Biology subjects

Kari, L.

Publications and source records attributed to Kari, L..

13 recordsLinked to original sources

bioRxiv2026

Beyond phylogeny: Genome-wide DNA sequence patterns suggest DNA physical properties associated with thermal adaptation in extremophile microbes

Temperature is a fundamental constraint on biological systems, yet how it is reflected in genome sequence organization remains unclear. Here, we show that genome-wide distributions of short DNA sequences contain a robust signal of thermal adaptation that is largely independent of phylogeny. Using Structural Topic Modelling (STM), a machine-learning approach for identifying groups of co-occurring sequence motifs, we analyze canonical 6-mer and 9-mer frequency profiles of bacterial and archaeal genome proxies (randomly sampled genomic regions) and identify motif families systematically associated with thermophiles and psychrophiles. In bacterial thermophiles, the identified motif families are dominated by highly specific, overrepresented and co-occurring C- and G-stacked hexamers, and a distinct family of CG-periodic hexamers recurring across multiple temperature comparisons. In contrast, bacterial psychrophile-associated motifs are dominated by low-complexity A-, T-, and AT-run hexamers. Thermophilic archaea generally exhibit a distinct CTAG-centred hexamer family, suggesting that different domains may adapt to similar environmental constraints through different sequence-level solutions. However, this domain-level contrast is not absolute: in a targeted analysis of two thermophilic bacterium-archaeon pairs, we find unusually similar frequencies of all the STM-identified thermophile-associated hexamer families, suggesting that shared high-temperature environments can, in specific cases, partially override phylogenetic divergence. Notably, the identified motif families constitute only a small and highly selective subset of the vast space of possible G+C-rich or A+T-rich sequences. This indicates that thermal adaptation is associated with specific sequence architectures rather than broad shifts in nucleotide composition. Accordingly, the observed signal cannot be explained by overall base composition alone, but instead arises from structured combinations and positional arrangements of nucleotides within short sequence contexts. Related motif families are recovered at both k = 6 and k = 9, indicating that the signal reflects systematic shifts in genome-wide sequence organization rather than isolated sequence motifs. These patterns are consistent with known sequence-dependent DNA physical properties documented in biochemical and bio-physical studies, including differences in base-stacking interactions and conformational flexibility. Together, our results suggest that genome-wide sequence organization reflects sequence-dependent DNA physical properties associated with thermal adaptation, revealing a previously underappreciated physical layer of genomic information beyond phylogenetic history.

bioinformatics↗

bioRxiv2025

Genome-wide Pervasiveness and Localized Variation of k-mer-based Genomic Signatures in Eukaryotes

Genomic signatures are taxon-specific patterns in nucleotide sequence composition observed across different regions of a genome, used in the taxonomic classification of organisms and in inferring their evolutionary relationships. However, the nature and extent of the pervasiveness of a genomic signature across the expanse of a Telomere-to-Telomere (T2T) assembly, especially across the functionally diverse sequence elements and highly repetitive regions, remain counterintuitive and underexplored. This study aims to bridge this knowledge gap by systematically investigating the pervasiveness and variation of the genomic signature across the human genome and the genome of each of three other eukaryotic species from different kingdoms. Using the alignment-free k-mer-based Frequency Chaos Game Representation (FCGR) of DNA sequences, this study qualitatively and quantitatively analyzes the variations of the genomic signature along an entire genome. Qualitative analysis is first performed through visual inspection of FCGR patterns across different chromosomes of a species. In parallel, a quantitative analysis evaluates the variation of the genomic signature within a genome by comparing eight distance measures to identify the optimal one for the datasets in this study. By taking an intragenomic perspective with detailed analysis of chromosome landscapes these analyses reveal that, while the genomic signature is preserved in most genomic regions, exceptions exist in localized regions, such as tandem repetitions of short and long repeat units. Upon determining this pervasiveness, we assemble novel pipelines aimed at selecting a short contiguous representative genomic segment that encapsulates the sequence composition patterns characteristic of the entire genome. These representative segments are then used to assess intragenomic variation of the genomic signature, demonstrating that only a small proportion of segments (namely those characterized by regional density of short and long tandem repeats) show high distance values from the representative. No-tably, in the human genome, 80% of the segments have a distance of less than 0.24 (on a [0,1] DSSIM scale) from the representative. Moreover, we demonstrate that using these representative segments improves down-stream tasks, e.g., increasing one-nearest-neighbor (1-NN) taxonomic classification accuracy by 7% compared to selecting a random genomic segment to serve as a proxy of the genome. Lastly, this study presents a special-purpose graphical user interface (GUI) software tool, CGR-Diff, designed to provide both visual and quantitative comparisons of FCGRs of sample or user-provided DNA sequences, thereby facilitating intragenomic variation analysis of genomic signature within and across species.

