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Ali Bashir

  • ASSISTANT PROFESSOR Genetics and Genomic Sciences
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Education

  • Ph.D., University of California, San Diego
    Bioinformatics

  • B.S., University of California, Berkeley
    Bioengineering

Publications

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, Kasarskis A, Wang S, Eid J, Rank D, Redman JC, Steyert SR, Frimodt-Møller J, Struve C, Petersen AM, Krogfelt KA, Nataro JP, Schadt EE, Waldor MK. Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. The New England journal of medicine 2011 Aug; 365(8).

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 2011 Feb; 108(6).

Lo C, Bashir A, Bansal V, Bafna V. Strobe sequence design for haplotype assembly. BMC bioinformatics 2011; 12 Suppl 1.

Ritz A, Bashir A, Raphael BJ. Structural variation analysis with strobe reads. Bioinformatics (Oxford, England) 2010 May; 26(10).

Bashir A, Bansal V, Bafna V. Designing deep sequencing experiments: detecting structural variation and estimating transcript abundance. BMC genomics 2010; 11.

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 2010 Mar; 17(3).

Sindi S, Helman E, Bashir A, Raphael BJ. A geometric approach for classification and comparison of structural variants. Bioinformatics (Oxford, England) 2009 Jun; 25(12).

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, Zhang L, Sheridan A, Fu H, Hendrickson CL, Li B, Kotler L, Stuart JR, Malek JA, Manning JM, Antipova AA, Perez DS, Moore MP, Hayashibara KC, Lyons MR, Beaudoin RE, Coleman BE, Laptewicz MW, Sannicandro AE, Rhodes MD, Gottimukkala RK, Yang S, Bafna V, Bashir A, MacBride A, Alkan C, Kidd JM, Eichler EE, Reese MG, De La Vega FM, Blanchard AP. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome research 2009 Sep; 19(9).

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 2008 Apr; 4(4).

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, Tao Q, Aerni SJ, Brown RP, Bashir A, Gray JW, Cheng JF, de Jong P, Nefedov M, Ried T, Padilla-Nash HM, Collins CC. A sequence-based survey of the complex structural organization of tumor genomes. Genome biology 2008; 9(3).

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) 2007 Nov; 23(21).

Bansal V, Bashir A, Bafna V. Evidence for large inversion polymorphisms in the human genome from HapMap data. Genome research 2007 Feb; 17(2).

Bashir A, Ye C, Price AL, Bafna V. Orthologous repeats and mammalian phylogenetic inference. Genome research 2005 Jul; 15(7).

Inada DC, Bashir A, Lee C, Thomas BC, Ko C, Goff SA, Freeling M. Conserved noncoding sequences in the grasses. Genome research 2003 Sep; 13(9).

Industry Relationships

Physicians and scientists on the faculty of the Icahn School of Medicine at Mount Sinai often interact with pharmaceutical, device and biotechnology companies to improve patient care, develop new therapies and achieve scientific breakthroughs. In order to promote an ethical and transparent environment for conducting research, providing clinical care and teaching, Mount Sinai requires that salaried faculty inform the School of their relationships with such companies.

Dr. Bashir did not report having any of the following types of financial relationships with industry during 2012 and/or 2013: consulting, scientific advisory board, industry-sponsored lectures, service on Board of Directors, participation on industry-sponsored committees, equity ownership valued at greater than 5% of a publicly traded company or any value in a privately held company. Please note that this information may differ from information posted on corporate sites due to timing or classification differences.

Mount Sinai's faculty policies relating to faculty collaboration with industry are posted on our website at http://icahn.mssm.edu/about-us/services-and-resources/faculty-resources/handbooks-and-policies/faculty-handbook. Patients may wish to ask their physician about the activities they perform for companies.

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