Search Results - Inanc Birol

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  1. 1

    HLA alleles measured from COVID-19 patient transcriptomes reveal associations with disease prognosis in a New York cohort by René L. Warren, Inanc Birol

    Published in PeerJ (2021-10-01)
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  2. 2

    Models and data of AMPlify: a deep learning tool for antimicrobial peptide prediction by Chenkai Li, René L. Warren, Inanc Birol

    Published in BMC Research Notes (2023-02-01)
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  3. 3

    GoldPolish-target: targeted long-read genome assembly polishing by Emily Zhang, Lauren Coombe, Johnathan Wong, René L. Warren, Inanç Birol

    Published in BMC Bioinformatics (2025-03-01)
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  4. 4

    AIEdit: Alignment-free genome assembly polisher trained on spaced seed match patterns. by Parham Kazemi, Ivana Sánchez Olivares, René L Warren, Lauren Coombe, Inanc Birol

    Published in PLoS Computational Biology (2026-05-01)
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  5. 5

    DIDA: Distributed Indexing Dispatched Alignment. by Hamid Mohamadi, Benjamin P Vandervalk, Anthony Raymond, Shaun D Jackman, Justin Chu, Clay P Breshears, Inanc Birol

    Published in PLoS ONE (2015-01-01)
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  6. 6

    Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2 by Ka Ming Nip, Saber Hafezqorani, Kristina K. Gagalova, Readman Chiu, Chen Yang, René L. Warren, Inanc Birol

    Published in Nature Communications (2023-05-01)
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  7. 7

    Leaf pigmentation in Cannabis sativa: Characterization of anthocyanin biosynthesis in colorful Cannabis varieties by Kristina K. Gagalova, Yifan Yan, Shumin Wang, Till Matzat, Simone D. Castellarin, Inanc Birol, David Edwards, Mathias Schuetz

    Published in Plant Direct (2024-11-01)
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  8. 8

    Spaced Seed Data Structures for De Novo Assembly by Inanç Birol, Justin Chu, Hamid Mohamadi, Shaun D. Jackman, Karthika Raghavan, Benjamin P. Vandervalk, Anthony Raymond, René L. Warren

    Published in International Journal of Genomics (2015-01-01)
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  9. 9

    Whole genome duplication and enrichment of metal cation transporters revealed by de novo genome sequencing of extremely halotolerant black yeast Hortaea werneckii. by Metka Lenassi, Cene Gostinčar, Shaun Jackman, Martina Turk, Ivan Sadowski, Corey Nislow, Steven Jones, Inanc Birol, Nina Gunde Cimerman, Ana Plemenitaš

    Published in PLoS ONE (2013-01-01)
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  10. 10

    mtGrasp: Streamlined reference‐grade mitochondrial genome assembly and standardization to enhance metazoan mitogenome resources by Mark Louie D. Lopez, Cecilia L. Yang, Lauren Coombe, René L. Warren, Michael J. Allison, Jacob J. Imbery, Inanc Birol, Caren C. Helbing

    Published in Methods in Ecology and Evolution (2025-04-01)
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  11. 11

    Enabling robust environmental DNA assay design with “unikseq” for the identification of taxon‐specific regions within whole mitochondrial genomes by Michael J. Allison, René L. Warren, M. Louie Lopez, Neha Acharya‐Patel, Jacob J. Imbery, Lauren Coombe, Cecilia L. Yang, Inanc Birol, Caren C. Helbing

    Published in Environmental DNA (2023-09-01)
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  12. 12

    Long-insert sequence capture detects high copy numbers in a defence-related beta-glucosidase gene βglu-1 with large variations in white spruce but not Norway spruce by Tin Hang Hung, Ernest T. Y. Wu, Pauls Zeltiņš, Āris Jansons, Aziz Ullah, Nadir Erbilgin, Joerg Bohlmann, Jean Bousquet, Inanc Birol, Sonya M. Clegg, John J. MacKay

    Published in BMC Genomics (2024-01-01)
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  13. 13

    Genome-wide sequencing as a first-tier screening test for short tandem repeat expansions by Indhu-Shree Rajan-Babu, Junran J. Peng, Readman Chiu, IMAGINE Study, CAUSES Study, Chenkai Li, Arezoo Mohajeri, Egor Dolzhenko, Michael A. Eberle, Inanc Birol, Jan M. Friedman

    Published in Genome Medicine (2021-08-01)
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  14. 14

    Mining Amphibian and Insect Transcriptomes for Antimicrobial Peptide Sequences with rAMPage by Diana Lin, Darcy Sutherland, Sambina Islam Aninta, Nathan Louie, Ka Ming Nip, Chenkai Li, Anat Yanai, Lauren Coombe, René L. Warren, Caren C. Helbing, Linda M. N. Hoang, Inanc Birol

    Published in Antibiotics (2022-07-01)
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  15. 15

    Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes by Zhuyi Xue, René L. Warren, Ewan A. Gibb, Daniel MacMillan, Johnathan Wong, Readman Chiu, S. Austin Hammond, Chen Yang, Ka Ming Nip, Catherine A. Ennis, Abigail Hahn, Sheila Reynolds, Inanc Birol

    Published in BMC Genomics (2018-07-01)
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  16. 16

    AMPlify: attentive deep learning model for discovery of novel antimicrobial peptides effective against WHO priority pathogens by Chenkai Li, Darcy Sutherland, S. Austin Hammond, Chen Yang, Figali Taho, Lauren Bergman, Simon Houston, René L. Warren, Titus Wong, Linda M. N. Hoang, Caroline E. Cameron, Caren C. Helbing, Inanc Birol

    Published in BMC Genomics (2022-01-01)
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  17. 17

    Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics' GemCode Sequencing Data. by Lauren Coombe, René L Warren, Shaun D Jackman, Chen Yang, Benjamin P Vandervalk, Richard A Moore, Stephen Pleasance, Robin J Coope, Joerg Bohlmann, Robert A Holt, Steven J M Jones, Inanc Birol

    Published in PLoS ONE (2016-01-01)
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  18. 18

    Comparison of environmental DNA and SCUBA diving methods to survey keystone rockfish species on the Central Coast of British Columbia, Canada by Neha Acharya-Patel, Emma Groenwold, Matthew A. Lemay, Rute Clemente-Carvalho, Evan Morien, Sarah Dudas, Emily Rubidge, Cecilia Lingyu Yang, Lauren Coombe, René L. Warren, Alejandro Frid, Inanc Birol, Caren C. Helbing

    Published in Ecological Indicators (2024-03-01)
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  19. 19

    Genomic virulence features of Beauveria bassiana as a biocontrol agent for the mountain pine beetle population by Janet X. Li, Kleinberg X. Fernandez, Carol Ritland, Sharon Jancsik, Daniel B. Engelhardt, Lauren Coombe, René L. Warren, Marco J. van Belkum, Allan L. Carroll, John C. Vederas, Joerg Bohlmann, Inanc Birol

    Published in BMC Genomics (2023-07-01)
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  20. 20

    Associating Biological Activity and Predicted Structure of Antimicrobial Peptides from Amphibians and Insects by Amelia Richter, Darcy Sutherland, Hossein Ebrahimikondori, Alana Babcock, Nathan Louie, Chenkai Li, Lauren Coombe, Diana Lin, René L. Warren, Anat Yanai, Monica Kotkoff, Caren C. Helbing, Fraser Hof, Linda M. N. Hoang, Inanc Birol

    Published in Antibiotics (2022-11-01)
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