Literature DB >> 23212109

Computation as the mechanistic bridge between precision medicine and systems therapeutics.

J Hansen1, R Iyengar.   

Abstract

Over the past 50 years, like molecular cell biology, medicine and pharmacology have been driven by a reductionist approach. The focus on individual genes and cellular components as disease loci and drug targets has been a necessary step in understanding the basic mechanisms underlying tissue/organ physiology and drug action. Recent progress in genomics and proteomics, as well as advances in other technologies that enable large-scale data gathering and computational approaches, is providing new knowledge of both normal and disease states. Systems-biology approaches enable integration of knowledge from different types of data for precision medicine and systems therapeutics. In this review, we describe recent studies that contribute to these emerging fields and discuss how together these fields can lead to a mechanism-based therapy for individual patients.

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Year:  2012        PMID: 23212109      PMCID: PMC3963513          DOI: 10.1038/clpt.2012.199

Source DB:  PubMed          Journal:  Clin Pharmacol Ther        ISSN: 0009-9236            Impact factor:   6.875


  53 in total

1.  Subtype and pathway specific responses to anticancer compounds in breast cancer.

Authors:  Laura M Heiser; Anguraj Sadanandam; Wen-Lin Kuo; Stephen C Benz; Theodore C Goldstein; Sam Ng; William J Gibb; Nicholas J Wang; Safiyyah Ziyad; Frances Tong; Nora Bayani; Zhi Hu; Jessica I Billig; Andrea Dueregger; Sophia Lewis; Lakshmi Jakkula; James E Korkola; Steffen Durinck; François Pepin; Yinghui Guan; Elizabeth Purdom; Pierre Neuvial; Henrik Bengtsson; Kenneth W Wood; Peter G Smith; Lyubomir T Vassilev; Bryan T Hennessy; Joel Greshock; Kurtis E Bachman; Mary Ann Hardwicke; John W Park; Laurence J Marton; Denise M Wolf; Eric A Collisson; Richard M Neve; Gordon B Mills; Terence P Speed; Heidi S Feiler; Richard F Wooster; David Haussler; Joshua M Stuart; Joe W Gray; Paul T Spellman
Journal:  Proc Natl Acad Sci U S A       Date:  2011-10-14       Impact factor: 11.205

Review 2.  Merging systems biology with pharmacodynamics.

Authors:  Ravi Iyengar; Shan Zhao; Seung-Wook Chung; Donald E Mager; James M Gallo
Journal:  Sci Transl Med       Date:  2012-03-21       Impact factor: 17.956

Review 3.  Fabry disease.

Authors:  Ana Lía Tarabuso
Journal:  Skinmed       Date:  2011 May-Jun

Review 4.  Treatment of HER2-positive breast cancer: current status and future perspectives.

Authors:  Carlos L Arteaga; Mark X Sliwkowski; C Kent Osborne; Edith A Perez; Fabio Puglisi; Luca Gianni
Journal:  Nat Rev Clin Oncol       Date:  2011-11-29       Impact factor: 66.675

Review 5.  Microarrays, deep sequencing and the true measure of the transcriptome.

Authors:  John H Malone; Brian Oliver
Journal:  BMC Biol       Date:  2011-05-31       Impact factor: 7.431

6.  Clinical application of a systems model of apoptosis execution for the prediction of colorectal cancer therapy responses and personalisation of therapy.

Authors:  Suzanne Hector; Markus Rehm; Jasmin Schmid; Joan Kehoe; Niamh McCawley; Patrick Dicker; Frank Murray; Deborah McNamara; Elaine W Kay; Caoimhin G Concannon; Heinrich J Huber; Jochen H M Prehn
Journal:  Gut       Date:  2011-11-14       Impact factor: 23.059

Review 7.  Systems pharmacology: network analysis to identify multiscale mechanisms of drug action.

Authors:  Shan Zhao; Ravi Iyengar
Journal:  Annu Rev Pharmacol Toxicol       Date:  2012       Impact factor: 13.820

Review 8.  Exploiting the cancer genome: strategies for the discovery and clinical development of targeted molecular therapeutics.

Authors:  Timothy A Yap; Paul Workman
Journal:  Annu Rev Pharmacol Toxicol       Date:  2012       Impact factor: 13.820

9.  The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity.

Authors:  Jordi Barretina; Giordano Caponigro; Nicolas Stransky; Kavitha Venkatesan; Adam A Margolin; Sungjoon Kim; Christopher J Wilson; Joseph Lehár; Gregory V Kryukov; Dmitriy Sonkin; Anupama Reddy; Manway Liu; Lauren Murray; Michael F Berger; John E Monahan; Paula Morais; Jodi Meltzer; Adam Korejwa; Judit Jané-Valbuena; Felipa A Mapa; Joseph Thibault; Eva Bric-Furlong; Pichai Raman; Aaron Shipway; Ingo H Engels; Jill Cheng; Guoying K Yu; Jianjun Yu; Peter Aspesi; Melanie de Silva; Kalpana Jagtap; Michael D Jones; Li Wang; Charles Hatton; Emanuele Palescandolo; Supriya Gupta; Scott Mahan; Carrie Sougnez; Robert C Onofrio; Ted Liefeld; Laura MacConaill; Wendy Winckler; Michael Reich; Nanxin Li; Jill P Mesirov; Stacey B Gabriel; Gad Getz; Kristin Ardlie; Vivien Chan; Vic E Myer; Barbara L Weber; Jeff Porter; Markus Warmuth; Peter Finan; Jennifer L Harris; Matthew Meyerson; Todd R Golub; Michael P Morrissey; William R Sellers; Robert Schlegel; Levi A Garraway
Journal:  Nature       Date:  2012-03-28       Impact factor: 49.962

