Cancer | Raunak Shrestha

Y-box Binding Protein-1 is Crucial in Acquired Drug Resistance Development in Metastatic Clear-Cell Renal Cell Carcinoma

NM D'Costa, MR Lowerison, PA Raven, Z Tan, ME Roberts, Raunak Shrestha, MW Urban, CU Monjaras-Avila, HZ Oo, A Hurtado-Coll, C Chavez-Munoz, AI So

Identification of Predictive Gene Signature to Guide Precision Oncology of Clear-Cell Renal Cell Carcinoma

NM D'Costa, D Cina, Raunak Shrestha, RH Bell, YLin, H Asghari, CU Monjaras-Avila, C Kollmannsberger, F Hach, CI Chavez-Munoz, AI So

Pan-cancer Analysis of Whole Genomes

The PCAWG Project, conducted by the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes, employed comprehensive whole genome sequencing and integrated analysis techniques on more than 2,600 primary cancers and their corresponding normal tissues from 38 different tumor types.

PCAWG Consortium

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

BAP1 Haploinsufficiency Predicts a Distinct Immunogenic Class of Malignant Peritoneal Mesothelioma

Malignant peritoneal mesothelioma (PeM) is a rare and fatal cancer originating from the abdominal lining. Our study revealed that BAP1 could serve as a prognostic and predictive biomarker for immunotherapy in PeM.

Raunak Shrestha, N Nabavi, Y Lin, F Mo, S Anderson, S Volik, H H Adomat, D Lin, H Xue, X Dong, R Shukin, RH Bell, B McConeghy, A Haegert, S Brahmbhatt, E Li, HZ Oo, A Hurtado-Coll, L Fazli, J Zhou, Y McConnell, A McCart, A Lowy, GB Morin, T Chen, M Daugaard, SC Sahinalp, F Hach, S Le Bihan, ME Gleave, Y Wang, A Churg, CC Collins

BAP1 Haploinsufficiency Predicts a Distinct Immunogenic Class of Malignant Peritoneal Mesothelioma

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

BIRC6-targeting as potential therapy for advanced, enzalutamide-resistant prostate cancer

ISU Luk, Raunak Shrestha, H Xue, F Zhang, D Lin, A Haegert, R Wu, X Dong, CC Collins, A Zoubeidi, ME Gleave, PW Gout, Y Wang

Heterogeneity in the inter-tumor transcriptome of high risk prostate cancer

AW Wyatt, F Mo, K Wang, B McConeghy, S Brahmbhatt, L Jong, DM Mitchell, RL Johnston, A Haegert, E Li, J Liew, J Yeung, Raunak Shrestha, A Lapuk, A McPherson, R Shukin, RH Bell, S Anderson, J Bishop, A Hurtado-Coll, H Xiao, AM Chinnaiyan, R Mehra, D Lin, Y Wang, L Fazli, ME Gleave, S Volik, CC Collins

A Meta-Analysis Approach for Characterizing Pan-Cancer Mechanisms of Drug Sensitivity in Cell Lines

K Wang, Raunak Shrestha, AW Wyatt, A Reddy, J Lehar, Y Wang, A Lapuk, CC Collins