Literature DB >> 19252506

The role of predictive modelling in rationally re-engineering biological systems.

Tie Koide1, Wyming Lee Pang, Nitin S Baliga.   

Abstract

Technologies to synthesize and transplant a complete genome into a cell have opened limitless potential to redesign organisms for complex, specialized tasks. However, large-scale re-engineering of a biological circuit will require systems-level optimization that will come from a deep understanding of operational relationships among all the constituent parts of a cell. The integrated framework necessary for conducting such complex bioengineering requires the convergence of systems and synthetic biology. Here, we review the status of these rapidly developing interdisciplinary fields of biology and provide a perspective on plausible venues for their merger.

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Year:  2009        PMID: 19252506      PMCID: PMC2734281          DOI: 10.1038/nrmicro2107

Source DB:  PubMed          Journal:  Nat Rev Microbiol        ISSN: 1740-1526            Impact factor:   60.633


  101 in total

1.  Genome-wide location and function of DNA binding proteins.

Authors:  B Ren; F Robert; J J Wyrick; O Aparicio; E G Jennings; I Simon; J Zeitlinger; J Schreiber; N Hannett; E Kanin; T L Volkert; C J Wilson; S P Bell; R A Young
Journal:  Science       Date:  2000-12-22       Impact factor: 47.728

Review 2.  From words to literature in structural proteomics.

Authors:  Andrej Sali; Robert Glaeser; Thomas Earnest; Wolfgang Baumeister
Journal:  Nature       Date:  2003-03-13       Impact factor: 49.962

Review 3.  The digital code of DNA.

Authors:  Leroy Hood; David Galas
Journal:  Nature       Date:  2003-01-23       Impact factor: 49.962

Review 4.  Minimal protein-folding systems in hyperthermophilic archaea.

Authors:  Pongpan Laksanalamai; Timothy A Whitehead; Frank T Robb
Journal:  Nat Rev Microbiol       Date:  2004-04       Impact factor: 60.633

Review 5.  Reconstruction of genetic circuits.

Authors:  David Sprinzak; Michael B Elowitz
Journal:  Nature       Date:  2005-11-24       Impact factor: 49.962

Review 6.  Bridging from molecular simulation to biochemical networks.

Authors:  Matthias Stein; Razif R Gabdoulline; Rebecca C Wade
Journal:  Curr Opin Struct Biol       Date:  2007-03-28       Impact factor: 6.809

Review 7.  Microbiology in the post-genomic era.

Authors:  Duccio Medini; Davide Serruto; Julian Parkhill; David A Relman; Claudio Donati; Richard Moxon; Stanley Falkow; Rino Rappuoli
Journal:  Nat Rev Microbiol       Date:  2008-05-13       Impact factor: 60.633

8.  Evolvability and hierarchy in rewired bacterial gene networks.

Authors:  Mark Isalan; Caroline Lemerle; Konstantinos Michalodimitrakis; Carsten Horn; Pedro Beltrao; Emanuele Raineri; Mireia Garriga-Canut; Luis Serrano
Journal:  Nature       Date:  2008-04-17       Impact factor: 49.962

Review 9.  Bacterial targeted tumour therapy-dawn of a new era.

Authors:  Ming Q Wei; Asferd Mengesha; David Good; Jozef Anné
Journal:  Cancer Lett       Date:  2008-01-18       Impact factor: 8.679

10.  Evolved orthogonal ribosomes enhance the efficiency of synthetic genetic code expansion.

Authors:  Kaihang Wang; Heinz Neumann; Sew Y Peak-Chew; Jason W Chin
Journal:  Nat Biotechnol       Date:  2007-06-24       Impact factor: 54.908

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  16 in total

Review 1.  Engineering ecosystems and synthetic ecologies.

Authors:  Michael T Mee; Harris H Wang
Journal:  Mol Biosyst       Date:  2012-10

2.  Identification of alterations in the Jacobian of biochemical reaction networks from steady state covariance data at two conditions.

Authors:  Philipp Kügler; Wei Yang
Journal:  J Math Biol       Date:  2013-05-26       Impact factor: 2.259

Review 3.  Unraveling interactions in microbial communities - from co-cultures to microbiomes.

Authors:  Justin Tan; Cristal Zuniga; Karsten Zengler
Journal:  J Microbiol       Date:  2015-05-03       Impact factor: 3.422

Review 4.  Reverse engineering systems models of regulation: discovery, prediction and mechanisms.

