İB
İnanç Birol
SoftwarebioinformaticsGenomicsGenomeGenome, HumanTranscriptomeAlgorithmsHigh-Throughput Nucleotide SequencinggenomicsGene Expression Profiling
On Valency
published · living versionsW_26xzgw86·v1 · currentpublished
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
with Keith R. Bradnam, Joseph N. Fass, Anton Alexandrov, Paul Baranay +86
1 version
Preprints & journals
177 papers in the corpus · 1995–2026biHash: bisulfite-aware recursive nucleotide hashing10.64898/2026.10.19.760264v1 · wong, j., Birol, I.2026 · 0 citationsbioRxiv
ntSynt-viz: visualizing synteny patterns across multiple genomes.42690038 · Coombe, Lauren, Warren, René L, Birol, Inanc2026 · 22 citationsJournal of evolutionary biology. 2026;39(10):1280-1288
Population-scale disease-associated tandem repeat analysis reveals locus and ancestry-specific insights.42686677 · Rajan-Babu, Indhu-Shree, Chiu, Readman, Weisburd, Ben et al.2026 · 1 citationNature communications. 2026;17(1)
Genome misassembly detection using Stash: A data structure based on stochastic tile hashing.42441722 · Sarvar, Armaghan, Coombe, Lauren, Birol, Inanc2026 · 0 citationsPloS one. 2026;21(7):e0333729
Pathogen-specific antimicrobial activity prediction with biological large language model-based methods10.64898/2026.05.23.727347v1 · Ucar, B., Demirsoy, E., Salehi, A. et al.2026 · 0 citationsbioRxiv
Efficacy and safety evaluation of artificial intelligence-identified antimicrobial peptides targeting avian pathogenic Escherichia coli in broiler chickens.42135842 · Demirsoy, Emre, Parkin, Teagan I, Mihalynuk, Shaeleen E et al.2026 · 1 citationJournal of animal science and biotechnology. 2026;17(1)
AIEdit: Alignment-free genome assembly polisher trained on spaced seed match patterns.42090425 · Kazemi, Parham, Sánchez Olivares, Ivana, Warren, René L et al.2026 · 0 citationsPLoS computational biology. 2026;22(5):e1014245
ntStat: k-mer characterization using occurrence statistics in raw sequencing data.41920843 · Kazemi, Parham, Coombe, Lauren, Warren, René L et al.2026 · 0 citationsPLoS computational biology. 2026;22(4):e1014158
aaKomp: Alignment-free amino acid k-mer matching for genome completeness assessment at scale10.64898/2026.03.19.713078v1 · Wong, J., Coombe, L., Warren, R. L. et al.2026 · 0 citationsbioRxiv
AMPSeek: A Workflow for Predicting Antimicrobial Peptide Activity, Three-Dimensional Structure, and Toxicity.41711565 · Zhang, Emily, Ucar, Berke, Salehi, Ali et al.2026 · 0 citationsCurrent protocols. 2026;6(2):e70325
Concordance and divergence between self-declared ancestry and genome-derived ancestry composition in 10 250 participants from the HostSeq cohort.42492085 · Warren, René L, Coombe, Lauren, Birol, Inanc2026 · 0 citationsGenome. 2026;69:1-12
ntSynt: multi-genome synteny detection using minimizer graph mappings.41462254 · Coombe, Lauren, Kazemi, Parham, Wong, Johnathan et al.2025 · 10 citationsBMC biology. 2025;23(1):367
ntRoot: computational inference of human ancestry at scale from genomic data.41383407 · Warren, René L, Coombe, Lauren, Wong, Johnathan et al.2025 · 5 citationsBioinformatics advances. 2025;5(1):vbaf287
Efficacy and safety evaluation of artificial intelligence-identified antimicrobial peptides for use against avian pathogenic Escherichia coli in the poultry industry10.1101/2025.09.15.675954v3 · Demirsoy, E., Parkin, T. I., Mihalynuk, S. E. et al.2025 · 0 citationsbioRxiv
Antimicrobial peptides with high bioactivity against MDR isolates: Addressing public health concerns.40695040 · Salehi, Ali, Yanai, Anat, Richter, Amelia et al.2025 · 2 citationsMicrobial pathogenesis. 2025;207:107893