10.  Systematic identification of genomic markers of drug sensitivity in cancer cells.

Authors:  Mathew J Garnett; Elena J Edelman; Sonja J Heidorn; Chris D Greenman; Anahita Dastur; King Wai Lau; Patricia Greninger; I Richard Thompson; Xi Luo; Jorge Soares; Qingsong Liu; Francesco Iorio; Didier Surdez; Li Chen; Randy J Milano; Graham R Bignell; Ah T Tam; Helen Davies; Jesse A Stevenson; Syd Barthorpe; Stephen R Lutz; Fiona Kogera; Karl Lawrence; Anne McLaren-Douglas; Xeni Mitropoulos; Tatiana Mironenko; Helen Thi; Laura Richardson; Wenjun Zhou; Frances Jewitt; Tinghu Zhang; Patrick O'Brien; Jessica L Boisvert; Stacey Price; Wooyoung Hur; Wanjuan Yang; Xianming Deng; Adam Butler; Hwan Geun Choi; Jae Won Chang; Jose Baselga; Ivan Stamenkovic; Jeffrey A Engelman; Sreenath V Sharma; Olivier Delattre; Julio Saez-Rodriguez; Nathanael S Gray; Jeffrey Settleman; P Andrew Futreal; Daniel A Haber; Michael R Stratton; Sridhar Ramaswamy; Ultan McDermott; Cyril H Benes
Journal:  Nature       Date:  2012-03-28       Impact factor: 49.962

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  15 in total

1.  Radiopharmaceutical therapy in the era of precision medicine.

Authors:  George Sgouros; David M Goldenberg
Journal:  Eur J Cancer       Date:  2014-06-19       Impact factor: 9.162

Review 2.  Screening out irrelevant cell-based models of disease.

Authors:  Peter Horvath; Nathalie Aulner; Marc Bickle; Anthony M Davies; Elaine Del Nery; Daniel Ebner; Maria C Montoya; Päivi Östling; Vilja Pietiäinen; Leo S Price; Spencer L Shorte; Gerardo Turcatti; Carina von Schantz; Neil O Carragher
Journal:  Nat Rev Drug Discov       Date:  2016-09-12       Impact factor: 84.694

3.  Harnessing Human Microphysiology Systems as Key Experimental Models for Quantitative Systems Pharmacology.

Authors:  D Lansing Taylor; Albert Gough; Mark E Schurdak; Lawrence Vernetti; Chakra S Chennubhotla; Daniel Lefever; Fen Pei; James R Faeder; Timothy R Lezon; Andrew M Stern; Ivet Bahar
Journal:  Handb Exp Pharmacol       Date:  2019

Review 4.  Augmenting Surgery via Multi-scale Modeling and Translational Systems Biology in the Era of Precision Medicine: A Multidisciplinary Perspective.

Authors:  Ghassan S Kassab; Gary An; Edward A Sander; Michael I Miga; Julius M Guccione; Songbai Ji; Yoram Vodovotz
Journal:  Ann Biomed Eng       Date:  2016-03-25       Impact factor: 3.934

5.  Systems pharmacology-based integration of human and mouse data for drug repurposing to treat thoracic aneurysms.

Authors:  Jens Hansen; Josephine Galatioto; Cristina I Caescu; Pauline Arnaud; Rhodora C Calizo; Bart Spronck; Sae-Il Murtada; Roshan Borkar; Alan Weinberg; Evren U Azeloglu; Maria Bintanel-Morcillo; James M Gallo; Jay D Humphrey; Guillaume Jondeau; Catherine Boileau; Francesco Ramirez; Ravi Iyengar
Journal:  JCI Insight       Date:  2019-06-06

6.  A Perspective on Implementing a Quantitative Systems Pharmacology Platform for Drug Discovery and the Advancement of Personalized Medicine.

Authors:  Andrew M Stern; Mark E Schurdak; Ivet Bahar; Jeremy M Berg; D Lansing Taylor
Journal:  J Biomol Screen       Date:  2016-03-08

7.  In silico model-based inference: a contemporary approach for hypothesis testing in network biology.

Authors:  David J Klinke
Journal:  Biotechnol Prog       Date:  2014-08-26

8.  Temporal Patterns of Circulating Inflammation Biomarker Networks Differentiate Susceptibility to Nosocomial Infection Following Blunt Trauma in Humans.

Authors:  Rami A Namas; Yoram Vodovotz; Khalid Almahmoud; Othman Abdul-Malak; Akram Zaaqoq; Rajaie Namas; Qi Mi; Derek Barclay; Brian Zuckerbraun; Andrew B Peitzman; Jason Sperry; Timothy R Billiar
Journal:  Ann Surg       Date:  2016-01       Impact factor: 12.969

9.  Mathematical modeling of folate metabolism.

Authors:  John C Panetta; Steven W Paugh; William E Evans
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2013-05-22

10.  Improving natural product research translation: From source to clinical trial.

Authors:  Barbara C Sorkin; Adam J Kuszak; Gregory Bloss; Naomi K Fukagawa; Freddie Ann Hoffman; Mahtab Jafari; Bruce Barrett; Paula N Brown; Frederic D Bushman; Steven J Casper; Floyd H Chilton; Christopher S Coffey; Mario G Ferruzzi; D Craig Hopp; Mairead Kiely; Daniel Lakens; John B MacMillan; David O Meltzer; Marco Pahor; Jeffrey Paul; Kathleen Pritchett-Corning; Sara K Quinney; Barbara Rehermann; Kenneth D R Setchell; Nisha S Sipes; Jacqueline M Stephens; D Lansing Taylor; Hervé Tiriac; Michael A Walters; Dan Xi; Giovanna Zappalá; Guido F Pauli
Journal:  FASEB J       Date:  2019-12-10       Impact factor: 5.834

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