OligoCOOL: A mobile application for nucleotide sequence analysis

Khorsand, Babak; Khammari, Anahita; Shirvanizadeh, Niloofar; Zahiri, Javad; Arab, Seyed Shahriar

doi:10.1002/bmb.21213

Cited by 5 publications

(2 citation statements)

References 13 publications

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“…This form of network visualization led to the comprehension of connections between metabolites and studies. Next, bipartite network projection that is extensively used for compacting data about bipartite networks was obtained 23–25 . Network projection was employed to streamline bipartite networks by converting them into unipartite networks.…”

Section: Methodsmentioning

confidence: 99%

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Metabolite signature of human malignant thyroid tissue: A systematic review and meta‐analysis

Razavi,

Khorsand,

Salehipour

et al. 2024

Cancer Medicine

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BackgroundThyroid cancer (TC) is the predominant malignancy within the endocrine system. However, the standard method for TC diagnosis lacks the capability to identify the pathological condition of all thyroid lesions. The metabolomics approach has the potential to manage this problem by identifying differential metabolites.AimsThis study conducted a systematic review and meta‐analysis of the NMR‐based metabolomics studies in order to identify significant altered metabolites associated with TC.MethodsA systematic search of published literature in any language in three databases including Embase, PubMed, and Scopus was conducted. Out of 353 primary articles, 12 studies met the criteria for inclusion in the systematic review. Among these, five reports belonging to three articles were eligible for meta‐analysis. The correlation coefficient of the orthogonal partial least squares discriminant analysis, a popular model in the multivariate statistical analysis of metabolomic data, was chosen for meta‐analysis. The altered metabolites were chosen based on the fact that they had been found in at least three studies.ResultsIn total, 49 compounds were identified, 40 of which were metabolites. The increased metabolites in thyroid lesions compared normal samples included lactate, taurine, alanine, glutamic acid, glutamine, leucine, lysine, phenylalanine, serine, tyrosine, valine, choline, glycine, and isoleucine. Lipids were the decreased compounds in thyroid lesions. Lactate and alanine were increased in malignant versus benign thyroid lesions, while, myo‐inositol, scyllo‐inositol, citrate, choline, and phosphocholine were found to be decreased. The meta‐analysis yielded significant results for three metabolites of lactate, alanine, and citrate in malignant versus benign specimens.DiscussionIn this study, we provided a concise summary of 12 included metabolomic studies, making it easier for future researchers to compare their results with the prior findings.ConclusionIt appears that the field of TC metabolomics will experience notable advancement, leading to the discovery of trustworthy diagnostic and prognostic biomarkers.

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Section: Methodsmentioning

confidence: 99%

“…Next, bipartite network projection that is extensively used for compacting data about bipartite networks was obtained. 23 , 24 , 25 Network projection was employed to streamline bipartite networks by converting them into unipartite networks. This conversion aided in the more efficient analysis of the relationships within the data.…”

Section: Methodsmentioning

confidence: 99%

Metabolite signature of human malignant thyroid tissue: A systematic review and meta‐analysis

Razavi,

Khorsand,

Salehipour

et al. 2024

Cancer Medicine

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A computational approach to assessing the prognostic implications of BRAF and RAS mutations in patients with papillary thyroid carcinoma

Haghzad,

Khorsand,

Razavi

et al. 2024

Endocrine

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PeptiHub: a curated repository of precisely annotated cancer-related peptides with advanced utilities for peptide exploration and discovery

Zareei,

Khorsand,

Dantism

et al. 2024

Database

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Peptihub (https://bioinformaticscollege.ir/peptihub/) is a meticulously curated repository of cancer-related peptides (CRPs) that have been documented in scientific literature. A diverse collection of CRPs is included in the PeptiHub, showcasing a spectrum of effects and activities. While some peptides demonstrated significant anticancer efficacy, others exhibited no discernible impact, and some even possessed alternative non-drug functionalities, including drug carrier or carcinogenic attributes. Presently, Peptihub houses 874 CRPs, subjected to evaluation across 10 distinct organism categories, 26 organs, and 438 cell lines. Each entry in the database is accompanied by easily accessible 3D conformations, obtained either experimentally or through predictive methodology. Users are provided with three search frameworks offering basic, advanced, and BLAST sequence search options. Furthermore, precise annotations of peptides enable users to explore CRPs based on their specific activities (anticancer, no effect, insignificant effect, carcinogen, and others) and their effectiveness (rate and IC50) under cancer conditions, specifically within individual organs. This unique property facilitates the construction of robust training and testing datasets. Additionally, PeptiHub offers 1141 features with the convenience of selecting the most pertinent features to address their specific research questions. Features include aaindex1 (in six main subcategories: alpha propensities, beta propensity, composition indices, hydrophobicity, physicochemical properties, and other properties), amino acid composition (Amino acid Composition and Dipeptide Composition), and Grouped Amino Acid Composition (Grouped amino acid composition, Grouped dipeptide composition, and Conjoint triad) categories. These utilities not only speed up machine learning-based peptide design but also facilitate peptide classification. Database URL: https://bioinformaticscollege.ir/peptihub/

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OligoCOOL: A mobile application for nucleotide sequence analysis

Cited by 5 publications

References 13 publications

Metabolite signature of human malignant thyroid tissue: A systematic review and meta‐analysis

Metabolite signature of human malignant thyroid tissue: A systematic review and meta‐analysis

A computational approach to assessing the prognostic implications of BRAF and RAS mutations in patients with papillary thyroid carcinoma

PeptiHub: a curated repository of precisely annotated cancer-related peptides with advanced utilities for peptide exploration and discovery

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