Conserved Sequence Identification Within Large Genomic Datasets Using 'Unikseq2': Application in Environmental DNA Assay Development.40642868 · Lopez, Mark Louie D, Warren, René L, Allison, Michael J et al.2025 · 5 citationsMolecular ecology resources. 2025;25(7):e70014
Concordance and dissonance: A genome-wide analysis of self-declared versus inferred ancestry in 10,250 participants from the HostSeq cohort10.1101/2025.06.10.658783v3 · Warren, R. L., Birol, I.2025 · 0 citationsbioRxiv
Correction: Streaming Long-Read Sequence Alignments for HLA Predictions Using HLAminer.40323714 · Warren, René L, Birol, Inanc2025 · 1 citationCurrent protocols. 2025;5(5):e70144
Monitoring marine pollution effects through targeted environmental DNA (eDNA) testing in the Pacific northwest.40294512 · Acharya-Patel, Neha, Cram, Karen, Groenwold, Emma T et al.2025 · 5 citationsMarine pollution bulletin. 2025;216:118036
Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation.39638560 · Porter, Vanessa L, Ng, Michelle, O'Neill, Kieran et al.2025 · 13 citationsGenome research. 2025;35(4):653-670
Mining the UniProtKB/Swiss-Prot database for antimicrobial peptides.40100125 · Li, Chenkai, Sutherland, Darcy, Salehi, Ali et al.2025 · 8 citationsProtein science : a publication of the Protein Society. 2025;34(4):e70083
GoldPolish-target: targeted long-read genome assembly polishing.40055584 · Zhang, Emily, Coombe, Lauren, Wong, Johnathan et al.2025 · 4 citationsBMC bioinformatics. 2025;26(1):78
Streaming Long-Read Sequence Alignments for HLA Predictions Using HLAminer.40145684 · Warren, René L, Birol, Inanc2025 · 1 citationCurrent protocols. 2025;5(3):e70124
Leaf pigmentation in Cannabis sativa: Characterization of anthocyanin biosynthesis in colorful Cannabis varieties.39600728 · Gagalova, Kristina K, Yan, Yifan, Wang, Shumin et al.2026 · 7 citationsPlant direct. 2024;8(11):e70016
De novo synthetic antimicrobial peptide design with a recurrent neural network.38988311 · Li, Chenkai, Sutherland, Darcy, Richter, Amelia et al.2024 · 20 citationsProtein science : a publication of the Protein Society. 2024;33(8):e5088
Structure-aware deep learning model for peptide toxicity prediction.39196703 · Ebrahimikondori, Hossein, Sutherland, Darcy, Yanai, Anat et al.2024 · 35 citationsProtein science : a publication of the Protein Society. 2024;33(7):e5076
A comprehensive tandem repeat catalog of the human genome.38947075 · Chiu, Readman, Rajan-Babu, Indhu-Shree, Friedman, Jan M et al.2026 · 19 citationsmedRxiv : the preprint server for health sciences. 2024
Conifers Concentrate Large Numbers of NLR Immune Receptor Genes on One Chromosome.38787537 · Woudstra, Yannick, Tumas, Hayley, van Ghelder, Cyril et al.2024 · 7 citationsGenome biology and evolution. 2024;16(6)
ntEmbd: Deep learning embedding for nucleotide sequences.38746190 · Hafezqorani, Saber, Nip, Ka Ming, Birol, Inanc2024 · 2 citationsbioRxiv : the preprint server for biology. 2024
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.38714098 · Corrie, Lorissa M, Kuecks-Winger, Haley, Ebrahimikondori, Hossein et al.2024 · 3 citationsComparative biochemistry and physiology. Part D, Genomics & proteomics. 2024;50:101238
Multi-genome synteny detection using minimizer graph mappings10.1101/2024.02.07.579356v2 · Coombe, L., Kazemi, P., Wong, J. et al.2024 · 29 citationsbioRxiv
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.38281030 · Hung, Tin Hang, Wu, Ernest T Y, Zeltiņš, Pauls et al.2024 · 6 citationsBMC genomics. 2024;25(1):118
Establishing association between HLA-C*04:01 and severe COVID-19.38273454 · Warren, René L, Abraham, Rohan, Calingo, Marc et al.2024 · 1 citationHLA. 2024;103(1):e15355
