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Ali Bashir, Ph.D. - Publications

Affiliations: 
2009 Bioinformatics University of California, San Diego, La Jolla, CA 
Area:
Bioinformatics Biology
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48 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
2024 Linderman MD, Wallace J, van der Heyde A, Wieman E, Brey D, Shi Y, Hansen P, Shamsi Z, Liu J, Gelb BD, Bashir A. NPSV-deep: a deep learning method for genotyping structural variants in short read genome sequencing data. Bioinformatics (Oxford, England). PMID 38444093 DOI: 10.1093/bioinformatics/btae129  0.405
2022 Gibson WS, Rodriguez OL, Shields K, Silver CA, Dorgham A, Emery M, Deikus G, Sebra R, Eichler EE, Bashir A, Smith ML, Watson CT. Characterization of the immunoglobulin lambda chain locus from diverse populations reveals extensive genetic variation. Genes and Immunity. PMID 36539592 DOI: 10.1038/s41435-022-00188-2  0.389
2021 Linderman MD, Paudyal C, Shakeel M, Kelley W, Bashir A, Gelb BD. NPSV: A simulation-driven approach to genotyping structural variants in whole-genome sequencing data. Gigascience. 10. PMID 34195837 DOI: 10.1093/gigascience/giab046  0.394
2020 Rodriguez OL, Gibson WS, Parks T, Emery M, Powell J, Strahl M, Deikus G, Auckland K, Eichler EE, Marasco WA, Sebra R, Sharp AJ, Smith ML, Bashir A, Watson CT. A Novel Framework for Characterizing Genomic Haplotype Diversity in the Human Immunoglobulin Heavy Chain Locus. Frontiers in Immunology. 11: 2136. PMID 33072076 DOI: 10.3389/fimmu.2020.02136  0.328
2020 Zook JM, Hansen NF, Olson ND, Chapman L, Mullikin JC, Xiao C, Sherry S, Koren S, Phillippy AM, Boutros PC, Sahraeian SME, Huang V, Rouette A, Alexander N, Mason CE, ... ... Bashir A, et al. A robust benchmark for detection of germline large deletions and insertions. Nature Biotechnology. PMID 32541955 DOI: 10.1038/S41587-020-0538-8  0.517
2019 Oliveira PH, Ribis JW, Garrett EM, Trzilova D, Kim A, Sekulovic O, Mead EA, Pak T, Zhu S, Deikus G, Touchon M, Lewis-Sandari M, Beckford C, Zeitouni NE, Altman DR, ... ... Bashir A, et al. Epigenomic characterization of Clostridioides difficile finds a conserved DNA methyltransferase that mediates sporulation and pathogenesis. Nature Microbiology. PMID 31768029 DOI: 10.1038/S41564-019-0613-4  0.376
2019 Sullivan MJ, Altman DR, Chacko KI, Ciferri B, Webster E, Pak TR, Deikus G, Lewis-Sandari M, Khan Z, Beckford C, Rendo A, Samaroo F, Sebra R, Karam-Howlin R, Dingle T, ... ... Bashir A, et al. A complete genome screening program of clinical methicillin-resistant isolates identifies the origin and progression of a neonatal intensive care unit outbreak. Journal of Clinical Microbiology. PMID 31578260 DOI: 10.1128/Jcm.01261-19  0.441
2019 Rodriguez OL, Ritz A, Sharp AJ, Bashir A. MsPAC: A tool for haplotype-phased structural variant detection. Bioinformatics (Oxford, England). PMID 31397844 DOI: 10.1093/Bioinformatics/Btz618  0.495
2019 Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, ... ... Bashir A, et al. Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nature Communications. 10: 1784. PMID 30992455 DOI: 10.1038/S41467-018-08148-Z  0.529
2018 Altman DR, Sullivan MJ, Chacko KI, Balasubramanian D, Pak TR, Sause WE, Kumar K, Sebra R, Deikus G, Attie O, Rose H, Lewis M, Fulmer Y, Bashir A, Kasarskis A, et al. Genome plasticity of -defective during clinical infection. Infection and Immunity. PMID 30061376 DOI: 10.1128/Iai.00331-18  0.307
