Maura F, Rajanna AR, Ziccheddu B, Poos AM, Derkach A, Maclachlan K, Durante M, Diamond B, Papadimitriou M, Davies F, Boyle EM, Walker B, Hultcrantz M, Silva A, Hampton O, Teer JK, Siegel EM, Bolli N, Jackson GH, Kaiser M, Pawlyn C, Cook G, Kazandjian D, Stein C, Chesi M, Bergsagel L, Mai EK, Goldschmidt H, Weisel KC, Fenk R, Raab MS, Van Rhee F, Usmani S, Shain KH, Weinhold N, Morgan G, Landgren O. Genomic Classification and Individualized Prognosis in Multiple Myeloma. J Clin Oncol. 2024. JCO2301277. Epub 2024 Jan 09. doi:10.1200/JCO.23.01277. PubMed PMID: 38194610. (Q1, Cancer Research, Medicine, Oncology. IF=42.1)
Bishop R, Miller A, Froid M, Nerlakanti N, Li T, Frieling J, Nasr M, Nyman K, Sudalagunta P, Canevarolo R, Silva AS, Shain K, Lynch C, Basanta D. The bone ecosystem facilitates multiple myeloma relapse and the evolution of heterogeneous drug resistant disease. Nature Communications. 2024. doi:10.1038/s41467-024-46594-0. (Q1 Biochemistry, Genetics and Molecular Biology. IF=14.7)
Sudalagunta P, Canevarolo R, Meads M, Silva M, Zhao X, Cubitt C, DeAvila G, Alugubelli R, Logothetis C, Tungesvik A, Zhang Q, Hampton O, Teer J, Welsh E, Yoder S, Shah B, Tao J, Hazlehurst L, Gatenby R, Sullivan D, Alsina M, Nishihori T, Brayer J, Cleveland J, Dalton W, Gillies R, DeCastro A, Domelen D, Chai Y, Walker C, Wang F, Landesman Y, Baz R, Silva AS*, Shain K*. Functional transcriptomic landscape informs novel therapeutic strategies in multiple myeloma. Cancer Research 2024. PubMed PMID: 39476082. *Co-senior authors. (Q1 Cancer Research, Oncology. IF=12.5)
Bishop R, Li T, Alugubelli R, Nasr M, Nyman K, Sudalagunta P, Meads M, Frieling J, Nerlakanti N, Tauro M, Hampton O, Fang B, Grant S, Koomen J, Silva A, Shain K, Lynch C. Acid Ceramidase Controls Proteasome Inhibitor Resistance and is a Tractable Therapeutic Target for the Treatment of Refractory Multiple Myeloma. Haematologica 2024. PubMed PMID: 39633543. (Q1 Hematology. IF=8.2)
Li L, Hu X, Nkwocha J, Kmieciak M, Mann H, Meads M, Shain K, Alugubelli R, Silva A, Sudalagunta P, Canevarolo R, Zhou L, Grant S. Combined Mek1/2 And Atr Inhibition Promotes Myeloma Cell Death Through A Stat3‑Dependent Mechanism In Vitro And In Vivo. British Journal of Haematology 2024 Oct. PubMed PMID: 39379134. (Q1 Hematology. IF=5.1)
Freeman C, Noble J, Menges M, Villanueva R, Nakashima J, Figura N, Tonseth RP, Idiaquez D, Skelson L, Smith E, Abraham-Miranda J, Corallo S, De Avila G, Castaneda Puglianini O, Liu H, Alsina M, Nishihori T, Shain K, Baz R, Blue B, Grajales‑Cruz A, Koomen J, Atkins R, Hansen D, Silva A.S., Kim J, Balagurunathan Y, Locke F. Tumor burden quantified by Soluble B-Cell Maturation Antigen and Metabolic Tumor Volume determine myeloma CAR-T outcomes. Blood 2024. PubMed PMID: 39652773. (Q1 Hematology, Cell Biology, Immunology. IF=21.0)
