A Systems Approach To Generating Functional Novelties

The Systems Biology concept

(Cornish-Bowden, Cardenas et al. 2007; Van Norman and Benfey 2009; Vidal 2009; Arkin and Schaffer 2011; Lucas, Laplaze et al. 2011)

Systems/Network properties and function

(Milo, Itzkovitz et al. 2004; Marder and Goaillard 2006; Sharan and Ideker 2006; Balaji, Babu et al. 2007; Daniels, Chen et al. 2008; Sole and Valverde 2008; Tagkopoulos, Liu et al. 2008; Altay and Emmert-Streib 2010; DeLong and Nusbaum 2010; Draghi, Parsons et al. 2010; Masel and Trotter 2010; Veiga, Dutta et al. 2010; de Ruiter and van der Boom 2011; Emmert-Streib and Dehmer 2011; Ma'ayan 2011)

Metabolism, physiology and neurobiology

(Agrawal, Padmanabhan et al. 2009; Schadt 2009; Szymanski, Jozefczuk et al. 2009; Wang and Zhang 2009; DeLong and Nusbaum 2010; Piedrafita, Montero et al. 2010; Kim, Fang et al. 2011; Klosinska, Crutchfield et al. 2011; Noble 2011)

Transcriptional regulation

(Balaji and Aravind 2007; Balaji, Babu et al. 2007; Madan Babu, Balaji et al. 2007; Jothi, Balaji et al. 2009; Perez and Groisman 2009; Altay and Emmert-Streib 2010; Nowick and Stubbs 2010; White and Sharrocks 2010; Lan and Mezic 2011)

Protein networks

(Yang, Siganos et al. 2006; Gierasch and Gershenson 2009; Vora, Hottes et al. 2009; Katz and Privman 2010; Lieber, Elemento et al. 2010; Ranea, Morilla et al. 2010; Foss, Radulovic et al. 2011)

RNA networks

(Mattick 2001; Mattick 2004; Lee, Risom et al. 2007; Mattick 2007; Amaral, Dinger et al. 2008; Amaral and Mattick 2008; Dinger, Amaral et al. 2008; Mattick 2009; Mattick 2011)

Cell biology and single-cell analysis

(Balaji, Babu et al. 2007; Parkhomchuk, Amstislavskiy et al. 2009; Bergquist, Dickman et al. 2010; Gray, Lukes et al. 2010; Costanzo, Baryshnikova et al. 2011; Magtanong, Ho et al. 2011)

Evolvability

(Carroll 2005; Yang, Siganos et al. 2006; Lamm and Jablonka 2008; Goodarzi, Elemento et al. 2009; Goodarzi, Hottes et al. 2009; Masel and Trotter 2010; Chen and Lin 2011; Papp, Notebaart et al. 2011)

Apoptosis and genome stability

(Castro, Dalmolin et al. 2008)

Multicellularity

(Foster, Parkinson et al. 2007; Foster 2009; Foster 2011; Regot, Macia et al. 2011)

Development & morphogenesis

(Mattick 2001; Mattick 2004; Mattick 2007; Amaral, Dinger et al. 2008; Amaral and Mattick 2008; Dinger, Amaral et al. 2008; Fujimoto, Ishihara et al. 2008; Heimberg, Sempere et al. 2008; Mattick 2009; Moroz 2009; Beldade, Mateus et al. 2011; Conceicao, Long et al. 2011; Lowe, Kellis et al. 2011; Moczek, Sultan et al. 2011; Saenko, Marialva et al. 2011; Ten Tusscher and Hogeweg 2011; Wang and Sommer 2011)

Stress response

(Dent, Yacoub et al. 2003; Kuhn, Heiner et al. 2005; Xu, Charles et al. 2005; Palotai, Szalay et al. 2008; Carlson 2009; Lawless, Pearson et al. 2009; Eldh, Ekstrom et al. 2010; Goodarzi, Bennett et al. 2010; Mittelman and Wilson 2010; de Nadal, Ammerer et al. 2011; Falik, Mordoch et al. 2011; Lee, Seo et al. 2011; Locke, Young et al. 2011; Mahbub, Haque et al. 2011; Seo, Chern et al. 2011; Siomi and Siomi 2011; Takekawa, Kubota et al. 2011; Tenev, Bianchi et al. 2011; Leung and Levesque 2012; Leung and Levesque 2012; Tentner, Lee et al. 2012)

Informatic and mathematical analysis

(Kauffman 1969; Kauffman and Levin 1987; Song, Havlin et al. 2005; Kwon and Cho 2007; Fernandes, Annibale et al. 2010; Katz and Privman 2010; Rosenfeld 2011; Ten Tusscher and Hogeweg 2011)

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