Literature DB >> 18436781

From genotype to phenotype: systems biology meets natural variation.

Philip N Benfey1, Thomas Mitchell-Olds.   

Abstract

The promise that came with genome sequencing was that we would soon know what genes do, particularly genes involved in human diseases and those of importance to agriculture. We now have the full genomic sequence of human, chimpanzee, mouse, chicken, dog, worm, fly, rice, and cress, as well as those for a wide variety of other species, and yet we still have a lot of trouble figuring out what genes do. Mapping genes to their function is called the "genotype-to-phenotype problem," where phenotype is whatever is changed in the organism when a gene's function is altered.

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Year:  2008        PMID: 18436781      PMCID: PMC2727942          DOI: 10.1126/science.1153716

Source DB:  PubMed          Journal:  Science        ISSN: 0036-8075            Impact factor:   47.728


  18 in total

1.  Modeling the organization of the WUSCHEL expression domain in the shoot apical meristem.

Authors:  Henrik Jönsson; Marcus Heisler; G Venugopala Reddy; Vikas Agrawal; Victoria Gor; Bruce E Shapiro; Eric Mjolsness; Elliot M Meyerowitz
Journal:  Bioinformatics       Date:  2005-06       Impact factor: 6.937

2.  Relating three-dimensional structures to protein networks provides evolutionary insights.

Authors:  Philip M Kim; Long J Lu; Yu Xia; Mark B Gerstein
Journal:  Science       Date:  2006-12-22       Impact factor: 47.728

3.  Positive selection at the protein network periphery: evaluation in terms of structural constraints and cellular context.

Authors:  Philip M Kim; Jan O Korbel; Mark B Gerstein
Journal:  Proc Natl Acad Sci U S A       Date:  2007-12-12       Impact factor: 11.205

4.  Influence of metabolic network structure and function on enzyme evolution.

Authors:  Dennis Vitkup; Peter Kharchenko; Andreas Wagner
Journal:  Genome Biol       Date:  2006-05-09       Impact factor: 13.583

5.  Why highly expressed proteins evolve slowly.

Authors:  D Allan Drummond; Jesse D Bloom; Christoph Adami; Claus O Wilke; Frances H Arnold
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-21       Impact factor: 11.205

6.  The evolutionary rate of a protein is influenced by features of the interacting partners.

Authors:  Takashi Makino; Takashi Gojobori
Journal:  Mol Biol Evol       Date:  2006-01-11       Impact factor: 16.240

7.  Epistasis and balanced polymorphism influencing complex trait variation.

Authors:  Juergen Kroymann; Thomas Mitchell-Olds
Journal:  Nature       Date:  2005-05-05       Impact factor: 49.962

8.  Association of the ADAM33 gene with asthma and bronchial hyperresponsiveness.

Authors:  Paul Van Eerdewegh; Randall D Little; Josée Dupuis; Richard G Del Mastro; Kathy Falls; Jason Simon; Dana Torrey; Sunil Pandit; Joyce McKenny; Karen Braunschweiger; Alison Walsh; Ziying Liu; Brooke Hayward; Colleen Folz; Susan P Manning; Alicia Bawa; Lisa Saracino; Michelle Thackston; Youssef Benchekroun; Neva Capparell; Mei Wang; Ron Adair; Yun Feng; JoAnn Dubois; Michael G FitzGerald; Hui Huang; René Gibson; Kristina M Allen; Alex Pedan; Melvyn R Danzig; Shelby P Umland; Robert W Egan; Francis M Cuss; Steuart Rorke; Joanne B Clough; John W Holloway; Stephen T Holgate; Tim P Keith
Journal:  Nature       Date:  2002-07-10       Impact factor: 49.962

9.  Ab initio genotype-phenotype association reveals intrinsic modularity in genetic networks.

Authors:  Noam Slonim; Olivier Elemento; Saeed Tavazoie
Journal:  Mol Syst Biol       Date:  2006-01-31       Impact factor: 11.429

10.  Evolutionary and physiological importance of hub proteins.

Authors:  Nizar N Batada; Laurence D Hurst; Mike Tyers
Journal:  PLoS Comput Biol       Date:  2006-06-05       Impact factor: 4.475

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  77 in total

Review 1.  At the heart of computational modelling.

Authors:  S A Niederer; N P Smith
Journal:  J Physiol       Date:  2012-01-23       Impact factor: 5.182

2.  Mapping cell fate decisions that occur during soybean defense responses.

Authors:  Prachi D Matsye; Ranjit Kumar; Parsa Hosseini; Christina M Jones; Arianne Tremblay; Nadim W Alkharouf; Benjamin F Matthews; Vincent P Klink
Journal:  Plant Mol Biol       Date:  2011-10-11       Impact factor: 4.076

3.  Genome-wide gene and pathway analysis.

Authors:  Li Luo; Gang Peng; Yun Zhu; Hua Dong; Christopher I Amos; Momiao Xiong
Journal:  Eur J Hum Genet       Date:  2010-05-05       Impact factor: 4.246

Review 4.  Mutation and the evolution of ageing: from biometrics to system genetics.

Authors:  Kimberly A Hughes
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2010-04-27       Impact factor: 6.237

5.  The evolutionary history of the Arabidopsis lyrata complex: a hybrid in the amphi-Beringian area closes a large distribution gap and builds up a genetic barrier.

Authors:  Roswitha Schmickl; Marte H Jørgensen; Anne K Brysting; Marcus A Koch
Journal:  BMC Evol Biol       Date:  2010-04-08       Impact factor: 3.260

6.  Common clinical practice versus new PRIM score in predicting coronary heart disease risk.

Authors:  Ruth Frikke-Schmidt; Anne Tybjærg-Hansen; Peter Schnohr; Gorm B Jensen; Børge G Nordestgaard
Journal:  Atherosclerosis       Date:  2010-07-27       Impact factor: 5.162

Review 7.  Systems Biology for Smart Crops and Agricultural Innovation: Filling the Gaps between Genotype and Phenotype for Complex Traits Linked with Robust Agricultural Productivity and Sustainability.

Authors:  Anil Kumar; Rajesh Kumar Pathak; Sanjay Mohan Gupta; Vikram Singh Gaur; Dinesh Pandey
Journal:  OMICS       Date:  2015-10

8.  Genetic regulatory network motifs constrain adaptation through curvature in the landscape of mutational (co)variance.

Authors:  Tyler D Hether; Paul A Hohenlohe
Journal:  Evolution       Date:  2013-12-04       Impact factor: 3.694

9.  Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids.

Authors:  Guangming He; Xiaopeng Zhu; Axel A Elling; Liangbi Chen; Xiangfeng Wang; Lan Guo; Manzhong Liang; Hang He; Huiyong Zhang; Fangfang Chen; Yijun Qi; Runsheng Chen; Xing-Wang Deng
Journal:  Plant Cell       Date:  2010-01-19       Impact factor: 11.277

Review 10.  Garrod's Croonian Lectures (1908) and the charter 'Inborn Errors of Metabolism': albinism, alkaptonuria, cystinuria, and pentosuria at age 100 in 2008.

Authors:  Charles R Scriver
Journal:  J Inherit Metab Dis       Date:  2008-10-12       Impact factor: 4.982

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