Identification (biology)
View article: The 2016 revision to the World Health Organization classification of myeloid neoplasms and acute leukemia
The 2016 revision to the World Health Organization classification of myeloid neoplasms and acute leukemia Open
The World Health Organization (WHO) classification of tumors of the hematopoietic and lymphoid tissues was last updated in 2008. Since then, there have been numerous advances in the identification of unique biomarkers associated with some …
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Maftools: efficient and comprehensive analysis of somatic variants in cancer Open
Numerous large-scale genomic studies of matched tumor-normal samples have established the somatic landscapes of most cancer types. However, the downstream analysis of data from somatic mutations entails a number of computational and statis…
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Discovering governing equations from data by sparse identification of nonlinear dynamical systems Open
Significance Understanding dynamic constraints and balances in nature has facilitated rapid development of knowledge and enabled technology, including aircraft, combustion engines, satellites, and electrical power. This work develops a nov…
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MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis Open
We present a new update to MetaboAnalyst (version 4.0) for comprehensive metabolomic data analysis, interpretation, and integration with other omics data. Since the last major update in 2015, MetaboAnalyst has continued to evolve based on …
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PHASTER: a better, faster version of the PHAST phage search tool Open
PHASTER (PHAge Search Tool - Enhanced Release) is a significant upgrade to the popular PHAST web server for the rapid identification and annotation of prophage sequences within bacterial genomes and plasmids. Although the steps in the phag…
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mixOmics: An R package for ‘omics feature selection and multiple data integration Open
The advent of high throughput technologies has led to a wealth of publicly available 'omics data coming from different sources, such as transcriptomics, proteomics, metabolomics. Combining such large-scale biological data sets can lead to …
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RepeatModeler2 for automated genomic discovery of transposable element families Open
The accelerating pace of genome sequencing throughout the tree of life is driving the need for improved unsupervised annotation of genome components such as transposable elements (TEs). Because the types and sequences of TEs are highly var…
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HMDB 4.0: the human metabolome database for 2018 Open
The Human Metabolome Database or HMDB (www.hmdb.ca) is a web-enabled metabolomic database containing comprehensive information about human metabolites along with their biological roles, physiological concentrations, disease associations, c…
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The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications Open
UNITE (https://unite.ut.ee/) is a web-based database and sequence management environment for the molecular identification of fungi. It targets the formal fungal barcode-the nuclear ribosomal internal transcribed spacer (ITS) region-and off…
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Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data Open
Decontam improves the quality of metagenomic and marker-gene sequencing by identifying and removing contaminant DNA sequences. Decontam integrates easily with existing MGS workflows and allows researchers to generate more accurate profiles…
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In Defense of the Triplet Loss for Person Re-Identification Open
In the past few years, the field of computer vision has gone through a revolution fueled mainly by the advent of large datasets and the adoption of deep convolutional neural networks for end-to-end learning. The person re-identification su…
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Random Erasing Data Augmentation Open
In this paper, we introduce Random Erasing, a new data augmentation method for training the convolutional neural network (CNN). In training, Random Erasing randomly selects a rectangle region in an image and erases its pixels with random v…
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The DisGeNET knowledge platform for disease genomics: 2019 update Open
One of the most pressing challenges in genomic medicine is to understand the role played by genetic variation in health and disease. Thanks to the exploration of genomic variants at large scale, hundreds of thousands of disease-associated …
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Genomewide Association Study of Severe Covid-19 with Respiratory Failure Open
We identified a 3p21.31 gene cluster as a genetic susceptibility locus in patients with Covid-19 with respiratory failure and confirmed a potential involvement of the ABO blood-group system. (Funded by Stein Erik Hagen and others.).
