Ali Bashir

17 papers B 1Journal 14Unranked 1
YearRankTypeTitle / Venue / Authors
2026 J jnl
Fold-CP: A Context Parallelism Framework for Biomolecular Modeling.
CoRR
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
2024 J jnl
NPSV-deep: a deep learning method for genotyping structural variants in short read genome sequencing data.
Bioinform.
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
2022 J jnl
Automated Deep Aberration Detection from Chromosome Karyotype Images.
CoRR
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
2020 J jnl
MsPAC: a tool for haplotype-phased structural variant detection.
Bioinform.
Oscar L. Rodriguez, Anna M. Ritz, Andrew J. Sharp, Ali Bashir
2016 J jnl
Alpha-CENTAURI: assessing novel centromeric repeat sequence variation with long read sequencing.
Bioinform.
Volkan Sevim, Ali Bashir, Chen-Shan Chin, Karen H. Miga
2014 J jnl
Characterization of structural variants with single molecule and hybrid sequencing approaches.
Bioinform.
Anna M. Ritz, Ali Bashir, Suzanne S. Sindi, David Hsu, Iman Hajirasouliha, Benjamin J. Raphael
2014 J jnl
Detecting epigenetic motifs in low coverage and metagenomics settings.
BMC Bioinform.
Noam D. Beckmann, Sashank Karri, Gang Fang, Ali Bashir
2014 J jnl
Resolving complex tandem repeats with long reads.
Bioinform.
Ajay Ummat, Ali Bashir
2011 J jnl
Strobe sequence design for haplotype assembly.
BMC Bioinform.
Christine Lo, Ali Bashir, Vikas Bansal, Vineet Bafna
2011 — conf
Workshop: Characterization of structural variants with next generation DNA sequencing.
ICCABS
Benjamin J. Raphael, Suzanne S. Sindi, Anna M. Ritz, Ali Bashir
2010 J jnl
Optimizing PCR Assays for DNA-Based Cancer Diagnostics.
J. Comput. Biol.
Ali Bashir, Qing Lu, Dennis Carson, Benjamin J. Raphael, Yu-Tsueng Liu, Vineet Bafna
2010 J jnl
Structural variation analysis with strobe reads.
Bioinform.
Anna M. Ritz, Ali Bashir, Benjamin J. Raphael
2009 J jnl
A geometric approach for classification and comparison of structural variants.
Bioinform.
Suzanne S. Sindi, Elena Helman, Ali Bashir, Benjamin J. Raphael
2009 — —
Computational methods for analyzing and detecting genomic structural variation : applications to cancer.
Ali Bashir
2009 B conf
Optimizing PCR Assays for DNA Based Cancer Diagnostics.
RECOMB
Ali Bashir, Qing Lu, Dennis Carson, Benjamin J. Raphael, Yu-Tsueng Liu, Vineet Bafna
2008 J jnl
Evaluation of Paired-End Sequencing Strategies for Detection of Genome Rearrangements in Cancer.
PLoS Comput. Biol.
Ali Bashir, Stanislav Volik, Colin C. Collins, Vineet Bafna, Benjamin J. Raphael
2007 J jnl
Optimization of primer design for the detection of variable genomic lesions in cancer.
Bioinform.
Ali Bashir, Yu-Tsueng Liu, Benjamin J. Raphael, Dennis Carson, Vineet Bafna