Advances in Omics and Bioinformatics Tools for Phyllosphere Studies

2021 ◽  
pp. 240-253
Author(s):  
Hina Bansal
Keyword(s):  
Bioinformatics Tools

Integrating Bioinformatics Strategies in Cancer Immunotherapy: Current and Future Perspectives

2020 ◽  
Vol 23 (8) ◽  
pp. 687-698 ◽  
Author(s):  
Houda N. Washah ◽  
Elliasu Y. Salifu ◽  
Opeyemi Soremekun ◽  
Ahmed A. Elrashedy ◽  
Geraldene Munsamy ◽  
...  
Keyword(s):  
Cancer Immunotherapy ◽  
Therapeutic Potential ◽  
Cell Cancer ◽  
Full Potential ◽  
Future Perspectives ◽  
The Past ◽  
Bioinformatics Tools ◽  
Treatment Paradigm ◽  
Immunotherapy Of Cancer ◽  
Significant Attention

For the past few decades, the mechanisms of immune responses to cancer have been exploited extensively and significant attention has been given into utilizing the therapeutic potential of the immune system. Cancer immunotherapy has been established as a promising innovative treatment for many forms of cancer. Immunotherapy has gained its prominence through various strategies, including cancer vaccines, monoclonal antibodies (mAbs), adoptive T cell cancer therapy, and immune checkpoint therapy. However, the full potential of cancer immunotherapy is yet to be attained. Recent studies have identified the use of bioinformatics tools as a viable option to help transform the treatment paradigm of several tumors by providing a therapeutically efficient method of cataloging, predicting and selecting immunotherapeutic targets, which are known bottlenecks in the application of immunotherapy. Herein, we gave an insightful overview of the types of immunotherapy techniques used currently, their mechanisms of action, and discussed some bioinformatics tools and databases applied in the immunotherapy of cancer. This review also provides some future perspectives in the use of bioinformatics tools for immunotherapy.

scholarly journals Rare Variants Imputation in Admixed Populations: Comparison Across Reference Panels and Bioinformatics Tools

2019 ◽  
Vol 10 ◽  
Author(s):  
Sanjeev Sariya ◽  
Joseph H. Lee ◽  
Richard Mayeux ◽  
Badri N. Vardarajan ◽  
Dolly Reyes-Dumeyer ◽  
...  
Keyword(s):  
Rare Variants ◽  
Bioinformatics Tools

scholarly journals Whole-Genome Sequencing for Investigating a Health Care-Associated Outbreak of Carbapenem-Resistant Acinetobacter baumannii

Diagnostics ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 201
Author(s):  
Sang Mee Hwang ◽  
Hee Won Cho ◽  
Tae Yeul Kim ◽  
Jeong Su Park ◽  
Jongtak Jung ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Acinetobacter Baumannii ◽  
Genome Sequencing ◽  
Snp Analysis ◽  
Whole Genome ◽  
Phylogenetic Tree Analysis ◽  
Web Based ◽  
Hospital Outbreak ◽  
Carbapenem Resistant ◽  
Bioinformatics Tools

Carbapenem-resistant Acinetobacter baumannii (CRAB) outbreaks in hospital settings challenge the treatment of patients and infection control. Understanding the relatedness of clinical isolates is important in distinguishing outbreak isolates from sporadic cases. This study investigated 11 CRAB isolates from a hospital outbreak by whole-genome sequencing (WGS), utilizing various bioinformatics tools for outbreak analysis. The results of multilocus sequence typing (MLST), single nucleotide polymorphism (SNP) analysis, and phylogenetic tree analysis by WGS through web-based tools were compared, and repetitive element polymerase chain reaction (rep-PCR) typing was performed. Through the WGS of 11 A. baumannii isolates, three clonal lineages were identified from the outbreak. The coexistence of blaOXA-23, blaOXA-66, blaADC-25, and armA with additional aminoglycoside-inactivating enzymes, predicted to confer multidrug resistance, was identified in all isolates. The MLST Oxford scheme identified three types (ST191, ST369, and ST451), and, through whole-genome MLST and whole-genome SNP analyses, different clones were found to exist within the MLST types. wgSNP showed the highest discriminatory power with the lowest similarities among the isolates. Using the various bioinformatics tools for WGS, CRAB outbreak analysis was applicable and identified three discrete clusters differentiating the separate epidemiologic relationships among the isolates.

scholarly journals Epigenetic dysregulation of immune-related pathways in cancer: bioinformatics tools and visualization

2021 ◽  
Author(s):  
Anders Berglund ◽  
Ryan M. Putney ◽  
Imene Hamaidi ◽  
Sungjune Kim
Keyword(s):  
Patient Outcome ◽  
Immune Responses ◽  
Cancer Cells ◽  
Immune Evasion ◽  
Epigenetic Regulation ◽  
Current Evidence ◽  
Immune Recognition ◽  
Bioinformatics Tools ◽  
Visualization Techniques ◽  
Cancer Bioinformatics

AbstractCancer immune evasion is one of the hallmarks of carcinogenesis. Cancer cells employ multiple mechanisms to avoid immune recognition and suppress antitumor immune responses. Recently, accumulating evidence has indicated that immune-related pathways are epigenetically dysregulated in cancer. Most importantly, the epigenetic footprint of immune-related pathways is associated with the patient outcome, underscoring the crucial need to understand this process. In this review, we summarize the current evidence for epigenetic regulation of immune-related pathways in cancer and describe bioinformatics tools, informative visualization techniques, and resources to help decipher the cancer epigenome.

scholarly journals Synthesis and Bioinformatic Characterization of New Schiff Bases with Possible Applicability in Brain Disorders

