Advanced Computational Genomics Tools: Network Analysis and Gene Regulation


We are pleased to announce a hands-on workshop on advanced computational genomics analysis. The workshop will cover tools developed in Prof. Ron Shamir's group for analyzing (1) gene and microRNA expression, (2) cis-regulatory sequences, (3) protein networks, and other high-throughput functional genomics data.

SPIKE is a database of human signaling pathways constructed by domain experts. It provides flexible, user-guided pathway visualization, enables superposition of functional omic data, and reveals novel functional interplays between network components. SPIKE’s capabilities within the EXPANDER workflow will be demonstrated.

AMADEUS is a platform for genome-scale detection of known and novel cis-regulatory motifs, such as transcription factors and microRNA binding sites. It stands out among motif-discovery tools in accuracy, running time, range of applications, and ease of use.

Module-Map and Cytoscape: Cytoscape is an excellent platform developed by several research labs for visualizing molecular networks and integrating them with a plethora of functional data and ad-hoc algorithms. We shall provide a basic tutorial on Cytoscape and use it to demonstrate module-map, our new tool for analyzing two networks simultaneously.

Organizers: Prof. Ron Shamir and Yaron Orenstein, School of Computer Science, Tel Aviv University.

Instructors: Yaron Orenstien, David Amar and Dorit Sagir, School of Computer Science, Tel Aviv University.

Workshop date and time: Tuesday, 8/4/2014 10:15-14:00

Number of Participants: up to 30 people.

Location: PC Classroom/SGI classroom, 09 Sherman Building, Tel Aviv University.

Campus map

Please note that although the workshops are free of charge, the subscription is obligatory and the registration period ends three working days before the workshop. To register, please fill the registration form.


10:15-10:25 Introduction, experimental design

10:25-11:15 Amadeus

11:15-11:25 break

11:25-13:15 Cytoscape

13:15-13:25 break

13:25-14:00 Spike

Tutorials will be combined with the presentations

Cytoscape materials:

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