Optimization of primer design for the detection of variable genomic lesions in cancer. - Ali Bashir; Yu-Tsueng Liu; Benjamin J. Raphael; Dennis Carson; Vineet Bafna (Bioinform., 2007)

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)

A geometric approach for classification and comparison of structural variants. - Suzanne S. Sindi; Elena Helman; Ali Bashir; Benjamin J. Raphael (Bioinform., 2009)

Computational methods for analyzing and detecting genomic structural variation : applications to cancer. - Ali Bashir (2009)

Structural variation analysis with strobe reads. - Anna M. Ritz; Ali Bashir; Benjamin J. Raphael (Bioinform., 2010)

Optimizing PCR Assays for DNA-Based Cancer Diagnostics. - Ali Bashir; Qing Lu; Dennis Carson; Benjamin J. Raphael; Yu-Tsueng Liu; Vineet Bafna (J. Comput. Biol., 2010)

Workshop: Characterization of structural variants with next generation DNA sequencing. - Benjamin J. Raphael; Suzanne S. Sindi; Anna M. Ritz; Ali Bashir (ICCABS, 2011)

Strobe sequence design for haplotype assembly. - Christine Lo; Ali Bashir; Vikas Bansal 001; Vineet Bafna (BMC Bioinform., 2011)

Characterization of structural variants with single molecule and hybrid sequencing approaches. - Anna M. Ritz; Ali Bashir; Suzanne S. Sindi; David Hsu; Iman Hajirasouliha; Benjamin J. Raphael (Bioinform., 2014)

Resolving complex tandem repeats with long reads. - Ajay Ummat; Ali Bashir (Bioinform., 2014)

Detecting epigenetic motifs in low coverage and metagenomics settings. - Noam D. Beckmann; Sashank Karri; Gang Fang; Ali Bashir (BMC Bioinform., 2014)

Alpha-CENTAURI: assessing novel centromeric repeat sequence variation with long read sequencing. - Volkan Sevim; Ali Bashir; Chen-Shan Chin; Karen H. Miga (Bioinform., 2016)

MsPAC: a tool for haplotype-phased structural variant detection. - Oscar L. Rodriguez; Anna M. Ritz; Andrew J. Sharp; Ali Bashir (Bioinform., 2020)

Automated Deep Aberration Detection from Chromosome Karyotype Images. - Zahra Shamsi; Drew Bryant; Jacob Wilson; Xiaoyu Qu; Avinava Dubey; Konik Kothari; Mostafa Dehghani 001; Mariya Chavarha; Valerii Likhosherstov; Brian Williams; Michael Frumkin; Fred Appelbaum; et al. (CoRR, 2022)