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HMDB 5.0: the Human Metabolome Database for 2022 Open
The Human Metabolome Database or HMDB (https://hmdb.ca) has been providing comprehensive reference information about human metabolites and their associated biological, physiological and chemical properties since 2007. Over the past 15 year…
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Time to Treatment and Mortality during Mandated Emergency Care for Sepsis Open
More rapid completion of a 3-hour bundle of sepsis care and rapid administration of antibiotics, but not rapid completion of an initial bolus of intravenous fluids, were associated with lower risk-adjusted in-hospital mortality. (Funded by…
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VoxCeleb: A Large-Scale Speaker Identification Dataset Open
Most existing datasets for speaker identification contain samples obtained under quite constrained conditions, and are usually hand-annotated, hence limited in size. The goal of this paper is to generate a large scale text-independent spea…
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The ENCODE Blacklist: Identification of Problematic Regions of the Genome Open
Functional genomics assays based on high-throughput sequencing greatly expand our ability to understand the genome. Here, we define the ENCODE blacklist- a comprehensive set of regions in the human, mouse, worm, and fly genomes that have a…
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AACR Project GENIE: Powering Precision Medicine through an International Consortium Open
The AACR Project GENIE is an international data-sharing consortium focused on generating an evidence base for precision cancer medicine by integrating clinical-grade cancer genomic data with clinical outcome data for tens of thousands of c…
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MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics Open
Thanks to the development of high‐throughput sequencing technologies, target enrichment sequencing of nuclear ultraconserved DNA elements (UCEs) now allows routine inference of phylogenetic relationships from thousands of genomic markers. …
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3D Semantic Parsing of Large-Scale Indoor Spaces Open
In this paper, we propose a method for semantic parsing the 3D point cloud of an entire building using a hierarchical approach: first, the raw data is parsed into semantically meaningful spaces (e.g. rooms, etc) that are aligned into a can…
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SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information Open
Mass spectrometry is a predominant experimental technique in metabolomics and related fields, but metabolite structural elucidation remains highly challenging. We report SIRIUS 4 (https://bio.informatik.uni-jena.de/sirius/), which provides…
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A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor Open
Single-cell RNA sequencing (scRNA-seq) is widely used to profile the transcriptome of individual cells. This provides biological resolution that cannot be matched by bulk RNA sequencing, at the cost of increased technical noise and data co…
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Machine Learning for Medical Imaging Open
Machine learning is a technique for recognizing patterns that can be applied to medical images. Although it is a powerful tool that can help in rendering medical diagnoses, it can be misapplied. Machine learning typically begins with the m…
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A Systematic Study of Sustainable Development Goal (SDG) Interactions Open
Sustainable development goals (SDGs) have set the 2030 agenda to transform our world by tackling multiple challenges humankind is facing to ensure well‐being, economic prosperity, and environmental protection. In contrast to conventional d…
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CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins Open
CRISPR (clustered regularly interspaced short palin-dromic repeats) arrays and their associated (Cas) proteins confer bacteria and archaea adaptive immunity against exogenous mobile genetic elements, such as phages or plasmids. CRISPRCasFi…
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DeepDTA: deep drug–target binding affinity prediction Open
Motivation The identification of novel drug–target (DT) interactions is a substantial part of the drug discovery process. Most of the computational methods that have been proposed to predict DT interactions have focused on binary classific…
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Three-Dimensional in Vitro Cell Culture Models in Drug Discovery and Drug Repositioning Open
Drug development is a lengthy and costly process that proceeds through several stages from target identification to lead discovery and optimization, preclinical validation and clinical trials culminating in approval for clinical use. An im…
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Publicly Available Clinical Open
Contextual word embedding models such as ELMo and BERT have dramatically improved performance for many natural language processing (NLP) tasks in recent months. However, these models have been minimally explored on specialty corpora, such …
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PharmMapper 2017 update: a web server for potential drug target identification with a comprehensive target pharmacophore database Open
The PharmMapper online tool is a web server for potential drug target identification by reversed pharmacophore matching the query compound against an in-house pharmacophore model database. The original version of PharmMapper includes more …