bioinformatics↗

bioRxiv2025

Life at the extremes: Maximally divergent microbes with similar genomic signatures linked to extreme environments

Extreme environments impose strong mutation and selection pressures that drive distinctive, yet understudied, genomic adaptations in extremophiles. In this study, we identify 15 bacterium-archaeon pairs that exhibit highly similar k-mer-based genomic signatures despite maximal taxonomic divergence, suggesting that shared environmental conditions can produce convergent, genome-wide patterns that transcend evolutionary distance. To uncover these patterns, we developed a computational pipeline to select a composite genome proxy assembled from non-contiguous subsequences of the genome. Using supervised machine learning on a curated dataset of 693 extremophile microbial genomes, we found that 6-mers and 100 kbp genome proxy lengths provide the best balance between classification accuracy and computational efficiency. Our results provide conclusive evidence of the pervasive nature of k-mer-based patterns across the genome, and uncover the presence of taxonomic and environmental components that persist across all regions of the genome. The 15 bacterium-archaeon pairs identified by our method as having similar genomic signatures were validated through multiple independent analyses, including 3-mer frequency profile comparisons, phenotypic trait similarity, and geographic co-occurrence data. These complementary validations confirmed that extreme environmental pressures can override traditionally recognized taxonomic components at the whole-genome level. Together, these findings reveal that adaptation to extreme conditions can carry robust, taxonomic domain-spanning imprints on microbial genomes, offering new insight into the relationship between environmental mutagenesis and selection and genome-wide evolutionary convergence.

bioinformatics↗

bioRxiv2023

Environment and taxonomy shape the genomic signature of prokaryotic extremophiles

This study provides comprehensive quantitative evidence suggesting that adaptations to extreme temperatures and pH imprint a discernible environmental component in the genomic signature of microbial extremophiles. Both supervised and unsupervised machine learning algorithms were used to analyze genomic signatures, each computed as the k-mer frequency vector of a 500 kbp DNA fragment arbitrarily selected to represent a genome. Computational experiments classified/clustered genomic signatures extracted from a curated dataset of [~]700 extremophile (temperature, pH) bacteria and archaea genomes, at multiple scales of analysis, 1 [≤]k [≤]6. The supervised learning resulted in high accuracies for taxonomic classifications at 2 [≤]k [≤]6, and medium to medium-high accuracies for environment category classifications of the same datasets at 3 [≤]k [≤]6. For k = 3, our findings were largely consistent with amino acid compositional biases and codon usage patterns in coding regions, previously attributed to extreme environment adaptations. The unsupervised learning of unlabelled sequences identified several exemplars of hyperthermophilic organisms with large similarities in their genomic signatures, in spite of belonging to different domains in the Tree of Life.

bioinformatics↗

bioRxiv2023

iDeLUCS: A deep learning interactive tool for alignment-free clustering of DNA sequences

SummaryWe present an interactive Deep Learning-based software tool for Unsupervised Clustering of DNA Sequences (iDeLUCS), that detects genomic signatures and uses them to cluster DNA sequences, without the need for sequence alignment or taxonomic identifiers. iDeLUCS is scalable and user-friendly: Its graphical user interface, with support for hardware acceleration, allows the practitioner to fine-tune the different hyper-parameters involved in the training process without requiring extensive knowledge of deep learning. The performance of iDeLUCS was evaluated on a diverse set of datasets: several real genomic datasets from organisms in kingdoms Animalia, Protista, Fungi, Bacteria, and Archaea, three datasets of viral genomes, a dataset of simulated metagenomic reads from microbial genomes, and multiple datasets of synthetic DNA sequences. The performance of iDeLUCS was compared to that of two classical clustering algorithms (k-means++ and GMM) and two clustering algorithms specialized in DNA sequences (MeShClust v3.0 and DeLUCS), using both intrinsic cluster evaluation metrics and external evaluation metrics. In terms of unsupervised clustering accuracy, iDeLUCS outperforms the two classical algorithms by an average of [~] 20%, and the two specialized algorithms by an average of [~] 12%, on the datasets of real DNA sequences analyzed. Overall, our results indicate that iDeLUCS is a robust clustering method suitable for the clustering of large and diverse datasets of unlabelled DNA sequences. Availability and implementationiDeLUCS is available at our github repository under the terms of the MIT licence. Contactpmillana@uwaterloo.ca Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2022

