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Machine Learning Links T-cell Function and Spatial Localization to Neoadjuvant Immunotherapy and Clinical Outcome in Pancreatic Cancer.
Blise KE, Sivagnanam S, Betts CB, Betre K, Kirchberger N, Tate BJ, Furth EE, Dias Costa A, Nowak JA, Wolpin BM, Vonderheide RH, Goecks J, Coussens LM, Byrne KT. Blise KE, et al. Among authors: sivagnanam s. Cancer Immunol Res. 2024 May 2;12(5):544-558. doi: 10.1158/2326-6066.CIR-23-0873. Cancer Immunol Res. 2024. PMID: 38381401
Leukocyte Heterogeneity in Pancreatic Ductal Adenocarcinoma: Phenotypic and Spatial Features Associated with Clinical Outcome.
Liudahl SM, Betts CB, Sivagnanam S, Morales-Oyarvide V, da Silva A, Yuan C, Hwang S, Grossblatt-Wait A, Leis KR, Larson W, Lavoie MB, Robinson P, Dias Costa A, Väyrynen SA, Clancy TE, Rubinson DA, Link J, Keith D, Horton W, Tempero MA, Vonderheide RH, Jaffee EM, Sheppard B, Goecks J, Sears RC, Park BS, Mori M, Nowak JA, Wolpin BM, Coussens LM. Liudahl SM, et al. Among authors: sivagnanam s. Cancer Discov. 2021 Aug;11(8):2014-2031. doi: 10.1158/2159-8290.CD-20-0841. Epub 2021 Mar 16. Cancer Discov. 2021. PMID: 33727309 Free PMC article.
Neoadjuvant Selicrelumab, an Agonist CD40 Antibody, Induces Changes in the Tumor Microenvironment in Patients with Resectable Pancreatic Cancer.
Byrne KT, Betts CB, Mick R, Sivagnanam S, Bajor DL, Laheru DA, Chiorean EG, O'Hara MH, Liudahl SM, Newcomb C, Alanio C, Ferreira AP, Park BS, Ohtani T, Huffman AP, Väyrynen SA, Dias Costa A, Kaiser JC, Lacroix AM, Redlinger C, Stern M, Nowak JA, Wherry EJ, Cheever MA, Wolpin BM, Furth EE, Jaffee EM, Coussens LM, Vonderheide RH. Byrne KT, et al. Among authors: sivagnanam s. Clin Cancer Res. 2021 Aug 15;27(16):4574-4586. doi: 10.1158/1078-0432.CCR-21-1047. Epub 2021 Jun 10. Clin Cancer Res. 2021. PMID: 34112709 Free PMC article. Clinical Trial.
Machine learning links T cell function and spatial localization to neoadjuvant immunotherapy and clinical outcome in pancreatic cancer.
Blise KE, Sivagnanam S, Betts CB, Betre K, Kirchberger N, Tate B, Furth EE, Dias Costa A, Nowak JA, Wolpin BM, Vonderheide RH, Goecks J, Coussens LM, Byrne KT. Blise KE, et al. Among authors: sivagnanam s. bioRxiv [Preprint]. 2023 Oct 23:2023.10.20.563335. doi: 10.1101/2023.10.20.563335. bioRxiv. 2023. PMID: 37961410 Free PMC article. Updated. Preprint.
Deciphering the Immune Complexity in Esophageal Adenocarcinoma and Pre-Cancerous Lesions With Sequential Multiplex Immunohistochemistry and Sparse Subspace Clustering Approach.
Sundaram S, Kim EN, Jones GM, Sivagnanam S, Tripathi M, Miremadi A, Di Pietro M, Coussens LM, Fitzgerald RC, Chang YH, Zhuang L. Sundaram S, et al. Among authors: sivagnanam s. Front Immunol. 2022 May 19;13:874255. doi: 10.3389/fimmu.2022.874255. eCollection 2022. Front Immunol. 2022. PMID: 35663986 Free PMC article.
The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution.
Rozenblatt-Rosen O, Regev A, Oberdoerffer P, Nawy T, Hupalowska A, Rood JE, Ashenberg O, Cerami E, Coffey RJ, Demir E, Ding L, Esplin ED, Ford JM, Goecks J, Ghosh S, Gray JW, Guinney J, Hanlon SE, Hughes SK, Hwang ES, Iacobuzio-Donahue CA, Jané-Valbuena J, Johnson BE, Lau KS, Lively T, Mazzilli SA, Pe'er D, Santagata S, Shalek AK, Schapiro D, Snyder MP, Sorger PK, Spira AE, Srivastava S, Tan K, West RB, Williams EH; Human Tumor Atlas Network. Rozenblatt-Rosen O, et al. Cell. 2020 Apr 16;181(2):236-249. doi: 10.1016/j.cell.2020.03.053. Cell. 2020. PMID: 32302568 Free PMC article. Review.
MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging.
Schapiro D, Sokolov A, Yapp C, Chen YA, Muhlich JL, Hess J, Creason AL, Nirmal AJ, Baker GJ, Nariya MK, Lin JR, Maliga Z, Jacobson CA, Hodgman MW, Ruokonen J, Farhi SL, Abbondanza D, McKinley ET, Persson D, Betts C, Sivagnanam S, Regev A, Goecks J, Coffey RJ, Coussens LM, Santagata S, Sorger PK. Schapiro D, et al. Among authors: sivagnanam s. Nat Methods. 2022 Mar;19(3):311-315. doi: 10.1038/s41592-021-01308-y. Epub 2021 Nov 25. Nat Methods. 2022. PMID: 34824477 Free PMC article.
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