Reconstructing tumor genome architectures. - Benjamin J. Raphael; Stanislav Volik; Colin C. Collins; Pavel A. Pevzner (ECCB, 2003)

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)

Optimally discriminative subnetwork markers predict response to chemotherapy. - Phuong Dao; Kendric Wang; Colin C. Collins; Martin Ester; Anna Lapuk; Süleyman Cenk Sahinalp (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)

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)

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 (RECOMB, 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 (WABI, 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)

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 (RECOMB, 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)

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)

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)

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)

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)

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 006; Andrew W. McPherson; Colin C. Collins; Milan Radovich; Haixu Tang; Süleyman Cenk Sahinalp (Bioinform., 2018)

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)

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)

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)

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)

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)

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)

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., 2024)