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Manuscripts

Yang J, Lim JT, Victor P, Chen C, Khawaja H, Schnellmann RG, Roe DJ, Gokhale PC, DeCaprio JA, Padi M. Integrative analysis reveals therapeutic potential of pyrvinium pamoate in Merkel cell carcinoma. https://www.biorxiv.org/content/10.1101/2023.11.01.565218v1

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Collins-McMillen D, Pessoa DDO, Zarrella K, Huntley M, Moorman NJ, Kamil JP, Caposio P, Padi M, Goodrum FD. Viral and host network analysis of the human cytomegalovirus transcriptome in latency. https://www.biorxiv.org/content/10.1101/2024.05.21.594597v1

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Publications

  1. Chen C, Padi M. Flexible modeling of regulatory networks improves transcription factor activity estimation. NPJ Systems Biology and Applications. 2024 May 28;10(1):58.

  2. Buss LG, Pessoa DDO, Snider JM, Padi M, Martinez JA, Limesand KH. Metabolomics analysis of pathways underlying radiation-induced salivary gland dysfunction stages. PLoS One. 2023 Nov 20;18(11):e0294355.

  3. Ben Guebila M, Wang T, Lopes-Ramos CM, Fanfani V, Weighill D, Burkholz R, Schlauch D, Paulson JN, Altenbuchinger M, Shutta KH, Sonawane AR, Lim J, Calderer G, van IJzendoorn DGP, Morgan D, Marin A, Chen CY, Song Q, Saha E, DeMeo DL, Padi M, Platig J, Kuijjer ML, Glass K, Quackenbush J. The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks. Genome Biology. 2023 Mar 9;24(1):45. 

  4. Bauman JE, Hsu CH, Centuori S, Guillen-Rodriguez J, Garland L, Ho E, Padi M, Bageerathan V, Bengtson L, Wojtowicz M, Szabo E, Chow HHS. Randomized crossover clinical trial evaluating detoxification of tobacco carcinogens by broccoli seed and sprout extract in current smokers. Cancers (Basel). 2022 Apr 24;14(9):2129.

  5. Ryniawec JM, Coope MR, Loertscher E, Bageerathan V, Pessoa DDO, Warfel NA, Cress AE*, Padi M*, Rogers GC*. GLUT3/SLC2A3 is an endogenous marker of hypoxia in prostate cancer cell lines and patient-derived xenograft tumors. Diagnostics (Basel). 2022 Mar 10;12(3):676.

  6. Parker SS, Ly KT, Grant AD, Sweetland J, Wang AM, Parker JD, Roman MR, Saboda K, Roe DJ, Padi M, Wolgemuth CW, Langlais PR, Mouneimne G. EVL and MIM/MTSS1 regulate actin cytoskeletal remodeling to promote dendritic filopodia in developing neurons. Journal of Cell Biology. 2023 May 1;222(5):e202106081.

  7. Grant A, Xicola R, Nguyen V, Lim J, Thorne C, Salhia B, Llor X, Ellis N, Padi M. Molecular Drivers of Tumor Progression in Microsatellite Stable APC Mutation-Negative Colorectal Cancers. Scientific Reports. 2021 Dec 6;11(1):23507.

  8. Watson AW, Grant AD, Harman M, Parker SS, Roman M, Forte B, Castro R, Reichner J, Franck C, Padi M, Romanoski C, Mouneimne G. Breast tumor stiffness instructs bone metastasis via maintenance of mechanical memory. Cell Reports. 2021 Jun 29; 35(13):109293.

  9. Meeks L, Pessoa DDO, Martinez JA, Limesand KH, Padi M. Integration of metabolomics and transcriptomics reveals convergent pathways driving radiation-induced salivary gland dysfunction. Physiological Genomics. 2021 Feb 1. doi: 10.1152/physiolgenomics.00127.2020.

  10. Lim JT, Chen C, Grant AD, Padi M. Generating ensembles of gene regulatory networks to assess robustness of disease modules. Frontiers in Genetics. 2021 Jan 14;11:603264.

  11. Lim JT, Singh N, Leuvano LA, Calvert VS, Petricoin EF, Teachey DT, Lock RB, Padi M, Kraft AS, Padi SKR. PIM kinase inhibitors block the growth of primary T-cell acute lymphoblastic leukemia: Resistance mechanisms identified by network modeling analysis. Molecular Cancer Therapeutics. 2020 Sep;19(9):1809-1821.

  12. Grant AD, Vail P, Padi M, Witkiewicz AK, Knudsen ES. Interrogating Mutant Allele Expression via Customized Reference Genomes to Define Influential Cancer Mutations. Scientific Reports. 2019 Sep 4;9(1):12766.

  13. Pearson T*, Caporaso JG*, Yellowhair M, Bokulich NA, Padi M, Roe DJ, Wertheim BC, Linhart M, Martinez JA, Bilagody C, Hornstra H, Alberts DA, Lance P, Thompson PA. Effects of ursodeoxycholic acid on the gut microbiome and colorectal adenoma development. Cancer Medicine. 2019 Jan 16. DOI: 10.1002/cam4.1965.

  14. Sharma A, Halu A, Decano JL, Padi M, Liu YY, Prasad RB, Fadista J, Santolini M, Menche J, Weiss ST, Vidal M, Silverman EK, Aikawa M, Barabási AL, Groop L, Loscalzo J. Controllability in an islet specific regulatory network identifies the transcriptional factor NFATC4, which regulates Type 2 Diabetes associated genes. NPJ Systems Biology and Applications. 2018 Jul 3;4:25.