Persi E, Sudalagunta P, Wolf Y, Canevarolo R, Damaghi M, Shain K, Silva AS*, Koonin E*. Genome-level Selection in Tumors as a Universal Marker of Resistance to Therapy. Nature Communications 2025. PubMed PMID: 40664650. *Co-senior authors
Meads MB, Zhao X, Noyes D, Sudalagunta PR, Achille A, Zhang C, Canevarolo RR, Silva M, Magaletti D, DeAvila D, Toska S, Oates A, Lastorino D, Idiaquez DW, Song J, Sansil SS, Yoder SJ, Grajales‑Cruz AF, Blue B, Freeman CL, Kim J, Alsina M, Brayer J, Silva AS, Song X, Shain KH, Baz R. Target antigen and plasma cell phenotype are critical factors for sensitivity to response‑adapted daratumumab therapy. Blood 2025. PubMed PMID: 40983035
Maura F, Bergsagel L, Ziccheddu B, Kumar S, Maclachlan K, Derkach A, Garces J-J, Firestone R, Braggio E, Asmann Y, Durante M, Diamond BT, Papadimitriou M, Hultcrantz M, Castellano G, Marella A, Lionetti M, Matera A, Maeda A, Pioggia S, Da Via M, Leongamornlert D, De Magistris C, DeAvila D, Sudalagunta PR, Canevarolo RR, Siegel EM, Agius P, Teer J, McPherson A, Yamashita Y, Silva A, Blaney P, Baz R, Patel K, Campbell P, Fonseca R, Orlowski R, Shain K, Bolli N, Usmani S, Rajkumar V, Morgan G, Landgren O. Genomics define malignant transformation in myeloma precursor conditions. J Clin Oncol, In Press.
Canevarolo R, Sudalagunta PR, 31 more & Silva AS. Epigenetic Plasticity Drives Carcinogenesis and Multi-Therapy Resistance in Multiple Myeloma. Under review at Nature Communications. https://doi.org/10.21203/rs.3.rs-6306816/v1
Di Meo F, Albano F, Cesarano A, Wang Y, Kale B, Shain K, Silva A, Kurihara N, Tenshin H, Jellyman D, Song X, Ghaffari S, Mesa H, Freeman C, Creelan B, Zhao X, Meads M, Marino S, Rodriguez PC, Locke F, Hwu P, Roodman D, Mansilla-Soto J, Perna F. Developing SEMA4A-directed CAR T cells to overcome low BCMA antigen density in Multiple Myeloma. Cancer Cell, In Press.
Churchman ML, Lu X, McKean DM, Radmacher MD, Zhang Q, Rounbehler RJ, Tan AC, Shaw TI, Obermayer A, Grass GD, Spakowicz D, Tarhini AA, Shain KH, Canevarolo RR, Meads MB, Silva AS, Sudalagunta PR, Manley BJ, Huntsman S, Collyar D, Kolesar JM, Evers BM, Single N, Edge SB, Johnson CS, Weiner GJ, McCarter MD, Borges VF, Horne L, Lillard JW Jr, Mudaranthakam DP, White J, Libutti S, Ganesan S, Riedlinger GM, Loughran TP Jr, Halme DG, Johns MA, Arciero C, Salhia B, Naqash AR, Shriver CD, Lee KP, Schneider BP, Nix DA, Fillmore GC, Colman H, Ulrich CM, Springer BC, Pollock R, Vucic EA, Sherman J, Jain AK, Dalton WS, Agius P, Siegel EM. The Oncology Research Information Exchange Network (ORIEN) – Building a Real‑World Collaborative, Patient‑driven Infrastructure for Discovery Research and Precision Oncology. Under Review at Nature Medicine.
Tauro M, Li T, Sudalagunta PR, Meads M, Alugubelli RR, Lawrence NJ, Lawrence H, Gunawan S, Tran TH, Shay G, Schonbrunn E, Bishop RT, Nasr M, Cleveland JL, Silva AS, Shain KH, Lynch CC. Unc‑51 Like Kinase 3 (ULK3) is essential for autophagy and cell survival in multiple myeloma. Under Review at Nature Communications.
