networks | Raunak Shrestha

Identification of Conserved Evolutionary Trajectories in Tumors

Delighted to share our paper describing an algorithm CONETT to identify Conserved Evolutionary Trajectory Tree from multiple tumors. This paper will be presented at the #ISMB2020 conference next week. @cenksahinalp https://t.

E Hodzic, Raunak Shrestha, S Malikic, CC Collins, K Litchfield, S Turajlic, SC Sahinalp

Pathway and network analysis of more than 2,500 whole cancer genomes

MA Reyna, D Haan, M Paczkowska, LPC Verbeke, M Vazquez, A Kahraman, S Pulido-Tamayo, J Barenboim, L Wadi, P Dhingra, Raunak Shrestha, G Getz, MS Lawrence, JS Pedersen, MA Rubin, DA Wheeler, S Brunak, JMG Izarzugaza, E Khurana, K Marchal, C von Mering, SC Sahinalp, A Valencia, J Reimand, JM Stuart, BJ Raphael, PCAWG Consortium

Combinatorial Detection of Conserved Alteration Patterns for Identifying Cancer Subnetworks

We introduce a novel combinatorial method, cd-CAP, for simultaneous detection of connected subnetworks of an interaction network where genes exhibit conserved alteration patterns across tumor samples.

E Hodzic, Raunak Shrestha, K Zhu, K Cheng, CC Collins, SC Sahinalp

Combinatorial Detection of Conserved Alteration Patterns for Identifying Cancer Subnetworks

Visualize and cluster one-mode projection of a bi-partite graph

Often bioinformaticians are interested to visualize if there is any kind of relation between the Modules. This problem can be modeled as the conversion of two-mode network (bipartite graph) to one-mode network of Modules and visualize the resulting one-mode network. Here, I attempt to demonstrate how this can be achieved using R.

Raunak Shrestha

Apr 20, 2016 4 min read networks, data viz