  15. Padi M, Quackenbush J. Detecting phenotype-driven transitions in regulatory network structure. NPJ Systems Biology and Applications. 2018 Apr 19;4:16.

  16. Cheng J, Park DE, Berrios C, White EA, Arora R, Yoon R, Branigan T, Xiao T, Westerling T, Federation A, Zeid R, Strober B, Swanson SK, Florens L, Bradner JE, Brown M, Howley PM, Padi M, Washburn MP, DeCaprio JA. Merkel cell polyomavirus recruits MYCL to the EP400 complex to promote oncogenesis. PLoS Pathogens. 2017 Oct 13;13(10):e1006668.

  17. Berrios C*, Padi M*, Keibler MA, Park DE, Molla V, Cheng J, Lee SM, Stephanopoulos G, Quackenbush J, DeCaprio JA. Merkel cell polyomavirus small T antigen promotes pro-glycolytic metabolic perturbations required for transformation. PLoS Pathogens. 2016 Nov 23;12(11):e1006020.

  18. Fischer M, Grossmann P, Padi M, DeCaprio JA. Integration of TP53, DREAM, MMB-FOXM1 and RB-E2F target gene analyses identifies cell cycle gene regulatory networks. Nucleic Acids Research. 2016 Jul 27;44(13):6070-86.

  19. Malleshaiah M, Padi M, Rue P, Quackenbush J, Martinez-Arias A, Gunawardena J. Nac1 coordinates a sub-network of pluripotency factors to regulate embryonic stem cell differentiation. Cell Reports. 2016 Feb 9;14(5):1181-94.

  20. Padi M, Quackenbush J. Integrating transcriptional and protein interaction networks to prioritize condition-specific master regulators. BMC Systems Biology. 2015 Nov 14;9(1):80.

  21. Fine DA*, Rozenblatt-Rosen O*, Padi M, Korkhin A, James RL, Adelmant G, Yoon R, Guo L, Berrios C, Zhang Y, Calderwood MA, Velmurgan S, Cheng J, Marto JA, Hill DE, Cusick ME, Vidal M, Florens L, Washburn MP, Litovchick L, Decaprio JA. Identification of FAM111A as an SV40 Host Range Restriction and Adenovirus Helper Factor. PLoS Pathogens. 2012 Oct;8(10).

  22. Rozenblatt-Rosen O*, Deo RC*, Padi M*, Adelmant G*, Calderwood MA, Rolland T, Grace M, Dricot A, Askenazi M, Tavares M, Pevzner SJ, Abderazzaq F, Byrdsong D, Carvunis AR, Chen AA, Cheng J, Correll M, Duarte M, Fan C, Feltkamp MC, Ficarro SB, Franchi R, Garg BK, Gulbahce N, Hao T, Holthaus AM, James R, Korkhin A, Litovchick L, Mar JC, Pak TR, Rabello S, Rubio R, Shen Y, Singh S, Spangle JM, Tasan M, Wanamaker S, Webber JT, Roecklein-Canfield J, Johannsen E, Barabási AL, Beroukhim R, Kieff E, Cusick ME, Hill DE, Münger K, Marto JA, Quackenbush J, Roth FP, DeCaprio JA, Vidal M. Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins. Nature. 2012 Jul 26;487(7408):491-5.

  23. Gulbahce N*, Yan H*, Dricot A, Padi M, Byrdsong D, Franchi R, Lee DS, Rozenblatt-Rosen O, Mar JC, Calderwood MA, Baldwin A, Zhao B, Santhanam B, Braun P, Simonis N, Huh KW, Hellner K, Grace M, Chen A, Rubio R, Marto JA, Christakis NA, Kieff E, Roth FP, Roecklein-Canfield J, Decaprio JA, Cusick ME, Quackenbush J, Hill DE, Münger K, Vidal M, Barabási AL. Viral perturbations of host networks reflect disease etiology. PLoS Computational Biology. 2012;8(6).

  24. Müller GA, Quaas M, Schümann M, Krause E, Padi M, Fischer M, Litovchick L., Decaprio JA, Engeland K. The CHR promoter element controls cell cycle-dependent gene transcription and binds the DREAM and MMB complexes. Nucleic Acids Research. 2012 Feb;40(4):1561-78.

  25. Gewurz BE, Mar JC, Padi M, Zhao B, Shinners NP, Takasaki K, Bedoya E, Zou JY, Cahir-McFarland E, Quackenbush J, Kieff E. Canonical NF-kappaB activation is essential for Epstein-Barr virus latent membrane protein 1 TES2/CTAR2 gene regulation. Journal of Virology. 2011 Jul; 85(13):6764-73.

  26. Denef F*, Esole M*, Padi M*. Orientiholes. Journal of High Energy Physics. 2010; 1003, 045.

  27. Anninos D*, Li W*, Padi M*, Song W*, Strominger A*.Warped AdS3 black holes. Journal of High Energy Physics. 2009; 0903, 130.

  28. Gaiotto D*, Li W*, Padi M*.Non-supersymmetric attractor flow in symmetric spaces. Journal of High Energy Physics. 2007; 0712, 093.

  29. Kats Y*, Motl L*, Padi M*.Higher-order corrections to mass-charge relation of extremal black holes. Journal of High Energy Physics, 2007; 0712, 068.

  30. Black MR, Padi M, Cronin SB, Lin YM, Rabin O, McClure T, Dresselhaus G, Hagelstein PL, Dresselhaus MS. Intersubband transitions in bismuth nanowires.  Applied Physics Letters. 2000; 77, 25, 4142-4144.

© 2024 by Padi Lab.

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