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Analysis workflow
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Clear cell renal cell carcinoma (ccRCC) is the dominant subtype of renal cancer. With currently available therapies, cure of advanced and metastatic ccRCC is achieved only in rare cases. Here, we developed a workflow integrating different -omics technologies to identify ccRCC-specific HLA-presented peptides as potential drug targets for ccRCC immunotherapy.
24p
vibransone
28-03-2024
2
1
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Ebook "Difference gel electrophoresis: Methods and protocols" provides a comprehensive update of this key method on gel-based proteomics. Chapters present an introduction into the development of methods on principles of differential protein labeling and two-dimensional gel electrophoresis, techniques on optimized proteomic workflows using advanced mass spectrometry for protein identification, and the application of those methods in basic biological research, pathobiology and applied biomarker discovery.
310p
lucchinguyen
28-12-2023
6
2
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Ebook "Logistics transportation systems" compiles multiple topics on transportation logistics systems from both qualitative and quantitative perspectives, providing detailed examples of real-world logistics workflows. It explores the key concepts and problem-solving techniques required by researchers and logistics professionals to effectively manage the continued expansion of logistics transportation systems, which is expected to reach an estimated 25 billion tons in the United States alone by 2045.
444p
phuong10693
20-06-2023
5
0
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Our study documented communication workflows across adult day care centers (ADCs) and primary care providers (PCPs) around complex needs of persons living with dementia (PLWD). We also identified barriers and facilitators to productive communication in clinical decision support and clinical information systems.
9p
vighostrider
25-05-2023
7
2
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The DNA metabarcoding approach has become one of the most used techniques to study the taxa composition of various sample types. To deal with the high amount of data generated by the high-throughput sequencing process, a bioinformatics workflow is required and the QIIME2 platform has emerged as one of the most reliable and commonly used.
14p
vihagrid
30-01-2023
8
3
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In this study, we introduce a simple three-step workflow for a universally applicable RI system, to be used in GC×GC analysis of ignitable liquid residue (ILR) for arson investigations. The proposed RI system applies a combination of two well-established GC RI systems: non-isothermal Kovats (K) index in the first dimension and Lee (L) index in the second dimension.
10p
viginny
23-12-2022
11
3
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Structural elucidation of compounds detected with liquid chromatography coupled to high resolution mass spectrometry is a challenging and time-consuming step in the workflow of non-targeted analysis and often requires manual validation of the results. Retention time, alongside exact mass, isotope pattern, fragmentation spectra, and collision cross-section, is valuable information for ruling out unlikely structures and increasing the confidence in others.
12p
viginny
23-12-2022
6
2
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Velocity model technique is routinely used to convert data from the time-to-depth domain to support prospect evaluation, reservoir modelling, well engineering, and further drilling operation. In Vietnam, the conventional velocity model building workflow oversimplifies the interval velocities as only well interval velocities are populated into 2D grids for depth conversion or oversimplified calibration interval velocities by applying a single scaling factor function.
7p
viharry
14-12-2022
8
4
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In this paper, this drawback was intended to be addressed by the use of hexanol-based supramolecular solvents (SUPRAS) with restrictedaccess properties. The aim was to develop a fast and interference-free sample treatment workflow for the determination of opioids, cocaine, amphetamines and their metabolites in human hair.
11p
vironald
15-12-2022
5
2
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Sequencing errors are key confounding factors for detecting low-frequency genetic variants that are important for cancer molecular diagnosis, treatment, and surveillance using deep next-generation sequencing (NGS). However, there is a lack of comprehensive understanding of errors introduced at various steps of a conventional NGS workflow, such as sample handling, library preparation, PCR enrichment, and sequencing. In this study, we use current NGS technology to systematically investigate these questions.
15p
vigalileogalilei
27-02-2022
14
2
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Vector-borne diseases (VBDs) impact both human and veterinary medicine and pose special public health challenges. The main bacterial vector-borne pathogens (VBPs) of importance in veterinary medicine include Anaplasma spp., Bartonella spp., Ehrlichia spp., and Spotted Fever Group Rickettsia.
10p
vidarwin
23-02-2022
11
1
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Cytoscape is one of the most successful network biology analysis and visualization tools, but because of its interactive nature, its role in creating reproducible, scalable, and novel workflows has been limited. We describe Cytoscape Automation (CA), which marries Cytoscape to highly productive workflow systems, for example, Python/R in Jupyter/RStudio.
15p
vielonmusk
30-01-2022
19
1
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We present the software Condition-specific Regulatory Units Prediction (CRUP) to infer from epigenetic marks a list of regulatory units consisting of dynamically changing enhancers with their target genes. The workflow consists of a novel pre-trained enhancer predictor that can be reliably applied across cell types and species, solely based on histone modification ChIP-seq data.
23p
vielonmusk
30-01-2022
12
0
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Existing workflows for the analysis of multi-omic microbiome datasets are lab-specific and often result in sub-optimal data usage. Here we present IMP, a reproducible and modular pipeline for the integrated and reference-independent analysis of coupled metagenomic and metatranscriptomic data.
21p
vialfrednobel
29-01-2022
9
0
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High-throughput CRISPR screens have shown great promise in functional genomics. We present MAGeCK-VISPR, a comprehensive quality control (QC), analysis, and visualization workflow for CRISPR screens. MAGeCK-VISPR defines a set of QC measures to assess the quality of an experiment, and includes a maximum-likelihood algorithm to call essential genes simultaneously under multiple conditions.
13p
viaristotle
29-01-2022
12
0
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Single-cell RNA-sequencing (scRNA-seq) technologies and associated analysis methods have rapidly developed in recent years. This includes preprocessing methods, which assign sequencing reads to genes to create count matrices for downstream analysis.
32p
viarchimedes
26-01-2022
16
0
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MAESTRO provides functions for preprocessing, alignment, quality control, expression and chromatin accessibility quantification, clustering, differential analysis, and annotation. By modeling gene regulatory potential from chromatin accessibilities at the single-cell level, MAESTRO outperforms the existing methods for integrating the cell clusters between scRNAseq and scATAC-seq.
28p
viarchimedes
26-01-2022
9
0
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Lecture UML based modeling and analysis: Detailing use cases scenarios and workflows present the content: main success scenario, other scenarios (successes or failures), user management, register user, organization of use case models, UML 2.0 activity diagrams, process order, data flow and control flow, dataflow networks, partitioning of activities,...
21p
bachkhinhdaluu
03-12-2021
18
0
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The workflow or framework includes the following steps: data processing, sequence clustering, taxonomic assignment, and data visualization. Moreover, we also like to catch readers’ attention to the information about bacterial communities living in the ocean as most marine microorganisms are unculturable, especially residing in coral reefs, namely, bacteria are associated with the coral Acropora tenuis in this case.
11p
spiritedaway36
25-11-2021
8
1
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High-throughput sequencing (HTS) technologies are increasingly applied to analyse complex microbial ecosystems by mRNA sequencing of whole communities, also known as metatranscriptome sequencing. This approach is at the moment largely limited to prokaryotic communities and communities of few eukaryotic species with sequenced genomes. For eukaryotes the analysis is hindered mainly by a low and fragmented coverage of the reference databases to infer the community composition, but also by lack of automated workflows for the task.
17p
vilarryellison
29-10-2021
11
1
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