Article
Oncology
Richard J. Sove, Babita K. Verma, Hanwen Wang, Won Jin Ho, Mark Yarchoan, Aleksander S. Popel
Summary: This study uses quantitative systems pharmacology (QSP) framework to conduct a virtual clinical trial for nivolumab and ipilimumab in HCC patients. The model incorporates detailed biological mechanisms of immune cell-cancer cell interactions and generates virtual patients for the trial. The predictions of the model are consistent with clinically observed outcomes, demonstrating the potential of QSP models in patient selection and trial design.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2022)
Article
Geriatrics & Gerontology
Daigo Okada
Summary: This study identified 17 age-related proteins produced by a single tissue and a single cell type through integrative data mining, which may be valuable for understanding age-related changes in the plasma proteome and inter-tissue networks.
Article
Oncology
Hanwen Wang, Huilin Ma, Richard J. Sove, Leisha A. Emens, Aleksander S. Popel
Summary: This study introduces a modular quantitative systems pharmacology (QSP) platform for predicting immunotherapy efficacy and identifying predictive biomarkers. Virtual clinical trials were conducted using a virtual patient cohort generated by the model, with retrospective analysis and model validation based on clinical trial data.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2021)
Article
Nutrition & Dietetics
V. A. Shiva Ayyadurai, Prabhakar Deonikar
Summary: Aging is a result of cellular damage caused by biochemical processes, and plant-derived bioactive molecules have been shown to ameliorate oxidative stress. This study uses a computational systems biology approach to uncover the mechanisms of action of bioactive compounds from fruit/berry/vegetable juice powder in mitigating oxidative stress. The compounds in juice powder affected two oxidative stress pathways by reducing reactive oxygen species production and increasing antioxidant enzyme production. The combination of bioactive compounds in juice powder attenuates aging by affecting multiple oxidative stress pathways.
Article
Geriatrics & Gerontology
Emerson Santiago, David F. Moreno, Murat Acar
Summary: Aging is a complex phenomenon of functional decay in biological organisms, with the cause(s) still poorly understood. Computational biology offers a unique opportunity to generate models that can help us understand the fundamental nature of aging, identify unaccounted aging factors, and demonstrate the mechanics of aging.
EXPERIMENTAL GERONTOLOGY
(2021)
Article
Immunology
Mohamed Helmy, Kumar Selvarajoo
Summary: The majority of human genome consists of non-coding genes, with about half made up of transposable elements, including endogenous retroviruses. While generally harmless, endogenous retroviruses have been linked to inflammatory diseases and cancer, posing a challenge in elucidating the mechanistic understanding between them.
FRONTIERS IN IMMUNOLOGY
(2021)
Review
Biochemical Research Methods
Peter D. Karp, Peter E. Midford, Richard Billington, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Wai Kit Ong, Pallavi Subhraveti, Ron Caspi, Carol Fulcher, Ingrid M. Keseler, Suzanne M. Paley
Summary: The development of Pathway Tools software enables researchers to construct biological knowledge resources more efficiently, develop metabolic flux models, and interpret high-throughput data using pathway information.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Oncology
Lunan Liu, Chao Ma, Zhuoyu Zhang, Matthew T. Witkowski, Iannis Aifantis, Saba Ghassemi, Weiqiang Chen
Summary: The study established a computational model for CAR T-cell therapy, successfully predicting diverse responses of leukemia patients to treatment and identifying critical determinants related to patient responses. Combining peak and accumulated values of CAR T-cells or early-stage CAR T-cell dynamics can predict patient responses, which has significant implications for clinical treatment and management.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2022)
News Item
Multidisciplinary Sciences
Ewen Callaway
Summary: Analysis of protein shapes reveals unexpected forms and connections.
Editorial Material
Multidisciplinary Sciences
Jeffrey A. Farrell
Summary: CellOracle, a computational tool, can predict the interaction of gene networks in programming cell identity during embryonic development. This tool will contribute to a better understanding of the regulation of development.