Jiang Q, Sudalagunta P, Meads M, Zhao X, Achille A, Noyes D, Silva M, Canevarolo R, Shain K, Silva A, Zhang W. TLCellClassifier: Machine Learning Based Cell Classification for Bright‑Field Time‑Lapse Images. Biorxiv 2024. doi:10.1101/2024.06.11.598552
Mariano S, Assis LH de P, Correa J, Canevarolo RR, Migita NA, Sudalagunta PR, Azevedo AC de, Meidanis J, Brandalise SR, Silva AS, Yunes JA. ELDA: A Real‑Time Microscopy‑Based Drug Screening Assay for Personalized Therapy in Acute Lymphoblastic Leukemia. Under Review at Frontiers in Oncology.
Hammami MB, Canevarolo RR, Silva AS, Alsina M, Kumar N, Baz RC, Shain KH. Navigating the evolving management of smoldering multiple myeloma. Under Review at HemaSphere.
Burger K, Meads M, Sudalagunta P, Fernandez M, Oliveira P, Canevarolo R, Alugubelli R,Tungsevik A, Avila G, Silva M, Distler A, Dai H, Kulkarni A, Hampton O, Koomen J, Roush W, Monastyrskyi A,Berglund A,Silva A, Cleveland J, Shain K. CK1δ/CK1ε Signaling is Necessary to Sustain mitochondrial Metabolism and Cell Survival in Multiple Myeloma. Submitted to Cancer Discovery.
Canevarolo R, Meads M, Silva M, Sudalagunta P, Avila G, Alugubelli R, Tungesvik A, Bell E, Burger K, Kulkarni A, Hampton O, Jiang Z, Dai H, Cubitt C, Teer J, Welsh E, Yoder S, Shah B, Tao J, Hazlehurst L, Gatenby R, Sullivan D, Alsina M, Nishihori T, Brayer J, Cleveland J, Dalton W, Gillies R, Baz R, Shain K, Silva A. Dynamic super-enhancer core regulatory circuits and epigenetic landscapes drive malignant progression and refractory disease in multiple myeloma. Pre-print version.
Hasipek M, Grabowski D,Guan Y, Alugubelli R,Tiwari A, Gu X, deAvila G, Silva A, Meads M, Parker Y, Lindner D, Saunthararajah Y, Shain K, Maciejewski J, Reu F, Phillips J, Jha B. Therapeutic Targeting of Protein Disulfide Isomerase PDIA1 in Multiple Myeloma. Under review at Cancers.
Koomen D, Meads M, Magaletti D, Guingab-Cagmat J, Oliveira P, Fang B, Liu M, Welsh E, Meke L, Jiang Z, Hampton O, Tungesvik A, De Avila G, Alugubelli R, Nishihori T, Silva A, Eschrich S, Garrett T, Koomen J, Shain K. Metabolic Changes are Associated with Melphalan Resistance in Multiple Myeloma. Under Review at Journal of Proteome Research.
Mostofa AGM, Distler A, Meads MB, Sahakian E, Powers JJ, Achille A, Noyes D, Wright G, Ramakrishnan R, Nguyen T, Avilla G, Silva A, Sudalagunta P, Renatino-Canevarolo R, Silva MD, Alugubelli R, Dai H, Kulkarni A, Dalton WS, Hampton O, Welsh E, Teer J, Tungesvik A, Pinilla-Ibarz J, Sotomayor EM, Shain KH and Brayer J. Key Functional Analysis of HDAC11 In Plasma Cell Development and Multiple Myeloma Survival. Manuscript under review at Blood.
