Publications

PubMed | Google Scholar | Computer Science Bibliography (dblp)

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 (2020). Pathway and network analysis of more than 2,500 whole cancer genomes. Nature Communications.

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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 (2019). BAP1 Haploinsufficiency Predicts a Distinct Immunogenic Class of Malignant Peritoneal Mesothelioma. Genome Medicine.

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E Hodzic, Raunak Shrestha, K Zhu, K Cheng, CC Collins, SC Sahinalp (2019). Combinatorial Detection of Conserved Alteration Patterns for Identifying Cancer Subnetworks. GigaScience.

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EE Gill, LS Chan, GL Winsor, N Dobson, R Lo, SJH Sui, BK Dhillon, PK Taylor, Raunak Shrestha, CoSpencer, REW Hancock, PJ Unrau, FSL Brinkman (2018). High-throughput detection of RNA processing in bacteria. BMC Genomics.

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H Sharifi-Noghabi, Y Liu, N Erho, Raunak Shrestha, M Alshalalfa, E Davicioni, CC Collins, M Ester (2018). Deep Genomic Signature for early metastasis prediction in Prostate Cancer. (in submission).

DOI Preprint

M Yamada, J Tang, J Lugo-Martinez, E Hodzic, Raunak Shrestha, A Saha, H Ouyang, D Yin, H Mamitsuka, SC Sahinalp, P Radivojac, F Menczer, Y Chang (2018). Ultra High-Dimensional Nonlinear Feature Selection for Big Biological Data. IEEE Transactions on Knowledge and Data Engineering.

DOI Journal

Raunak Shrestha, E Hodzic, T Sauerwald, P Dao, K Wang, J Yeung, S Anderson, F Vandin, G Haffari, CC Collins, SC Sahinalp (2017). HIT'nDRIVE: Patient-Specific Multi-Driver Gene Prioritization for Precision Oncology. Genome Research.

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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 (2016). BIRC6-targeting as potential therapy for advanced, enzalutamide-resistant prostate cancer. Clinical Cancer Research.

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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 (2014). Heterogeneity in the inter-tumor transcriptome of high risk prostate cancer. Genome Biology.

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K Wang, Raunak Shrestha, AW Wyatt, A Reddy, J Lehar, Y Wang, A Lapuk, CC Collins (2014). A Meta-Analysis Approach for Characterizing Pan-Cancer Mechanisms of Drug Sensitivity in Cell Lines. PLoS ONE.

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