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Abbas Salavaty

Bioinformatician & Systems Biologist
ResearchGate

EDUCATION

Master of Science in Molecular and Cellular Biology-Biochemistry

Master thesis: Functional analysis and annotation of lung adenocarcinoma prognostic long non-coding RNAs

GPA: 3.82 / 4

University of Kashan

Kashan, Iran

2016-2018

Bachelor of Science in Genetics

GPA: 3.72 / 4

Shahid Chamran University of Ahvaz

Ahvaz, Iran

2011-2015

AWARDS AND HONORS

Ranked 2nd among all M.Sc. students in Biochemistry, University of Kashan

2018

Ranked among the top 4% of participants in the National University Entrance Exam, Iran

2011

PUBLICATIONS, PRESENTATIONS, AND ABSTRACTS

Publications

Potential role of RAB6C-AS1 long noncoding RNA in different cancers

ABSTRACT

Background: Long non-coding RNAs (lncRNAs) refer to a group of non-protein coding RNAs that are usually more than 200 nucleotides. These long transcripts play significant roles in diverse cellular processes mostly through epigenetic mechanisms. Thus, dysregulation of lncRNAs is associated with various diseases especially cancer. This study aims to investigate the probable roles of RAB6C-AS1 lncRNA in different cancers.

Methods: Real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was applied for the analysis of RAB6C-AS1 lncRNA amplification in gastric cancer (GC) samples compared with normal ones. Also, several online and offline datasets and tools were used to analyze the relation between RAB6C-AS1 lncRNA and different cancers.

Results: The end result of our analyses indicated that RAB6C-AS1 is over-expressed in 40 percent of under-investigation GC specimens. Also, the results demonstrated a true relation between RAB6C-AS1 over-expression and higher GC tumor grades. However, bioinformatic analyses showed that while RAB6C-AS1 possibly functions as an oncogene in some cancer types including prostate and breast cancers, it might have a tumor suppressive function in some others including brain tumors.

Conclusions: We found that RAB6C-AS1 lncRNA is mostly over-expressed in GC. Also, based on bioinformatic and systems biology analyses, RAB6C-AS1 might function either as an oncogenic factor or tumor suppressor in a tissue-specific manner. Thus, RAB6C-AS1 could be considered as a candidate biomarker for various malignancies especially prostate and brain cancers. According to our results, RAB6C-AS1 has a notable prognostic value for brain lower grade glioma patients.

KEYWORDS: bioinformatic analysis; cancer gene; long noncoding RNA (lncRNA); RAB6C‐AS1; systems biology

PubMed ResearchGate

Long non-coding RNA LINC00987 may function as a tumor suppressor in lung adenocarcinoma

ABSTRACT

Long non-coding RNAs (lncRNAs) are a group of transcripts over 200 nucleotides in length that do not code for proteins. The association of the dysregulation of numerous lncRNAs with several malignancies, including lung cancer, has been frequently reported. This study aims to inspect the association of genomic and transcriptomic alterations to the lncRNA LINC00987 with lung adenocarcinoma, a subtype of lung cancer, using a bioinformatic approach. To this end, we used three publically available online databases, cBioPortal, the International Cancer Genome Consortium Data Portal and the GEPIA web server. In short, our results demonstrated that LINC00987 expression might have a tumor suppressive role in lung adenocarcinoma and levels of expression could be of prognostic value for this cancer type.

KEYWORDS: LINC00987; Lung adenocarcinoma; Tumor suppressor lncRNA; Genotranscriptomic analysis; Bioinformatics

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Bioinformatic analysis of circadian expression of oncogenes and tumor suppressor genes

