Colin C. Collins

Publication Activity (10 Years)

Years Active: 2003-2024
Publications (10 Years): 12

Top Topics

Nucleotide Sequences

Profile Hidden Markov Models

Gene Expression

False Positives

Top Venues

J. Comput. Biol.

Publications

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)
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) (2021)
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) (2020)
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) (2020)
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) (2020)
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) (2019)
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) (2019)
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) (2018)
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) (2018)
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) (2017)
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) (2017)
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)
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) (2014)
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)
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 (2014)
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) (2012)
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)
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)
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 (2011)
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) (2011)
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) (2011)
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)
Benjamin J. Raphael, Stanislav Volik, Colin C. Collins, Pavel A. Pevzner
Reconstructing tumor genome architectures. ECCB (2003)