Ali Bashir

According to our database, Ali Bashir authored at least 16 papers between 2007 and 2026.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2026

Fold-CP: A Context Parallelism Framework for Biomolecular Modeling.

Dejun Lin, Simon K. S. Chu, Vishanth Iyer, Youhan Lee, John St. John, Kevin Boyd, Brian Roland, Xiaowei Ren, Guoqing Zhou, Zhonglin Cao, Polina Binder, Yuliya Zhautouskaya, Jakub Zakrzewski, Maximilian Stadler, Kyle Gion, Yuxing Peng, Xi Chen, Tianjing Zhang, Philipp Junk, Michelle Dimon, Pawel Gniewek, Fabian Ortega, McKinley Polen, Ivan Grubisic, Ali Bashir, Graham Holt, Danny Kovtun, Matthias Grass, Luca Naef, Rui Wang, Jian Peng, Anthony B. Costa, Saee Paliwal, Eddie Calleja, Timur Rvachov, Neha Tadimeti, Roy Tal, Emine Küçükbenli

CoRR, March, 2026

2024

NPSV-deep: a deep learning method for genotyping structural variants in short read genome sequencing data.

Michael D. Linderman, Jacob Wallace, Alderik van der Heyde, Eliza Wieman, Daniel Brey, Yiran Shi, Peter Hansen, Zahra Shamsi, Jeremiah Liu, Bruce D. Gelb, Ali Bashir

Bioinform., 2024

2022

Automated Deep Aberration Detection from Chromosome Karyotype Images.

Zahra Shamsi, Drew Bryant, Jacob Wilson, Xiaoyu Qu, Avinava Dubey, Konik Kothari, Mostafa Dehghani, Mariya Chavarha, Valerii Likhosherstov, Brian Williams, Michael Frumkin, Fred Appelbaum, Krzysztof Choromanski, Ali Bashir, Min Fang

CoRR, 2022

2020

MsPAC: a tool for haplotype-phased structural variant detection.

Oscar L. Rodriguez, Anna M. Ritz, Andrew J. Sharp, Ali Bashir

Bioinform., 2020

2016

Alpha-CENTAURI: assessing novel centromeric repeat sequence variation with long read sequencing.

Volkan Sevim, Ali Bashir, Chen-Shan Chin, Karen H. Miga

Bioinform., 2016

2014

Detecting epigenetic motifs in low coverage and metagenomics settings.

Noam D. Beckmann, Sashank Karri, Gang Fang, Ali Bashir

BMC Bioinform., 2014

Resolving complex tandem repeats with long reads.

Ajay Ummat, Ali Bashir

Bioinform., 2014

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

2011

Strobe sequence design for haplotype assembly.

Christine Lo, Ali Bashir, Vikas Bansal, Vineet Bafna

BMC Bioinform., 2011

Workshop: Characterization of structural variants with next generation DNA sequencing.

Benjamin J. Raphael, Suzanne S. Sindi, Anna M. Ritz, Ali Bashir

Proceedings of the IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, 2011

2010

Structural variation analysis with strobe reads.

Anna M. Ritz, Ali Bashir, Benjamin J. Raphael

Bioinform., 2010

2009

Computational methods for analyzing and detecting genomic structural variation : applications to cancer.

Ali Bashir

PhD thesis, 2009

A geometric approach for classification and comparison of structural variants.

Suzanne S. Sindi, Elena Helman, Ali Bashir, Benjamin J. Raphael

Bioinform., 2009

Optimizing PCR Assays for DNA Based Cancer Diagnostics.

Ali Bashir, Qing Lu, Dennis Carson, Benjamin J. Raphael, Yu-Tsueng Liu, Vineet Bafna

Proceedings of the Research in Computational Molecular Biology, 2009

2008

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

2007

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