MT-MAG: Accurate and interpretable machine learning based taxonomic assignment of metagenome-assembled genomes, with a partial classification option

We propose MT-MAG, a novel machine learning-based software tool for the complete or partial hierarchically-structured taxonomic classification of metagenome-assembled genomes (MAGs). MT-MAG is alignment-free, with k-mer frequencies being the only feature used to distinguish a DNA sequence from another (herein k = 7). MT-MAG is capable of classifying large and diverse metagenomic datasets: a total of 245.68 Gbp in the training sets, and 9.6 Gbp in the test sets analyzed in this study. In addition to complete classifications, MT-MAG offers a "partial classification" option, whereby a classification at a higher taxonomic level is provided for MAGs that cannot be classified to the Species level. MT-MAG outputs complete or partial classification paths, and interpretable numerical classification confidences of its classifications, at all taxonomic ranks. To assess the performance of MT-MAG, we define a "weighted classification accuracy," with a weighting scheme reflecting the fact that partial classifications at different ranks are not equally informative. For the two benchmarking datasets analyzed (genomes from human gut microbiome species, and bacterial and archaeal genomes assembled from cow rumen metagenomic sequences), MT-MAG achieves an average of 87.32% in weighted classification accuracy. At the Species level, MT-MAG outperforms DeepMicrobes, the only other comparable software tool, by an average of 34.79% in weighted classification accuracy. In addition, MT-MAG is able to completely classify an average of 67.70% of the sequences at the Species level, compared with DeepMicrobes which only classifies 47.45%. Moreover, MT-MAG provides additional information for sequences that it could not classify at the Species level, resulting in the partial or complete classification of 95.13%, of the genomes in the datasets analyzed. Lastly, unlike other taxonomic assignment tools (e.g., GDTB-Tk), MT-MAG is an alignment-free and genetic marker-free tool, able to provide additional bioinformatics analysis to confirm existing or tentative taxonomic assignments.

bioinformatics↗

bioRxiv2021

SomaticSiMu: a mutational signature simulator

SummarySomaticSiMu is an in silico simulator of single and double base substitutions, and single base insertions and deletions in an input genomic sequence to mimic mutational signatures. SomaticSiMu outputs simulated DNA sequences and mutational catalogues with imposed mutational signatures. The tool is the first mutational signature simulator featuring a graphical user interface, control of mutation rates, and built-in visualization tools of the simulated mutations. Simulated datasets are useful as a ground truth to test the accuracy and sensitivity of DNA sequence classification tools and mutational signature extraction tools under different experimental scenarios. The reliability of SomaticSiMu was affirmed by 1) supervised machine learning classification of simulated sequences with different mutation types and burdens, and 2) mutational signature extraction from simulated mutational catalogs. Availability and ImplementationSomaticSiMu is written in Python 3.8.3. The open-source code, documentation, and tutorials are available at https://github.com/HillLab/SomaticSiMu under the terms of the Creative Commons Attribution 4.0 International License. Contactkhill22@uwo.ca Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2021