ABSTRACT

BACKGROUND: Circadian rhythms are physiological and behavioral cycles with a period of approximately 24 hours that control various functions including gene expression. Circadian disruption is associated with a variety of diseases, especially cancer. Although some of the oncogenes and tumor suppressor genes (TSGs) are known as clock-controlled genes (CCGs), the analysis and annotation of circadian expression of most human oncogenes and TSGs are still lacking. This study aims to investigate the circadian expression of a list of human oncogenes and TSGs. METHODS: A bioinformatic analysis was conducted on a gene library comprising 120 genes to investigate the circadian expression of human oncogenes and TSGs. To achieve this purpose, the genotranscriptomic data were retrieved from COSMIC and analyzed by R statistical software. Furthermore, the acquired data were analyzed at the transcriptomic and proteomic levels using several publicly available databases. Also, the significance of all analyses was confirmed statistically. RESULTS: Altogether, our results indicated that 7 human oncogenes/TSGs may be expressed and function in a circadian manner. These oncogenes/TSGs showed a circadian expression pattern at CircaDB database and associated with at least one of the circadian genes/CCGs based on both genotranscriptomic and correlation analyses. CONCLUSIONS: Although 4 of 7 finally outputted genes have been previously reported to be clock controlled, heretofore there is no report about the circadian expression of 3 other genes. Considering the importance of oncogenes/TSGs in the initiation and progression of cancer, further studies are suggested for the identification of exact circadian expression patterns of these 3 human oncogenes/TSGs.

KEYWORDS: Oncogenes; bioinformatic analysis; circadian expression; tumor suppressor genes (TSGs)

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Tissue Specific Expression Levels of Apoptosis Involved Genes Have Correlations with Codon and Amino Acid Usage

ABSTRACT

Different mechanisms, including transcriptional and post transcriptional processes, regulate tissue specific expression of genes. In this study, we report differences in gene/protein compositional features between apoptosis involved genes selectively expressed in human tissues. We found some correlations between codon/amino acid usage and tissue specific expression level of genes. The findings can be significant for understanding the translational selection on these features. The selection may play an important role in the differentiation of human tissues and can be considered for future studies in diagnosis of some diseases such as cancer.

KEYWORDS: apoptosis; codon; gene expression regulation; translation

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Genomic rearrangement screening of the BRCA1 from seventy Iranian high-risk breast cancer families

ABSTRACT

BACKGROUND: The second leading cause of cancer deaths in women is breast cancer. Germline mutations in susceptibility breast cancer gene BRCA1 increase the lifetime risk of breast cancer. Eighty-one large genomic rearrangements (LGRs) have been reported up to date in BRCA1 gene, and evaluation of these rearrangements helps with precise risk assessment in high-risk individuals. In this study, we have investigated LGRs in BRCA1 among Iranian high-risk breast cancer families. MATERIALS AND METHODS: Seventy patients with breast cancer who were identified negative for point mutations or small deletions/insertions of BRCA1 gene were selected. Deletions and duplications of BRCA1 gene were evaluated using multiplex ligation-dependent probe amplification (MLPA). RESULTS: Two deletions, deletion of exons 1A/1B-2 and exon 24, were detected in two patients with breast cancer. The former alteration was found in a woman with a strong family history of breast cancer while the latter one was detected in a woman with early onset of breast cancer. CONCLUSION: Although our data confirm that LGRs in BRCA1 comprise a relatively small proportion of mutations in hereditary breast cancer in the Iranian population, MLPA analysis might be considered for screening of LGRs in high-risk individuals. It is worth to note that our results are consistent with previous studies in various Asian and European countries.

KEYWORDS: BRCA1 gene; breast cancer; large genomic rearrangements; multiplex ligation-dependent probe amplification

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The potential role of PHF6 as an oncogene: a genotranscriptomic/proteomic meta-analysis

ABSTRACT

Epigenetic complexes control various pathways within the cells. Their abnormalities can be involved in the initiation and the progression of different types of cancer. Nucleosome remodeling and deacetylase (NuRD) is an epigenetic complex that comprises several subunits such as PHF6. Although PHF6 is reported as a tumor suppressor in some of the hematopoietic malignancies, its function is still challenging in other cancers. Our study aimed at investigating the role of PHF6 in different types of cancer. We conducted a meta-analysis of PHF6 in human cancers at genomic, transcriptomic, and proteomic levels. For this purpose, we acquired the data from several databases, and tried to statistically integrate and analyze the data in order to find the potential role of PHF6 in different tumors. The results demonstrated that although PHF6 has been previously known as a tumor suppressor gene, it was remarkably overexpressed in many cancer types such as breast and colorectal cancers. Notably, PHF6 was under-expressed in a few types of cancer, including esophageal tumors. Moreover, the results indicated that although the mutation rate of PHF6 is relatively low, it is mutated in some tumor types. In addition, our data for 40 epigenetic genes showed that missense and nonsense mutations were associated with overexpression and under-expression, respectively. Our results suggest that PHF6 may function as an oncogenic factor in several types of cancer. We also hypothesize that PHF6 may also play its role in a tissue-specific manner. Our findings suggest further investigations regarding the exact role of PHF6 in tumor types.

