KLEAT: Cleavage Site Analysis of Transcriptomes. - Inanç Birol; Anthony Raymond; Readman Chiu; Ka Ming Nip; Shaun D. Jackman; Maayan Kreitzman; T. Roderick Docking; Catherine A. Ennis; A. Gordon Robertson; Aly Karsan (Pacific Symposium on Biocomputing, 2015)

Deep profiling of multitube flow cytometry data. - Kieran O'Neill; Nima Aghaeepour; Jeremy Parker; Donna Hogge; Aly Karsan; Bakul Dalal; Ryan Remy Brinkman (Bioinform., 2015)

Graph-based Semi-supervised Gene Mention Tagging. - Golnar Sheikhshab; Elizabeth Starks; Aly Karsan; Anoop Sarkar; Inanç Birol (BioNLP@ACL, 2016)

Assembling draft genomes using contiBAIT. - Kieran O'Neill; Mark Hills 004; Mike Gottlieb; Matthew Borkowski; Aly Karsan; Peter M. Lansdorp (Bioinform., 2017)

GraphNER: Using Corpus Level Similarities and Graph Propagation for Named Entity Recognition. - Golnar Sheikhshab; Elizabeth Starks; Aly Karsan; Readman Chiu; Anoop Sarkar; Inanç Birol (IPDPS Workshops, 2018)