Colin C. Collins

24 papers B 3C 2Journal 19
YearRankTypeTitle / Venue / Authors
2025 J jnl
scMUSCL: multi-source transfer learning for clustering scRNA-seq data.
Bioinform.
Arash Khoeini, Funda Sar, Yen-Yi Lin, Colin C. Collins, Martin Ester
2024 J jnl
Phenotype prediction from single-cell RNA-seq data using attention-based neural networks.
Bioinform.
Yuzhen Mao, Yen-Yi Lin, Nelson K. Y. Wong, Stanislav Volik, Funda Sar, Colin C. Collins, Martin Ester
2021 J jnl
Out-of-distribution generalization from labelled and unlabelled gene expression data for drug response prediction.
Nat. Mach. Intell.
Hossein Sharifi-Noghabi, Parsa Alamzadeh Harjandi, Olga I. Zolotareva, Colin C. Collins, Martin Ester
2020 J jnl
AITL: Adversarial Inductive Transfer Learning with input and output space adaptation for pharmacogenomics.
Bioinform.
Hossein Sharifi-Noghabi, Shuman Peng, Olga I. Zolotareva, Colin C. Collins, Martin Ester
2020 J jnl
CircMiner: accurate and rapid detection of circular RNA through splice-aware pseudo-alignment scheme.
Bioinform.
Hossein Asghari, Yen-Yi Lin, Yang Xu, Ehsan Haghshenas, Colin C. Collins, Faraz Hach
2020 J jnl
Identification of conserved evolutionary trajectories in tumors.
Bioinform.
Ermin Hodzic, Raunak Shrestha, Salem Malikic, Colin C. Collins, Kevin Litchfield, Samra Turajlic, Süleyman Cenk Sahinalp
2019 J jnl
Alignment-free clustering of UMI tagged DNA molecules.
Bioinform.
Baraa Orabi, Emre Erhan, Brian McConeghy, Stanislav V. Volik, Stephane Le Bihan, Robert Bell, Colin C. Collins, Cédric Chauve, Faraz Hach
2019 J jnl
MOLI: multi-omics late integration with deep neural networks for drug response prediction.
Bioinform.
Hossein Sharifi-Noghabi, Olga I. Zolotareva, Colin C. Collins, Martin Ester
2018 J jnl
Computational identification of micro-structural variations and their proteogenomic consequences in cancer.
Bioinform.
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
2018 J jnl
MechRNA: prediction of lncRNA mechanisms from RNA-RNA and RNA-protein interactions.
Bioinform.
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
2017 J jnl
Clonality Inference from Single Tumor Samples Using Low-Coverage Sequence Data.
J. Comput. Biol.
Nilgun Donmez, Salem Malikic, Alexander W. Wyatt, Martin E. Gleave, Colin C. Collins, Süleyman Cenk Sahinalp
2017 J jnl
SiNVICT: ultra-sensitive detection of single nucleotide variants and indels in circulating tumour DNA.
Bioinform.
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
2016 B conf
Clonality Inference from Single Tumor Samples Using Low Coverage Sequence Data.
RECOMB
Nilgun Donmez, Salem Malikic, Alexander W. Wyatt, Martin E. Gleave, Colin C. Collins, Süleyman Cenk Sahinalp
2014 B conf
HIT'nDRIVE: Multi-driver Gene Prioritization Based on Hitting Time.
RECOMB
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
2014 J jnl
ORMAN: Optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms.
Bioinform.
Phuong Dao, Ibrahim Numanagic, Yen-Yi Lin, Faraz Hach, Emre Karakoç, Nilgun Donmez, Colin C. Collins, Evan E. Eichler, Süleyman Cenk Sahinalp
2014 J jnl
ShatterProof: operational detection and quantification of chromothripsis.
BMC Bioinform.
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
2012 C conf
CLIIQ: Accurate Comparative Detection and Quantification of Expressed Isoforms in a Population.
WABI
Yen-Yi Lin, Phuong Dao, Faraz Hach, Marzieh Bakhshi, Fan Mo, Anna Lapuk, Colin C. Collins, Süleyman Cenk Sahinalp
2012 B conf
Discovery of Complex Genomic Rearrangements in Cancer Using High-Throughput Sequencing.
RECOMB
Andrew W. McPherson, Chunxiao Wu, Alexander Wyatt, Sohrab P. Shah, Colin C. Collins, Süleyman Cenk Sahinalp
2012 J jnl
Dissect: detection and characterization of novel structural alterations in transcribed sequences.
Bioinform.
Deniz Yörükoglu, Faraz Hach, Lucas Swanson, Colin C. Collins, Inanç Birol, Süleyman Cenk Sahinalp
2011 J jnl
Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data.
Bioinform.
Andrew W. McPherson, Chunxiao Wu, Iman Hajirasouliha, Fereydoun Hormozdiari, Faraz Hach, Anna Lapuk, Stanislav Volik, Sohrab P. Shah, Colin C. Collins, Süleyman Cenk Sahinalp
2011 J jnl
Detection of recurrent rearrangement breakpoints from copy number data.
BMC Bioinform.
Anna M. Ritz, Pamela L. Paris, Michael Ittmann, Colin C. Collins, Benjamin J. Raphael
2011 J jnl
Optimally discriminative subnetwork markers predict response to chemotherapy.
Bioinform.
Phuong Dao, Kendric Wang, Colin C. Collins, Martin Ester, Anna Lapuk, Süleyman Cenk Sahinalp
2008 J jnl
Evaluation of Paired-End Sequencing Strategies for Detection of Genome Rearrangements in Cancer.
PLoS Comput. Biol.
Ali Bashir, Stanislav Volik, Colin C. Collins, Vineet Bafna, Benjamin J. Raphael
2003 C conf
Reconstructing tumor genome architectures.
ECCB
Benjamin J. Raphael, Stanislav Volik, Colin C. Collins, Pavel A. Pevzner