Our Publications


 

Books Edited

 

 
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Translational Bioinformatics for Therapeutic Development

Springer, 2021

Edited by Joseph Markowitz

 

Included Articles

Perkins RM, Markowitz J. Development and Optimization of Clinical Informatics Infrastructure to Support Bioinformatics at an Oncology Center. Methods Mol Biol. 2021;2194:1-19. doi:10.1007/978-1-0716-0849-4_1

Lin TA, Eroglu Z, Carvajal R, Markowitz J. Cohort Identification for Translational Bioinformatics Studies. Methods Mol Biol. 2021;2194:35-44. doi:10.1007/978-1-0716-0849-4_3

Sun J, Kroeger JL, Markowitz J. Introduction to Multiparametric Flow Cytometry and Analysis of High-Dimensional Data. Methods Mol Biol. 2021;2194:239-253. doi:10.1007/978-1-0716-0849-4_13

Markowitz J. Preface. Methods Mol Biol. 2021;2194:v-vii. doi:10.1007/978-1-0716-0849-4


 

Journal Articles

2022

Yu X, Cen L, Chen YA, Markowitz J, Shaw T, Tsai K, Conejo-Garcia J, and Wang X. Tumor Expression Quantitative Trait Methylation Screening Reveals Distinct CpG Panels for Deconvolving Cancer Immune Signatures. Cancer Res. 2022;82(9):1724-1735. doi:10.1158/0008-5472.CAN-21-3113

Cheng P, Chen X, Dalton R, Calescibetta A, So T, Gilvary D, Ward G, Smith V, Eckard S, Fox JA, Guenot J, Markowitz J, Cleveland JL, Wright KL, Eksioglu, EA. Immunodepletion of MDSC by AMV564, a novel bivalent, bispecific CD33/CD3 T cell engager, ex vivo in MDS and melanoma. Mol Ther. 2022;30(6):2315-2326. doi:10.1016/j.ymthe.2022.02.005

2021

Creed JH, Wilson CM, Soupir AC, Colin-Leitzinger CM, Kimmel GJ, Ospina OE, Chakiryan NH, Markowitz J, Peres LC, Coghill A, Fridley BL. spatialTIME and iTIME: R package and Shiny application for visualization and analysis of immunofluorescence data. Bioinformatics. 2021;37(23):4584-4586. doi:10.1093/bioinformatics/btab757

Haymaker C, Johnson DH, Murthy R, Bentebibel SE, Uemura MI, Hudgens CW, Safa H, James M, Andtbacka RHI, Johnson DB, Shaheen M, Davies MA, Rahimian S, Chunduru SK, Milton DR, Tetzlaff MT, Overwijk WW, Hwu P, Gabrail N, Agrawal S, Doolittle G, Puzanov I, Markowitz J, Bernatchez C, Diab A. Tilsotolimod with Ipilimumab Drives Tumor Responses in Anti-PD-1 Refractory Melanoma. Cancer Discov. 2021;11(8):1996-2013. doi:10.1158/2159-8290.CD-20-1546

Hicks JK, Howard R, Reisman P, Adashek JI, Fields KK, Gray JE, McIver B, McKee K, O’Leary MF, Perkins RM, Robinson E, Tandon A, Teer JK, Markowitz J, Rollison DE. Integrating Somatic and Germline Next-Generation Sequencing Into Routine Clinical Oncology Practice. JCO Precis Oncol. 2021;5:PO.20.00513. Published 2021 May 20. doi:10.1200/PO.20.00513

2020

Bunch BL, Kodumudi KN, Scott E, Morse J, Weber AM, Berglund AE, Pilon-Thomas S, Markowitz J. Anti-tumor efficacy of plasmid encoding emm55 in a murine melanoma model. Cancer Immunol Immunother. 2020;69(12):2465-2476. doi:10.1007/s00262-020-02634-4

Garg SK, Welsh EA, Fang B, Hernandez YI, Rose T, Gray J, Koomen JM, Berglund A, Mulé JJ, Markowitz J. Multi-Omics and Informatics Analysis of FFPE Tissues Derived from Melanoma Patients with Long/Short Responses to Anti-PD1 Therapy Reveals Pathways of Response. Cancers. 2020;12(12):3515. doi:10.3390/cancers12123515