KEYWORDS: Epigenetics; Meta-analysis; NuRD; PHF6

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Carcinogenic effects of circadian disruption: an epigenetic viewpoint

ABSTRACT

Circadian rhythms refer to the endogenous rhythms that are generated to synchronize physiology and behavior with 24-h environmental cues. These rhythms are regulated by both external cues and molecular clock mechanisms in almost all cells. Disruption of circadian rhythms, which is called circadian disruption, affects many biological processes within the body and results in different long-term diseases, including cancer. Circadian regulatory pathways result in rhythmic epigenetic modifications and the formation of circadian epigenomes. Aberrant epigenetic modifications, such as hypermethylation, due to circadian disruption may be involved in the transformation of normal cells into cancer cells. Several studies have indicated an epigenetic basis for the carcinogenic effects of circadian disruption. In this review, I first discuss some of the circadian genes and regulatory proteins. Then, I summarize the current evidence related to the epigenetic modifications that result in circadian disruption. In addition, I explain the carcinogenic effects of circadian disruption and highlight its potential role in different human cancers using an epigenetic viewpoint. Finally, the importance of chronotherapy in cancer treatment is highlighted.

KEYWORDS: Cancer; Epigenetics; Circadian rhythms; Circadian disruption; Chronotherapy

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HOTAIR: an oncogenic long non-coding RNA in different cancers

ABSTRACT

Long non-coding RNAs (lncRNAs) refer to a group of RNAs that are usually more than 200 nucleotides and are not involved in protein generation. Instead, lncRNAs are involved in different regulatory processes, such as regulation of gene expression. Different lncRNAs exist throughout the genome. LncRNAs are also known for their roles in different human diseases such as cancer. HOTAIR is an lncRNA that plays a role as an oncogenic molecule in different cancer cells, such as breast, gastric, colorectal, and cervical cancer cells. Therefore, HOTAIR expression level is a potential biomarker for diagnostic and therapeutic purposes in several cancers. This RNA takes part in epigenetic regulation of genes and plays an important role in different cellular pathways by interacting with Polycomb Repressive Complex 2 (PRC2). In this review, we describe the molecular function and regulation of HOTAIR and its role in different types of cancers.

KEYWORDS: HOTAIR; cancer; epigenetic; long non-coding RNA (lncRNA)

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Manuscripts submitted for publication

Survival analysis and functional annotation of long non-coding RNAs in lung adenocarcinoma. Submitted to the journal of Frontiers in Genetics
Cutaneous melanoma; malignant transformation and current pharmaceuticals. Submitted to Cancer Biology and Medicine

Presentations and Abstracts

Application of nanobioinformatics in drug design and delivery systems

Global Meet on Nanomedicine & Healthcare New Orleans, USA November 2017

 

ABSTRACT

Nanobioinformatics is a convergent field which integrates the science of nanotechnology with bioinformatics. Nanobioinformatics has the potential to solve problems regarding high throughput genomics data, novel biomarker discovery, complex biological systems, computer-aided drug design (CADD), and nanobiology. Also, nanobioinformatics can be used for devising and designing of different nanosystems. In this context, for instance, bioinformatics can efficiently facilitate identification of multiplexed probes in a nanoparticle. Nano drugs are capable of cell targeting, penetration, and controlled release. Today, the application of nanobiotechnology in drug delivery systems is well-known. Bioinformatics is an important predictive approach for designing nano-transport systems for specific drugs. Also, integration of the power of two chem/bioinformatic techniques, molecular dynamics (MD) and docking, with statistics can help prediction of the efficiency of drug loading in nanoparticles. In addition, in the context of in-silico drug design, nano-design through nanoscale simulation and modeling requires cheminformatic and bioinformatic techniques such as MD simulations, quantitative structure–activity relationship (QSAR), molecular mechanics and quantum mechanics. A growing number of publically available databases such as NanoParticle Ontology and Chemical Entities of Biological Interest can be used to retrieve required data for nanobioinformatic drug design. Altogether, nanobioinformatics is a novel multidisciplinary field with many potential capabilities in drug design and delivery systems which may significantly accelerate the treatment many deadly diseases including cancer.

