Algorithms | 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

HIT'nDRIVE: Patient-Specific Multi-Driver Gene Prioritization for Precision Oncology

An algorithm to identify cancer driver genes in individual cancer patients by measuring the influence of gene alterations on perturbing transcriptional networks.

Raunak Shrestha, E Hodzic, T Sauerwald, P Dao, K Wang, J Yeung, S Anderson, F Vandin, G Haffari, CC Collins, SC Sahinalp

HIT'nDRIVE: Patient-Specific Multi-Driver Gene Prioritization for Precision Oncology

HIT'nDRIVE: Multi-driver gene prioritization based on hitting time

Raunak Shrestha, E Hodzic, J Yeung, K Wang, T Sauerwald, P Dao, S Anderson, H Beltran, MA Rubin, CC Collins, G Haffari, SC Sahinalp