583.e6. doi: 10.1016/j.immuni.2023.09.013. Epub 2023 Oct 30. Immunity. 2023. PMID: 37909039 Free PMC article.
Relationships among Inflammatory Biomarkers and Objectively Assessed Physical Activity and Sleep during and after Chemotherapy for Gynecologic Malignancies.
Tometich DB, Hoogland AI, Small BJ, Janelsins MC, Bryant C, Rodriguez Y, Gonzalez BD, Li X, Bulls HW, James BW, Arboleda B, Colon-Echevarria C, Townsend MK, Tworoger SS, Rodriguez P, Oswald LB, Bower JE, Apte SM, Wenham RM, Chon HS, Shahzad MM, Jim HSL. Tometich DB, et al. Cancers (Basel). 2023 Jul 30;15(15):3882. doi: 10.3390/cancers15153882. Cancers (Basel). 2023. PMID: 37568698 Free PMC article.
Relationships among Inflammatory Biomarkers and Self-Reported Treatment-Related Symptoms in Patients Treated with Chemotherapy for Gynecologic Cancer: A Controlled Comparison.
Hoogland AI, Small BJ, Oswald LB, Bryant C, Rodriguez Y, Gonzalez BD, Li X, Janelsins MC, Bulls HW, James BW, Arboleda B, Colon-Echevarria C, Townsend MK, Tworoger SS, Rodriguez PC, Bower JE, Apte SM, Wenham RM, Jim HSL. Hoogland AI, et al. Cancers (Basel). 2023 Jun 29;15(13):3407. doi: 10.3390/cancers15133407. Cancers (Basel). 2023. PMID: 37444517 Free PMC article.
Neglected no more: B cell-mediated anti-tumor immunity.
Conejo-Garcia JR, Biswas S, Chaurio R, Rodriguez PC. Conejo-Garcia JR, et al. Semin Immunol. 2023 Jan;65:101707. doi: 10.1016/j.smim.2022.101707. Epub 2022 Dec 15. Semin Immunol. 2023. PMID: 36527759 Free PMC article. Review.
On the illusion of auxotrophy: met15Δ yeast cells can grow on inorganic sulfur, thanks to the previously uncharacterized homocysteine synthase Yll058w.
Van Oss SB, Parikh SB, Castilho Coelho N, Wacholder A, Belashov I, Zdancewicz S, Michaca M, Xu J, Kang YP, Ward NP, Yoon SJ, McCourt KM, McKee J, Ideker T, VanDemark AP, DeNicola GM, Carvunis AR. Van Oss SB, et al. J Biol Chem. 2022 Dec;298(12):102697. doi: 10.1016/j.jbc.2022.102697. Epub 2022 Nov 13. J Biol Chem. 2022. PMID: 36379252 Free PMC article.
Ablation of the endoplasmic reticulum stress kinase PERK induces paraptosis and type I interferon to promote anti-tumor T cell responses.
Mandula JK, Chang S, Mohamed E, Jimenez R, Sierra-Mondragon RA, Chang DC, Obermayer AN, Moran-Segura CM, Das S, Vazquez-Martinez JA, Prieto K, Chen A, Smalley KSM, Czerniecki B, Forsyth P, Koya RC, Ruffell B, Cubillos-Ruiz JR, Munn DH, Shaw TI, Conejo-Garcia JR, Rodriguez PC. Mandula JK, et al. Cancer Cell. 2022 Oct 10;40(10):1145-1160.e9. doi: 10.1016/j.ccell.2022.08.016. Epub 2022 Sep 22. Cancer Cell. 2022. PMID: 36150390 Free PMC article.
Affinity-matured DLL4 ligands as broad-spectrum modulators of Notch signaling.
Gonzalez-Perez D, Das S, Antfolk D, Ahsan HS, Medina E, Dundes CE, Jokhai RT, Egan ED, Blacklow SC, Loh KM, Rodriguez PC, Luca VC. Gonzalez-Perez D, et al. Nat Chem Biol. 2023 Jan;19(1):9-17. doi: 10.1038/s41589-022-01113-4. Epub 2022 Sep 1. Nat Chem Biol. 2023. PMID: 36050494 Free PMC article.
IgA-Dominated Humoral Immune Responses Govern Patients' Outcome in Endometrial Cancer.
Mandal G, Biswas S, Anadon CM, Yu X, Gatenbee CD, Prabhakaran S, Payne KK, Chaurio RA, Martin A, Innamarato P, Moran C, Powers JJ, Harro CM, Mine JA, Sprenger KB, Rigolizzo KE, Wang X, Curiel TJ, Rodriguez PC, Anderson AR, Saglam O, Conejo-Garcia JR. Mandal G, et al. Cancer Res. 2022 Mar 1;82(5):859-871. doi: 10.1158/0008-5472.CAN-21-2376. Cancer Res. 2022. PMID: 34949671 Free PMC article.
