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PFP-WGAN: Protein function prediction by discovering gene ontology term correlations with generative adversarial networks
, Article PLoS ONE ; Volume 16, Issue 2 , 2021 ; 19326203 (ISSN) ; Soleymani, M ; Rabiee, H. R ; Kaazempur Mofrad, M. R ; Sharif University of Technology
Public Library of Science
2021
Abstract
Understanding the functionality of proteins has emerged as a critical problem in recent years due to significant roles of these macro-molecules in biological mechanisms. However, in-laboratory techniques for protein function prediction are not as efficient as methods developed and processed for protein sequencing. While more than 70 million protein sequences are available today, only the functionality of around one percent of them are known. These facts have encouraged researchers to develop computational methods to infer protein functionalities from their sequences. Gene Ontology is the most well-known database for protein functions which has a hierarchical structure, where deeper terms are...
A Novel Method to Improve Binning of Metagenomic Sequence Fragments by Using Gene Ontology Graphs
, M.Sc. Thesis Sharif University of Technology ; Beigy, Hamid (Supervisor) ; Marashi, Amir (Supervisor)
Abstract
Bacteria are the first organisms, and ath the same time, the most diverse forms of life that appeared on the earth and without their functions living on the earth would not be possible. Therefore, recognition of bacteria is greatly important and can lead to the recognition of new genes, production of new antibiotics and anti-cancer compounds, etc. The problem of identifying the bacterial genome from DNA sequences obtained directly from environmental samples is known as Metagenomics. One of the main stages of Metagenomics is the binning of genetic components and because bio-marker based binning methods are only able to bin 1% of bacterial species, bio-marker free methods have been considered...
TripletProt: Deep Representation Learning of Proteins Based On Siamese Networks
, Article IEEE/ACM Transactions on Computational Biology and Bioinformatics ; Volume 19, Issue 6 , 2022 , Pages 3744-3753 ; 15455963 (ISSN) ; Asgari, E ; McHardy, A. C ; Mofrad, M. R. K ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2022
Abstract
Pretrained representations have recently gained attention in various machine learning applications. Nonetheless, the high computational costs associated with training these models have motivated alternative approaches for representation learning. Herein we introduce TripletProt, a new approach for protein representation learning based on the Siamese neural networks. Representation learning of biological entities which capture essential features can alleviate many of the challenges associated with supervised learning in bioinformatics. The most important distinction of our proposed method is relying on the protein-protein interaction (PPI) network. The computational cost of the generated...
CircWalk: a novel approach to predict CircRNA-disease association based on heterogeneous network representation learning
, Article BMC Bioinformatics ; Volume 23, Issue 1 , 2022 ; 14712105 (ISSN) ; Kashaninia, E ; Mardani, B ; Rabiee, H. R ; Sharif University of Technology
BioMed Central Ltd
2022
Abstract
Background: Several types of RNA in the cell are usually involved in biological processes with multiple functions. Coding RNAs code for proteins while non-coding RNAs regulate gene expression. Some single-strand RNAs can create a circular shape via the back splicing process and convert into a new type called circular RNA (circRNA). circRNAs are among the essential non-coding RNAs in the cell that involve multiple disorders. One of the critical functions of circRNAs is to regulate the expression of other genes through sponging micro RNAs (miRNAs) in diseases. This mechanism, known as the competing endogenous RNA (ceRNA) hypothesis, and additional information obtained from biological datasets...
The association of clinicopathological characterizations of colorectal cancer with membrane-bound mucins genes and LncRNAs
, Article Pathology Research and Practice ; Volume 233 , 2022 ; 03440338 (ISSN) ; Entezari, M ; Rejali, L ; Nazemalhosseini-Mojarad, E ; Maghsoudloo, M ; Asadzadeh Aghdaei, H ; Zali, M. R ; Hushmandi, K ; Rabiee, N ; Makvandi, P ; Ashrafizadeh, M ; Hashemi, M ; Sharif University of Technology
Elsevier GmbH
2022
Abstract
Background: Colorectal cancer (CRC) is one of the most common malignancies in the world and has a high mortality rate. It is believed that dysfunction in the expression of mucins and aberrant expression of some lncRNAs are associated with the occurrence and development of CRC. Therefore, the aim of the present study was to investigate the expression of MUC15, MUC16, MUC20, PCAT1, CCAT1 and HOTAIR genes in colorectal cancer and its relationship with clinicopathological variables. Materials and methods: This research was prospective case-control study. Tumors from CRC patients were collected from the Taleghani Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran. RNA...
Genome annotation and comparative genomic analysis of Bacillus subtilis MJ01, a new bio-degradation strain isolated from oil-contaminated soil
, Article Functional and Integrative Genomics ; Volume 18, Issue 5 , 2018 , Pages 533-543 ; 1438793X (ISSN) ; Niazi, A ; Deihimi, T ; Taghavi, S. M ; Ayatollahi, S ; Ebrahimie, E ; Sharif University of Technology
Springer Verlag
2018
Abstract
One of the main challenges in elimination of oil contamination from polluted environments is improvement of biodegradation by highly efficient microorganisms. Bacillus subtilis MJ01 has been evaluated as a new resource for producing biosurfactant compounds. This bacterium, which produces surfactin, is able to enhance bio-accessibility to oil hydrocarbons in contaminated soils. The genome of B. subtilis MJ01 was sequenced and assembled by PacBio RS sequencing technology. One big contig with a length of 4,108,293 bp without any gap was assembled. Genome annotation and prediction of gene showed that MJ01 genome is very similar to B. subtilis spizizenii TU-B-10 (95% similarity). The comparison...
Dna-Rna hybrid (R-loop): From a unified picture of the mammalian telomere to the genome-wide profile
, Article Cells ; Volume 10, Issue 6 , 2021 ; 20734409 (ISSN) ; Sharifi Zarchi, A ; Kianmehr, L ; Sharif University of Technology
MDPI
2021
Abstract
Local three-stranded DNA/RNA hybrid regions of genomes (R-loops) have been detected either by binding of a monoclonal antibody (DRIP assay) or by enzymatic recognition by RNaseH. Such a structure has been postulated for mouse and human telomeres, clearly suggested by the identification of the complementary RNA Telomeric repeat-containing RNA “TERRA”. However, the tremendous disparity in the information obtained with antibody-based technology drove us to investigate a new strategy. Based on the observation that DNA/RNA hybrids in a triplex complex genome co-purify with the double-stranded chromosomal DNA fraction, we developed a direct preparative approach from total protein-free cellular...
Pan-cancer analysis of microRNA expression profiles highlights microRNAs enriched in normal body cells as effective suppressors of multiple tumor types: A study based on TCGA database
, Article PLoS ONE ; Volume 17, Issue 4 April , 2022 ; 19326203 (ISSN) ; Kamal, A ; Es, H. A ; Farhadi, F ; Ebrahimi, M ; Chitsaz, H ; Sharifi Zarchi, A ; Baharvand, H ; Sharif University of Technology
Public Library of Science
2022
Abstract
Background MicroRNAs (miRNAs) are frequently deregulated in various types of cancer. While antisense oligonucleotides are used to block oncomiRs, delivery of tumour-suppressive miRNAs holds great potential as a potent anti-cancer strategy. Here, we aim to determine, and functionally analyse, miRNAs that are lowly expressed in various types of tumour but abundantly expressed in multiple normal tissues. Methods The miRNA sequencing data of 14 cancer types were downloaded from the TCGA dataset. Significant differences in miRNA expression between tumor and normal samples were calculated using limma package (R programming). An adjusted p value < 0.05 was used to compare normal versus tumor miRNA...