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CytoSpectre: a tool for spectral analysis of oriented structures on cellular ...
Background Orientation and the degree of isotropy are important in many biological systems such as the sarcomeres of cardiomyocytes and other fibrillar structures of the... -
Towards a phenome-wide catalog of human clinical traits impacted by genetic a...
Background Racial/ethnic differences for commonly measured clinical variables are well documented, and it has been postulated that population-specific genetic factors may play a... -
ClonoCalc and ClonoPlot: immune repertoire analysis from raw files to publica...
Background Next generation sequencing (NGS) technologies enable studies and analyses of the diversity of both T and B cell receptors (TCR and BCR) in human and animal systems to... -
SnoReport 2.0: new features and a refined Support Vector Machine to improve s...
Background snoReport uses RNA secondary structure prediction combined with machine learning as the basis to identify the two main classes of small nucleolar RNAs, the box H/ACA... -
AutoSOME: a clustering method for identifying gene expression modules without...
Abstract Background Clustering the information content of large high-dimensional gene expression datasets has widespread application in "omics" biology. Unfortunately, the... -
"CellProfiler Tracer: exploring and validating high-throughput, time-lapse mi...
Background Time-lapse analysis of cellular images is an important and growing need in biology. Algorithms for cell tracking are widely available; what researchers have been... -
An Eigenvalue test for spatial principal component analysis
AbstractBackgroundThe spatial Principal Component Analysis (sPCA, Jombart 2008) is designed to investigate non-random spatial distributions of genetic variation. Unfortunately,... -
MetaDiff: differential isoform expression analysis using random-effects meta-...
Background RNA sequencing (RNA-Seq) allows an unbiased survey of the entire transcriptome in a high-throughput manner. A major application of RNA-Seq is to detect differential... -
A generic schema and data collection forms applicable to diverse entomologica...
Background Standardized schemas, databases, and public data repositories are needed for the studies of malaria vectors that encompass a remarkably diverse array of designs and... -
Handling missing rows in multi-omics data integration: multiple imputation in...
Background In omics data integration studies, it is common, for a variety of reasons, for some individuals to not be present in all data tables. Missing row values are... -
QUADrATiC: scalable gene expression connectivity mapping for repurposing FDA-...
Background Gene expression connectivity mapping has proven to be a powerful and flexible tool for research. Its application has been shown in a broad range of research topics,... -
Leveraging 3D chemical similarity, target and phenotypic data in the identifi...
Background Drug-target identification is crucial to discover novel applications for existing drugs and provide more insights about mechanisms of biological actions, such as... -
Tackling the challenges of matching biomedical ontologies
Background Biomedical ontologies pose several challenges to ontology matching due both to the complexity of the biomedical domain and to the characteristics of the ontologies... -
Badapple: promiscuity patterns from noisy evidence.
Background Bioassay data analysis continues to be an essential, routine, yet challenging task in modern drug discovery and chemical biology research. The challenge is to infer... -
Hybrid open access—A longitudinal study
Abstract This study estimates the development of hybrid open access (OA), i.e. articles published openly on the web within subscription-access journals. Included in the study... -
The growth process of higher education institutions and public policies
This paper investigates the growth over time of the size of higher education institutions (HEIs), as measured by the number of academic staff, and its association with HEI and... -
Addressing inaccuracies in BLOSUM computation improves homology search perfor...
Background BLOSUM matrices belong to the most commonly used substitution matrix series for protein homology search and sequence alignments since their publication in 1992. In... -
"MRMPlus: an open source quality control and assessment tool for SRM/MRM assa...
Background Selected and multiple reaction monitoring involves monitoring a multiplexed assay of proteotypic peptides and associated transitions in mass spectrometry runs. To... -
Pattern measures of sedentary behaviour in adults: A literature review
Objective: With sensors, we are increasingly able to assess sitting behaviour during the day. However, there is no consensus among researchers on the best outcome measures for... -
Optimal prediction of decisions and model selection in social dilemmas using ...
Abstract Advancing our understanding of human behavior hinges on the ability of theories to unveil the mechanisms underlying such behaviors. Measuring the ability of theories...