2018 Linderman MD, Sanderson SC, Bashir A, Diaz GA, Kasarskis A, Zinberg R, Mahajan M, Suckiel SA, Zweig M, Schadt EE. Impacts of incorporating personal genome sequencing into graduate genomics education: a longitudinal study over three course years. Bmc Medical Genomics. 11: 5. PMID 29382336 DOI: 10.1186/S12920-018-0319-0  0.439
2017 Watson CT, Matsen FA, Jackson KJL, Bashir A, Smith ML, Glanville J, Breden F, Kleinstein SH, Collins AM, Busse CE. Comment on "A Database of Human Immune Receptor Alleles Recovered from Population Sequencing Data". Journal of Immunology (Baltimore, Md. : 1950). 198: 3371-3373. PMID 28416712 DOI: 10.4049/Jimmunol.1700306  0.33
2017 Bashir A, Attie O, Sullivan M, Sebra R, Singh KV, Altman D, Pak T, Dutta J, Chacko K, Webster E, Lewis M, Hamula C, Delli Carpini KW, Murray BE, Kasarskis A, et al. Genomic confirmation of vancomycin-resistant Enterococcus transmission from deceased donor to liver transplant recipient. Plos One. 12: e0170449. PMID 28301471 DOI: 10.1371/Journal.Pone.0170449  0.398
2016 Zook JM, Catoe D, McDaniel J, Vang L, Spies N, Sidow A, Weng Z, Liu Y, Mason CE, Alexander N, Henaff E, McIntyre AB, Chandramohan D, Chen F, Jaeger E, ... ... Bashir A, et al. Extensive sequencing of seven human genomes to characterize benchmark reference materials. Scientific Data. 3: 160025. PMID 27271295 DOI: 10.1038/Sdata.2016.25  0.498
2016 Sevim V, Bashir A, Chin CS, Miga KH. Alpha-CENTAURI: assessing novel centromeric repeat sequence variation with long read sequencing. Bioinformatics (Oxford, England). PMID 27153570 DOI: 10.1093/Bioinformatics/Btw101  0.491
2016 Sullivan M, Altman D, Webster E, Lewis M, Khan Z, Beckford C, Ciferri B, Deikus G, Rendo A, Samaroo F, Sebra R, Wallach F, Patel G, Hamula C, Bashir A, et al. Continuous Surveillance by Whole-Genome Sequencing to Identify and Manage Methicillin-Resistant Staphylococcus aureus Outbreaks Open Forum Infectious Diseases. 3. DOI: 10.1093/Ofid/Ofw194.82  0.414
2016 Webster E, Chacko K, Sullivan M, Pak T, Ciferri B, Beckford C, Lewis M, Fang G, Altman D, Hamula C, Huprikar S, Sebra R, Schadt E, Kasarskis A, Van Bakel H, ... Bashir A, et al. Comparative Genomics and Assessment of Strain Diversity, Pathogenicity and Transmission of Clostridium difficile Isolates From a Hospital Setting Open Forum Infectious Diseases. 3. DOI: 10.1093/Ofid/Ofw194.50  0.341
2016 Pak T, Sullivan M, Attie O, Webster E, Kasarskis A, Bakel HV, Bashir A. PathogenDB: A Modular Software Suite Integrating Genomic Clinical Microbiology and Epidemiology Open Forum Infectious Diseases. 3. DOI: 10.1093/Ofid/Ofw172.1181  0.357
2015 Franzén O, Hu J, Bao X, Itzkowitz SH, Peter I, Bashir A. Improved OTU-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering. Microbiome. 3: 43. PMID 26434730 DOI: 10.1186/S40168-015-0105-6  0.394
2015 Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Hsi-Yang Fritz M, Konkel MK, Malhotra A, Stütz AM, Shi X, Paolo Casale F, ... ... Bashir A, et al. An integrated map of structural variation in 2,504 human genomes. Nature. 526: 75-81. PMID 26432246 DOI: 10.1038/Nature15394  0.436
2015 Pak TR, Altman DR, Attie O, Sebra R, Hamula CL, Lewis M, Deikus G, Newman LC, Fang G, Hand J, Patel G, Wallach F, Schadt EE, Huprikar S, van Bakel H, ... ... Bashir A, et al. Whole-genome sequencing identifies emergence of a quinolone resistance mutation in a case of Stenotrophomonas maltophilia bacteremia. Antimicrobial Agents and Chemotherapy. PMID 26324280 DOI: 10.1128/Aac.01723-15  0.486
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  0.449
