Related papers: A network approach to analyzing highly recombinant…
Understanding how viral mutant spectra organize and explore genotype space is essential for unraveling the mechanisms driving evolution at the finest scale. Here we use deep-sequencing data of an amplicon in the A2 protein of the RNA…
Improving the efficiency of malaria diagnosis is one of the main goals of current malaria research. We have recently developed a magneto-optical (MO) method which allows high-sensitivity detection of malaria pigment (hemozoin) crystals via…
Malaria is a life-threatening mosquito-borne blood disease, hence early detection is very crucial for health. The conventional method for the detection is a microscopic examination of Giemsa-stained blood smears, which needs a highly…
In medical genetics, each genetic variant is evaluated as an independent entity regarding its clinical importance. However, in most complex diseases, variant combinations in specific gene networks, rather than the presence of a particular…
Reconstructing interactions from observational data is a critical need for investigating natural biological networks, wherein network dimensionality (i.e. number of interacting components) is usually high and interactions are time-varying.…
The epidemiological behavior of Plasmodium vivax malaria occurs across spatial scales including within-host, population, and metapopulation levels. On the within-host scale, P. vivax sporozoites inoculated in a host may form latent…
Bacteria pose unique challenges for genome-wide association studies (GWAS) because of strong structuring into distinct strains and substantial linkage disequilibrium across the genome. While methods developed for human studies can correct…
RNA viruses form genetically diverse populations structured as mutant spectra, or quasispecies, whose internal organization influences their evolutionary and adaptive dynamics. While genetic diversity has been extensively characterized, the…
Motivation: Machine learning methods can be used to support scientific discovery in healthcare-related research fields. However, these methods can only be reliably used if they can be trained on high-quality and curated datasets. Currently,…
Viroids are small circular single-stranded infectious RNAs that are characterized by a relatively high mutation level. Knowledge of their sequence heterogeneity remains largely elusive, and, as yet, no strategy attempting to address this…
The article presents an application of Hidden Markov Models (HMMs) for pattern recognition on genome sequences. We apply HMM for identifying genes encoding the Variant Surface Glycoprotein (VSG) in the genomes of Trypanosoma brucei (T.…
We describe the Microbial Community Reconstruction ({\bf MCR}) Problem, which is fundamental for microbiome analysis. In this problem, the goal is to reconstruct the identity and frequency of species comprising a microbial community, using…
Sequence differences between the strains of bacteria comprising host-associated and environmental microbiota may play a role in community assembly and influence the resilience of microbial communities to disturbances. Tools for…
The diversity of virus populations within single infected hosts presents a major difficulty for the natural immune response as well as for vaccine design and antiviral drug therapy. Recently developed pyrophosphate based sequencing…
RNA virus populations will undergo processes of mutation and selection resulting in a mixed population of viral particles. High throughput sequencing of a viral population subsequently contains a mixed signal of the underlying clones. We…
Complex distribution networks are pervasive in biology. Examples include nutrient transport in the slime mold \emph{Physarum polycephalum} as well as mammalian and plant venation. Adaptive rules are believed to guide development of these…
Malaria is considered one of the deadliest diseases in today world which causes thousands of deaths per year. The parasites responsible for malaria are scientifically known as Plasmodium which infects the red blood cells in human beings.…
Plasmodium falciparum 70 kDa heat shock proteins (PfHsp70s) are expressed at all stages of the pathogenic erythrocytic phase of the malaria parasite lifecycle. There are six PfHsp70s, all of which have orthologues in other plasmodial…
In this paper, we suggested eleven protein targets to be used as possible vaccines against Plasmodium falciparum causative agent of almost two to three million deaths per year. A comprehensive analysis of protein target have been selected…
Understanding genetic variation, e.g., through mutations, in organisms is crucial to unravel their effects on the environment and human health. A fundamental characterization can be obtained by solving the haplotype assembly problem, which…