Review
Biochemical Research Methods
Anna Niarakis, Dagmar Waltemath, James Glazier, Falk Schreiber, Sarah M. Keating, David Nickerson, Claudine Chaouiya, Anne Siegel, Vincent Noel, Henning Hermjakob, Tomas Helikar, Sylvain Soliman, Laurence Calzone
Summary: This article highlights the importance of using computational models in systems biology to study complex system dynamics. It discusses the need for improving the reusability of these models and their ability to reproduce virtual experiments through proper model annotation in community-supported and standardized formats.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Pharmacology & Pharmacy
Pukar Khanal, Vishal S. Patil, Vishwambhar V. Bhandare, Priyanka P. Patil, B. M. Patil, Prarambh S. R. Dwivedi, Kunal Bhattacharya, Darasaguppe R. Harish, Subarna Roy
Summary: The aim of this study was to investigate the mechanism of action of diosgenin against breast cancer using system biology tools and experimental validation. Diosgenin-regulated domains associated with breast cancer were identified and diosgenin-protein-pathway associations were established. Molecular docking and dynamics simulations confirmed the binding affinity of diosgenin with key proteins, and functional assays validated its effects on cell proliferation, cytotoxicity, and the Warburg effect.
FRONTIERS IN PHARMACOLOGY
(2023)
Article
Oncology
Vardges Tserunyan, Stacey D. Finley
Summary: CAR therapy is a revolutionary approach to cancer treatment that involves engineering immune cells with an artificial receptor to recognize and eliminate tumor cells. Systems and computational biology techniques have been used to understand the mechanisms and improve the design of CAR therapy.
SEMINARS IN CANCER BIOLOGY
(2023)
Review
Cell Biology
Cara C. Hardy, Ron Korstanje
Summary: Age-associated alterations in bladder control have a significant impact on millions of older adults, bringing economic and quality of life burdens to their families. Understanding the effects of aging on the brain-bladder axis and identifying genetic targets related to functional outcomes are crucial for improving therapeutic options for older adults. Changes in both the central nervous system and the bladder itself contribute to age-related alterations in bladder control.
Review
Physiology
Karim Azer, Chanchala D. Kaddi, Jeffrey S. Barrett, Jane P. F. Bai, Sean T. McQuade, Nathaniel J. Merrill, Benedetto Piccoli, Susana Neves-Zaph, Luca Marchetti, Rosario Lombardo, Silvia Parolo, Selva Rupa Christinal Immanuel, Nitin S. Baliga
Summary: This paper reviews the history of mathematical biology and pharmacology models, highlights some gaps and challenges in the development and application of systems pharmacology models, and proposes an integrated strategy to overcome these challenges by leveraging advances in adjacent fields.
FRONTIERS IN PHYSIOLOGY
(2021)
Review
Cell Biology
A. E. Morgan, K. M. Mooney, S. J. Wilkinson, N. A. Pickles, M. T. Mc Auley
AGEING RESEARCH REVIEWS
(2016)
Article
Biology
A. E. Morgan, K. M. Mooney, S. J. Wilkinson, N. A. Pickles, M. T. Mc Auley
Article
Nutrition & Dietetics
A. E. Morgan, K. M. Mooney, S. J. Wilkinson, N. A. Pickles, M. T. Mc Auley
PROCEEDINGS OF THE NUTRITION SOCIETY
(2017)
Article
Biology
Amy Elizabeth Morgan, Mark Tomas Mc Auley
Review
Cell Biology
Tara Warren, Roisin McAllister, Amy Morgan, Taranjit Singh Rai, Victoria McGilligan, Matthew Ennis, Christopher Page, Catriona Kelly, Aaron Peace, Bernard M. Corfe, Mark Mc Auley, Steven Watterson
Summary: The overlap between vitamin D and cholesterol metabolism pathways is significant, yet our understanding of their independent and co-regulation is limited. Research highlights the relationships between vitamin D supplementation, total cholesterol, and LDL-C status, as well as the consistency between latitude, vitamin D, and cholesterol status. Furthermore, some results cannot be explained with current knowledge of molecular mechanisms.
Article
Biochemistry & Molecular Biology
Amy E. Morgan, Katie D. Acutt, Mark T. Mc Auley
BIOSCIENCE REPORTS
(2020)
Review
Biochemistry & Molecular Biology
Mark T. Mc Auley, Alvaro Martinez Guimera, David Hodgson, Neil Mcdonald, Kathleen M. Mooney, Amy E. Morgan, Carole J. Proctor
BIOSCIENCE REPORTS
(2017)
Review
Endocrinology & Metabolism
Amy Morgan, Kathleen Mooney, Mark. Mc Auley
EXPERT REVIEW OF ENDOCRINOLOGY & METABOLISM
(2016)
