Papers 10,000
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#1Robert Warmerdam (UMCG: University Medical Center Groningen)H-Index: 3
#2Pauline Lanting (UMCG: University Medical Center Groningen)H-Index: 5
Last. Lude Franke (UMCG: University Medical Center Groningen)H-Index: 104
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Motivation null Identifying sample mix-ups in biobanks is essential to allow the repurposing of genetic data for clinical pharmacogenetics. Pharmacogenetic advice based on the genetic information of another individual is potentially harmful. Existing methods for identifying mix-ups are limited to datasets in which additional omics data (e.g., gene expression) is available. Cohorts lacking such data can only use sex, which can reveal only half of the mix-ups. Here, we describe Idefix, a method fo...
#2Paul ZahariasH-Index: 5
Last. Tandy WarnowH-Index: 70
view all 0 authors...
#1Thea Van Rossum (EBI: European Bioinformatics Institute)
#2Paul Igor Costea (EBI: European Bioinformatics Institute)H-Index: 1
Last. Peer Bork (Yonsei University)H-Index: 223
view all 7 authors...
Summary null Taxonomic analysis of microbial communities is well supported at the level of species and strains. However, species can contain significant phenotypic diversity and strains are rarely widely shared across global populations. Stratifying the diversity between species and strains can identify "subspecies", which are a useful intermediary. High-throughput identification and profiling of subspecies is not yet supported in the microbiome field. Here, we use an operational definition of s...
Last. Min Xu (CMU: Carnegie Mellon University)H-Index: 21
view all 8 authors...
Cryo-Electron Tomography (cryo-ET) is a 3D imaging technology that enables the visualization of subcellular structures in situ at near-atomic resolution. Cellular cryo-ET images help in resolving the structures of macromolecules and determining their spatial relationship in a single cell, which has broad significance in cell and structural biology. Subtomogram classification and recognition constitute a primary step in the systematic recovery of these macromolecular structures. Supervised deep l...
#1Miroslav Kratochvíl (University of Luxembourg)H-Index: 6
#2Laurent Heirendt (University of Luxembourg)H-Index: 9
Last. Wei Gu (University of Luxembourg)H-Index: 18
view all 12 authors...
Summary null COBREXA.jl is a Julia package for scalable, high-performance constraint-based reconstruction and analysis of very large-scale biological models. Its primary purpose is to facilitate the integration of modern high performance computing environments with the processing and analysis of large-scale metabolic models of challenging complexity. We report the architecture of the package, and demonstrate how the design promotes analysis scalability on several use-cases with multi-organism co...
Motivation null CRISPR/Cas9-based technology allows for the functional analysis of genetic variants at single nucleotide resolution whilst maintaining genomic context (Findlay et al., 2018). This approach, known as saturation genome editing (SGE), a form of deep mutational scanning (DMS), systematically alters each position in a target region to explore its function. SGE experiments require the design and synthesis of oligonucleotide variant libraries which are introduced into the genome. This t...
#1Lucas S.P. Rudden (Durham University)H-Index: 2
#2Samuel C. Musson (Durham University)H-Index: 1
Last. Matteo T. Degiacomi (Durham University)H-Index: 23
view all 4 authors...
Motivation null The implementation of biomolecular modelling methods and analyses can be cumbersome, often carried out with in-house software re-implementing common tasks, and requiring the integration of diverse software libraries. null Results null We present Biobox, a Python-based toolbox facilitating the implementation of biomolecular modelling methods. null Availability null Biobox is freely available on, along with its API and interactive Jupyter notebook...
#1Zongyang Du (NKU: Nankai University)H-Index: 1
#2Zhenling Peng (SDU: Shandong University)H-Index: 1
Last. Jianyi Yang (NKU: Nankai University)H-Index: 28
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MOTIVATION Significant progress has been achieved in distance-based protein folding, due to improved prediction of inter-residue distance by deep learning. Many efforts are thus made to improve distance prediction in recent years. However, it remains unknown what is the best way of objectively assessing the accuracy of predicted distance. RESULTS A total of 19 metrics were proposed to measure the accuracy of predicted distance. These metrics were discussed and compared quantitatively on three be...
#1Guy Shtar (BGU: Ben-Gurion University of the Negev)H-Index: 3
#2Lior Rokach (BGU: Ben-Gurion University of the Negev)H-Index: 6
Last. Maya Berlin (TAU: Tel Aviv University)H-Index: 7
view all 6 authors...
Motivation null Teratogenic drugs can cause severe fetal malformation and therefore have critical impact on the health of the fetus, yet the teratogenic risks are unknown for most approved drugs. This paper proposes an explainable machine learning model for classifying pregnancy drug safety based on multimodal data and suggests an orthogonal ensemble for modeling multimodal data. To train the proposed model, we created a set of labeled drugs by processing over 100,000 textual responses collected...
#1Thomas Y. Sheffield (Oak Ridge Institute for Science and Education)H-Index: 3
#2Jason Brown (EPA: Environmental Protection Agency)H-Index: 1
Last. Richard S. Judson (EPA: Environmental Protection Agency)H-Index: 78
view all 5 authors...
SUMMARY Many applications of chemical screening are performed in concentration or dose-response mode, and it is necessary to extract appropriate parameters, including whether the chemical/assay pair is active and if so, what are concentrations where activity is seen. Typically, multiple mathematical models or curve shapes are tested against the data to assess the best fit. There are several commercial programs used for this purpose as well as open-source libraries. A widely used system for manag...
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