Publications by authors named "Inanc Birol"

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

Nat Commun· May 2023

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ntRoot: computational inference of human ancestry at scale from genomic data.
René L Warren, Lauren Coombe, Johnathan Wong, Parham Kazemi, Inanc Birol

Bioinform Adv· December 2025

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Conserved Sequence Identification Within Large Genomic Datasets Using 'Unikseq2': Application in Environmental DNA Assay Development.
Mark Louie D Lopez, René L Warren, Michael J Allison, Lauren Coombe, Jacob J Imbery, Inanc Birol

Mol Ecol Resour· October 2025

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Antimicrobial peptides with high bioactivity against MDR isolates: Addressing public health concerns.
Ali Salehi, Anat Yanai, Amelia Richter, Chenkai Li, Darcy Sutherland, Inanc Birol

Microb Pathog· October 2025

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Monitoring marine pollution effects through targeted environmental DNA (eDNA) testing in the Pacific northwest.
Neha Acharya-Patel, Karen Cram, Emma T Groenwold, Hajeong Lee, Abigail G Keller, Inanc Birol

Mar Pollut Bull· July 2025

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Correction: Streaming Long-Read Sequence Alignments for HLA Predictions Using HLAminer.
René L Warren, Inanc Birol

Curr Protoc· May 2025

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Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation.
Vanessa L Porter, Michelle Ng, Kieran O'Neill, Signe MacLennan, Richard D Corbett, Inanc Birol

Genome Res· April 2025

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Mining the UniProtKB/Swiss-Prot database for antimicrobial peptides.
Chenkai Li, Darcy Sutherland, Ali Salehi, Amelia Richter, Diana Lin, Inanc Birol

Protein Sci· April 2025

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

BMC Bioinformatics· March 2025

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Streaming Long-Read Sequence Alignments for HLA Predictions Using HLAminer.
René L Warren, Inanc Birol

Curr Protoc· March 2025

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

Plant Direct· November 2024

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De novo synthetic antimicrobial peptide design with a recurrent neural network.
Chenkai Li, Darcy Sutherland, Amelia Richter, Lauren Coombe, Anat Yanai, Inanc Birol

Protein Sci· August 2024

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Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.
Francisco J Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark Diekhans, Sílvia Carbonell-Sala, Inanc Birol

Nat Methods· July 2024

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Structure-aware deep learning model for peptide toxicity prediction.
Hossein Ebrahimikondori, Darcy Sutherland, Anat Yanai, Amelia Richter, Ali Salehi, Inanc Birol

Protein Sci· July 2024

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Transcriptomic profiling of Rana [Lithobates] catesbeiana back skin during natural and thyroid hormone-induced metamorphosis under different temperature regimes with particular emphasis on innate immune system components.
Lorissa M Corrie, Haley Kuecks-Winger, Hossein Ebrahimikondori, Inanc Birol, Caren C Helbing

Comp Biochem Physiol Part D Genomics Proteomics· June 2024

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Conifers Concentrate Large Numbers of NLR Immune Receptor Genes on One Chromosome.
Yannick Woudstra, Hayley Tumas, Cyril van Ghelder, Tin Hang Hung, Joana J Ilska, Inanc Birol

Genome Biol Evol· June 2024

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A comprehensive tandem repeat catalog of the human genome.
Readman Chiu, Indhu-Shree Rajan-Babu, Jan M Friedman, Inanc Birol

medRxiv· June 2024

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ntEmbd: Deep learning embedding for nucleotide sequences.
Saber Hafezqorani, Ka Ming Nip, Inanc Birol

bioRxiv· May 2024

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Establishing association between HLA-C*04:01 and severe COVID-19.
René L Warren, Rohan Abraham, Marc Calingo, Jean-Michel Garant, Steven J M Jones, Inanc Birol

HLA· January 2024

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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.
Tin Hang Hung, Ernest T Y Wu, Pauls Zeltiņš, Āris Jansons, Aziz Ullah, Inanc Birol

BMC Genomics· January 2024

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Assembly and annotation of the black spruce genome provide insights on spruce phylogeny and evolution of stress response.
Theodora Lo, Lauren Coombe, Kristina K Gagalova, Alex Marr, René L Warren, Inanç Birol

G3 (Bethesda)· December 2023

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Genomic structures and regulation patterns at HPV integration sites in cervical cancer.
Vanessa L Porter, Kieran O'Neill, Signe MacLennan, Richard D Corbett, Michelle Ng, Inanc Birol

bioRxiv· November 2023

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aaHash: recursive amino acid sequence hashing.
Johnathan Wong, Parham Kazemi, Lauren Coombe, René L Warren, Inanç Birol

Bioinform Adv· November 2023

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Genomic virulence features of Beauveria bassiana as a biocontrol agent for the mountain pine beetle population.
Janet X Li, Kleinberg X Fernandez, Carol Ritland, Sharon Jancsik, Daniel B Engelhardt, Inanc Birol

BMC Genomics· July 2023

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Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.
Francisco J Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark Diekhans, Sílvia Carbonell-Sala, Inanc Birol

bioRxiv· July 2023

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