2015 Pendleton M, Sebra R, Pang AW, Ummat A, Franzen O, Rausch T, Stütz AM, Stedman W, Anantharaman T, Hastie A, Dai H, Fritz MH, Cao H, Cohain A, Deikus G, ... ... Bashir A, et al. Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nature Methods. PMID 26121404 DOI: 10.1038/Nmeth.3454  0.477
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  0.441
2015 Khedimi R, Patel G, Kohli-Seth R, Hamula C, Pak T, Altman D, Lewis M, Somers E, Sebra R, Bakel HV, Bashir A, Kasarskis A, Wallach F, Huprikar S. Non-clonal Outbreak of Burkholderia Cepacia Complex in the Intensive Care Unit Confirmed by Genomic Analysis and Eradicated After Terminal Cleaning of the Unit Open Forum Infectious Diseases. 2. DOI: 10.1093/Ofid/Ofv133.223  0.329
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  0.506
2014 Stoesser N, Giess A, Batty EM, Sheppard AE, Walker AS, Wilson DJ, Didelot X, Bashir A, Sebra R, Kasarskis A, Sthapit B, Shakya M, Kelly D, Pollard AJ, Peto TE, et al. Genome sequencing of an extended series of NDM-producing Klebsiella pneumoniae isolates from neonatal infections in a Nepali hospital characterizes the extent of community- versus hospital-associated transmission in an endemic setting. Antimicrobial Agents and Chemotherapy. 58: 7347-57. PMID 25267672 DOI: 10.1128/Aac.03900-14  0.369
2014 Beckmann ND, Karri S, Fang G, Bashir A. Detecting epigenetic motifs in low coverage and metagenomics settings. Bmc Bioinformatics. 15: S16. PMID 25253358 DOI: 10.1186/1471-2105-15-S9-S16  0.473
2014 Altman DR, Sebra R, Hand J, Attie O, Deikus G, Carpini KW, Patel G, Rana M, Arvelakis A, Grewal P, Dutta J, Rose H, Shopsin B, Daefler S, Schadt E, ... ... Bashir A, et al. Transmission of methicillin-resistant Staphylococcus aureus via deceased donor liver transplantation confirmed by whole genome sequencing. American Journal of Transplantation : Official Journal of the American Society of Transplantation and the American Society of Transplant Surgeons. 14: 2640-4. PMID 25250641 DOI: 10.1111/Ajt.12897  0.347
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  0.491
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  0.395
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  0.436
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  0.507
2012 Hu J, Bashir A, Pendleton M, Pei Z, Itzkowitz S, Peter I. Multiple Bar-Coding 16S Sequencing by Pacbio RS Platform to Study the Gut Microbiome in Ashkenazi Jews With Crohn’s Disease: P-261 Inflammatory Bowel Diseases. 18. DOI: 10.1097/00054725-201212001-00294  0.318
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  0.677
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  0.535
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  0.689
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  0.512
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  0.582
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  0.667
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  0.483
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  0.546
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  0.652
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  0.458
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  0.593
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  0.673
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  0.59
2003 Inada DC, Bashir A, Lee C, Thomas BC, Ko C, Goff SA, Freeling M. Conserved noncoding sequences in the grasses. Genome Research. 13: 2030-41. PMID 12952874 DOI: 10.1101/Gr.1280703  0.345
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