24 papers · ranked by Valyu relevance
Sean A. S. Anderson, Sachin Kaushik, Daniel R. Matute
A powerful but poorly understood analysis in ecology and evolutionary biology is the comparative study of lineage-pair traits. “Lineage-pair traits” are characters like ‘diet niche overlap’ and ‘strength of reproductive isolation’ that are defined for pairs of lineages instead of individual taxa. Comparative tests for…
Haibao Tang, Vivek Krishnakumar, Xiaofei Zeng, Zhougeng Xu + 8 more
'Adam Taranto' 'Johnathan S. Lomas' 'Yixing Zhang' 'Yumin Huang' 'Yibin Wang' 'Won Cheol Yim' 'Jisen Zhang' 'Xingtan Zhang'] Title: Abstract The life cycle of genome builds spans interlocking pillars of assembly, annotation, and comparative genomics to drive biological insights. While tools exist to address each pillar…
Ioannis G. Kiachidis, Dimitrios Baltatzis
To fight against the evolution of malware and its development, the specific methodologies that are applied by the malware analysts are crucial. Yet, this is something often overlooked in the relevant bibliography or in the formal and informal training of the relevant professionals. There are only two generic and…
Kalen Clifton, Vivien Jiang, Rafael dos Santos Peixoto, Srujan Singh + 3 more
Comparative analysis of spatial transcriptomics (ST) data is needed to identify genes that spatially change in their expression patterns between conditions, such as in diseased versus healthy tissues. Existing methods, including those developed for and adapted from non-spatial transcriptomics, generally focus on…
Yansong Huang, Zherui Zhang, Ao Jiao, Yuxin Ma + 1 more
Based on the identified considerations and analytical tasks, we have developed a visual analytics framework to support comparative analysis between EMO algorithms. Our framework consists of two main stages in the workflow: Similarity Modeling. As a data preprocessing stage, the logs recording the evolutionary processes…
Philip S. Rosenberg, Adalberto Miranda-Filho, David C. Whiteman
Background Cancer surveillance researchers analyze incidence or mortality rates jointly indexed by age group and calendar period using age-period-cohort models. Many studies consider age- and period-specific rates in two or more strata defined by sex, race/ethnicity, etc. A comprehensive characterization of trends and…
Carl M. Kobel, Velma T. E. Aho, Ove Øyås, Niels Nørskov-Lauritsen + 2 more
Here, we present CompareM2, a genomes-to-report pipeline for comparative analysis of bacterial and archaeal genomes derived from isolates and metagenomic assemblies. CompareM2 is easy to install and operate, and integrates community-adopted tools to perform genome quality control and annotation, taxonomic and…
Kun-Ting Chen, Arnaud Prouzeau, Joshua Langmead, Ryan T Whitelock-Jones + 5 more
'Ryan T Whitelock-Jones' 'Lee Lawrence' 'Tim Dwyer' 'Christophe Hurter' 'Daniel Weiskopf' 'Sarah Goodwin'] We present a novel, web-based visual eye-tracking analytics tool called Gazealytics. Our open-source toolkit features a unified combination of gaze analytics features that support flexible exploratory analysis…
Ali Zeytoon-Nejad
This paper presents a novel quantitative approach for comparative economic studies, addressing limitations in current classifcation methods. Conventional approaches in comparative economics often rely on ad hoc and categorical classifcations, leading to subjective judgments and disregarding the continuous nature of the…
Fabricio Almeida-Silva, Yves Van de Peer
Comparative genomics has become an indispensable part of modern biology due to the advancements in high-throughput sequencing technologies and the accumulation of genomic data in public databases. However, the quality of genomic data and the choice of parameters used in software tools used for comparative genomics can…
Zachary Konkel, Jason C. Slot
Comparative genomics comprises analyses that investigate the genetic basis of organismal biology and ecology, which have also been applied to high throughput trait screening for applied purposes. The number of fungal genomes deposited in publicly available databases are currently in exponential growth. Due to the…
Alexander R. Bennett, Jon Lundstrøm, Sayantani Chatterjee, Morten Thaysen-Andersen + 1 more
