A5041517753- DNA and Biological Computing
- semigroups and automata theory
- Advanced biosensing and bioanalysis techniques
- Algorithms and Data Compression
- Modular Robots and Swarm Intelligence
- Genomics and Phylogenetic Studies
- Cellular Automata and Applications
- Fractal and DNA sequence analysis
- Machine Learning in Bioinformatics
- Advanced Algebra and Logic
- Chemical Synthesis and Analysis
- Machine Learning and Algorithms
- Natural Language Processing Techniques
- Coding theory and cryptography
- Protist diversity and phylogeny
- Logic, programming, and type systems
- Advanced Graph Theory Research
- RNA and protein synthesis mechanisms
- Computability, Logic, AI Algorithms
- DNA and Nucleic Acid Chemistry
- SARS-CoV-2 and COVID-19 Research
- Evolutionary Algorithms and Applications
- Optimization and Search Problems
- Genetic diversity and population structure
- Advanced Combinatorial Mathematics
University of Waterloo
2017-2024
Western University
2008-2017
University of Hawaii–West Oahu
2010
University of Massachusetts Amherst
2008
University of California, Berkeley
2008
The University of Texas at Austin
2008
Conference Board
2008
Springer Nature (Germany)
2008
Penn Center for AIDS Research
2008
Carnegie Mellon University
2008
The 2019 novel coronavirus (renamed SARS-CoV-2, and generally referred to as the COVID-19 virus) has spread 184 countries with over 1.5 million confirmed cases. Such major viral outbreaks demand early elucidation of taxonomic classification origin virus genomic sequence, for strategic planning, containment, treatment. This paper identifies an intrinsic signature uses it together a machine learning-based alignment-free approach ultra-fast, scalable, highly accurate whole genomes. proposed...
Natural computing builds a bridge between computer science and natural sciences.
For many disease-causing virus species, global diversity is clustered into a taxonomy of subtypes with clinical significance. In particular, the classification infections among human immunodeficiency type 1 (HIV-1) routine component management, and there are now algorithms available for this purpose. Although several these similar in accuracy speed, majority proprietary require laboratories to transmit HIV-1 sequence data over network remote servers. This potentially exposes sensitive...
Abstract As of February 20, 2020, the 2019 novel coronavirus (renamed to COVID-19) spread 30 countries with 2130 deaths and more than 75500 confirmed cases. COVID-19 is being compared infamous SARS coronavirus, which resulted, between November 2002 July 2003, in 8098 cases worldwide a 9.6% death rate 774 deaths. Though has 2.8% as 20 February, 75752 few weeks (December 8, 2020) are alarming, likely under-reported given comparatively longer incubation period. Such outbreaks demand elucidation...
Although software tools abound for the comparison, analysis, identification, and classification of genomic sequences, taxonomic remains challenging due to magnitude datasets intrinsic problems associated with classification. The need exists an approach tool that addresses limitations existing alignment-based methods, as well challenges recently proposed alignment-free methods.We propose a novel combination supervised Machine Learning Digital Signal Processing, resulting in ML-DSP: ultrafast,...
We present a novel De ep L earning method for the U nsupervised C lustering of DNA S equences (DeLUCS) that does not require sequence alignment, homology, or (taxonomic) identifiers. DeLUCS uses Frequency Chaos Game Representations ( FCGR ) primary sequences, and generates “mimic” FCGRs to self-learn data patterns (genomic signatures) through optimization multiple neural networks. A majority voting scheme is then used determine final cluster assignment each sequence. The clusters learned by...
We propose a computational method to measure and visualize interrelationships among any number of DNA sequences allowing, for example, the examination hundreds or thousands complete mitochondrial genomes. An "image distance" is computed each pair graphical representations sequences, distances are visualized as Molecular Distance Map: Each point on map represents sequence, spatial proximity between two points reflects degree structural similarity corresponding sequences. The representation...
Abstract Background Studies exploring the potential of Chaos Game Representations (CGR) genomic sequences to act as “genomic signatures” (to be species- and genome-specific) showed that CGR patterns nuclear organellar DNA same organism can very different. While hypothesis CGRs mitochondrial signatures was validated for a snapshot all sequenced genomes available in NCBI GenBank sequence database, our knowledge no such extensive analysis exists date. Results We analyzed an dataset, totalling...
Machine Learning with Digital Signal Processing and Graphical User Interface (MLDSP-GUI) is an open-source, alignment-free, ultrafast, computationally lightweight, standalone software tool interactive GUI for comparison analysis of DNA sequences. MLDSP-GUI a general-purpose that can be used variety applications such as taxonomic classification, disease virus subtype evolutionary analyses, among others.MLDSP-GUI cross-platform compatible, available under the terms Creative Commons Attribution...