Identification of Immunogenic MHC Class II Human HER3 Peptides that Mediate Anti-HER3 CD4+ Th1 Responses and Potential Use as a Cancer Vaccine.
Basu A, Albert GK, Awshah S, Datta J, Kodumudi KN, Gallen C, Beyer A, Smalley KSM, Rodriguez PC, Duckett DR, Forsyth PA, Soyano A, Koski GK, Lima Barros Costa R, Han H, Soliman H, Lee MC, Kalinski P, Czerniecki BJ. Basu A, et al. Cancer Immunol Res. 2022 Jan;10(1):108-125. doi: 10.1158/2326-6066.CIR-21-0454. Epub 2021 Nov 16. Cancer Immunol Res. 2022. PMID: 34785506 Free PMC article.
Inhibition of the BTK-IDO-mTOR axis promotes differentiation of monocyte-lineage dendritic cells and enhances anti-tumor T cell immunity.
Sharma MD, Pacholczyk R, Shi H, Berrong ZJ, Zakharia Y, Greco A, Chang CS, Eathiraj S, Kennedy E, Cash T, Bollag RJ, Kolhe R, Sadek R, McGaha TL, Rodriguez P, Mandula J, Blazar BR, Johnson TS, Munn DH. Sharma MD, et al. Immunity. 2021 Oct 12;54(10):2354-2371.e8. doi: 10.1016/j.immuni.2021.09.005. Epub 2021 Oct 5. Immunity. 2021. PMID: 34614413 Free PMC article.
Deep Learning of Histopathology Images at the Single Cell Level.
Lee K, Lockhart JH, Xie M, Chaudhary R, Slebos RJC, Flores ER, Chung CH, Tan AC. Lee K, et al. Front Artif Intell. 2021 Sep 10;4:754641. doi: 10.3389/frai.2021.754641. eCollection 2021. Front Artif Intell. 2021. PMID: 34568816 Free PMC article. Review.
Single-Cell Characterization of the Immune Microenvironment of Melanoma Brain and Leptomeningeal Metastases.
Smalley I, Chen Z, Phadke M, Li J, Yu X, Wyatt C, Evernden B, Messina JL, Sarnaik A, Sondak VK, Zhang C, Law V, Tran N, Etame A, Macaulay RJB, Eroglu Z, Forsyth PA, Rodriguez PC, Chen YA, Smalley KSM. Smalley I, et al. Clin Cancer Res. 2021 Jul 15;27(14):4109-4125. doi: 10.1158/1078-0432.CCR-21-1694. Epub 2021 May 25. Clin Cancer Res. 2021. PMID: 34035069 Free PMC article.
The inhibitory receptor TIM-3 limits activation of the cGAS-STING pathway in intra-tumoral dendritic cells by suppressing extracellular DNA uptake.
de Mingo Pulido Á, Hänggi K, Celias DP, Gardner A, Li J, Batista-Bittencourt B, Mohamed E, Trillo-Tinoco J, Osunmakinde O, Peña R, Onimus A, Kaisho T, Kaufmann J, McEachern K, Soliman H, Luca VC, Rodriguez PC, Yu X, Ruffell B. de Mingo Pulido Á, et al. Immunity. 2021 Jun 8;54(6):1154-1167.e7. doi: 10.1016/j.immuni.2021.04.019. Epub 2021 May 11. Immunity. 2021. PMID: 33979578 Free PMC article.
Targeted Therapy Given after Anti-PD-1 Leads to Prolonged Responses in Mouse Melanoma Models through Sustained Antitumor Immunity.
Phadke MS, Chen Z, Li J, Mohamed E, Davies MA, Smalley I, Duckett DR, Palve V, Czerniecki BJ, Forsyth PA, Noyes D, Adeegbe DO, Eroglu Z, Nguyen KT, Tsai KY, Rix U, Burd CE, Chen YA, Rodriguez PC, Smalley KSM. Phadke MS, et al. Cancer Immunol Res. 2021 May;9(5):554-567. doi: 10.1158/2326-6066.CIR-20-0905. Epub 2021 Mar 2. Cancer Immunol Res. 2021. PMID: 33653716 Free PMC article.
IgA transcytosis and antigen recognition govern ovarian cancer immunity.
Biswas S, Mandal G, Payne KK, Anadon CM, Gatenbee CD, Chaurio RA, Costich TL, Moran C, Harro CM, Rigolizzo KE, Mine JA, Trillo-Tinoco J, Sasamoto N, Terry KL, Marchion D, Buras A, Wenham RM, Yu X, Townsend MK, Tworoger SS, Rodriguez PC, Anderson AR, Conejo-Garcia JR. Biswas S, et al. Nature. 2021 Mar;591(7850):464-470. doi: 10.1038/s41586-020-03144-0. Epub 2021 Feb 3. Nature. 2021. PMID: 33536615 Free PMC article.