KEYWORDS: Nanobioinformatics; Bioinformatics; Drug design; Drug delivery

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Meta-analysis of RAG2 using a genotranscriptomic/proteomic approach: suggestive of its oncogenic role

5th International Conference on Proteomics & Bioinformatics OMICS Group, Valencia, Spain September 2015

 

ABSTRACT

Epigenetic modifications are implicated in various intracellular changes that altogether result in regulation of proteinic content within the cells. These epigenetic modifications are exerted mostly by epigenetic complexes such as PRC2 and ASCOM which their misregulation is implicated in development of different diseases including cancer. Herein a genotranscriptomic/proteomic metaanalysis is done using different databases such as COSMIC, cBioPortal and The Human Protein Atlas to investigate the oncogenic role of RAG2, a component of ASCOM complex. In addition, the similarities between mutation distribution of RAG2 and JARID2, a component of PRC2 and also between their over/under expression may be suggestive of the association between PRC2 and ASCOM.

KEYWORDS: Cancer; Epigenetic complexes; ASCOM; RAG2; Over/Under expression; Meta-analysis

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Books

Next Generation Sequencing Technologies in Medical Genetics (Translation)

Co-translator of “Next Generation Sequencing Technologies in Medical Genetics” book

ISBN: 978-600-356-502-9; National Bibliography Number (NBN): 4282468 Shahid Chamran University of Ahvaz; 2015 Supervisor: Dr. Maryam Naderi Soorki   NBN Page

SKILLS

Bioinformatics and Systems Biology

Genomics (cancer genomics), Epigenomics (familiar with epigenetic modifications/gene regulation), NGS data analysis, Transcriptomics (RNA-seq and microarray data analysis), Proteomics (protein sequence and structure analysis), Interactomics, Investigation of protein-protein interactions, visualization and analysis of biological networks, homology modelling, function prediction, …

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Programming languages and skills

R, Linux, Python, Machine learning (Basic)

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Statistics

Biostatistics, Computational Biology, Data mining, Meta-analysis

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Scientific writing

Academic writing and working with Reference manager (EndNote, Mendeley, Citavi)

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Computer skills

MS Office, Adobe Photoshop, Adobe Illustrator

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CERTIFICATES

Workshop on Application of Next-Generation Sequencing in Cancer Diagnosis and Management

Isfahan University of Medical Sciences, Department of Genetics and Molecular Biology

OMICSTM

BGI Tech

Isfahan, Iran

October 2015

Bioinformatics workshop

Shahid Chamran University of Ahvaz

Ahvaz, Iran

June 2014

PROFESSIONAL EXPERIENCES

Affiliations

  • Professional Member of Cancer Epigenetics Society (ID Number: 1537)
    2018-present
  • Member of Young Researchers and Elite Club, Iran
    2016-present
  • Research fellow (Bioinformatician), Al-Zahra Medical Genetics Laboratory, Isfahan, Isfahan, Iran
    2015-2018
  • Member of National Elites Foundation, Iran
    2015-present
  • Member of Complex Biological Systems Alliance (CBSA), a global non-profit research consortium
    2015-present

Editorial and reviewer

  • Reviewer, Journal of Rare Diseases Research & Treatment
    2017
  • Reviewer, Molecular Neurobiology
    2017
  • Editor, AMOR: Advances in Modern Oncology Research
    2015-present
  • Reviewer, MOJPB: MedCrave Online Journal of Proteomics & Bioinformatics
    2014-2016

Teaching experiences

  • Cancer Systems Biology Workshop
    Tehran University of Medical Sciences, Tehran, Iran, 2018
  • Manuscript Writing Workshop
    University of Kashan, Kashan, Iran, 2016
  • Secondary school-level courses in English language
    Ghalamchi Educational Foundation
    Isfahan, Iran, 2015

INTERESTS

RESEARCH INTERESTS

  • Melanoma and lung cancer
  • Bioinformatic analysis of cancer initiation/progression causes
  • Epigenetic basis of carcinogenesis

TEACHING INTERESTS

  • Graduate/undergraduate-level courses in Bioinformatics
  • Graduate/undergraduate-level courses in Systems Biology
  • Graduate/undergraduate-level courses in Molecular Oncology