Assembly and annotation of the black spruce genome provide insights on spruce phylogeny and evolution of stress response.37875130 · Lo, Theodora, Coombe, Lauren, Gagalova, Kristina K et al.2024 · 13 citationsG3 (Bethesda, Md.). 2023;14(1)
Genomic structures and regulation patterns at HPV integration sites in cervical cancer.37961641 · Porter, Vanessa L, O'Neill, Kieran, MacLennan, Signe et al.2026 · 3 citationsbioRxiv : the preprint server for biology. 2023
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.37546854 · Pardo-Palacios, Francisco J, Wang, Dingjie, Reese, Fairlie et al.2024 · 265 citationsbioRxiv : the preprint server for biology. 2023
Genomic virulence features of Beauveria bassiana as a biocontrol agent for the mountain pine beetle population.37430186 · Li, Janet X, Fernandez, Kleinberg X, Ritland, Carol et al.2023 · 8 citationsBMC genomics. 2023;24(1):390
Linear time complexity de novo long read genome assembly with GoldRush.37217507 · Wong, Johnathan, Coombe, Lauren, Nikolić, Vladimir et al.2023 · 29 citationsNature communications. 2023;14(1):2906
Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2.37217540 · Nip, Ka Ming, Hafezqorani, Saber, Gagalova, Kristina K et al.2023 · 51 citationsNature communications. 2023;14(1):2940
aaHash: recursive amino acid sequence hashing.37214907 · Wong, Johnathan, Kazemi, Parham, Coombe, Lauren et al.2023 · 1 citationbioRxiv : the preprint server for biology. 2023
HostSeq: a Canadian whole genome sequencing and clinical data resource.37131148 · Yoo, S, Garg, E, Elliott, L T et al.2023 · 14 citationsBMC genomic data. 2023;24(1):26
ntLink: A Toolkit for De Novo Genome Assembly Scaffolding and Mapping Using Long Reads.37039735 · Coombe, Lauren, Warren, René L, Wong, Johnathan et al.2023 · 46 citationsCurrent protocols. 2023;3(4):e733
Characterization and simulation of metagenomic nanopore sequencing data with Meta-NanoSim.36939007 · Yang, Chen, Lo, Theodora, Nip, Ka Ming et al.2023 · 18 citationsGigaScience. 2023;12
Models and data of AMPlify: a deep learning tool for antimicrobial peptide prediction.36732807 · Li, Chenkai, Warren, René L, Birol, Inanc2023 · 26 citationsBMC research notes. 2023;16(1):11
Associating Biological Activity and Predicted Structure of Antimicrobial Peptides from Amphibians and Insects.36551368 · Richter, Amelia, Sutherland, Darcy, Ebrahimikondori, Hossein et al.2022 · 22 citationsAntibiotics (Basel, Switzerland). 2022;11(12)
ntHash2: recursive spaced seed hashing for nucleotide sequences.36000872 · Kazemi, Parham, Wong, Johnathan, Nikolić, Vladimir et al.2022 · 20 citationsBioinformatics (Oxford, England). 2022;38(20):4812-4813
The western redcedar genome reveals low genetic diversity in a self-compatible conifer.36109148 · Shalev, Tal J, Gamal El-Dien, Omnia, Yuen, Macaire M S et al.2022 · 37 citationsGenome research. 2022;32(10):1952-1964
Spruce giga-genomes: structurally similar yet distinctive with differentially expanding gene families and rapidly evolving genes.35789009 · Gagalova, Kristina K, Warren, René L, Coombe, Lauren et al.2022 · 35 citationsThe Plant journal : for cell and molecular biology. 2022;111(5):1469-1485
Mining Amphibian and Insect Transcriptomes for Antimicrobial Peptide Sequences with rAMPage.35884206 · Lin, Diana, Sutherland, Darcy, Aninta, Sambina Islam et al.2022 · 24 citationsAntibiotics (Basel, Switzerland). 2022;11(7)
RResolver: efficient short-read repeat resolution within ABySS.35729491 · Nikolić, Vladimir, Afshinfard, Amirhossein, Chu, Justin et al.2022 · 1 citationBMC bioinformatics. 2022;23(1):246
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