Modern bioinformatics
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The increasing complexity of data streams and computational processes in modern clinical health information systems makes reproducibility challenging. Clinical natural language processing (NLP) pipelines are routinely leveraged for the secondary use of data. Workflow management systems (WMS) have been widely used in bioinformatics to handle the reproducibility bottleneck.
12p vighostrider 25-05-2023 2 2 Download
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Protein classification is a task of paramount importance in various fields of biology. Despite the great momentum of modern implementation of protein classification, machine learning techniques such as Random Forest and Neural Network could not always be used for several reasons: Data collection, unbalanced classification or labelling of the data.
18p vihagrid 30-01-2023 5 3 Download
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The progress of medicine, science, technology, education, and culture improves, year by year, quality of life and life expectancy of the populace. The modern human has a chance to further improve the quality and duration of his/her life and the lives of his/her loved ones by bringing their lifestyle in line with their sequenced individual genomes.
23p vibeauty 23-10-2021 19 1 Download
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Modern metagenomic analysis of complex microbial communities produces large amounts of sequence data containing information on the microbiome in terms of bacterial, archaeal, viral and eukaryotic composition. The bioinformatics tools available are mainly devoted to profiling the bacterial and viral fractions and only a few software packages consider fungi.
7p visilicon2711 20-08-2021 10 1 Download
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Ontological concepts are useful for many different biomedical tasks. Concepts are difficult to recognize in text due to a disconnect between what is captured in an ontology and how the concepts are expressed in text. There are many recognizers for specific ontologies, but a general approach for concept recognition is an open problem.
29p vikentucky2711 26-11-2020 11 1 Download
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Modern DNA sequencing methods produce vast amounts of data that often requires mapping to a reference genome. Most existing programs use the number of mismatches between the read and the genome as a measure of quality.
17p vikentucky2711 26-11-2020 13 0 Download
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Integrating and analyzing heterogeneous genome-scale data is a huge algorithmic challenge for modern systems biology. Bipartite graphs can be useful for representing relationships across pairs of disparate data types, with the interpretation of these relationships accomplished through an enumeration of maximal bicliques.
18p vikentucky2711 26-11-2020 10 0 Download
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Ongoing advancements in cloud computing provide novel opportunities in scientific computing, especially for distributed workflows. Modern web browsers can now be used as high-performance workstations for querying, processing, and visualizing genomics’ “Big Data” from sources like The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) without local software installation or configuration.
12p vikentucky2711 26-11-2020 11 0 Download
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Understanding the relationship between diseases based on the underlying biological mechanisms is one of the greatest challenges in modern biology and medicine. Exploring disease-disease associations by using system-level biological data is expected to improve our current knowledge of disease relationships, which may lead to further improvements in disease diagnosis, prognosis and treatment.
13p vikentucky2711 26-11-2020 7 1 Download
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In modern biomedical research of complex diseases, a large number of demographic and clinical variables, herein called phenomic data, are often collected and missing values (MVs) are inevitable in the data collection process. Since many downstream statistical and bioinformatics methods require complete data matrix, imputation is a common and practical solution.
12p vikentucky2711 26-11-2020 14 0 Download
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Cellular organelles with genomes of their own (e.g. plastids and mitochondria) can pass genetic sequences to other organellar genomes within the cell in many species across the eukaryote phylogeny.
13p vikentucky2711 24-11-2020 9 1 Download
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Today’s modern research of B and T cell antigen receptors (the immunoglobulins (IG) or antibodies and T cell receptors (TR)) forms the basis for detailed analyses of the human adaptive immune system.
10p vikentucky2711 24-11-2020 7 1 Download
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Modern biotechnologies often result in high-dimensional data sets with many more variables than observations (n p). These data sets pose new challenges to statistical analysis: Variable selection becomes one of the most important tasks in this setting.
17p vikentucky2711 24-11-2020 10 1 Download
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The need for precise and stable taxonomic classification is highly relevant in modern microbiology. Parallel to the explosion in the amount of sequence data accessible, there has also been a shift in focus for classification methods.
13p vikentucky2711 24-11-2020 9 1 Download
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Computing alignments between two or more sequences are common operations frequently performed in computational molecular biology. The continuing growth of biological sequence databases establishes the need for their efficient parallel implementation on modern accelerators.
13p vioklahoma2711 19-11-2020 14 1 Download
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Biological/genetic data is a complex mix of various forms or topologies which makes it quite difficult to analyze. An abundance of such data in this modern era requires the development of sophisticated statistical methods to analyze it in a reasonable amount of time.
14p vioklahoma2711 19-11-2020 10 1 Download
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Adverse drug events (ADEs) constitute one of the leading causes of post-therapeutic death and their identification constitutes an important challenge of modern precision medicine. Unfortunately, the onset and effects of ADEs are often underreported complicating timely intervention.
17p vioklahoma2711 19-11-2020 14 1 Download
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Modern methods for mining biomolecular interactions from literature typically make predictions based solely on the immediate textual context, in effect a single sentence. No prior work has been published on extending this context to the information automatically gathered from the whole biomedical literature.
12p vioklahoma2711 19-11-2020 6 1 Download
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Cytotoxicity assays have been used by researchers to screen for cytotoxicity in compound libraries. Researchers can either look for cytotoxic compounds or screen “hits” from initial high-throughput drug screens for unwanted cytotoxic effects before investing in their development as a pharmaceutical.
7p vioklahoma2711 19-11-2020 6 1 Download
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Understanding complicated networks of interactions and chemical components is essential to solving contemporary problems in modern biology, especially in domains such as cancer and systems research. In these domains, biological pathway data is used to represent chains of interactions that occur within a given biological process.
13p vioklahoma2711 19-11-2020 10 1 Download