Related papers: Pan-genome Analysis of Angiosperm Plastomes using …
Motivation: Alternative splicing is an important mechanism in which the regions of pre-mRNAs are differentially joined in order to form different transcript isoforms. Alternative splicing is involved in the regulation of normal…
Tumors often contain multiple subpopulations of cancerous cells defined by distinct somatic mutations. We describe a new method, PhyloWGS, that can be applied to WGS data from one or more tumor samples to reconstruct complete genotypes of…
Tumor microenvironment has complex effects on tumorigenesis and metastasis. However, there is still a lack of comprehensive understanding of the relationship among molecular and cellular characteristics in tumor microenvironment, clinical…
The Quadrant-Slope Index (QSI) method was created in order to detect subtle patterns of organization in tumor images that have metaplastic elements, such as streams of spindle cells [1]. However, metaplastic tumors also have nuclei that may…
We present molecular phylogenetic investigation of Thuidiaceae, especially on Thudium and Pelekium. Three chloroplast sequences (trnL-F, rps4, and atpB-rbcL) and one nuclear sequence (ITS) were analyzed. Data partitions were analyzed…
A looming question that must be solved before robotic plant phenotyping capabilities can have significant impact to crop improvement programs is scalability. High Throughput Phenotyping (HTP) uses robotic technologies to analyze crops in…
Mining gene expression profiles has proven valuable for identifying signatures serving as surrogates of cancer phenotypes. However, the similarities of such signatures across different cancer types have not been strong enough to conclude…
A key challenge in genomics is to identify genetic variants that distinguish patients with different survival time following diagnosis or treatment. While the log-rank test is widely used for this purpose, nearly all implementations of the…
Affordable, high-quality whole-genome assemblies have made it possible to construct rich pangenomes that capture haplotype diversity across many species. As these datasets grow, they motivate the development of specialized techniques…
The exploration of cellular heterogeneity within the tumor microenvironment (TME) via single-cell RNA sequencing (scRNA-seq) is essential for understanding cancer progression and response to therapy. Current scRNA-seq approaches, however,…
One of the important questions in biological evolution is to know if certain changes along protein coding genes have contributed to the adaptation of species. This problem is known to be biologically complex and computationally very…
Parallel coordinates plot (PCP) is an excellent tool for multivariate visualization and analysis, but it may fail to reveal inherent structures for datasets with a large number of items. In this paper, we propose a suite of novel…
Pan-genome analysis is a standard procedure to decipher genome heterogeneity and diversification of bacterial species. Specie evolution is traced by defining and comparing the core (conserved), accessory (dispensable) and unique…
The grammars used in grammar-based Genetic Programming (GP) methods have a significant impact on the quality of the solutions generated since they define the search space by restricting the solutions to its syntax. In this work, we propose…
Cretaceous-Cenozoic history of angiosperms led to the a certain character of the distribution of taxa of different levels (the number of species and genera in families, species/genera ratio in families, the number of species in the genera).…
The Kolmogorov-Arnold stochasticity parameter technique is applied for the first time to the study of cancer genome sequencing, to reveal mutations. Using data generated by next generation sequencing technologies, we have analyzed the exome…
Genome editing allows scientists to change an organism's DNA. One promising genome editing protocol, already validated in living organisms, is based on clustered regularly interspaced short palindromic repeats (CRISPR)/Cas protein-nucleic…
We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…
The characterization of Tumor MicroEnvironment (TME) is challenging due to its complexity and heterogeneity. Relatively consistent TME characteristics embedded within highly specific tissue features, render them difficult to predict. The…
In this work, we applied the Chaos Game Representation (CGR) to the complete human genomic sequence T2T-CHM13v2.0, analyzing the entire chromosome assembly and each chromosome separately, including mitochondrial DNA. Multifractal spectra…