Zhao X, Wang MY, Jiang H, Lwin T, Park PM, Gao J, Meads MB, Ren Y, Li T, Sun J, Fahmi NA, Singh S, Sehgal L, Wang X, Silva AS, Sotomayor EM, Shain KH, Cleveland JL, Wang M, Zhang W, Qi J, Shah BD, Tao J. Transcriptional programming drives Ibrutinib-resistance evolution in mantle cell lymphoma. Cell Rep. 2021;34(11):108870. PMID: 33730585
Tichacek CJ, Tafreshi NK, Kil H, Engelman RW, Doligalski ML, Budzevich MM, Gage KL, McLaughlin ML, Wadas TJ, Silva A, Moros E, Morse DL. Biodistribution and Multicompartment Pharmacokinetic Analysis of a Targeted alpha Particle Therapy. Mol Pharm. 2020;17(11):4180-8. PMID: 32960613
Enderling H, Altrock PM, Andor N, Basanta D, Brown JS, Gatenby RA, Marusyk A, Rejniak KA, Silva A, Anderson ARA. High School Internship Program in Integrated Mathematical Oncology (HIP IMO): Five-Year Experience at Moffitt Cancer Center. B Math Biol. 2020;82(7). PMID: 32648152
Sudalagunta PR, Silva M, Canevarolo R, Meads M, Shain KH, Silva AS. A pharmacodynamic model of clinical synergy in multiple myeloma. EBioMedicine. 2020 Apr;54:102716. PMID: 32268267
Zhao X, Ren Y, Lawlor M, Shah BD, Park PMC, Lwin T, Wang X, Liu K, Wang M, Gao J, Li T, Xu M, Silva AS, Lee K, Zhang T, Koomen JM, Jiang H, Sudalagunta PR, Meads MB, Cheng F, Bi C, Fu K, Fan H, Dalton WS, Moscinski LC, Shain KH, Sotomayor EM, Wang GG, Gray NS, Cleveland JL, Qi J, Tao J. BCL2 Amplicon Loss and Transcriptional Remodeling Drives ABT-199 Resistance in B Cell Lymphoma Models. Cancer Cell. 2019;35(5):752-66.e9. PMID: 31085176
Ren Y, Bi C, Zhao X, Lwin T, Wang C, Yuan J, Silva AS, Shah BD, Fang B, Li T, Koomen JM, Jiang H, Chavez JC, Pham LV, Sudalagunta PR, Wan L, Wang X, Dalton WS, Moscinski LC, Shain KH, Vose J, Cleveland JL, Sotomayor EM, Fu K, Tao J. PLK1 stabilizes a MYC-dependent kinase network in aggressive B cell lymphomas. J Clin Invest. 2018;128(12):5517-30. PMID: 30260324
Shah B, Zhao X, Silva AS, Shain KH, Tao J. Resistance to Ibrutinib in B Cell Malignancies: One Size Does Not Fit All. Trends Cancer. 2018 Mar;4(3):197-206. PMID: 29506670
Maley CC, Aktipis A, Graham TA, Sottoriva A, Boddy AM, Janiszewska M, Silva A, Gerlinger M, Yuan Y, Pienta KJ, Anderson KS, Gatenby R, Swanton C, Posada D, Wu C, Polyak K, Anderson A, Brown JS, Greaves M, Shibata D. Classifying the evolutionary and ecological features of neoplasms. Nat Rev Cancer. 2017 Oct;17(10):605-619. PMID: 28912577
Emmons MF, Anreddy N, Cuevas J, Prater K, McLaughlin M, Silva A, and Hazlehurst LA. MTI-101 treatment inducing activation of Stim1 and TRPC1 expression is a determinant of response in multiple myeloma. Sci Rep. 2017 Jun 2;7(1):2685. PMID: 28578393
Silva AS, Silva MC, Sudalagunta P, Distler A, Jacobson T, Collins A, Song J, Chen D, Chen L, Cubitt C, Baz R, Perez L, Rebatchouk D, Dalton W, Greene J, Gatenby R, Gillies R, Sontag E, Meads MB, Shain KH. An ex vivo platform for the prediction of clinical response in multiple myeloma. Cancer Res. 2017 Jun 15;77(12):3336-3351. PMID: 28400475
Xiaohong Z, Lwin T, Silva A, Shah B, Tao J, Fang B, Zhang L, Li J, Meads M, Jacobson T, Silva M, Distler A, Zhang L, Han Y, Moscinski L, Koomen J, Dalton W, Shain K, Wang M, Sotomayor E, Tao J. Unification of environment-mediated and Acquired Ibrutinib Resistance in B Cell Malignancies. Nat Commun. 2017 Apr 18;8:14920. PMID: 28416797
