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ORCIDColin C. Collins
Person information
- affiliation: Vancouver Prostate Centre, BC, Canada
- affiliation: University of British Columbia, Department of Urologic Sciences, Vancouver, BC, Canada
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Journal Articles
- 2024
[j18]Yuzhen Mao, Yen-Yi Lin
, Nelson K. Y. Wong, Stanislav Volik, Funda Sar, Colin C. Collins, Martin Ester:
Phenotype prediction from single-cell RNA-seq data using attention-based neural networks. Bioinform. 40(2) (2024)- 2021
- [j17]Hossein Sharifi-Noghabi, Parsa Alamzadeh Harjandi, Olga I. Zolotareva, Colin C. Collins, Martin Ester:
Out-of-distribution generalization from labelled and unlabelled gene expression data for drug response prediction. Nat. Mach. Intell. 3(11): 962-972 (2021) - 2020
- [j16]Hossein Asghari, Yen-Yi Lin, Yang Xu, Ehsan Haghshenas, Colin C. Collins, Faraz Hach:
CircMiner: accurate and rapid detection of circular RNA through splice-aware pseudo-alignment scheme. Bioinform. 36(12): 3703-3711 (2020) - [j15]Hossein Sharifi-Noghabi, Shuman Peng, Olga I. Zolotareva, Colin C. Collins, Martin Ester:
AITL: Adversarial Inductive Transfer Learning with input and output space adaptation for pharmacogenomics. Bioinform. 36(Supplement-1): i380-i388 (2020) - [j14]Ermin Hodzic, Raunak Shrestha, Salem Malikic, Colin C. Collins, Kevin Litchfield, Samra Turajlic, Süleyman Cenk Sahinalp:
Identification of conserved evolutionary trajectories in tumors. Bioinform. 36(Supplement-1): i427-i435 (2020) - 2019
- [j13]Baraa Orabi, Emre Erhan, Brian McConeghy, Stanislav V. Volik, Stephane Le Bihan, Robert Bell, Colin C. Collins, Cédric Chauve, Faraz Hach:
Alignment-free clustering of UMI tagged DNA molecules. Bioinform. 35(11): 1829-1836 (2019) - [j12]Hossein Sharifi-Noghabi, Olga I. Zolotareva, Colin C. Collins, Martin Ester:
MOLI: multi-omics late integration with deep neural networks for drug response prediction. Bioinform. 35(14): i501-i509 (2019) - 2018
- [j11]Yen-Yi Lin, Alexander Gawronski, Faraz Hach, Sujun Li, Ibrahim Numanagic, Iman Sarrafi, Swati Mishra, Andrew W. McPherson, Colin C. Collins, Milan Radovich, Haixu Tang, Süleyman Cenk Sahinalp:
Computational identification of micro-structural variations and their proteogenomic consequences in cancer. Bioinform. 34(10): 1672-1681 (2018) - [j10]Alexander Gawronski, Michael Uhl, Yajia Zhang, Yen-Yi Lin, Yashar S. Niknafs, Varune R. Ramnarine, Rohit Malik, Felix Feng, Arul M. Chinnaiyan, Colin C. Collins, Süleyman Cenk Sahinalp, Rolf Backofen:
MechRNA: prediction of lncRNA mechanisms from RNA-RNA and RNA-protein interactions. Bioinform. 34(18): 3101-3110 (2018) - 2017
- [j9]Can Kockan, Faraz Hach, Iman Sarrafi, Robert H. Bell, Brian McConeghy, Kevin Beja, Anne Haegert, Alexander W. Wyatt, Stanislav Volik, Kim N. Chi, Colin C. Collins, Süleyman Cenk Sahinalp:
SiNVICT: ultra-sensitive detection of single nucleotide variants and indels in circulating tumour DNA. Bioinform. 33(1): 26-34 (2017) - [j8]Nilgun Donmez, Salem Malikic, Alexander W. Wyatt, Martin E. Gleave, Colin C. Collins, Süleyman Cenk Sahinalp:
