## Sunday, April 29, 2012

### abstract for talk at Harvard Systems Biology [i0hsb]

Molecular Networks: The Next-generation Annotation for Personal Genomes

Mark Gerstein

Yale University

My talk will be concerned the analysis of networks and the use of

networks as a "next-generation annotation" for interpreting personal

genomes. I will initially describe current approaches to genome

annotation in terms of one-dimension browser tracks. Then I will

describe various aspects of networks. In particular, I will touch on

the following topics: (1) I will show how analyzing the structure of

the regulatory network indicates that it has a hierarchical layout

with the "middle-managers" acting as information-flow bottlenecks and

with more "influential" TFs on top. (2) I will show that most human

variation occurs at the periphery of the network. (3) I will compare

the topology and variation of the regulatory network to the call graph

of a computer operating system, showing that they have different

patterns of variation. (4) I will talk about web-based tools for the

analysis of networks (TopNet and tYNA).

http://networks.gersteinlab.org

http://tyna.gersteinlab.org

Comparing genomes to computer operating systems in terms of the

topology and evolution of their regulatory control networks.

KK Yan, G Fang, N Bhardwaj, RP Alexander, M Gerstein (2010). Proc Natl

Acad Sci U S A 107:9186-91.

Analysis of diverse regulatory networks in a hierarchical context

shows consistent tendencies for collaboration in the middle levels.

N Bhardwaj, KK Yan, MB Gerstein (2010). Proc Natl Acad Sci U S A 107:6841-6.

Positive selection at the protein network periphery: evaluation in

terms of structural constraints and cellular context.

PM Kim, JO Korbel, MB Gerstein (2007). Proc Natl Acad Sci U S A 104:20274-9.

The tYNA platform for comparative interactomics: a web tool for

managing, comparing and mining multiple networks.

KY Yip, H Yu, PM Kim, M Schultz, M Gerstein (2006). Bioinformatics 22:2968-70.

## Saturday, April 21, 2012

### abstract for talk at UCLA [i0ucla]

Analysis of Molecular Networks

Mark Gerstein

Yale University

My talk will be concerned the analysis of networks and the use of

networks as a "next-generation annotation" for interpreting personal

genomes. I will initially describe current approaches to genome

annotation in terms of one-dimension browser tracks. Then I will

describe various aspects of networks. In particular, I will touch on

the following topics: (1) I will show how analyzing the structure of

the regulatory network indicates that it has a hierarchical layout

with the "middle-managers" acting as information-flow bottlenecks and

with more "influential" TFs on top. (2) I will show that most human

variation occurs at the periphery of the network. (3) I will compare

the topology and variation of the regulatory network to the call graph

of a computer operating system, showing that they have different

patterns of variation. (4) I will talk about web-based tools for the

analysis of networks (TopNet and tYNA).

http://networks.gersteinlab.org

http://tyna.gersteinlab.org

Comparing genomes to computer operating systems in terms of the

topology and evolution of their regulatory control networks.

KK Yan, G Fang, N Bhardwaj, RP Alexander, M Gerstein (2010). Proc Natl

Acad Sci U S A 107:9186-91.

Analysis of diverse regulatory networks in a hierarchical context

shows consistent tendencies for collaboration in the middle levels.

N Bhardwaj, KK Yan, MB Gerstein (2010). Proc Natl Acad Sci U S A 107:6841-6.

Positive selection at the protein network periphery: evaluation in

terms of structural constraints and cellular context.

PM Kim, JO Korbel, MB Gerstein (2007). Proc Natl Acad Sci U S A 104:20274-9.

The tYNA platform for comparative interactomics: a web tool for

managing, comparing and mining multiple networks.

KY Yip, H Yu, PM Kim, M Schultz, M Gerstein (2006). Bioinformatics 22:2968-70.

## Saturday, April 14, 2012

### abstract for talk at CMU [i0cmu12]

Analysis of Molecular Networks

Mark Gerstein

Yale University

My talk will be concerned the analysis of networks and the use of

networks as a "next-generation annotation" for interpreting personal

genomes. I will initially describe current approaches to genome

annotation in terms of one-dimension browser tracks. Then I will

describe various aspects of networks. In particular, I will touch on

the following topics: (1) I will show how analyzing the structure of

the regulatory network indicates that it has a hierarchical layout

with the "middle-managers" acting as information-flow bottlenecks and

with more "influential" TFs on top. (2) I will show that most human

variation occurs at the periphery of the network. (3) I will compare

the topology and variation of the regulatory network to the call graph

of a computer operating system, showing that they have different

patterns of variation. (4) I will talk about web-based tools for the

analysis of networks (TopNet and tYNA).

http://networks.gersteinlab.org

http://tyna.gersteinlab.org

Comparing genomes to computer operating systems in terms of the

topology and evolution of their regulatory control networks.

KK Yan, G Fang, N Bhardwaj, RP Alexander, M Gerstein (2010). Proc Natl

Acad Sci U S A 107:9186-91.

Analysis of diverse regulatory networks in a hierarchical context

shows consistent tendencies for collaboration in the middle levels.

N Bhardwaj, KK Yan, MB Gerstein (2010). Proc Natl Acad Sci U S A 107:6841-6.

Positive selection at the protein network periphery: evaluation in

terms of structural constraints and cellular context.

PM Kim, JO Korbel, MB Gerstein (2007). Proc Natl Acad Sci U S A 104:20274-9.

The tYNA platform for comparative interactomics: a web tool for

managing, comparing and mining multiple networks.

KY Yip, H Yu, PM Kim, M Schultz, M Gerstein (2006). Bioinformatics 22:2968-70.

## Thursday, April 12, 2012

### abstract for talk at UMD Center for Bioinformatics and Computational Biology [i0cbcb]

Analysis of Molecular Networks

Mark Gerstein

Yale University

My talk will be concerned the analysis of networks and the use of

networks as a "next-generation annotation" for interpreting personal

genomes. I will initially describe current approaches to genome

annotation in terms of one-dimension browser tracks. Then I will

describe various aspects of networks. In particular, I will touch on

the following topics: (1) I will show how analyzing the structure of

the regulatory network indicates that it has a hierarchical layout

with the "middle-managers" acting as information-flow bottlenecks and

with more "influential" TFs on top. (2) I will show that most human

variation occurs at the periphery of the network. (3) I will compare

the topology and variation of the regulatory network to the call graph

of a computer operating system, showing that they have different

patterns of variation. (4) I will talk about web-based tools for the

analysis of networks (TopNet and tYNA).

http://networks.gersteinlab.org

http://tyna.gersteinlab.org

Comparing genomes to computer operating systems in terms of the

topology and evolution of their regulatory control networks.

KK Yan, G Fang, N Bhardwaj, RP Alexander, M Gerstein (2010). Proc Natl

Acad Sci U S A 107:9186-91.

Analysis of diverse regulatory networks in a hierarchical context

shows consistent tendencies for collaboration in the middle levels.

N Bhardwaj, KK Yan, MB Gerstein (2010). Proc Natl Acad Sci U S A 107:6841-6.

Positive selection at the protein network periphery: evaluation in

terms of structural constraints and cellular context.

PM Kim, JO Korbel, MB Gerstein (2007). Proc Natl Acad Sci U S A 104:20274-9.

The tYNA platform for comparative interactomics: a web tool for

managing, comparing and mining multiple networks.

KY Yip, H Yu, PM Kim, M Schultz, M Gerstein (2006). Bioinformatics 22:2968-70.