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Dr. Alida Palmisano

Bioinformatics Engineer, Computational & Systems Biology Branch

Research Interests

Computer scientist with expertise in software and database development, genomic data analysis and visualization, software for clinical trial management, and computational and systems biology.

Selected Publications (full list available here):

P. Zhang, A. Palmisano, R. Kumar, MC. Li, J.H. Doroshow, Y. Zhao
TPWshiny: an interactive R/Shiny app to explore cell line transcriptional responses to anti-cancer drugs
Bioinformatics 38 (2), 570-572, 2022

S Vural, A Palmisano, WC Reinhold, Y Pommier, BA Teicher, J Krushkal
Association of expression of epigenetic molecular factors with DNA methylation and sensitivity to chemotherapeutic agents in cancer cell lines
Clinical Epigenetics 13 (1), 1-23, 2021

A. Palmisano, S. Vural, Y. Zhao, D. Sonkin
MutSpliceDB: A database of splice sites variants with RNA-seq based evidence on effects on splicing
Human Mutation42 (4), 342-345, 2021

A.P. Chen, S. Kummar, N. Moore, L.V. Rubinstein, Y. Zhao, P.M. Williams, A. Palmisano, D. Sims, G. O'Sullivan Coyne, C. L. Rosenberger, M. Simpson, K. PS Raghav, F. Meric-Bernstam, S. Leong, S. Waqar, J. C Foster, M. M Konat�, B. Das, C. Karlovich, CJ Lih, E. Polley, R. Simon, MC Li, R. Piekarz, J. H. Doroshow.
Molecular Profiling-Based Assignment of Cancer Therapy (NCI-MPACT): A Randomized Multicenter Phase II Trial.
JCO Precision Oncology 5, 133-144, 2021

J. Krushkal, S. Negi, L.M. Yee, J.R. Evans, T. Grkovic, A. Palmisano, J. Fang, H. Sankaran, L.M. McShane, Y. Zhao, and B.R. O'Keefe.
Molecular genomic features associated with in vitro response of the NCI-60 cancer cell line panel to natural products.
Molecular oncology 15 (2), 381-406, 2021

A. Palmisano, J. Krushkal, M.C. Li, J. Fang, D. Sonkin, G. Wright, L. Yee, Y. Zhao, and L. McShane.
Bioinformatics Tools and Resources for Cancer Immunotherapy Study.
In Biomarkers for Immunotherapy of Cancer (pp. 649-678). Humana, New York, NY, 2020

DJ. Min, Y. Zhao, A. Monks, A. Palmisano, C. Hose, B.A. Teicher, J.H. Doroshow and R. Simon.
Identification of pharmacodynamic biomarkers and common molecular mechanisms of response to genotoxic agents in cancer cell lines.
Cancer chemotherapy and pharmacology, 84(4), pp.771-780. 2019

A. Palmisano, Y. Zhao and R. Simon.
D3Oncoprint: Stand-Alone Software to Visualize and Dynamically Explore Annotated Genomic Mutation Files.
JCO Clinical Cancer Informatics, nr. 2, p. 1-9, DOI: 10.1200/CCI.17.00050, 2018

A. Monks, Y. Zhao, C. Hose, H. Hamed, J. Krushkal, J. Fang, D. Sonkin, A. Palmisano, E.C. Polley, L.K. Fogli, M.M. Konate, S.B. Miller, M.A. Simpson, A.R. Voth, MC. Li, E. Harris, X. Wu, J.W. Connelly, A. Rapisarda, B.A. Teicher, R. Simon and J.H. Doroshow.
The NCI Transcriptional Pharmacodynamics Workbench: a tool to examine dynamic expression profiling of therapeutic response in the NCI-60 cell line panel.
Cancer Research, 78(24), pp.6807-6817, 2018

A. Palmisano, Y. Zhao, MC Li, E. C. Polley, and R. M. Simon.
OpenGeneMed: a portable, flexible and customizable informatics hub for the coordination of next-generation sequencing studies in support of precision medicine trials.
Briefings in Bioinformatics, 2016

A. Palmisano, J. Zamborszky, C. Oguz, and A. Csikasz-Nagy.
Molecular network dynamics of cell cycle control: periodicity of Start and Finish.
In Cell Cycle Synchronization, Springer, 2016

Y. Zhao, E. Polley, M.C. Li, C.J. Lih, A. Palmisano, D. Sims, L. Rubinstein, B. Conley, A. Chen, P.M. Williams, S. Kummar, J.H. Doroshow, and R.M. Simon.
GeneMed: an informatics hub for the coordination of next-generation sequencing studies that support precision oncology clinical trials.
Cancer Informatics, 2015

A. Palmisano, S. Hoops, L. T. Watson, T. C. Jones, J. J. Tyson, and C. A. Shaffer. JigCell Run Manager (JC-RM): a tool for managing large sets of biochemical model parametrizations. BMC Systems Biology, 9(1):1, 2015

A. Palmisano, S. Hoops, L. T. Watson, T. C. Jones, J. J. Tyson, and C. A. Shaffer. Multistate model builder (MSMB): a flexible editor for compact biochemical models. BMC Systems Biology, 8(1):42, 2014

C. Oguz, A. Palmisano, T. Laomettachit, L. T. Watson, W. T. Baumann, and J. J. Tyson. A stochastic model correctly predicts changes in budding yeast cell cycle dynamics upon periodic expression of cln2. PloS One, 9(5):e96726, 2014

F. Ferrezuelo, N. Colomina, A. Palmisano, E. Gari, C. Gallego, A. Csikasz-Nagy, and M. Aldea. The critical size is set at a single-cell level by growth rate to attain homeostasis and adaptation. Nature Communications, 3:1012, 2012

P. Ballarini, T. Mazza, A. Palmisano, and A. Csikasz-Nagy. Studying irreversible transitions in a model of cell cycle regulation. Electronic Notes in Theoretical Computer Science, 232:39, 2009