Literature DB >> 21808261

Systems-biology approaches for predicting genomic evolution.

Balázs Papp1, Richard A Notebaart, Csaba Pál.   

Abstract

Is evolution predictable at the molecular level? The ambitious goal to answer this question requires an understanding of the mutational effects that govern the complex relationship between genotype and phenotype. In practice, it involves integrating systems-biology modelling, microbial laboratory evolution experiments and large-scale mutational analyses - a feat that is made possible by the recent availability of the necessary computational tools and experimental techniques. This Review investigates recent progresses in mapping evolutionary trajectories and discusses the degree to which these predictions are realistic.

Mesh:

Year:  2011        PMID: 21808261     DOI: 10.1038/nrg3033

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  91 in total

1.  KEGG: kyoto encyclopedia of genes and genomes.

Authors:  M Kanehisa; S Goto
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

Review 2.  Comparative systems biology: from bacteria to man.

Authors:  Bas Teusink; Hans V Westerhoff; Frank J Bruggeman
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2010 Sep-Oct

3.  Genome evolution and adaptation in a long-term experiment with Escherichia coli.

Authors:  Jeffrey E Barrick; Dong Su Yu; Sung Ho Yoon; Haeyoung Jeong; Tae Kwang Oh; Dominique Schneider; Richard E Lenski; Jihyun F Kim
Journal:  Nature       Date:  2009-10-18       Impact factor: 49.962

4.  Something from nothing: bridging the gap between constraint-based and kinetic modelling.

Authors:  Kieran Smallbone; Evangelos Simeonidis; David S Broomhead; Douglas B Kell
Journal:  FEBS J       Date:  2007-10-08       Impact factor: 5.542

Review 5.  The danger of metabolic pathways with turbo design.

Authors:  B Teusink; M C Walsh; K van Dam; H V Westerhoff
Journal:  Trends Biochem Sci       Date:  1998-05       Impact factor: 13.807

6.  Modular epistasis in yeast metabolism.

Authors:  Daniel Segrè; Alexander Deluna; George M Church; Roy Kishony
Journal:  Nat Genet       Date:  2004-12-12       Impact factor: 38.330

7.  Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models.

Authors:  Nathan E Lewis; Kim K Hixson; Tom M Conrad; Joshua A Lerman; Pep Charusanti; Ashoka D Polpitiya; Joshua N Adkins; Gunnar Schramm; Samuel O Purvine; Daniel Lopez-Ferrer; Karl K Weitz; Roland Eils; Rainer König; Richard D Smith; Bernhard Ø Palsson
Journal:  Mol Syst Biol       Date:  2010-07       Impact factor: 11.429

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

9.  Programming cells by multiplex genome engineering and accelerated evolution.

Authors:  Harris H Wang; Farren J Isaacs; Peter A Carr; Zachary Z Sun; George Xu; Craig R Forest; George M Church
Journal:  Nature       Date:  2009-07-26       Impact factor: 49.962

10.  A genome-scale computational study of the interplay between transcriptional regulation and metabolism.

Authors:  Tomer Shlomi; Yariv Eisenberg; Roded Sharan; Eytan Ruppin
Journal:  Mol Syst Biol       Date:  2007-04-17       Impact factor: 11.429

View more
  48 in total

Review 1.  A road map for the development of community systems (CoSy) biology.

Authors:  Karsten Zengler; Bernhard O Palsson
Journal:  Nat Rev Microbiol       Date:  2012-03-27       Impact factor: 60.633

Review 2.  Plant metabolic modeling: achieving new insight into metabolism and metabolic engineering.

Authors:  Kambiz Baghalian; Mohammad-Reza Hajirezaei; Falk Schreiber
Journal:  Plant Cell       Date:  2014-10-24       Impact factor: 11.277

3.  Repeatability of adaptation in experimental populations of different sizes.

Authors:  Josianne Lachapelle; Joshua Reid; Nick Colegrave
Journal:  Proc Biol Sci       Date:  2015-04-22       Impact factor: 5.349

Review 4.  Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods.

Authors:  Nathan E Lewis; Harish Nagarajan; Bernhard O Palsson
Journal:  Nat Rev Microbiol       Date:  2012-02-27       Impact factor: 60.633

Review 5.  Culture history and population heterogeneity as determinants of bacterial adaptation: the adaptomics of a single environmental transition.

Authors:  Ben Ryall; Gustavo Eydallin; Thomas Ferenci
Journal:  Microbiol Mol Biol Rev       Date:  2012-09       Impact factor: 11.056

6.  Biophysics of protein evolution and evolutionary protein biophysics.

Authors:  Tobias Sikosek; Hue Sun Chan
Journal:  J R Soc Interface       Date:  2014-11-06       Impact factor: 4.118

7.  Fisher's geometrical model emerges as a property of complex integrated phenotypic networks.

Authors:  Guillaume Martin
Journal:  Genetics       Date:  2014-02-28       Impact factor: 4.562

Review 8.  Empirical fitness landscapes and the predictability of evolution.

Authors:  J Arjan G M de Visser; Joachim Krug
Journal:  Nat Rev Genet       Date:  2014-06-10       Impact factor: 53.242

Review 9.  How many molecular subtypes? Implications of the unique tumor principle in personalized medicine.

Authors:  Shuji Ogino; Charles S Fuchs; Edward Giovannucci
Journal:  Expert Rev Mol Diagn       Date:  2012-07       Impact factor: 5.225

10.  The mutational structure of metabolism in Caenorhabditis elegans.

Authors:  Sarah K Davies; Armand Leroi; Austin Burt; Jacob G Bundy; Charles F Baer
Journal:  Evolution       Date:  2016-08-24       Impact factor: 3.694

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.