Comparative glycomics data are an instance of compositional data defined by the Aitchison simplex, where measured glycans are parts of a whole, indicated by relative abundances, which are then compared between conditions. Applying traditional statistical analyses to this type of data often results in misleading…
Mirka Henninger, Simone Malejka, Johannes Titz
Researchers in psychology traditionally use analysis of variance to examine differences between multiple groups or conditions. A less well-known, but valuable alternative is contrast analysis - a simple statistical method for testing directional, theoretically motivated hypotheses that are defined prior to data…
Authors not listed
The study aims to build upon previous research by incorporating Density Functional Theory (DFT), specifically using the B3LYP functional, to improve the computational methodology for analyzing chlorobutadiene (TCBD) compounds. DFT is chosen for its ability to account for electron correlation effects beyond the…
Gao Jiang, Juan-Yu Zheng, Shu-Ning Ren, Weilun Yin + 3 more
'Yun Li' 'Hou-Ling Wang'] Background Current RNA-seq analysis software for RNA-seq data tends to use similar parameters across different species without considering species-specific differences. However, the suitability and accuracy of these tools may vary when analyzing data from different species, such as humans…
Alexander Muacevic, John R Adler, Frederick Strale Jr.
Using simulated data with duplicate observational data points, this research aims to highlight the notable efficiency of repeated measures analysis of variance (ANOVA) compared to one-way ANOVA as a more powerful statistical model. One of the principal advantages of repeated measures ANOVA is its design, in which each…
Hunter Dlugas, Xiang Zhang, Seongho Kim
In mass spectrometry (MS)-based metabolomics, compound identification relies on Liquid Chromatography-MS (LC-MS) and Gas Chromatography-MS (GC-MS). The most popular and efficient approach for this purpose is the comparison of similarity scores between experimental spectra and reference spectra. Among the various single…
Authors not listed
Background: Pharmaceutical batch scheduling in multi-reactor configurations presents complex optimization challenges under operational uncertainty, yet limited research addresses how parallel processing capacity affects heuristic performance and predictive modeling. Objectives: This study investigated scheduling…
Hélio Amante Miot
Many different study designs involve the analysis of the same subject (or experimental unit) in different situations or under repeated conditions ([gf0100]). This occurs in longitudinal time-dependent assessments (for example, before and after measures, clinical trials, studies of the progress over time of…
Yueqi Lu, Quan Zou
The study of plant genomics has significantly deepened our understanding of plant evolution and adaptation from a microscopic perspective [1,2]. The abundance of plant genomic data has empowered researchers to uncover molecular-level insights into plants’ ecological adaptability, stress resilience, and pest and disease…
Zijian Ding, Joel Chan
Analysis through Rapid Prototyping, Iteration and Curation Authors: ['Zijian Ding' 'Joel Chan'] Complex data analysis inherently seeks unexpected insights through exploratory visual analysis methods, transcending logical, stepby-step processing. However, existing interfaces such as notebooks and dashboards have…
James Swift, Matthew Arran Turner, James Christopher Reynolds
A rapid headspace analysis method for the authenticity testing of whiskies of different brands and years was developed for a low cost, deployable atmospheric pressure ionisation mass spectrometer, which required minimal sample preparation. Principal component analysis was applied to the time-averaged mass spectra, the…
Authors not listed
As time-resolved x-ray absorption spectroscopy experiments become more prevalent, new tools are required to process and analyze the large amounts of data measured efficiently. To address this growing demand, we developed autoXAS: a python package for easy, fast, and reproducible processing and analysis of in-situ and…
Authors not listed
Aluminum titanium nitride (AlxTi1-xN, 0<x<1) is a critical hard coating material for cutting tools due to its exceptional hardness, thermal stability, wear resistance, and oxidation resistance, all of which are influenced by its Al content. A common method to swiftly estimate the Al content is by the size of the…