Enriquez-Navas PM, Kam Y, Das T, Hassan S, Silva A, Foroutan P, Ruiz E, Martinez G, Minton S, Gillies RJ, Gatenby RA. Exploiting evolutionary principles to prolong tumor control in preclinical models of breast cancer. Sci Transl Med. 2016 Feb 24;8(327):327ra24. PMID: 26912903
Silva A, Durand S, Ribeiro M, Alsina M, Shain K, Baz R. An Evolutionary Approach for Personalized Therapy in Multiple Myeloma. Applied Mathematics, 2016, 7, 159-169. SciRP.org
Silva A, Jacobson T, Meads M, Distler A, Shain K. An Organotypic High Throughput System for Characterization of Drug Sensitivity of Primary Multiple Myeloma Cells. J Vis Exp. 2015 Jul 15;(101):e53070. PMID: 26274375
Khin ZP, Ribeiro MC, Jacobson T, Hazlehurst LA, Perez L, Baz R, Shain KH, Silva AS. A preclinical assay for chemosensitivity in multiple myeloma. Cancer Res. 2014 Jan 1;74(1):56-67. PMID: 24310398
Tafreshi NK, Silva A, Estrella VC, McCardle TW, Chen T, Jeune-Smith Y, Lloyd MC, Enkemann SA, Smalley KSM, Sondak VK, Vagner J, Morse DL. In Vivo and in Silico Pharmacokinetics and Biodistribution of a Melanocortin Receptor 1 Targeted Agent in Preclinical Models of Melanoma. Mol Pharm. 2013 Aug 5;10(8):3175-85. PMID: 23763620
Ribeiro MdLC, Silva AS, Bailey KM, Kumar NB, Sellers TA, et al. Buffer Therapy for Cancer. J Nutr Food Sci. 2012 Aug 15;2:6. PMID: 24371544
Silva AS, Kam Y, Khin Z, Minton S, Gillies RJ, Gatenby RA. Evolutionary approaches to prolong progression-free survival in breast cancer. Cancer Res. 2012 Dec 15;72(24):6362-70. PMID: 23066036
Silva AS, Gatenby RA. Adaptation to Survival in Germinal Center Is the Initial Step in Onset of Indolent Stage of Multiple Myeloma. Mol Pharm. 2011 Dec 5;8(6):2012-20. PMID: 21958215
Lee HO, Silva AS, Concilio S, Li YS, Slifker M, Gatenby RA, Cheng JD. Evolution of tumor invasiveness: the adaptive tumor microenvironment landscape model. Cancer Res. 2011 Oct 15;71(20):6327-37. PMID: 21859828
Silva AS, Anderson AR, Gatenby RA. A multiscale model of the bone marrow and hematopoiesis. Math Biosci Eng. 2011 Apr;8(2):643-58. PMID: 21631151
Assumpcao JG, Ganazza MA, de Araujo M, Silva AS, Scrideli CA, Brandalise SR, Yunes JA. Detection of clonal immunoglobulin and T-cell receptor gene rearrangements in childhood acute lymphoblastic leukemia using a low-cost PCR strategy. Pediatr Blood Cancer. 2010 Dec 15;55(7):1278-86. PMID: 20730889
Silva AS, Gatenby RA. A theoretical quantitative model for evolution of cancer chemotherapy resistance. Biol Direct. 2010 Apr 20;5:25. PMID: 20406443
Silva AS, Gatenby RA, Gillies RJ, Yunes JA. A Quantitative Theoretical Model for Development of Malignancy in Ductal Carcinoma In Situ. J Theor Biol. 2010 Feb 21;262(4):601-13. PMID: 19887072
Gatenby RA, Silva AS, Gillies RJ, Frieden BR. Adaptive Therapy. Cancer Res. 2009 Jun 1;69(11):4894-903. PMID: 19487300
Silva AS, Yunes JA, Gillies RJ, Gatenby RA. The potential role of systemic buffers in reducing intratumoral pHe and acid-mediated invasion. Cancer Res. 2009 Mar 15;69(6):2677-84. PMID: 19276380
Silva AS, Yunes JA. Conservation of glycolytic oscillations in Saccharomyces cerevisiae and human pancreatic beta-cells: a study of metabolic robustness. Genet Mol Res. 2006 Aug 31;5(3):525-35. PMID: 17117368