Sun J, Kirichenko DA, Chung JL, Carr MJ, Eroglu Z, Khushalani N, Markowitz J, Messina JL, Sondak VK, Zager JS, Patel SY. Perioperative Outcomes of Melanoma Patients Undergoing Surgery After Receiving Immunotherapy or Targeted Therapy. World J Surg. 2020;44(4):1283-1293. doi:10.1007/s00268-019-05314-2

Garg SK, Ott MJ, Mostofa AGM, Chen Z, Chen YA, Kroeger J, Cao B, Mailloux AW, Agrawal A, Schaible BJ, Sarnaik A, Weber JS, Berglund AE, Mule JJ, Markowitz J. Multi-Dimensional Flow Cytometry Analyses Reveal a Dichotomous Role for Nitric Oxide in Melanoma Patients Receiving Immunotherapy. Front Immunol. 2020;11:164. doi:10.3389/fimmu.2020.00164

Eroglu Z, Eatrides J, Naqvi SMH, Kim Y, Rich J, Babacan NA, Brohl AS, Markowitz J, Sarnaik A, Zager J, Khushalnai N, Sondak VK, Messina J. Neoadjuvant BRAF-targeted therapy in regionally advanced and oligometastatic melanoma. Pigment Cell Melanoma Res. 2020;33(1):86-95. doi:10.1111/pcmr.12813

2019

Eroglu Z, Holmen SL, Chen Q, Khushalani N, Amaravadi R, Thomas R, Ahmed KA, Tawbi H, Chandra S, Markowitz J, Smalley I, Liu JKC, Chen YA, Najjar YG, Karreth FA, Abate-Daga D, Glitza IC, Sosman JA, Sondak VK, Bosenberg M, Herlyn M, Atkins MB, Kluger H, Margolin K, Forsyth PA, Davies MA, Smalley KSM. Melanoma central nervous system metastases: An update to approaches, challenges, and opportunities. Pigment Cell Melanoma Res. 2019;32(3):458-469. doi:10.1111/pcmr.12771

Suarez-Kelly LP, Levine KM, Olencki TE, Del Campo SEM, Streacker EA, Brooks TR, Karpa VI, Markowitz J, Bingman AK, Geyer SM, Kendra KL, Carson WE. A pilot study of interferon-alpha-2b dose reduction in the adjuvant therapy of high-risk melanoma. Cancer Immunol Immunother. 2019;68(4):619-629. doi:10.1007/s00262-019-02308-w

2018

Eroglu Z, Chen YA, Gibney GT, Weber JS, Kudchadkar RR, Khushalani NI, Markowitz J, Brohl AS, Tetteh LF, Ramadam H, Arnone G, Li J, Zhao X, Sharma R, Darville LNF, Fang B, Smalley I, Messina JL, Koomen JM, Sondak VK, Smalley KSM. Combined BRAF and HSP90 Inhibition in Patients with Unresectable BRAFV600E-Mutant Melanoma. Clin Cancer Res. 2018;24(22):5516-5524. doi:10.1158/1078-0432.CCR-18-0565

Johnson DB, Bordeaux JM, Kim JY, Vaupel CA, Rimm DL, Ho TH, Joseph RW, Daud AI, Conry RM, Gaughan EM, Hernandez-Aya LF, Dimou A, Funchain P, Smithy JW, Witte JS, McKee SB, Ko J, Wrangle J, Dabbas B, Tangri S, Lameh J, Hall JM, Markowitz J, Balko JM, Dakappagari NK. Quantitative Spatial Profiling of PD-1/PD-L1 Interaction and HLA-DR/IDO-1 Predicts Improved Outcomes of anti-PD-1 Therapies in Metastatic Melanoma. Clin Cancer Res. 2018;24(21):5250-5260. doi:10.1158/1078-0432.CCR-18-0309

Latchana N, DiVincenzo MJ, Regan K, Abrams Z, Zhang X, Jacob NK, Gru AA, Fadda P, Markowitz J, Howard JH, Carson WE 3rd. Alterations in patient plasma microRNA expression profiles following resection of metastatic melanoma. J Surg Oncol. 2018;118(3):501-509. doi:10.1002/jso.25163

