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Gerstein Lab: Networks

Portal for networks research in the Gerstein Lab. The structure and behavior of many biological (and other) systems can be effectively represented as networks. We have several projects related to this topic. Below, we provide links to the various software developed in our group for declaring, visualizing, and analyzing networks. We also provide access to our databases containing network representations of several systems. Finally, links to our network-related publications are provided. A lightweight sema...

http://networks.gersteinlab.org/

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Gerstein Lab: Networks | networks.gersteinlab.org Reviews
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Portal for networks research in the Gerstein Lab. The structure and behavior of many biological (and other) systems can be effectively represented as networks. We have several projects related to this topic. Below, we provide links to the various software developed in our group for declaring, visualizing, and analyzing networks. We also provide access to our databases containing network representations of several systems. Finally, links to our network-related publications are provided. A lightweight sema...
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1 networks
2 software and servers
3 papers
4 formerly topnet
5 and cbhd newsletter
6 defective cliques
7 yeasthub
8 databases and datasets
9 metagenomics dynamics
10 net hierarchy
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networks,software and servers,papers,formerly topnet,and cbhd newsletter,defective cliques,yeasthub,databases and datasets,metagenomics dynamics,net hierarchy,and s cerevisiae,intint,sandy,interolog,d melanogaster,and h pylori,phosphorylome,echipchip
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Gerstein Lab: Networks | networks.gersteinlab.org Reviews

https://networks.gersteinlab.org

Portal for networks research in the Gerstein Lab. The structure and behavior of many biological (and other) systems can be effectively represented as networks. We have several projects related to this topic. Below, we provide links to the various software developed in our group for declaring, visualizing, and analyzing networks. We also provide access to our databases containing network representations of several systems. Finally, links to our network-related publications are provided. A lightweight sema...

INTERNAL PAGES

networks.gersteinlab.org networks.gersteinlab.org
1

Statistical Analysis of Network Dynamics

http://networks.gersteinlab.org/regulation/dynamics/index.html

Genomic analysis of regulatory network dynamics reveals large topological changes. Nicholas M Luscombe, Madan M Babu, Haiyuan Yu, Michael Snyder, Sarah A Teichmann and Mark Gerstein.

2

::::YALE GERSTEIN LAB::::

http://networks.gersteinlab.org/intint/index.html

A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data. Ronald Jansen, Haiyuan Yu, Dov Greenbaum, Yuval Kluger, Nevan J. Krogan, Sambath Chung, Andrew Emili, Michael Snyder, Jack F. Greenblatt, Mark Gerstein. Science, 2003, Oct 17; 302(5644): 449-53. Assessing the Limits of Genomic Data Integration for Predicting Protein-Protein Interactions. Jason Lu, Yu Xia, Alberto Paccanaro, Haiyuan Yu, Mark Gerstein. Genome Research, In press. Last modified March 2004.

3

Graph properties calculation

http://networks.gersteinlab.org/genome/interactions/networks/core.html

Start to use TopNet. Upload your own dataset here. Both category datasets and interaction dataset can be accepted. Calculate the topology parameters: diameter, average links and clustering coefficient. The data to be calculated can be freely selected from given datasets or datasets uploaded by the user. Navigate within the interaction networks. Report all the neighbors of one node. Links from different interaction datasets are seperated by different colors. To enter the download page.

4

3-D Structural Analysis of the Interaction Network

http://networks.gersteinlab.org/structint

5

Phosphorylome Database

http://networks.gersteinlab.org/phosphorylome

More on protein chip.

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Gerstein Lab Abstracts: March 2013

http://abstracts.gersteinlab.org/2013_03_01_archive.html

Monday, March 25, 2013. Abstract for talk i0cmg - Comp Meth Prioritizing Var Exome Seq Pgenes trueLoF nethubs- 20130319-i0cmg. Filtering out Artifacts Due to Pseudogenes. Certain genes have lots of similar pseudogenes. Which could confound variant calling. Finding True LoF Mutations. Not just stop codon finding: tricky if one takes into. Account splicing, NMD, indels, &c. Using High Network Connectivity. More connected genes in many networks have a. Greater chance of being disease causing. Patterns of va...

abstracts.gersteinlab.org abstracts.gersteinlab.org

Gerstein Lab Abstracts: May 2013

http://abstracts.gersteinlab.org/2013_05_01_archive.html

Thursday, May 16, 2013. Abstract for Talk at Harvard CCSB (i0farb). My talk will be concerned with 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-dimensional browser tracks. Here I will discuss. Approaches for annotating pseudogenes and also. For developing predictive models for gene expression. Analysis of networks (TopNet and tYNA). Understanding tran...

abstracts.gersteinlab.org abstracts.gersteinlab.org

Gerstein Lab Abstracts: December 2013

http://abstracts.gersteinlab.org/2013_12_01_archive.html

Thursday, December 5, 2013. Abstract for Talk at University of Connecticut Health Center (i0ccam). Plummeting sequencing costs have led to a great increase in the number. Of personal genomes. Interpreting the large number of variants in. Them, particularly in non-coding regions, is a central challenge for. Genomics. We investigate patterns of selection in DNA elements from. The ENCODE project using the full spectrum of sequence variants from. Very strong selection constraint, comparable to coding genes:.

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Links

http://www.linkgroup.hu/links.php

Groups working on networks and complex systems. Luigi F. Agnati:. Http:/ www.cibiotech.it/asp/dtglresponsabile.asp? Http:/ www.phys.psu.edu/ ralbert/. László A. Barabási:. Adam P. Arkin:. Http:/ gobi.lbl.gov/ aparkin/People/TheBoss.html. György Buzsáki:. Http:/ osiris.rutgers.edu/frontmid/indexmid.html. Http:/ www.cnn.group.cam.ac.uk/. Http:/ cyvision.ifsc.usp.br/Cyvision/. Gerald M. Edelman:. Http:/ www.nsi.edu/public/scientists/index.php. Http:/ www.santafe.edu/sfi/People/mgm/. Stuart A. Kaufmann:.

abstracts.gersteinlab.org abstracts.gersteinlab.org

Gerstein Lab Abstracts: November 2013

http://abstracts.gersteinlab.org/2013_11_01_archive.html

Saturday, November 30, 2013. Abstract for Talk at Keystone Big Data Symposium (i0keybdata). My talk will discuss Human Genome Analysis from a data science perspective. Plummeting sequencing costs have led to a great increase in the number. Of personal genomes. Interpreting the large number of variants in. Them, particularly in non-coding regions, is a central challenge for. One data science construct that is particularly useful for genome. Interpretation is networks. My talk will be concerned with the.

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networks.gersteinlab.org networks.gersteinlab.org

Gerstein Lab: Networks

Portal for networks research in the Gerstein Lab. The structure and behavior of many biological (and other) systems can be effectively represented as networks. We have several projects related to this topic. Below, we provide links to the various software developed in our group for declaring, visualizing, and analyzing networks. We also provide access to our databases containing network representations of several systems. Finally, links to our network-related publications are provided. A lightweight sema...

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