Other Quantitative Biology
Machine learning is a modern approach to problem-solving and task automation. In particular, machine learning is concerned with the development and applications of algorithms that can recognize patterns in data and use them for predictive…
It is widely acknowledged that there is a diversity problem in genomics stemming from the vast underrepresentation of non-European genetic ancestry populations. While many challenges exist to address this gap, a major complicating factor is…
The use of population descriptors like race, ethnicity, and ancestry in science, medicine and public health has a long, complicated, and at times dark history, particularly for genetics, given the field's perceived importance for…
The aim of the study is to analyze viruses using parameters obtained from distributions of nucleotide sequences in the viral RNA. Seeking for the input data homogeneity, we analyze single-stranded RNA viruses only. Two approaches are used…
Eight experiments were conducted to test an oregano-essential-oil-based product (PRO) on performance, gut health, and nutrient absorption capacity in broilers. The first three, up to 14d and without specific challenges, tested the effects…
Diabetes is considered as an critical comorbidity linked with the latest coronavirus disease 2019 (COVID-19) which spreads through Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-Cov-2). The diabetic patients have higher threat of…
The recent opinion article "A decade of molecular cell atlases" by Stephen Quake narrates the incredible single-cell genomics technology advances that have taken place over the last decade, and how they have translated to increasingly…
Nymphaea caerulea is a valuable freshwater aquatic plant, not only because of its ornamental value but also its extractions for chemical and medical uses. It is necessary to store its seeds as backup resources. Cryopreservation is the…
The COronaVIrus Disease 2019 (COVID-19) pandemic that has had the world in its grip from the beginning of 2020, has resulted in an unprecedented level of public interest and media attention on the field of mathematical epidemiology. Ever…
COVID-19 is now a global pandemic, and an effective vaccine may be many months away. Over 100 years ago, Spanish flu fatalities were attenuated when doctors began treating patients with blood plasma donated by recovered (or convalesced)…
Life is confronted with computation problems in a variety of domains including animal behavior, single-cell behavior, and embryonic development. Yet we currently do not know of a naturally existing biological system that is capable of…
The imminent release of tissue atlases combining multi-channel microscopy with single cell sequencing and other omics data from normal and diseased specimens creates an urgent need for data and metadata standards that guide data deposition,…
Here we examine the evolution of beta-2 microglobulin in terms of its hydropathic shapes, a theoretical construct that has revealed important trends. The dynamics of many proteins are largely driven by interactions between the protein…
The GFF3 format is a common, flexible tab-delimited format representing the structure and function of genes or other mapped features (https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md). However, with increasing…
The early detection of cancer is a challenging problem in medicine. The blood sera of cancer patients are enriched with heterogeneous secretory lipid bound extracellular vesicles (EVs), which present a complex repertoire of information and…
Colorectal cancer refers to the cancer from the dentate line to the junction of rectosigmoid colon, which is one of the most common malignant tumors of the digestive tract. The treatment of colorectal cancer is controversial, so…
Our understanding of radiation induced cellular damage has greatly improved over the past decades. Despite this progress, there are still many obstacles to fully understanding how radiation interacts with biologically relevant cellular…
We present an open source model that allows quantitative prediction of the effects of testing on the rate of spread of COVID-19 described by R, the reproduction number, and on the degree of quarantine, isolation and lockdown required to…
A possible explanation based on first principles for the appearance of the Omicron variant of the SARS-CoV-2 virus is proposed involving coinfection with HIV. The gist is that the resultant HIV-induced immunocompromise allows SARS-CoV-2…
Neuroinflammation is a significant aspect of many neurological diseases of Homo sapiens, and the genes that are differentially expressed in this process should be well understood to gather the nature of such diseases. We have conducted a…