Perez MC, Yu HM, Markowitz J. Severe thromboembolic phenomenon in the setting of pseudoprogression of melanoma brain metastases in response to combination immunotherapy. BMJ Case Rep. 2018;2018:bcr-2018-226089. doi:10.1136/bcr-2018-226089

Mullinax JE, Hall M, Prabhakaran S, Weber J, Khushalani N, Eroglu Z, Brohl AS, Markowitz J, Royster E, Richards A, Stark V, Zager JS, Kelley L, Cox C, Sondak VK, Mulé JJ, Pilon-Thomas S, Sarnaik AA. Combination of Ipilimumab and Adoptive Cell Therapy with Tumor-Infiltrating Lymphocytes for Patients with Metastatic Melanoma. Front Oncol. 2018;8:44. Published 2018 Mar 2. doi:10.3389/fonc.2018.00044

2017

Yarlagadda K, Hassani J, Markowitz J. The role of nitric oxide in melanoma. Biochim Biophys Acta Rev Cancer. 2017;1868(2):500-509. doi:10.1016/j.bbcan.2017.09.005

Markowitz J, Wang J, Vangundy Z, You J, Yildiz V, Yu L, Branson OE, Stiff AR,  Brooks TR, Biesiadecki B, Olencki T, Tridandapani S, Freitas MA, Papenfuss T, Phelps MA, Carson WE. Nitric oxide mediated inhibition of antigen presentation from DCs to CD4+ T cells in cancer and measurement of STAT1 nitration. Sci Rep. 2017;7(1):15424. doi:10.1038/s41598-017-14970-0

Wesolowski R, Duggan MC, Stiff A, Markowitz J, Trikha P, Levine KM, Schoenfield L, Abdel-Rasoul M, Layman R, Ramaswamy B, Macrae ER, Lustberg MB, Reinbolt RE, Mrozek E, Byrd JC, Caligiuri MA, Mace TA, Carson WE 3rd. Circulating myeloid-derived suppressor cells increase in patients undergoing neo-adjuvant chemotherapy for breast cancer. Cancer Immunol Immunother. 2017;66(11):1437-1447. doi:10.1007/s00262-017-2038-3

Creelan BC, Gabrilovich DI, Gray JE, Williams CC, Tanvetyanon T, Haura EB, Weber JS, Gibney GT, Markowitz J, Proksch JW, Reisman SA, McKee MD, Chin MP, Meyer CJ, Antonia SJ. Safety, pharmacokinetics, and pharmacodynamics of oral omaveloxolone (RTA 408), a synthetic triterpenoid, in a first-in-human trial of patients with advanced solid tumors. Onco Targets Ther. 2017;10:4239-4250. Published 2017 Aug 29. doi:10.2147/OTT.S136992 

Puri S, Markowitz J. The use of baseline biomarkers to predict outcome in melanoma patients treated with pembrolizumab. Ann Res Hosp. 2017;1:24. doi:10.21037/arh.2017.04.24

2016

Brohl AS, Khushalani NI, Eroglu Z, Markowitz J, Thapa R, Chen AY, Kudchadkar R, Weber JS. A phase IB study of ipilimumab with peginterferon alfa-2b in patients with unresectable melanoma. J Immunother Cancer. 2016;4:85. Published 2016 Dec 20. doi:10.1186/s40425-016-0194-1

Ozgun A, Sondak VK, Markowitz J. Resistance patterns to anti-PD-1 therapy in metastatic melanoma. Chin Clin Oncol. 2016;5(6):75. doi:10.21037/cco.2016.08.01

Markowitz J, Abrams Z, Jacob NK, Zhang X, Hassani JN, Latchana N, Wei L, Regan KE, Brooks TR, Uppati SR, Levine KM, Bekaii-Saab T, Kendra KL, Lesinski GB, Howard JH, Olencki T, Payne PR, Carson WE 3rd. MicroRNA profiling of patient plasma for clinical trials using bioinformatics and biostatistical approaches. Onco Targets Ther. 2016;9:5931-5941. Published 2016 Sep 29. doi:10.2147/OTT.S106288

Markowitz J, Mal TK, Yuan C, Courtney NB, Patel M, Stiff AR, Blachly J, Walker C, Eisfeld AK, de la Chapelle A, Carson WE 3rd. Structural characterization of NRAS isoform 5. Protein Sci. 2016;25(5):1069-1074. doi:10.1002/pro.2916