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Multiple assemblies
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Ebook "Computational modeling of biological systems: From molecules to pathways" provides an overview of the established computational methods used for modeling biologically and medically relevant systems. Computational modeling is emerging as a powerful new approach to study and manipulate biological systems. Multiple methods have been developed to model, visualize, and rationally alter systems at various length scales, starting from molecular modeling and design at atomic resolution to cellular pathways modeling and analysis.
360p
duongthandue0501
28-02-2024
6
1
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This paper presents the analysis of sensitivity and uncertainty for the infinite multiplication factor (kinf) for the VVR-M2 typed HEU and LEU fuel assemblies of the Dalat nuclear research reactor (DNRR) using the MCNP6.1-Whisper1.1 code.
14p
vimelindagates
18-07-2022
7
2
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Software design - Lecture 18. The main topics covered in this chapter include: relationships between classes; specialized form of association i-e weak association; assembling a class from other classes; aggregation and multiplicity; composition – container and contained classes;...
11p
haoasakura
30-05-2022
14
3
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Lecture Computer Architecture and Assembly Language Programming - Lesson 10: Bit manipulation provide students with knowledge about signed/unsigned numbers; multiplication; shift instructions; rotate instructions;...
18p
linyanjun_2408
23-04-2022
17
2
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SKESA is a DeBruijn graph-based de-novo assembler designed for assembling reads of microbial genomes sequenced using Illumina. Comparison with SPAdes and MegaHit shows that SKESA produces assemblies that have high sequence quality and contiguity, handles low-level contamination in reads, is fast, and produces an identical assembly for the same input when assembled multiple times with the same or different compute resources.
13p
vigalileogalilei
27-02-2022
13
1
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Accurate fusion transcript detection is essential for comprehensive characterization of cancer transcriptomes. Over the last decade, multiple bioinformatic tools have been developed to predict fusions from RNA-seq, based on either read mapping or de novo fusion transcript assembly.
16p
vielonmusk
30-01-2022
15
0
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The majority of eukaryotic genomes are unfinished due to the algorithmic challenges of assembling them. A variety of assembly and scaffolding tools are available, but it is not always obvious which tool or parameters to use for a specific genome size and complexity.
14p
vialfrednobel
29-01-2022
17
0
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We introduce STrain Resolution ON assembly Graphs (STRONG), which identifies strains de novo, from multiple metagenome samples. STRONG performs coassembly, and binning into metagenome assembled genomes (MAGs), and stores the coassembly graph prior to variant simplification.
34p
viarchimedes
26-01-2022
10
0
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While long-read sequencing allows for the complete assembly of bacterial genomes, long-read assemblies contain a variety of errors. Here, we present Trycycler, a tool which produces a consensus assembly from multiple input assemblies of the same genome. Benchmarking showed that Trycycler assemblies contained fewer errors than assemblies constructed with a single tool.
17p
viarchimedes
26-01-2022
9
0
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The majority of eukaryotic promoters utilize multiple transcription start sites (TSSs). How multiple TSSs are specified at individual promoters across eukaryotes is not understood for most species. In Saccharomyces cerevisiae, a preinitiation complex (PIC) comprised of Pol II and conserved general transcription factors (GTFs) assembles and opens DNA upstream of TSSs.
31p
viarchimedes
26-01-2022
7
0
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Quantitative structure–activity relationship (QSAR) analysis of 28 quinoline-arylamidine (CQArA) hybrids against two leukemia cells, K562 and Raji, was performed. Multiple linear regression (MLR) models were obtained by genetic algorithm. The best models involved the following descriptors: radial distribution function (RDF) descriptors, GETAWAY (GEometry, Topology, and Atom-Weights AssemblY) descriptor, bond information content index, and dipole moment. The best MLR models for K562 and Raji cells demonstrated satisfactory stability in internal and external validation.
16p
tudichquannguyet
29-11-2021
7
1
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New insights into the phylogenetics and population structure of the prairie falcon (Falco mexicanus)
Management requires a robust understanding of between- and within-species genetic variability, however such data are still lacking in many species. For example, although multiple population genetics studies of the peregrine falcon (Falco peregrinus) have been conducted, no similar studies have been done of the closelyrelated prairie falcon (F. mexicanus) and it is unclear how much genetic variation and population structure exists across the species’ range.
14p
vibeauty
23-10-2021
12
1
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Genomes rearrangements carry valuable information for phylogenetic inference or the elucidation of molecular mechanisms of adaptation. However, the detection of genome rearrangements is often hampered by current deficiencies in data and methods: Genomes obtained from short sequence reads have generally very fragmented assemblies, and comparing multiple gene orders generally leads to computationally intractable algorithmic questions.
15p
vibeauty
23-10-2021
11
0
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Relationships between an organism and its environment can be fundamental in the understanding how populations change over time and species arise. Local ecological conditions can shape variation at multiple levels, among these are the evolutionary history and trajectories of coding genes.
13p
visilicon2711
20-08-2021
9
1
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Obligate sulfur oxidizing chemolithoauthotrophic strains of Hydrogenovibrio crunogenus have been isolated from multiple hydrothermal vent associated habitats. However, a hydrogenase gene cluster (encoding the hydrogen converting enzyme and its maturation/assembly machinery) detected on the first sequenced H. crunogenus strain (XCL-2) suggested that hydrogen conversion may also play a role in this organism.
19p
visilicon2711
20-08-2021
12
1
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Sulforaphane is a natural isothiocyanate available from cruciferous vegetables with multiple characteristics including antioxidant, antitumor and anti-inflammatory effect. Single-molecule real-time (SMRT) sequencing has been used for long-read de novo assembly of plant genome.
13p
visilicon2711
20-08-2021
9
1
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The assembly of animal microbiomes is influenced by multiple environmental factors and host genetics, although the relative importance of these factors remains unclear. Bifidobacteria (genus Bifidobacterium, phylum Actinobacteria) are common first colonizers of gut microbiomes in humans and inhabit other mammals, social insects, food, and sewages.
12p
vijeeni2711
24-07-2021
11
0
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Advances in sequencing technologies have led to the release of reference genomes and annotations for multiple individuals within more well-studied systems. While each of these new genome assemblies shares significant portions of synteny between each other, the annotated structure of gene models within these regions can differ.
13p
vijeeni2711
24-07-2021
19
0
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Musculoskeletal Diseases (MSDs) are among the most prevalent health problems encountered in the workforce in Europe. Multiple risk factors contribute to their onset. In the present study, different individual risk factors for chronic tendinous pathology affecting the shoulder were analysed in a sample of workers from the automotive manufacturing sector.
8p
vimariana2711
22-12-2020
12
0
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The k-mer counting problem, which is to build the histogram of occurrences of every k-symbol long substring in a given text, is important for many bioinformatics applications. They include developing de Bruijn graph genome assemblers, fast multiple sequence alignment and repeat detection.
12p
viwyoming2711
16-12-2020
16
1
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