GeneComber: Combining Outputs of Gene Prediction Programs for Improved Results. - Sohrab P. Shah; Graham P. McVicker; Alan K. Mackworth; Sanja Rogic; B. F. Francis Ouellette (Bioinform., 2003)

Pegasys: software for executing and integrating analyses of biological sequences. - Sohrab P. Shah; David Y. M. He; Jessica N. Sawkins; Jeffrey C. Druce; Gerald T. Quon; Drew Lett; Grace X. Y. Zheng; Tao Xu; B. F. Francis Ouellette (BMC Bioinform., 2004)

Atlas - a data warehouse for integrative bioinformatics. - Sohrab P. Shah; Yong Huang; Tao Xu; Macaire Man Saint Yuen; John Ling; B. F. Francis Ouellette (BMC Bioinform., 2005)

A Novel Algorithm For the Analysis Of Array Cgh Data. - Mehrnoush Khojasteh; Bradley P. Coe; Sohrab P. Shah; Rabab K. Ward; Wan L. Lam; Calum MacAulay (ICASSP (2), 2006)

Integrating copy number polymorphisms into array CGH analysis using a robust HMM. - Sohrab P. Shah; Xiang Xuan; Ronald J. deLeeuw; Mehrnoush Khojasteh; Wan L. Lam; Raymond T. Ng; Kevin P. Murphy (ISMB (Supplement of Bioinformatics), 2006)

Modeling recurrent DNA copy number alterations in array CGH data. - Sohrab P. Shah; Wan L. Lam; Raymond T. Ng; Kevin P. Murphy (ISMB/ECCB (Supplement of Bioinformatics), 2007)

Model-based clustering of array CGH data. - Sohrab P. Shah; K-John Cheung Jr.; Nathalie A. Johnson; Guillaume Alain; Randy D. Gascoyne; Douglas E. Horsman; Raymond T. Ng; Kevin P. Murphy (Bioinform., 2009)

Robust hidden semi-Markov modeling of array CGH data. - Jiarui Ding; Sohrab P. Shah (BIBM, 2010)

SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors. - Rodrigo Goya; Mark G. F. Sun; Ryan D. Morin; Gillian Leung; Gavin Ha; Kimberley C. Wiegand; Janine Senz; Anamaria Crisan; Marco A. Marra; Martin Hirst; David G. Huntsman; Kevin P. Murphy; et al. (Bioinform., 2010)

Genomic analysis of a rare human tumor. - Steven J. M. Jones; Janessa Laskin; Yvonne Y. Li; Obi L. Griffith; Jianghong An; Mikhail Bilenky; Yaron S. N. Butterfield; Timothee Cezard; Eric Chuah; Richard Corbett; Anthony P. Fejes; Malachi Griffith; et al. (BMC Bioinform., 2010)

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)

deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data. - Andrew W. McPherson; Fereydoun Hormozdiari; Abdalnasser Zayed; Ryan Giuliany; Gavin Ha; Mark G. F. Sun; Malachi Griffith; Alireza Heravi Moussavi; Janine Senz; Nataliya Melnyk; Marina Pacheco; Marco A. Marra; et al. (PLoS Comput. Biol., 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)

Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data. - Jiarui Ding; Ali Bashashati; Andrew Roth; Arusha Oloumi; Kane Tse; Thomas Zeng 002; Gholamreza Haffari; Martin Hirst; Marco A. Marra; Anne Condon; Sam Aparicio; Sohrab P. Shah (Bioinform., 2012)

JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data. - Andrew Roth; Jiarui Ding; Ryan D. Morin; Anamaria Crisan; Gavin Ha; Ryan Giuliany; Ali Bashashati; Martin Hirst; Gulisa Turashvili; Arusha Oloumi; Marco A. Marra; Sam Aparicio; et al. (Bioinform., 2012)

A robust hidden semi-Markov model with application to aCGH data processing. - Jiarui Ding; Sohrab P. Shah (Int. J. Data Min. Bioinform., 2013)

Joint Inference of Genome Structure and Content in Heterogeneous Tumour Samples. - Andrew W. McPherson; Andrew Roth; Gavin Ha; Sohrab P. Shah; Cédric Chauve; Süleyman Cenk Sahinalp (CoRR, 2015)

densityCut: an efficient and versatile topological approach for automatic clustering of biological data. - Jiarui Ding; Sohrab P. Shah; Anne Condon (Bioinform., 2016)

12 Grand Challenges in Single-Cell Data Science. - David Laehnemann; Johannes Köster; Ewa Szczurek; Davis J. McCarthy; Stephanie C. Hicks; Mark D. Robinson; Catalina A. Vallejos; Niko Beerenwinkel; Kieran R. Campbell; Ahmed Mahfouz; Luca Pinello; Pavel Skums; et al. (PeerJ Prepr., 2019)

Integrated structural variation and point mutation signatures in cancer genomes using correlated topic models. - Tyler Funnell; Allen W. Zhang; Diljot Grewal; Steven McKinney; Ali Bashashati; Yi Kan Wang; Sohrab P. Shah (PLoS Comput. Biol., 2019)

Epiclomal: Probabilistic clustering of sparse single-cell DNA methylation data. - Camila P. E. de Souza; Mirela Andronescu; Tehmina Masud; Farhia Kabeer; Justina Biele; Emma Laks; Daniel Lai; Patricia Ye; Jazmine Brimhall; Beixi Wang; Edmund Su; Tony Hui; et al. (PLoS Comput. Biol., 2020)

Population Priors for Matrix Factorization. - Sohrab Salehi; Achille Nazaret; Sohrab P. Shah; David M. Blei (Trans. Mach. Learn. Res., 2024)