The genome as a read-write (RW) storage system

(Shapiro 1982; McClintock 1984; Shapiro 1991; Shapiro 1992; Shapiro 1993; Shapiro 1994; Shapiro 1997; Bellgard, Itoh et al. 1999; Jorgensen 2004; Shapiro 2005; Shapiro 2005; Shapiro 2007; Koonin and Wolf 2008; Koonin 2009; Koonin 2009; Pigliucci 2009; Shapiro 2009; D'Onofrio and An 2010)

Mobile genetic elements and genome change

(McClintock 1950; McClintock 1953; Bukhari 1977; Cohen and Shapiro 1980; Shapiro 1983; Purugganan and Wessler 1995; DeBerardinis, Goodier et al. 1998; Shapiro 1999; Evgen'ev, Zelentsova et al. 2000; Comfort 2001; Bowen and Jordan 2002; Craig 2002; Feschotte, Jiang et al. 2002; Kidwell 2002; Deininger, Moran et al. 2003; Kazazian 2004; Miller and Capy 2004; Biemont and Vieira 2005; Feschotte and Pritham 2007; Jurka, Kapitonov et al. 2007; Pritham and Feschotte 2007; Bohne, Brunet et al. 2008; Ray, Feschotte et al. 2008; Bourque 2009; Churakov, Kriegs et al. 2009; Oliver and Greene 2009; Pritham 2009; Shapiro 2010; Jurka, Bao et al. 2011; Oliver and Greene 2011)

Reverse transcription of RNA sequences into the genome

(DeBerardinis, Goodier et al. 1998; Brosius 1999; Hiller, Hetzer et al. 2000; Betrán, Thornton et al. 2002; Brosius 2003; von Sternberg and Shapiro 2005; Kriegs, Churakov et al. 2006; Xing, Wang et al. 2006; Moller-Krull, Delsuc et al. 2007; Volff and Brosius 2007; Baertsch, Diekhans et al. 2008; Bai, Casola et al. 2008; Conley, Piriyapongsa et al. 2008; Moller-Krull, Zemann et al. 2008; Churakov, Kriegs et al. 2009; Hancks, Ewing et al. 2009; Chen, Zou et al. 2011)

Formation of novel coding sequences and genetic loci

(Wessler 1988; Wessler, Baran et al. 1988; Purugganan and Wessler 1992; Varagona, Purugganan et al. 1992; Moran, DeBerardinis et al. 1999; Hiller, Hetzer et al. 2000; Long 2001; Betrán, Thornton et al. 2002; Long, Deutsch et al. 2003; Jiang, Bao et al. 2004; Brandt, Schrauth et al. 2005; Brandt, Veith et al. 2005; Krull, Brosius et al. 2005; Britten 2006; Xing, Wang et al. 2006; Arguello, Fan et al. 2007; Babushok, Ostertag et al. 2007; Bowen and Jordan 2007; Casola, Lawing et al. 2007; Krull, Petrusma et al. 2007; Piriyapongsa, Rutledge et al. 2007; Moller-Krull, Zemann et al. 2008; Hancks, Ewing et al. 2009; Chen, Zhang et al. 2010; Fu, Chen et al. 2010)

Regulatory signals and networks written in the genome

(McClintock 1956; Britten 1996; Britten 1996; McDonald, Matyunina et al. 1997; Comfort 1999; Shapiro 1999; Comfort 2001; Shapiro 2002; Jordan, Rogozin et al. 2003; Marino-Ramirez, Lewis et al. 2005; Shapiro and Sternberg 2005; von Sternberg and Shapiro 2005; Marino-Ramirez and Jordan 2006; Istrail, De-Leon et al. 2007; Piriyapongsa, Marino-Ramirez et al. 2007; Bai, Casola et al. 2008; Bourque, Leong et al. 2008; Conley, Piriyapongsa et al. 2008; Feschotte 2008; Jurka 2008; Polavarapu, Marino-Ramirez et al. 2008; Bourque 2009; Huda and Jordan 2009; Huda, Marino-Ramirez et al. 2010; Kunarso, Chia et al. 2010; Huda, Bowen et al. 2011)




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