DeLUCS: Deep Learning for Unsupervised Classification of DNA Sequences

We present a novel Deep Learning method for the Unsupervised Clustering of DNA Sequences (DeLUCS) that does not require sequence alignment, sequence homology, or (taxonomic) identifiers. DeLUCS uses Frequency Chaos Game Representations (FCGR) of primary DNA sequences, and generates "mimic" sequence FCGRs to self-learn data patterns (genomic signatures) through the optimization of multiple neural networks. A majority voting scheme is then used to determine the final cluster assignment for each sequence. The clusters learned by DeLUCS match true taxonomic groups for large and diverse datasets, with accuracies ranging from 77% to 100%: 2,500 complete vertebrate mitochondrial genomes, at taxonomic levels from sub-phylum to genera; 3,200 randomly selected 400 kbp-long bacterial genome segments, into clusters corresponding to bacterial families; three viral genome and gene datasets, averaging 1,300 sequences each, into clusters corresponding to virus subtypes. DeLUCS significantly outperforms two classic clustering methods (K-means++ and Gaussian Mixture Models) for unlabelled data, by as much as 47%. DeLUCS is highly effective, it is able to cluster datasets of unlabelled primary DNA sequences totalling over 1 billion bp of data, and it bypasses common limitations to classification resulting from the lack of sequence homology, variation in sequence length, and the absence or instability of sequence annotations and taxonomic identifiers. Thus, DeLUCS offers fast and accurate DNA sequence clustering for previously intractable datasets.

bioinformatics↗

bioRxiv2020

Machine learning-based analysis of genomes suggests associations between Wuhan 2019-nCoV and bat Betacoronaviruses

As of February 20, 2020, the 2019 novel coronavirus (renamed to COVID-19) spread to 30 countries with 2130 deaths and more than 75500 confirmed cases. COVID-19 is being compared to the infamous SARS coronavirus, which resulted, between November 2002 and July 2003, in 8098 confirmed cases worldwide with a 9.6% death rate and 774 deaths. Though COVID-19 has a death rate of 2.8% as of 20 February, the 75752 confirmed cases in a few weeks (December 8, 2019 to February 20, 2020) are alarming, with cases likely being under-reported given the comparatively longer incubation period. Such outbreaks demand elucidation of taxonomic classification and origin of the virus genomic sequence, for strategic planning, containment, and treatment. This paper identifies an intrinsic COVID-19 genomic signature and uses it together with a machine learning-based alignment-free approach for an ultra-fast, scalable, and highly accurate classification of whole COVID-19 genomes. The proposed method combines supervised machine learning with digital signal processing for genome analyses, augmented by a decision tree approach to the machine learning component, and a Spearmans rank correlation coefficient analysis for result validation. These tools are used to analyze a large dataset of over 5000 unique viral genomic sequences, totalling 61.8 million bp. Our results support a hypothesis of a bat origin and classify COVID-19 as Sarbecovirus, within Betacoronavirus. Our method achieves high levels of classification accuracy and discovers the most relevant relationships among over 5,000 viral genomes within a few minutes, ab initio, using raw DNA sequence data alone, and without any specialized biological knowledge, training, gene or genome annotations. This suggests that, for novel viral and pathogen genome sequences, this alignment-free whole-genome machine-learning approach can provide a reliable real-time option for taxonomic classification.

bioinformatics↗

bioRxiv2019

MLDSP-GUI: An alignment-free standalone tool with an interactive graphical user interface for DNA sequence comparison and analysis

SummaryMLDSP-GUI (Machine Learning with Digital Signal Processing) is an open-source, alignment-free, ultrafast, computationally lightweight, standalone software tool with an interactive Graphical User Interface (GUI) for comparison and analysis of DNA sequences. MLDSP-GUI is a general-purpose tool that can be used for a variety of applications such as taxonomic classification, disease classification, virus subtype classification, evolutionary analyses, among others.\n\nAvailabilityMLDSP-GUI is open-source, cross-platform compatible, and is available under the terms of the Creative Commons Attribution 4.0 International license (http://creativecommons.org/licenses/by/4.0/). The executable and dataset files are available at https://sourceforge.net/projects/mldsp-gui/.\n\nContactgrandha8@uwo.ca\n\nSupplementary informationSupplementary data are available online.

bioinformatics↗

bioRxiv2019

Highly reproducible murine model of oral Salmonella infection via inoculated food

