Search
Search Results
-
MaPPeRTrac: A Massively Parallel, Portable, and Reproducible Tractography Pipeline
Large-scale diffusion MRI tractography remains a significant challenge. Users must orchestrate a complex sequence of instructions that requires many...
-
Semiautomated pipeline for quantitative analysis of heart histopathology
BackgroundHeart diseases are among the leading causes of death worldwide, many of which lead to pathological cardiomyocyte hypertrophy and capillary...
-
A Novel Integrated Pipeline for Site-Specific Quantification of N-glycosylation
The site-specific N-glycosylation changes of human plasma immunoglobulin gamma molecules (IgGs) have been shown to modulate the immune response and...
-
Associations between the choroid plexus and tau in Alzheimer’s disease using an active learning segmentation pipeline
BackgroundThe cerebrospinal fluid (CSF), primarily generated by the choroid plexus (ChP), is the major carrier of the glymphatic system. The...
-
Test development, optimization and validation of a WGS pipeline for genetic disorders
BackgroundWith advances in massive parallel sequencing (MPS) technology, whole-genome sequencing (WGS) has gradually evolved into the first-tier...
-
An optimized GATK4 pipeline for Plasmodium falciparum whole genome sequencing variant calling and analysis
BackgroundAccurate variant calls from whole genome sequencing (WGS) of Plasmodium falciparum infections are crucial in malaria population genomics....
-
Identification of potent antimicrobial peptides via a machine-learning pipeline that mines the entire space of peptide sequences
Systematically identifying functional peptides is difficult owing to the vast combinatorial space of peptide sequences. Here we report a...
-
MetaPro: a scalable and reproducible data processing and analysis pipeline for metatranscriptomic investigation of microbial communities
BackgroundWhole microbiome RNASeq (metatranscriptomics) has emerged as a powerful technology to functionally interrogate microbial communities. A key...
-
ProbaStem, a pipeline towards the first high-resolution probabilistic atlas of the whole human brainstem
The brainstem plays an essential role in many vital functions, such as autonomic control, consciousness and sleep, motricity, somatic afferent...
-
A robust pipeline for ranking carrier frequencies of autosomal recessive and X-linked Mendelian disorders
Single gene disorders are individually rare but collectively common leading causes of neonatal and pediatric morbidity and mortality. Both parents or...
-
A Computational Pipeline for Predicting Cancer Neoepitopes
Mutant Peptide eXtractor and Informer (MuPeXI), by Bjerregaard et al. (Cancer Immunol Immunother CII 66:1123–1130, 2017), is a program which...
-
Computational Pipeline for the Detection of Plant RNA Viruses Using High-Throughput Sequencing
In this chapter, we describe a computational pipeline for the in silico detection of plant viruses by high-throughput sequencing (HTS) from total RNA...
-
Identification and characterization of two DMD pedigrees with large inversion mutations based on a long-read sequencing pipeline
Pathogenic large inversions are rarely reported on DMD gene due to the lack of effective detection methods. Here we report two DMD pedigrees and...
-
MetaboDirect: an analytical pipeline for the processing of FT-ICR MS-based metabolomic data
BackgroundMicrobiomes are now recognized as the main drivers of ecosystem function ranging from the oceans and soils to humans and bioreactors....
-
Topological Data Analysis Captures Task-Driven fMRI Profiles in Individual Participants: A Classification Pipeline Based on Persistence
BOLD-based fMRI is the most widely used method for studying brain function. The BOLD signal while valuable, is beset with unique vulnerabilities. The...
-
In Silico Pipeline to Identify Tumor-Specific Antigens for Cancer Immunotherapy Using Exome Sequencing Data
Tumor-specific antigens or neoantigens are peptides that are expressed only in cancer cells and not in healthy cells. Some of these molecules can...
-
Validation of aortic valve pressure gradient quantification using semi-automated 4D flow CMR pipeline
ObjectiveDoppler echocardiographic aortic valve peak velocity and peak pressure gradient assessment across the aortic valve (AV) is the mainstay for...
-
A Computational Pipeline to Investigate Longitudinal Blood Flow Changes in the Circle of Willis of Patients with Stable and Growing Aneurysms
Changes in cerebral blood flow are often associated with the initiation and development of different life-threatening medical conditions including...
-
Predicting Persistent Aneurysm Filling After Pipeline Embolization Device Treatment in Patients with Intracranial Aneurysm: Development and External Validation of a Nomogram Model
The pipeline embolization device (PED) is an effective endovascular treatment modality for intracranial aneurysm (IA), but nearly one-fifth of IAs...
-
HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi
BackgroundLinking the identity of wild microbes with their ecophysiological traits and environmental functions is a key ambition for microbial...
