22,252 Result(s)
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Bioinformatics
Computer Appl. in Life Sciences
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Article
Open AccessMETASEED: a novel approach to full-length 16S rRNA gene reconstruction from short read data
With the emergence of Oxford Nanopore technology, now the on-site sequencing of 16S rRNA from environments is available. Due to the error level and structure, the analysis of such data demands some database of...
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Open AccessBenchmarking and integrating human B-cell receptor genomic and antibody proteomic profiling
Immunoglobulins (Ig), which exist either as B-cell receptors (BCR) on the surface of B cells or as antibodies when secreted, play a key role in the recognition and response to antigenic threats. The capability...
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Open AccessexpHRD: an individualized, transcriptome-based prediction model for homologous recombination deficiency assessment in cancer
Homologous recombination deficiency (HRD) stands as a clinical indicator for discerning responsive outcomes to platinum-based chemotherapy and poly ADP-ribose polymerase (PARP) inhibitors. One of the conventio...
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Open AccessBuilding RadiologyNET: an unsupervised approach to annotating a large-scale multimodal medical database
The use of machine learning in medical diagnosis and treatment has grown significantly in recent years with the development of computer-aided diagnosis systems, often based on annotated medical radiology image...
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Open AccessHow the brain can be trained to achieve an intermittent control strategy for stabilizing quiet stance by means of reinforcement learning
The stabilization of human quiet stance is achieved by a combination of the intrinsic elastic properties of ankle muscles and an active closed-loop activation of the ankle muscles, driven by the delayed feedba...
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Characteristics of the Structural Connectivity in Patients with Brain Injury and Chronic Health Symptoms: A Pilot Study
Diffusion properties from diffusion tensor imaging (DTI) are exquisitely sensitive to white matter abnormalities incurred during traumatic brain injury (TBI), especially for those patients with chronic post-TB...
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Open AccessTranscriptome- and DNA methylation-based cell-type deconvolutions produce similar estimates of differential gene expression and differential methylation
Changing cell-type proportions can confound studies of differential gene expression or DNA methylation (DNAm) from peripheral blood mononuclear cells (PBMCs). We examined how cell-type proportions derived from...
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Open AccessA strategy to detect metabolic changes induced by exposure to chemicals from large sets of condition-specific metabolic models computed with enumeration techniques
The growing abundance of in vitro omics data, coupled with the necessity to reduce animal testing in the safety assessment of chemical compounds and even eliminate it in the evaluation of cosmetics, highlights...
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Open AccessSimSpliceEvol2: alternative splicing-aware simulation of biological sequence evolution and transcript phylogenies
SimSpliceEvol is a tool for simulating the evolution of eukaryotic gene sequences that integrates exon-intron structure evolution as well as the evolution of the sets of transcripts produced from genes. It tak...
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Open Accessgcplyr: an R package for microbial growth curve data analysis
Characterization of microbial growth is of both fundamental and applied interest. Modern platforms can automate collection of high-throughput microbial growth curves, necessitating the development of computati...
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Open AccessProcaryaSV: structural variation detection pipeline for bacterial genomes using short-read sequencing
Structural variations play an important role in bacterial genomes. They can mediate genome adaptation quickly in response to the external environment and thus can also play a role in antibiotic resistance. The...
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Open AccessClassifying Neuronal Cell Types Based on Shared Electrophysiological Information from Humans and Mice
The brain is an intricate system that controls a variety of functions. It consists of a vast number of cells that exhibit diverse characteristics. To understand brain function in health and disease, it is cruc...
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Open AccessGenerative Modelling of Cortical Receptor Distributions from Cytoarchitectonic Images in the Macaque Brain
Neurotransmitter receptor densities are relevant for understanding the molecular architecture of brain regions. Quantitative in vitro receptor autoradiography, has been introduced to map neurotransmitter recep...
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Open AccessComputational gastronomy: capturing culinary creativity by making food computable
Cooking, a quintessential creative pursuit, holds profound significance for individuals, communities, and civilizations. Food and cooking transcend mere sensory pleasure to influence nutrition and public healt...
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Open AccessDeepvirusclassifier: a deep learning tool for classifying SARS-CoV-2 based on viral subtypes within the coronaviridae family
In this study, we present DeepVirusClassifier, a tool capable of accurately classifying Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) viral sequences among other subtypes of the coronaviridae fa...
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Open AccessA comprehensive review of computational cell cycle models in guiding cancer treatment strategies
This article reviews the current knowledge and recent advancements in computational modeling of the cell cycle. It offers a comparative analysis of various modeling paradigms, highlighting their unique strengt...
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Open AccessUnsupervised modeling of mutational landscapes of adeno-associated viruses viability
Adeno-associated viruses 2 (AAV2) are minute viruses renowned for their capacity to infect human cells and akin organisms. They have recently emerged as prominent candidates in the field of gene therapy, prima...
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Open AccessFilter bank temporally local multivariate synchronization index for SSVEP-based BCI
Multivariate synchronization index (MSI) has been successfully applied for frequency detection in steady state visual evoked potential (SSVEP) based brain–computer interface (BCI) systems. However, the standar...
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Open AccessSGCP: a spectral self-learning method for clustering genes in co-expression networks
A widely used approach for extracting information from gene expression data employs the construction of a gene co-expression network and the subsequent computational detection of gene clusters, called modules. WG...
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Open AccessHitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2
Fungi play a key role in several important ecological functions, ranging from organic matter decomposition to symbiotic associations with plants. Moreover, fungi naturally inhabit the human body and can be ben...
