Research Papers/Topics in Bioinformatics

A mentorship and incubation program using project-based learning to build a professional bioinformatics pipeline in Kenya

Abstract: The demand for well-trained bioinformaticians to support genomics research continues to rise. Unfortunately, undergraduate training in Kenya does not prepare students for specialization in bioinformatics. Graduates are often unaware of the career opportunities in bioinformatics, and those who are may lack mentors to help them choose a specialization. The Bioinformatics Mentorship and Incubation Program seeks to bridge the gap by laying the foundation for a bioinformatics training p...

Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Abstract: In March 2021, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by four families (Aliusviridae, Crepuscuviridae, Myriaviridae, and Natareviridae), three subfamilies (Alpharhabdovirinae, Betarhabdovirinae, and Gammarhabdovirinae), 42 genera, and 200 species. Thirty-nine species were renamed and/or moved and seven species were abolished. This...

Structural and Functional Annotation of Hypothetical Proteins from the Microsporidia Species Vittaforma corneae ATCC 50505 Using in silico Approaches

Abstract: Microsporidia are spore-forming eukaryotes that are related to fungi but have unique traits that set them apart. They have compact genomes as a result of evolutionary gene loss associated with their complete dependency on hosts for survival. Despite having a relatively small number of genes, a disproportionately high percentage of the genes in microsporidia genomes code for proteins whose functions remain unknown (hypothetical proteins—HPs). Computational annotation of HPs has be...

Coding of tsetse repellents by olfactory sensory neurons: towards the improvement and the development of novel tsetse repellents

Abstract: Tsetse flies are the biological vectorsof human and animal trypanosomiasisand hence representant medical and veterinary importance. The sense of smell plays a significant role in tsetse and its ecological interaction, such as finding blood meal source, resting, and larvicidal sitesand for mating. Tsetse olfactory behaviour can be exploited for their management;however, olfactory studies in tsetse flies are still fragmentary. Here in my PhD thesis, usingscanning electron microscopy,...

Genome Sequence Of Tsetse Polydnavirus: Insights Into Symbiotic Virus Evolution

Abstract: Tsetse flies are the sole vectors of African trypanosomiasis in humans (sleeping sickness) and animals (nagana). The whole genome sequence of the tsetse fly Glossina morsitans morsitans revealed the presence of putative bracoviral sequences (n = 310) widely spread in the genome. These sequences are similar to those identified in parasitic braconid wasps. Bracoviruses (family Polydnaviridae) encode proteins that lower host immunity allowing for the development of parasitoid larvae i...

Modelling the Transmission Dynamics of African Animal Trypanosomiasis; A Case Study of Shimba Hills, Kwale County, Kenya

Abstract: African Animal Trypanosomiasis (AAT) is caused by parasites of the species Trypanosoma vivax, Trypanosoma congolense, and Trypanosoma rhodesiense. Of 48 sub-Saharan African nations, 36 have endemic cases of AAT. The disease is prevalent in savannah and woodland areas. It poses a major threat to livestock production and health in agro-pastoralist communities, many of which are located along the boundaries of wildlife reserves. Most epidemiological studies on AAT around Shimba Hills ...

Research and development of a weighted most recent common ancester algorithm for metagenomic taxonomic assignment

Abstract: The new generation of metagenomics has gained tremendous popularity in recent years. This has been majorly due to rapid advances in DNA sequencing technology, which has produced large amounts of sequence data in relatively shorter times, compared to conventional DNA sequencing methods. There is a need to taxonomically characterise these data by assigning individual sequence reads to their constituent taxa. However, there is lack of up-to-date and customized software tools to accomp...

Structure of the 40 S ribosomal subunit from Plasmodium falciparum By Homology and De novo modeling

Abstract: Generation of the three dimensional structures of macromolecules using in silico structural modeling technologies such as homology and de novo modeling has improved dramatically and increased the speed in which tertiary structures of organisms of interest can be generated. This is especially the case if a homologous crystal structure is already available. High resolution structures can be rapidly created using only their sequence information as input and thus increasing the speed o...

Characterization of dark and pale forms of frankliniella schultzei (trybom) – an ecological, biological, morphological and molecular approach

Abstract: Frankliniella schultzei Trybom is an important pest of ornamental and vegetable crops worldwide and a vector of Tospoviruses, which are plant viruses belonging to the family Bunyaviridae. It occurs as two color forms (dark and pale) which are morphologically very similar hence has been considered as one species. However, differences in vector competency and geographic spread has led to debate on whether they are one or separate species. Moreover, evidence is lacking on whether thes...

Comparison of the Patterns of Spread of Human Metapneumovirus (hmpv) and Respiratory Syncytial Virus (rsv) in Africa using virus sequence data

Abstract: Background: Human metapneumovirus(HMPV) and respiratory syncytial virus (RSV) are the leading causes of viral severe acute respiratory diseasein childhood. They are related viruses from the Pneumoviridaefamily andshow overlapping clinical, epidemiological and transmission features.Whether the two viruses also share similar patterns of geographic spread remains unknown; this may provide insight on common modalities of control. Materials and Methods:Using 232 HMPV and 842 RSV attachm...

Comparing Mitochondrial Gene Sequences of Aedes Aegypti in East Africa to the Global Anthropophilic Strain

Abstract: Advances in genotyping methods have shed more light into mosquito genetics and improved our understanding of vector-borne disease transmission cycles. Outside of Africa, Aedes aegypti, the main vector of arboviruses such as dengue, chikungunya, yellow fever, and Zika viruses, prefers humans for a blood meal, resting and breeding in close association with human settlements. However, in its native African ecology, both domestic (Aedes aegypti aegypti) and sylvatic (forest) (Aedes aeg...

Computational biology in proteomics

The broad application of proteomics in different biological and medical fields, as well as the diffusion of high-throughput platforms, leads to increasing volumes of available proteomics data. Computational proteomics is the data science concerned with the identification and quantification of proteins from numerous data and the biological interpretation of their concentration changes, posttranslational modifications, interactions, and subcellular localizations. Computational proteomics is a h...

Drought Responsive Genes In Tea Cultivars Grown In Kenya.

ABSTRACT Tea is one of the most popular non-alcoholic beverages worlwide, and a leading foreign exchange earner and source of livelihood to over three million people in Kenya. However, tea growing areas in Kenya experience abiotic stresses with drought been the most predominant. Tea plants tolerate drought through poorly understood physiological, cellular/biochemical and molecular processes. Development of tea cultivars adapted to water-deficit stress greatly relies on an understanding of me...

Effects Of Repetitive DNA And Epigenetics On Human Genome Regulation

The highly developed and specialized anatomical and physiological characteristics observed for eukaryotes in general and mammals in particular are underwritten by an elaborate and intricate process of genome regulation. This precise control of the location, timing and amplitude of gene expression is achieved by a variety of genetic and epigenetic tools and mechanisms. Such tools include cis- and trans- transcriptional regulation, epigenetic marks and chromosomal conformation in the nucleus [7...

Phylogenetic and In Silico Analysis of Niemann-pick type C1 (NPC1) Transporter Required for Ebola Viral Entry

Ebola  virus  (EBOV) has recently emerged as a highly virulent organism of concern to humans. The pathology behind the hemorrhagic fever within an EBOV host remains largely unclear, and demands rather novel therapeutics to effectively eradicate this virus. The Niemann-pick type C1 (NPC1) protein cholesterol transporter is required for EBOV entry and internalization into a mammalian host cell. On this premise, an organism’s NPC1  can  decide  the  virus-species  specificity.  Here, ...


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