Colin C. Collins

According to our database, Colin C. Collins authored at least 22 papers between 2003 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

Phenotype prediction from single-cell RNA-seq data using attention-based neural networks.

Yuzhen Mao, Yen-Yi Lin, Nelson K. Y. Wong, Stanislav Volik, Funda Sar, Colin C. Collins, Martin Ester

Bioinform., February, 2024

2021

Out-of-distribution generalization from labelled and unlabelled gene expression data for drug response prediction.

Hossein Sharifi-Noghabi, Parsa Alamzadeh Harjandi, Olga I. Zolotareva, Colin C. Collins, Martin Ester

Nat. Mach. Intell., 2021

2020

AITL: Adversarial Inductive Transfer Learning with input and output space adaptation for pharmacogenomics.

Hossein Sharifi-Noghabi, Shuman Peng, Olga I. Zolotareva, Colin C. Collins, Martin Ester

Bioinform., 2020

Identification of conserved evolutionary trajectories in tumors.

Ermin Hodzic, Raunak Shrestha, Salem Malikic, Colin C. Collins, Kevin Litchfield, Samra Turajlic, Süleyman Cenk Sahinalp

Bioinform., 2020

CircMiner: accurate and rapid detection of circular RNA through splice-aware pseudo-alignment scheme.

Hossein Asghari, Yen-Yi Lin, Yang Xu, Ehsan Haghshenas, Colin C. Collins, Faraz Hach

Bioinform., 2020

2019

MOLI: multi-omics late integration with deep neural networks for drug response prediction.

Hossein Sharifi-Noghabi, Olga I. Zolotareva, Colin C. Collins, Martin Ester

Bioinform., 2019

Alignment-free clustering of UMI tagged DNA molecules.

Baraa Orabi, Emre Erhan, Brian McConeghy, Stanislav V. Volik, Stephane Le Bihan, Robert Bell, Colin C. Collins, Cédric Chauve, Faraz Hach

Bioinform., 2019

2018

Computational identification of micro-structural variations and their proteogenomic consequences in cancer.

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

Bioinform., 2018

MechRNA: prediction of lncRNA mechanisms from RNA-RNA and RNA-protein interactions.

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

Bioinform., 2018

2017

Clonality Inference from Single Tumor Samples Using Low-Coverage Sequence Data.

Nilgun Donmez, Salem Malikic, Alexander W. Wyatt, Martin E. Gleave, Colin C. Collins, Süleyman Cenk Sahinalp

J. Comput. Biol., 2017

SiNVICT: ultra-sensitive detection of single nucleotide variants and indels in circulating tumour DNA.

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

Bioinform., 2017

2014

ShatterProof: operational detection and quantification of chromothripsis.

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

BMC Bioinform., 2014

ORMAN: Optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms.

Phuong Dao, Ibrahim Numanagic, Yen-Yi Lin, Faraz Hach, Emre Karakoç, Nilgun Donmez, Colin C. Collins, Evan E. Eichler, Süleyman Cenk Sahinalp

Bioinform., 2014

HIT'nDRIVE: Multi-driver Gene Prioritization Based on Hitting Time.

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

Proceedings of the Research in Computational Molecular Biology, 2014

2012

Dissect: detection and characterization of novel structural alterations in transcribed sequences.

Deniz Yörükoglu, Faraz Hach, Lucas Swanson, Colin C. Collins, Inanç Birol, Süleyman Cenk Sahinalp

Bioinform., 2012

CLIIQ: Accurate Comparative Detection and Quantification of Expressed Isoforms in a Population.

Yen-Yi Lin, Phuong Dao, Faraz Hach, Marzieh Bakhshi, Fan Mo, Anna Lapuk, Colin C. Collins, Süleyman Cenk Sahinalp

Proceedings of the Algorithms in Bioinformatics - 12th International Workshop, 2012

Discovery of Complex Genomic Rearrangements in Cancer Using High-Throughput Sequencing.

Andrew W. McPherson, Chunxiao Wu, Alexander Wyatt, Sohrab P. Shah, Colin C. Collins, Süleyman Cenk Sahinalp

Proceedings of the Research in Computational Molecular Biology, 2012

2011

Detection of recurrent rearrangement breakpoints from copy number data.

Anna M. Ritz, Pamela L. Paris, Michael Ittmann, Colin C. Collins, Benjamin J. Raphael

BMC Bioinform., 2011

Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data.

Andrew W. McPherson, Chunxiao Wu, Iman Hajirasouliha, Fereydoun Hormozdiari, Faraz Hach, Anna Lapuk, Stanislav Volik, Sohrab P. Shah, Colin C. Collins, Süleyman Cenk Sahinalp

Bioinform., 2011

Optimally discriminative subnetwork markers predict response to chemotherapy.

Phuong Dao, Kendric Wang, Colin C. Collins, Martin Ester, Anna Lapuk, Süleyman Cenk Sahinalp

Bioinform., 2011

2008

Evaluation of Paired-End Sequencing Strategies for Detection of Genome Rearrangements in Cancer.

Ali Bashir, Stanislav Volik, Colin C. Collins, Vineet Bafna, Benjamin J. Raphael

PLoS Comput. Biol., 2008

2003

Reconstructing tumor genome architectures.

Benjamin J. Raphael, Stanislav Volik, Colin C. Collins, Pavel A. Pevzner

Proceedings of the European Conference on Computational Biology (ECCB 2003), 2003