Browsing by Subject "Software"
Now showing items 1-20 of 43
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A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples.
(Genome Res, 2014-07)Unbiased next-generation sequencing (NGS) approaches enable comprehensive pathogen detection in the clinical microbiology laboratory and have numerous applications for public health surveillance, outbreak investigation, ... -
A functional analysis of the spacer of V(D)J recombination signal sequences.
(PLoS Biol, 2003-10)During lymphocyte development, V(D)J recombination assembles antigen receptor genes from component V, D, and J gene segments. These gene segments are flanked by a recombination signal sequence (RSS), which serves as the ... -
A new fully automated approach for aligning and comparing shapes.
(Anatomical record (Hoboken, N.J. : 2007), 2015-01)Three-dimensional geometric morphometric (3DGM) methods for placing landmarks on digitized bones have become increasingly sophisticated in the last 20 years, including greater degrees of automation. One aspect shared by ... -
A new phylogenetic data standard for computable clade definitions: the Phyloreference Exchange Format (Phyx).
(PeerJ, 2022-01)To be computationally reproducible and efficient, integration of disparate data depends on shared entities whose matching meaning (semantics) can be computationally assessed. For biodiversity data one of the most prevalent ... -
A robotics platform for automated batch fabrication of high density, microfluidics-based DNA microarrays, with applications to single cell, multiplex assays of secreted proteins.
(The Review of scientific instruments, 2011-09)Microfluidics flow-patterning has been utilized for the construction of chip-scale miniaturized DNA and protein barcode arrays. Such arrays have been used for specific clinical and fundamental investigations in which many ... -
A tutorial on Bayesian multi-model linear regression with BAS and JASP.
(Behavior research methods, 2021-12)Linear regression analyses commonly involve two consecutive stages of statistical inquiry. In the first stage, a single 'best' model is defined by a specific selection of relevant predictors; in the second stage, the regression ... -
Advances to Bayesian network inference for generating causal networks from observational biological data.
(Bioinformatics, 2004-12-12)MOTIVATION: Network inference algorithms are powerful computational tools for identifying putative causal interactions among variables from observational data. Bayesian network inference algorithms hold particular promise ... -
American Association of Physicists in Medicine Task Group 263: Standardizing Nomenclatures in Radiation Oncology.
(International journal of radiation oncology, biology, physics, 2018-03)A substantial barrier to the single- and multi-institutional aggregation of data to supporting clinical trials, practice quality improvement efforts, and development of big data analytics resource systems is the lack of ... -
apex: phylogenetics with multiple genes.
(Mol Ecol Resour, 2017-01)Genetic sequences of multiple genes are becoming increasingly common for a wide range of organisms including viruses, bacteria and eukaryotes. While such data may sometimes be treated as a single locus, in practice, a number ... -
Application description and policy model in collaborative environment for sharing of information on epidemiological and clinical research data sets.
(PLoS One, 2010-02-19)BACKGROUND: Sharing of epidemiological and clinical data sets among researchers is poor at best, in detriment of science and community at large. The purpose of this paper is therefore to (1) describe a novel Web application ... -
Assessment of LD matrix measures for the analysis of biological pathway association.
(Stat Appl Genet Mol Biol, 2010)Complex diseases will have multiple functional sites, and it will be invaluable to understand the cross-locus interaction in terms of linkage disequilibrium (LD) between those sites (epistasis) in addition to the haplotype-LD ... -
Automatic segmentation of seven retinal layers in SDOCT images congruent with expert manual segmentation.
(Opt Express, 2010-08-30)Segmentation of anatomical and pathological structures in ophthalmic images is crucial for the diagnosis and study of ocular diseases. However, manual segmentation is often a time-consuming and subjective process. This paper ... -
CMOS-based carbon nanotube pass-transistor logic integrated circuits.
(Nature communications, 2012-02)Field-effect transistors based on carbon nanotubes have been shown to be faster and less energy consuming than their silicon counterparts. However, ensuring these advantages are maintained for integrated circuits is a challenge. ... -
Compressive holography.
(2012)Compressive holography estimates images from incomplete data by using sparsity priors. Compressive holography combines digital holography and compressive sensing. Digital holography consists of computational image estimation ... -
Computational Methods for RNA Structure Validation and Improvement.
(Methods Enzymol, 2015)With increasing recognition of the roles RNA molecules and RNA/protein complexes play in an unexpected variety of biological processes, understanding of RNA structure-function relationships is of high current importance. ... -
CPAG: software for leveraging pleiotropy in GWAS to reveal similarity between human traits links plasma fatty acids and intestinal inflammation.
(Genome Biol, 2015-09-15)Meta-analyses of genome-wide association studies (GWAS) have demonstrated that the same genetic variants can be associated with multiple diseases and other complex traits. We present software called CPAG (Cross-Phenotype ... -
Creating and parameterizing patient-specific deep brain stimulation pathway-activation models using the hyperdirect pathway as an example.
(PloS one, 2017-01)<h4>Background</h4>Deep brain stimulation (DBS) is an established clinical therapy and computational models have played an important role in advancing the technology. Patient-specific DBS models are now common tools in both ... -
Detecting structure of haplotypes and local ancestry.
(Genetics, 2014-03)We present a two-layer hidden Markov model to detect the structure of haplotypes for unrelated individuals. This allows us to model two scales of linkage disequilibrium (one within a group of haplotypes and one between groups), ... -
f-treeGC: a questionnaire-based family tree-creation software for genetic counseling and genome cohort studies.
(BMC medical genetics, 2017-07-14)The Tohoku Medical Megabank project aims to create a next-generation personalized healthcare system by conducting large-scale genome-cohort studies involving three generations of local residents in the areas affected by ... -
FlowKit: A Python Toolkit for Integrated Manual and Automated Cytometry Analysis Workflows.
(Frontiers in immunology, 2021-01)An important challenge for primary or secondary analysis of cytometry data is how to facilitate productive collaboration between domain and quantitative experts. Domain experts in cytometry laboratories and core facilities ...