Molecules ◽  
2021 ◽  
Vol 26 (14) ◽  
pp. 4160
Author(s):  
Speranta Avram ◽  
Ana Maria Udrea ◽  
Diana Camelia Nuta ◽  
Carmen Limban ◽  
Adrian Cosmin Balea ◽  
...  
Keyword(s):  
Schiff Bases ◽  
Neurodegenerative Disorders ◽  
Aromatic Aldehydes ◽  
Brain Disorders ◽  
Ir And Nmr Spectroscopy ◽  
Bioinformatics Tools ◽  
Ft Ir ◽  
New Treatments ◽  
New Compounds

(1) Background: The research aims to find new treatments for neurodegenerative diseases, in particular, Alzheimer’s disease. (2) Methods: This article presents a bioinformatics and pathology study of new Schiff bases, (EZ)-N′-benzylidene-(2RS)-2-(6-chloro-9H-carbazol-2-yl)propanehydrazide derivatives, and aims to evaluate the drug-like, pharmacokinetic, pharmacodynamic and pharmacogenomic properties, as well as to predict the binding to therapeutic targets by applying bioinformatics, cheminformatics and computational pharmacological methods. (3) Results: We obtained these Schiff bases by condensing (2RS)-2-(6-chloro-9H-carbazol-2-yl)propanehydrazide with aromatic aldehydes, using the advantages of microwave irradiation. The newly synthesized compounds were characterized spectrally, using FT-IR and NMR spectroscopy, which confirmed their structure. Using bioinformatics tools, we noticed that all new compounds are drug-likeness features and may be proposed as potentially neuropsychiatric drugs (4) Conclusions: Using bioinformatics tools, we determined that the new compound 1e had a high potential to be used as a good candidate in neurodegenerative disorders treatment.

scholarly journals Bioinformatics Tools and Genomic Resources Available in Understanding the Structure and Function of Gossypium

10.5772/64325 ◽  
2016 ◽  
Author(s):  
Venkateswara R. Sripathi ◽  
Ramesh Buyyarapu ◽  
Siva P. Kumpatla ◽  
Abreeotta J. Williams ◽  
Seloame T. Nyaku ◽  
...  
Keyword(s):  
Structure And Function ◽  
Genomic Resources ◽  
Bioinformatics Tools ◽  
And Function

Frequently used bioinformatics tools overestimate the damaging effect of allelic variants

2017 ◽  
Vol 20 (1) ◽  
pp. 10-22 ◽  
Author(s):  
Line Lykke Andersen ◽  
Ewa Terczyńska-Dyla ◽  
Nanna Mørk ◽  
Carsten Scavenius ◽  
Jan J. Enghild ◽  
...  
Keyword(s):  
Allelic Variants ◽  
Bioinformatics Tools

scholarly journals Programmatic access to bioinformatics tools from EMBL-EBI update: 2017

2017 ◽  
Vol 45 (W1) ◽  
pp. W550-W553 ◽  
Author(s):  
Szymon Chojnacki ◽  
Andrew Cowley ◽  
Joon Lee ◽  
Anna Foix ◽  
Rodrigo Lopez
Keyword(s):  
Bioinformatics Tools ◽  
Programmatic Access

Proteomic Approaches to Tumor Marker Discovery

2002 ◽  
Vol 126 (12) ◽  
pp. 1518-1526 ◽  
Author(s):  
Alex J. Rai ◽  
Zhen Zhang ◽  
Jason Rosenzweig ◽  
Ie-ming Shih ◽  
Thang Pham ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Confidence Interval ◽  
Tumor Marker ◽  
Tumor Markers ◽  
Tumor Resection ◽  
Rapid Screening ◽  
Neoplastic Disease ◽  
Proteomic Profiling ◽  
Bioinformatics Tools ◽  
Potential Biomarkers

Abstract Context.—Current tumor markers for ovarian cancer still lack adequate sensitivity and specificity to be applicable in large populations. High-throughput proteomic profiling and bioinformatics tools allow for the rapid screening of a large number of potential biomarkers in serum, plasma, or other body fluids. Objective.—To determine whether protein profiles of plasma can be used to identify potential biomarkers that improve the detection of ovarian cancer. Design.—We analyzed plasma samples that had been collected between 1998 and 2001 from patients with sporadic ovarian serous neoplasms before tumor resection at various International Federation of Gynecology and Obstetrics stages (stage I [n = 11], stage II [n = 3], and stage III [n = 29]) and from women without known neoplastic disease (n = 38) using proteomic profiling and bioinformatics. We compared results between the patients with and without cancer and evaluated their discriminatory performance against that of the cancer antigen 125 (CA125) tumor marker. Results.—We selected 7 biomarkers based on their collective contribution to the separation of the 2 patient groups. Among them, we further purified and subsequently identified 3 biomarkers. Individually, the biomarkers did not perform better than CA125. However, a combination of 4 of the biomarkers significantly improved performance (P ≤ .001). The new biomarkers were complementary to CA125. At a fixed specificity of 94%, an index combining 2 of the biomarkers and CA125 achieves a sensitivity of 94% (95% confidence interval, 85%–100.0%) in contrast to a sensitivity of 81% (95% confidence interval, 68%–95%) for CA125 alone. Conclusions.—The combined use of bioinformatics tools and proteomic profiling provides an effective approach to screen for potential tumor markers. Comparison of plasma profiles from patients with and without known ovarian cancer uncovered a panel of potential biomarkers for detection of ovarian cancer with discriminatory power complementary to that of CA125. Additional studies are required to further validate these biomarkers.

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