Ali Bashir, Ph.D. - Publications

2009 Bioinformatics University of California, San Diego, La Jolla, CA 
Bioinformatics Biology

22 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2015 Linderman MD, Bashir A, Diaz GA, Kasarskis A, Sanderson SC, Zinberg RE, Mahajan M, Shah H, Suckiel S, Zweig M, Schadt EE. Preparing the next generation of genomicists: a laboratory-style course in medical genomics. Bmc Medical Genomics. 8: 47. PMID 26264128 DOI: 10.1186/S12920-015-0124-Y  0.84
2015 Smith CC, Zhang C, Lin KC, Lasater EA, Zhang Y, Massi E, Damon LE, Pendleton M, Bashir A, Sebra R, Perl A, Kasarskis A, Shellooe R, Tsang G, Carias H, et al. Characterizing and Overriding the Structural Mechanism of the Quizartinib-Resistant FLT3 "Gatekeeper" F691L Mutation with PLX3397. Cancer Discovery. 5: 668-79. PMID 25847190 DOI: 10.1158/2159-8290.Cd-15-0060  0.84
2015 Sanderson SC, Linderman MD, Zinberg R, Bashir A, Kasarskis A, Zweig M, Suckiel S, Shah H, Mahajan M, Diaz GA, Schadt EE. How do students react to analyzing their own genomes in a whole-genome sequencing course?: outcomes of a longitudinal cohort study. Genetics in Medicine : Official Journal of the American College of Medical Genetics. PMID 25634025 DOI: 10.1038/Gim.2014.203  0.84
2014 Ritz A, Bashir A, Sindi S, Hsu D, Hajirasouliha I, Raphael BJ. Characterization of structural variants with single molecule and hybrid sequencing approaches. Bioinformatics (Oxford, England). 30: 3458-66. PMID 25355789 DOI: 10.1093/Bioinformatics/Btu714  0.84
2014 Ummat A, Bashir A. Resolving complex tandem repeats with long reads. Bioinformatics (Oxford, England). 30: 3491-8. PMID 25028725 DOI: 10.1093/Bioinformatics/Btu437  0.84
2013 Sanderson SC, Linderman MD, Kasarskis A, Bashir A, Diaz GA, Mahajan MC, Shah H, Wasserstein M, Zinberg RE, Zweig M, Schadt EE. Informed decision-making among students analyzing their personal genomes on a whole genome sequencing course: a longitudinal cohort study. Genome Medicine. 5: 113. PMID 24373383 DOI: 10.1186/Gm518  0.84
2013 Katz LS, Petkau A, Beaulaurier J, Tyler S, Antonova ES, Turnsek MA, Guo Y, Wang S, Paxinos EE, Orata F, Gladney LM, Stroika S, Folster JP, Rowe L, Freeman MM, ... ... Bashir A, et al. Evolutionary dynamics of Vibrio cholerae O1 following a single-source introduction to Haiti. Mbio. 4. PMID 23820394 DOI: 10.1128/Mbio.00398-13  0.84
2012 Bashir A, Klammer AA, Robins WP, Chin CS, Webster D, Paxinos E, Hsu D, Ashby M, Wang S, Peluso P, Sebra R, Sorenson J, Bullard J, Yen J, Valdovino M, et al. A hybrid approach for the automated finishing of bacterial genomes. Nature Biotechnology. 30: 701-7. PMID 22750883 DOI: 10.1038/Nbt.2288  0.84
2011 Rasko DA, Webster DR, Sahl JW, Bashir A, Boisen N, Scheutz F, Paxinos EE, Sebra R, Chin CS, Iliopoulos D, Klammer A, Peluso P, Lee L, Kislyuk AO, Bullard J, et al. Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. The New England Journal of Medicine. 365: 709-17. PMID 21793740 DOI: 10.1056/Nejmoa1106920  0.84
2011 Lo C, Bashir A, Bansal V, Bafna V. Strobe sequence design for haplotype assembly. Bmc Bioinformatics. 12: S24. PMID 21342554 DOI: 10.1186/1471-2105-12-S1-S24  0.84
2011 Zhou D, Udpa N, Gersten M, Visk DW, Bashir A, Xue J, Frazer KA, Posakony JW, Subramaniam S, Bafna V, Haddad GG. Experimental selection of hypoxia-tolerant Drosophila melanogaster. Proceedings of the National Academy of Sciences of the United States of America. 108: 2349-54. PMID 21262834 DOI: 10.1073/Pnas.1010643108  0.84
2010 Bashir A, Bansal V, Bafna V. Designing deep sequencing experiments: detecting structural variation and estimating transcript abundance. Bmc Genomics. 11: 385. PMID 20565853 DOI: 10.1186/1471-2164-11-385  0.84
2010 Ritz A, Bashir A, Raphael BJ. Structural variation analysis with strobe reads. Bioinformatics (Oxford, England). 26: 1291-8. PMID 20378554 DOI: 10.7490/F1000Research.340.1  0.84
2010 Bashir A, Lu Q, Carson D, Raphael BJ, Liu YT, Bafna V. Optimizing PCR assays for DNA-based cancer diagnostics. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 369-81. PMID 20377451 DOI: 10.1089/Cmb.2009.0203  0.84
2009 McKernan KJ, Peckham HE, Costa GL, McLaughlin SF, Fu Y, Tsung EF, Clouser CR, Duncan C, Ichikawa JK, Lee CC, Zhang Z, Ranade SS, Dimalanta ET, Hyland FC, Sokolsky TD, ... ... Bashir A, et al. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Research. 19: 1527-41. PMID 19546169 DOI: 10.1101/Gr.091868.109  0.84
2009 Sindi S, Helman E, Bashir A, Raphael BJ. A geometric approach for classification and comparison of structural variants. Bioinformatics (Oxford, England). 25: i222-30. PMID 19477992 DOI: 10.1093/Bioinformatics/Btp208  0.84
2009 Bashir A, Lu Q, Carson D, Raphael B, Liu YT, Bafna V. Optimizing PCR assays for DNA based cancer diagnostics Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5541: 220-235. DOI: 10.1007/978-3-642-02008-7_17  0.84
2008 Bashir A, Volik S, Collins C, Bafna V, Raphael BJ. Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer. Plos Computational Biology. 4: e1000051. PMID 18404202 DOI: 10.1371/Journal.Pcbi.1000051  0.84
2008 Raphael BJ, Volik S, Yu P, Wu C, Huang G, Linardopoulou EV, Trask BJ, Waldman F, Costello J, Pienta KJ, Mills GB, Bajsarowicz K, Kobayashi Y, Sridharan S, Paris PL, ... ... Bashir A, et al. A sequence-based survey of the complex structural organization of tumor genomes. Genome Biology. 9: R59. PMID 18364049 DOI: 10.1186/Gb-2008-9-3-R59  0.84
2007 Bashir A, Liu YT, Raphael BJ, Carson D, Bafna V. Optimization of primer design for the detection of variable genomic lesions in cancer. Bioinformatics (Oxford, England). 23: 2807-15. PMID 17766270 DOI: 10.1093/Bioinformatics/Btm390  0.84
2007 Bansal V, Bashir A, Bafna V. Evidence for large inversion polymorphisms in the human genome from HapMap data. Genome Research. 17: 219-30. PMID 17185644 DOI: 10.1101/Gr.5774507  0.84
2005 Bashir A, Ye C, Price AL, Bafna V. Orthologous repeats and mammalian phylogenetic inference. Genome Research. 15: 998-1006. PMID 15998912 DOI: 10.1101/Gr.3493405  0.84
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