Complex Systems Biology Approach in Connecting PI3K-Akt and NF-κB Pathways in Prostate Cancer

Autor: Eswar Shankar, Michael C. Weis, Jayant Avva, Sanjeev Shukla, Meenakshi Shukla, Sree N. Sreenath, Sanjay Gupta

Publikováno v: Cells, Vol 8, Iss 3, p 201 (2019)

Phosphatidylinositol 3′-OH kinase (PI3K)-Akt and transcription factor NF-κB are important molecules involved in the regulation of cell proliferation, apoptosis, and oncogenesis. Both PI3K-Akt and Nuclear Factor-kappaB (NF-κB) are involved in the

Externí odkaz: https://doaj.org/article/3bf7f503c88e447a94daaf511b05829e

Dynamic expression profiles from static cytometry data: component fitting and conversion to relative, 'same scale' values.

Autor: Jayant Avva, Michael C Weis, R Michael Sramkoski, Sree N Sreenath, James W Jacobberger

Publikováno v: PLoS ONE, Vol 7, Iss 7, p e38275 (2012)

Cytometry of asynchronous proliferating cell populations produces data with an extractable time-based feature embedded in the frequency of clustered, correlated events. Here, we present a specific case of general methodology for calculating dynamic e

Externí odkaz: https://doaj.org/article/8f5e1168eaa74f8688181fbf0d8354b9

Sampling strategies to capture single-cell heterogeneity

Autor: James S. Malter, John D. Gordan, Lani F. Wu, Satwik Rajaram, Robert S. Warren, Jayant Avva, Chloe E. Atreya, Kathy Bonness, Steven J. Altschuler, Agnieszka K. Witkiewicz, Louise Heinrich

Publikováno v: Nature methods, vol 14, iss 10
Rajaram, S; Heinrich, LE; Gordan, JD; Avva, J; Bonness, KM; Witkiewicz, AK; et al.(2017). Sampling strategies to capture single-cell heterogeneity. NATURE METHODS, 14(10), 967-+. doi: 10.1038/NMETH.4427. UCSF: Retrieved from: http://www.escholarship.org/uc/item/9857d75s
Nature methods

Advances in single-cell technologies have highlighted the prevalence and biological significance of cellular heterogeneity. A critical question is how to design experiments that faithfully capture the true range of heterogeneity from samples of cellu

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::706787d0212cfc74f77dfd37e425282a
https://escholarship.org/uc/item/9857d75s

A data-driven, mathematical model of mammalian cell cycle regulation

Autor: Michael C. Weis, Sree N. Sreenath, Jayant Avva, James W. Jacobberger

Publikováno v: PLoS ONE
PLoS ONE, Vol 9, Iss 5, p e97130 (2014)

Few of >150 published cell cycle modeling efforts use significant levels of data for tuning and validation. This reflects the difficultly to generate correlated quantitative data, and it points out a critical uncertainty in modeling efforts. To devel

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3ca2236f4b7a98c3c423399f20bb7335
https://pubmed.ncbi.nlm.nih.gov/24824602

CytoSys: a tool for extracting cell-cycle-related expression dynamics from static data

Autor: Jayant, Avva, Michael C, Weis, Radina P, Soebiyanto, James W, Jacobberger, Sree N, Sreenath

Publikováno v: Methods in molecular biology (Clifton, N.J.). 717

Computational models of biological processes are important building blocks in Systems Biology studies. Calibration and validation are two important steps for moving a mathematical model to a computational model. While calibration refers to finding nu

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::339ef42faac025d6ab02c4870417fba3
https://pubmed.ncbi.nlm.nih.gov/21370031