Oral infection of mice with Salmonella Typhimurium is an important model system. In particular C57Bl/6 mice, which are susceptible to Salmonella, are used to study both systemic and gastrointestinal pathogenesis. Pretreatment with streptomycin disrupts the intestinal microbiota and results in colitis resembling human intestinal Salmonellosis. Oral gavage is typically used for delivery of both antibiotic and bacteria. Although convenient, this method requires a moderate level of expertise, can be stressful for experimental animals, and may lead to unwanted tracheal or systemic introduction of bacteria. Here, we demonstrate a simple method for oral infection of mice using small pieces of regular mouse chow inoculated with a known number of bacteria. Mice readily ate chow pieces containing up to 108 CFU Salmonella, allowing for a wide range of infectious doses. In mice pretreated with streptomycin, infection with inoculated chow resulted in less variability in numbers of bacteria recovered from tissues compared to oral gavage, and highly consistent infections even at doses as low as 103 Salmonella. Mice not treated with streptomycin, as well as resistant Nramp1 reconstituted C57Bl/6J mice, were also readily infected using this method. In summary, we show that foodborne infection of mice by feeding with pieces of chow inoculated with Salmonella results in infection comparable to oral gavage but represents a natural route of infection with fewer side effects and less variability among mice.

microbiology↗

bioRxiv2018

ML-DSP: Machine Learning with Digital Signal Processing for ultrafast, accurate, and scalable genome classification at all taxonomic levels

BackgroundAlthough methods and software tools abound for the comparison, analysis, identification, and taxonomic classification of the enormous amount of genomic sequences that are continuously being produced, taxonomic classification remains challenging. The difficulty lies within both the magnitude of the dataset and the intrinsic problems associated with classification. The need exists for an approach and software tool that addresses the limitations of existing alignment-based methods, as well as the challenges of recently proposed alignment-free methods.\n\nResultsWe combine supervised Machine Learning with Digital Signal Processing to design ML-DSP, an alignment-free software tool for ultrafast, accurate, and scalable genome classification at all taxonomic levels.\n\nWe test ML-DSP by classifying 7,396 full mitochondrial genomes from the kingdom to genus levels, with 98% classification accuracy. Compared with the alignment-based classification tool MEGA7 (with sequences aligned with either MUSCLE, or CLUSTALW), ML-DSP has similar accuracy scores while being significantly faster on two small benchmark datasets (2,250 to 67,600 times faster for 41 mammalian mitochondrial genomes). ML-DSP also successfully scales to accurately classify a large dataset of 4,322 complete vertebrate mtDNA genomes, a task which MEGA7 with MUSCLE or CLUSTALW did not complete after several hours, and had to be terminated. ML-DSP also outperforms the alignment-free tool FFP (Feature Frequency Profiles) in terms of both accuracy and time, being three times faster for the vertebrate mtDNA genomes dataset.\n\nConclusionsWe provide empirical evidence that ML-DSP distinguishes complete genome sequences at all taxonomic levels. Ultrafast and accurate taxonomic classification of genomic sequences is predicted to be highly relevant in the classification of newly discovered organisms, in distinguishing genomic signatures, in identifying mechanistic determinants of genomic signatures, and in evaluating genome integrity.

genomics↗

bioRxiv2018

An open-source k-mer based machine learning tool for fast and accurate subtyping of HIV-1 genomes

For many disease-causing virus species, global diversity is clustered into a taxonomy of subtypes with clinical significance. In particular, the classification of infections among the subtypes of human immunodeficiency virus type 1 (HIV-1) is a routine component of clinical management, and there are now many classification algorithms available for this purpose. Although several of these algorithms are similar in accuracy and speed, the majority are proprietary and require laboratories to transmit HIV-1 sequence data over the network to remote servers. This potentially exposes sensitive patient data to unauthorized access, and makes it impossible to determine how classifications are made and to maintain the data provenance of clinical bioinformatic workflows. We propose an open-source supervised and alignment-free subtyping method (KO_SCPCAPAMERISC_SCPCAP) that operates on k-mer frequencies in HIV-1 sequences. We performed a detailed study of the accuracy and performance of subtype classification in comparison to four state-of-the-art programs. Based on our testing data set of manually curated real-world HIV-1 sequences (n = 2, 784), Kameris obtained an overall accuracy of 97%, which matches or exceeds all other tested software, with a processing rate of over 1,500 sequences per second. Furthermore, our fully standalone general-purpose software provides key advantages in terms of data security and privacy, transparency and reproducibility. Finally, we show that our method is readily adaptable to subtype classification of other viruses including dengue, influenza A, and hepatitis B and C virus.

bioinformatics↗