Gerstein Lab Publications
Compilation of Network Papers from the Gerstein Lab Making Analogies between Biological and Non-biological Networks
In general, we are very interested in how analogies between biological networks and non-biological ones may yield useful insights and intuitions. We have published a bit on this in the past.
- Some of these analogies are made explicitly and are part of broad themes, in particular:
- the way variation impacts on the network -- Yan et al. ('10) [
callgraph] and Shou et al. ('11) [
- the way a biological regulatory hierarchy relates to a management one -- Bhardwaj et al. ('10) PNAS [nethier] or Yu et al. ('06) [
- Other explicit analogies are more 'one-off' comparisons
- Yu et al. ('07) [
netcmp] compares the control structures in assembly lines to metabolic pathways.
- Bhardwaj et al. ('10) Plos CB [
coreg-scaling] looks at scaling relationships in biological and social networks.
- Yu et al. ('07) [
funcsim] looks at the applicability of similarity measures on DAG classifications in a variety of contexts.
- Finally, some papers have more indirect associations -- for instance:
- Gerstein et al. ('12) [
encodenets] alludes to the way human regulatory hierarchy relates to a social one (eg 'More influential transcription factors tend to be better connected and higher in the hierarchy').
- Kim et al. ('07) [
netpossel] discusses how the greater variation on the periphery of biological networks is similar to that observed in computer networks (eg 'The parallels are particularly clear with respect to security considerations in computer networks.').
- All the themes are more fully developed in some talks -- for instance:
MB Gerstein, A Kundaje, M Hariharan, SG Landt, KK Yan, C Cheng, XJ Mu, E Khurana, J Rozowsky, R Alexander, R Min, P Alves, A Abyzov, N Addleman, N Bhardwaj, AP Boyle, P Cayting, A Charos, DZ Chen, Y Cheng, D Clarke, C Eastman, G Euskirchen, S Frietze, Y Fu, J Gertz, F Grubert, A Harmanci, P Jain, M Kasowski, P Lacroute, JJ Leng, J Lian, H Monahan, H O'Geen, Z Ouyang, EC Partridge, D Patacsil, F Pauli, D Raha, L Ramirez, TE Reddy, B Reed, M Shi, T Slifer, J Wang, L Wu, X Yang, KY Yip, G Zilberman-Schapira, S Batzoglou, A Sidow, PJ Farnham, RM Myers, SM Weissman, M Snyder (2012). Nature 489: 91-100.
C Shou, N Bhardwaj, HY Lam, KK Yan, PM Kim, M Snyder, MB Gerstein (2011). PLoS Comput Biol 7: e1001050.
N Bhardwaj, MB Carson, A Abyzov, KK Yan, H Lu, MB Gerstein (2010). PLoS Comput Biol 6: e1000755.
KK Yan, G Fang, N Bhardwaj, RP Alexander, M Gerstein (2010). Proc Natl Acad Sci U S A 107: 9186-91.
N Bhardwaj, KK Yan, MB Gerstein (2010). Proc Natl Acad Sci U S A 107: 6841-6.
PM Kim, JO Korbel, MB Gerstein (2007). Proc Natl Acad Sci U S A 104: 20274-9.
H Yu, R Jansen, G Stolovitzky, M Gerstein (2007). Bioinformatics 23: 2163-73.
H Yu, M Gerstein (2006). Proc Natl Acad Sci U S A 103: 14724-31.
H Yu, Y Xia, V Trifonov, M Gerstein (2006). Genome Biol 7: R55.
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