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1. MAGE: Strain Level Profiling of Metagenome Samples

   Metagenomic profiling from sequencing data aims to disentangle a microbial sample at lower ranks of taxonomy, such as species and strains. Deep...

   Vidushi Walia, V. G. Saipradeep, ... Naveen Sivadasan in Comparative Genomics

   Conference paper 2023
   

2. CONSULT-II: Taxonomic Identification Using Locality Sensitive Hashing

   Metagenomics is widely used to study the microbiome using environmental samples, and taxonomic classification of reads is a precursor to many...

   Ali Osman Berk Şapcı, Eleonora Rachtman, Siavash Mirarab in Comparative Genomics

   Conference paper 2023
   

3. OHMI: the ontology of host-microbiome interactions

   Background

   Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several...

   Yongqun He, Haihe Wang, ... Jihad S. Obeid in Journal of Biomedical Semantics

   Article Open access 30 December 2019
   

4. Symmetries and the Genetic Code

   This essay is devoted to a few results in investigating symmetries in the genetic coding system. The focus is on symmetry relationships in the...

   Sergey V. Petoukhov, Elena S. Petukhova, Vladimir V. Verevkin in Complex Symmetries

   Chapter 2021
   

5. Levels and building blocks—toward a domain granularity framework for the life sciences

   Background

   With the emergence of high-throughput technologies, Big Data and eScience, the use of online data repositories and the establishment of new...

   Lars Vogt in Journal of Biomedical Semantics

   Article Open access 28 January 2019
   

6. MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions

   Background

   MicrO is an ontology of microbiological terms, including prokaryotic qualities and processes, material entities (such as cell components),...

   Carrine E. Blank, Hong Cui, ... Ramona L. Walls in Journal of Biomedical Semantics

   Article Open access 12 April 2016
   

7. The Orthology Ontology: development and applications

   Background

   Computational comparative analysis of multiple genomes provides valuable opportunities to biomedical research. In particular, orthology...

   Jesualdo Tomás Fernández-Breis, Hirokazu Chiba, ... Ikuo Uchiyama in Journal of Biomedical Semantics

   Article Open access 04 June 2016
   

8. An Evolution Model for Sequence Length Based on Residue Insertion–Deletion Independent of Substitution: An Application to the GC Content in Bacterial Genomes

   We introduce here a gene evolution model which is an extension of the time-continuous stochastic IDIS model (Lèbre and Michel in J. Comput. Biol....

   Sophie Lèbre, Christian J. Michel in Bulletin of Mathematical Biology

   Article 30 May 2012
   

9. Computational methods in noncoding RNA research

   Non protein-coding RNAs (ncRNAs) are a research hotspot in bioinformatics. Recent discoveries have revealed new ncRNA families performing a variety...

   Ariane Machado-Lima, Hernando A. del Portillo, Alan Mitchell Durham in Journal of Mathematical Biology

   Article 04 September 2007

10. Information capacity of nucleotide sequences and Its applications

    The information capacity of nucleotide sequences is defined through the specific entropy of frequency dictionary of a sequence determined with...

    M. G. Sadovsky in Bulletin of Mathematical Biology

    Article 07 April 2006

11. A multiple sequence comparison method

    This article presents a new method for the comparison of multiple macromolecular sequences. It is based on a hierarchical sequence synthesis...

    A. K. C. Wong, S. C. Chan, D. K. Y. Chiu in Bulletin of Mathematical Biology

    Article 01 March 1993

12. A survey of multiple sequence comparison methods

    Multiple sequence comparison refers to the search for similarity in three or more sequences. This article presents a survey of the exhaustive...

    S. C. Chan, A. K. C. Wong, D. K. Y. Chiu in Bulletin of Mathematical Biology

    Article 01 July 1992

13. Mathematical tools for molecular genetics data: An annotated bibliography

    An annotated bibliography of mathematical and computer analyses of protein and nucleic acid sequences is presented. The major subject areas...

    John R. Jungck, Robert M. Friedman in Bulletin of Mathematical Biology

    Article 01 July 1984