Clonality Inference from Single Tumor Samples Using Low-Coverage Sequence Data. J. Comput. Biol. 24(6): 515-523 (2017) - 2014
- [j7]Phuong Dao, Ibrahim Numanagic, Yen-Yi Lin, Faraz Hach, Emre Karakoç, Nilgun Donmez, Colin C. Collins, Evan E. Eichler, Süleyman Cenk Sahinalp:
ORMAN: Optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms. Bioinform. 30(5): 644-651 (2014) - [j6]Shaylan K. Govind, Amin Zia, Pablo H. Hennings-Yeomans, John D. Watson, Michael Fraser, Catalina V. Anghel, Alexander Wyatt, Theodorus van der Kwast, Colin C. Collins, John D. McPherson, Robert G. Bristow, Paul C. Boutros:
ShatterProof: operational detection and quantification of chromothripsis. BMC Bioinform. 15: 78 (2014) - 2012
- [j5]Deniz Yörükoglu, Faraz Hach, Lucas Swanson, Colin C. Collins, Inanç Birol, Süleyman Cenk Sahinalp:
Dissect: detection and characterization of novel structural alterations in transcribed sequences. Bioinform. 28(12): 179-187 (2012) - 2011
- [j4]Andrew W. McPherson, Chunxiao Wu, Iman Hajirasouliha, Fereydoun Hormozdiari, Faraz Hach, Anna Lapuk, Stanislav Volik, Sohrab P. Shah, Colin C. Collins, Süleyman Cenk Sahinalp:
Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data. Bioinform. 27(11): 1481-1488 (2011) - [j3]Phuong Dao, Kendric Wang, Colin C. Collins, Martin Ester, Anna Lapuk, Süleyman Cenk Sahinalp:
Optimally discriminative subnetwork markers predict response to chemotherapy. Bioinform. 27(13): 205-213 (2011) - [j2]Anna M. Ritz, Pamela L. Paris, Michael Ittmann, Colin C. Collins, Benjamin J. Raphael:
Detection of recurrent rearrangement breakpoints from copy number data. BMC Bioinform. 12: 114 (2011) - 2008
- [j1]Ali Bashir, Stanislav Volik, Colin C. Collins, Vineet Bafna, Benjamin J. Raphael:
Evaluation of Paired-End Sequencing Strategies for Detection of Genome Rearrangements in Cancer. PLoS Comput. Biol. 4(4) (2008)
Conference and Workshop Papers
- 2016
- [c5]Nilgun Donmez, Salem Malikic, Alexander W. Wyatt, Martin E. Gleave, Colin C. Collins, Süleyman Cenk Sahinalp:
Clonality Inference from Single Tumor Samples Using Low Coverage Sequence Data. RECOMB 2016: 83-94 - 2014
- [c4]Raunak Shrestha, Ermin Hodzic, Jake Yeung, Kendric Wang, Thomas Sauerwald, Phuong Dao, Shawn Anderson, Himisha Beltran, Mark A. Rubin, Colin C. Collins, Gholamreza Haffari, Süleyman Cenk Sahinalp:
HIT'nDRIVE: Multi-driver Gene Prioritization Based on Hitting Time. RECOMB 2014: 293-306 - 2012
- [c3]Andrew W. McPherson, Chunxiao Wu, Alexander Wyatt, Sohrab P. Shah, Colin C. Collins, Süleyman Cenk Sahinalp:
Discovery of Complex Genomic Rearrangements in Cancer Using High-Throughput Sequencing. RECOMB 2012: 181-182 - [c2]Yen-Yi Lin, Phuong Dao, Faraz Hach, Marzieh Bakhshi, Fan Mo, Anna Lapuk, Colin C. Collins, Süleyman Cenk Sahinalp:
CLIIQ: Accurate Comparative Detection and Quantification of Expressed Isoforms in a Population. WABI 2012: 178-189 - 2003
- [c1]Benjamin J. Raphael, Stanislav Volik, Colin C. Collins, Pavel A. Pevzner:
Reconstructing tumor genome architectures. ECCB 2003: 162-171
Coauthor Index
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