Literature DB >> 33402669

A new precision medicine initiative at the dawn of exascale computing.

Ruth Nussinov1,2, Hyunbum Jang3, Guy Nir4,5,6, Chung-Jung Tsai3, Feixiong Cheng7,8.   

Abstract

Which signaling pathway and protein to select to mitigate the patient's expected drug resistance? The number of possibilities facing the physician is massive, and the drug combination should fit the patient status. Here, we briefly review current approaches and data and map an innovative patient-specific strategy to forecast drug resistance targets that centers on parallel (or redundant) proliferation pathways in specialized cells. It considers the availability of each protein in each pathway in the specific cell, its activating mutations, and the chromatin accessibility of its encoding gene. The construction of the resulting Proliferation Pathway Network Atlas will harness the emerging exascale computing and advanced artificial intelligence (AI) methods for therapeutic development. Merging the resulting set of targets, pathways, and proteins, with current strategies will augment the choice for the attending physicians to thwart resistance.

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Mesh:

Year:  2021        PMID: 33402669      PMCID: PMC7785737          DOI: 10.1038/s41392-020-00420-3

Source DB:  PubMed          Journal:  Signal Transduct Target Ther        ISSN: 2059-3635


  81 in total

Review 1.  Opportunities and challenges provided by crosstalk between signalling pathways in cancer.

Authors:  A Prahallad; R Bernards
Journal:  Oncogene       Date:  2015-05-18       Impact factor: 9.867

Review 2.  'Latent drivers' expand the cancer mutational landscape.

Authors:  Ruth Nussinov; Chung-Jung Tsai
Journal:  Curr Opin Struct Biol       Date:  2015-02-05       Impact factor: 6.809

3.  Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes.

Authors:  Brian J Beliveau; Eric F Joyce; Nicholas Apostolopoulos; Feyza Yilmaz; Chamith Y Fonseka; Ruth B McCole; Yiming Chang; Jin Billy Li; Tharanga Niroshini Senaratne; Benjamin R Williams; Jean-Marie Rouillard; Chao-ting Wu
Journal:  Proc Natl Acad Sci U S A       Date:  2012-12-11       Impact factor: 11.205

Review 4.  Network science in clinical trials: A patient-centered approach.

Authors:  Venkata S K Manem; Roberto Salgado; Philippe Aftimos; Christos Sotiriou; Benjamin Haibe-Kains
Journal:  Semin Cancer Biol       Date:  2017-12-24       Impact factor: 15.707

5.  The evolutionarily conserved MAPK/Erk signaling promotes ancestral T-cell immunity in fish via c-Myc-mediated glycolysis.

Authors:  Xiumei Wei; Yu Zhang; Cheng Li; Kete Ai; Kang Li; Huiying Li; Jialong Yang
Journal:  J Biol Chem       Date:  2020-01-29       Impact factor: 5.157

6.  Studying tumorigenesis through network evolution and somatic mutational perturbations in the cancer interactome.

Authors:  Feixiong Cheng; Peilin Jia; Quan Wang; Chen-Ching Lin; Wen-Hsiung Li; Zhongming Zhao
Journal:  Mol Biol Evol       Date:  2014-05-31       Impact factor: 16.240

7.  Variant cell cycles regulated by Notch signaling control cell size and ensure a functional blood-brain barrier.

Authors:  Jessica R Von Stetina; Laura E Frawley; Yingdee Unhavaithaya; Terry L Orr-Weaver
Journal:  Development       Date:  2018-02-13       Impact factor: 6.868

8.  Rare BRAF mutations in pancreatic neuroendocrine tumors may predict response to RAF and MEK inhibition.

Authors:  Amy Allen; Alice Can Ran Qin; Nitya Raj; Jiawan Wang; Sharmeen Uddin; Zhan Yao; Laura Tang; Paul A Meyers; Barry S Taylor; Michael F Berger; Rona Yaeger; Diane Reidy-Lagunes; Christine A Pratilas
Journal:  PLoS One       Date:  2019-06-03       Impact factor: 3.240

9.  A random walk-based method to identify driver genes by integrating the subcellular localization and variation frequency into bipartite graph.

Authors:  Junrong Song; Wei Peng; Feng Wang
Journal:  BMC Bioinformatics       Date:  2019-05-14       Impact factor: 3.169

10.  Visualizing DNA folding and RNA in embryos at single-cell resolution.

Authors:  Leslie J Mateo; Sedona E Murphy; Antonina Hafner; Isaac S Cinquini; Carly A Walker; Alistair N Boettiger
Journal:  Nature       Date:  2019-03-18       Impact factor: 49.962

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  8 in total

Review 1.  Allostery, and how to define and measure signal transduction.

Authors:  Ruth Nussinov; Chung-Jung Tsai; Hyunbum Jang
Journal:  Biophys Chem       Date:  2022-01-29       Impact factor: 2.352

Review 2.  Neurodevelopmental disorders, immunity, and cancer are connected.

Authors:  Ruth Nussinov; Chung-Jung Tsai; Hyunbum Jang
Journal:  iScience       Date:  2022-05-30

3.  Validation of a Liquid Biopsy Protocol for Canine BRAFV595E Variant Detection in Dog Urine and Its Evaluation as a Diagnostic Test Complementary to Cytology.

Authors:  Fabio Gentilini; Christopher J Palgrave; Michal Neta; Raimondo Tornago; Tommaso Furlanello; Jennifer S McKay; Federico Sacchini; Maria E Turba
Journal:  Front Vet Sci       Date:  2022-05-31

Review 4.  Anticancer drug resistance: An update and perspective.

Authors:  Ruth Nussinov; Chung-Jung Tsai; Hyunbum Jang
Journal:  Drug Resist Updat       Date:  2021-12-16       Impact factor: 18.500

5.  How can same-gene mutations promote both cancer and developmental disorders?

Authors:  Ruth Nussinov; Chung-Jung Tsai; Hyunbum Jang
Journal:  Sci Adv       Date:  2022-01-14       Impact factor: 14.136

Review 6.  AlphaFold, Artificial Intelligence (AI), and Allostery.

Authors:  Ruth Nussinov; Mingzhen Zhang; Yonglan Liu; Hyunbum Jang
Journal:  J Phys Chem B       Date:  2022-08-17       Impact factor: 3.466

7.  Monoclonal antibodies and Fc-fusion protein biologic medicines: A multinational cross-sectional investigation of accessibility and affordability in Asia Pacific regions between 2010 and 2020.

Authors:  Xinning Tong; Xue Li; Nicole L Pratt; Jodie B Hillen; Tyman Stanford; Michael Ward; Elizabeth E Roughead; Edward Chia-Cheng Lai; Ju-Young Shin; Franco W T Cheng; Kuan Peng; Chak Sing Lau; Wai Keung Leung; Ian C K Wong
Journal:  Lancet Reg Health West Pac       Date:  2022-06-24

Review 8.  Mechanism of activation and the rewired network: New drug design concepts.

Authors:  Ruth Nussinov; Mingzhen Zhang; Ryan Maloney; Chung-Jung Tsai; Bengi Ruken Yavuz; Nurcan Tuncbag; Hyunbum Jang
Journal:  Med Res Rev       Date:  2021-10-25       Impact factor: 12.388

  8 in total

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