Authors:  Justin Ashworth; Elisabeth J Wurtmann; Nitin S Baliga
Journal:  Curr Opin Biotechnol       Date:  2011-12-28       Impact factor: 9.740

Review 5.  Adaptation of cells to new environments.

Authors:  Aaron N Brooks; Serdar Turkarslan; Karlyn D Beer; Fang Yin Lo; Nitin S Baliga
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2010-12-31

Review 6.  Microfluidic devices for measuring gene network dynamics in single cells.

Authors:  Matthew R Bennett; Jeff Hasty
Journal:  Nat Rev Genet       Date:  2009-08-11       Impact factor: 53.242

7.  Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis.

Authors:  Marc T Facciotti; Wyming L Pang; Fang-yin Lo; Kenia Whitehead; Tie Koide; Ken-ichi Masumura; Min Pan; Amardeep Kaur; David J Larsen; David J Reiss; Linh Hoang; Ewa Kalisiak; Trent Northen; Sunia A Trauger; Gary Siuzdak; Nitin S Baliga
Journal:  BMC Syst Biol       Date:  2010-05-14

8.  Computational design of genomic transcriptional networks with adaptation to varying environments.

Authors:  Javier Carrera; Santiago F Elena; Alfonso Jaramillo
Journal:  Proc Natl Acad Sci U S A       Date:  2012-08-27       Impact factor: 11.205

Review 9.  Recent advances in 2D and 3D in vitro systems using primary hepatocytes, alternative hepatocyte sources and non-parenchymal liver cells and their use in investigating mechanisms of hepatotoxicity, cell signaling and ADME.

Authors:  Patricio Godoy; Nicola J Hewitt; Ute Albrecht; Melvin E Andersen; Nariman Ansari; Sudin Bhattacharya; Johannes Georg Bode; Jennifer Bolleyn; Christoph Borner; Jan Böttger; Albert Braeuning; Robert A Budinsky; Britta Burkhardt; Neil R Cameron; Giovanni Camussi; Chong-Su Cho; Yun-Jaie Choi; J Craig Rowlands; Uta Dahmen; Georg Damm; Olaf Dirsch; María Teresa Donato; Jian Dong; Steven Dooley; Dirk Drasdo; Rowena Eakins; Karine Sá Ferreira; Valentina Fonsato; Joanna Fraczek; Rolf Gebhardt; Andrew Gibson; Matthias Glanemann; Chris E P Goldring; María José Gómez-Lechón; Geny M M Groothuis; Lena Gustavsson; Christelle Guyot; David Hallifax; Seddik Hammad; Adam Hayward; Dieter Häussinger; Claus Hellerbrand; Philip Hewitt; Stefan Hoehme; Hermann-Georg Holzhütter; J Brian Houston; Jens Hrach; Kiyomi Ito; Hartmut Jaeschke; Verena Keitel; Jens M Kelm; B Kevin Park; Claus Kordes; Gerd A Kullak-Ublick; Edward L LeCluyse; Peng Lu; Jennifer Luebke-Wheeler; Anna Lutz; Daniel J Maltman; Madlen Matz-Soja; Patrick McMullen; Irmgard Merfort; Simon Messner; Christoph Meyer; Jessica Mwinyi; Dean J Naisbitt; Andreas K Nussler; Peter Olinga; Francesco Pampaloni; Jingbo Pi; Linda Pluta; Stefan A Przyborski; Anup Ramachandran; Vera Rogiers; Cliff Rowe; Celine Schelcher; Kathrin Schmich; Michael Schwarz; Bijay Singh; Ernst H K Stelzer; Bruno Stieger; Regina Stöber; Yuichi Sugiyama; Ciro Tetta; Wolfgang E Thasler; Tamara Vanhaecke; Mathieu Vinken; Thomas S Weiss; Agata Widera; Courtney G Woods; Jinghai James Xu; Kathy M Yarborough; Jan G Hengstler
Journal:  Arch Toxicol       Date:  2013-08-23       Impact factor: 5.153

10.  Regulatory consequences of gene translocation in bacteria.

Authors:  Dena H S Block; Razika Hussein; Lusha W Liang; Han N Lim
Journal:  Nucleic Acids Res       Date:  2012-07-24       Impact factor: 16.971

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