Afif Ben Mahmoud | Genomics | Excellence in Research

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Ā Dr. Afif Ben Mahmoud | Genomics | Excellence in Research Ā 

Ā Dr at Qatar Biomedical Research Institute,Ā  Qatar

Afif Ben Mahmoud, Ph.D., is a Senior Research Associate at the Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, in Doha, Qatar. A Tunisian national, Dr. Ben Mahmoud specializes in human molecular genetics and has dedicated over ten years to researching neurological disorders and genetic diseases. He holds a Ph.D. in Biological Sciences and has made significant contributions to understanding neurodevelopmental disorders through innovative research techniques and mentoring graduate students. His work emphasizes the identification of genetic factors in various disorders, making him a vital asset to the scientific community in Qatar and beyond.

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Education šŸŽ“

Dr. Ben Mahmoud earned his Ph.D. in Biological Sciences (Human Molecular Genetics) from the Faculty of Sciences of Sfax, University of Sfax, Tunisia, in 2015. Prior to this, he obtained a Masterā€™s degree in Genetics and Biodiversity from the Higher Institute of Biotechnology of Monastir, Tunisia, in 2009. His academic journey began with an Engineering degree in Animal Production from the Higher School of Agronomy of Mateur, University of Carthage, Tunisia, in 2007. This solid educational foundation has equipped him with the necessary skills and knowledge to excel in his research endeavors.

Experience šŸ’¼

Since 2019, Dr. Ben Mahmoud has served as a Senior Research Associate at the Qatar Biomedical Research Institute, where he identifies and characterizes candidate genes for neurodevelopmental disorders by analyzing whole exome and whole genome sequencing data. Before this, he was a Postdoctoral Researcher at the College of Medicine and Health Sciences, University of UAE, from 2016 to 2018, focusing on genomic and cellular studies of autosomal recessive disorders. He has also taught cell biology and genetics at various higher education institutions in Tunisia, contributing to the academic development of future scientists.

Awards and Honors šŸ†

Dr. Ben Mahmoud has received recognition for his contributions to genetic research and education. He participated in the development of cell lines using CRISPR-Cas9 technology at UAEU, which aims to better understand diseases. His work has been featured in multiple peer-reviewed publications, establishing him as an authority in his field. He has been actively involved in mentoring students, fostering the next generation of researchers, and enhancing the academic environment in which he works.

Research Focus šŸ”¬

Dr. Ben Mahmoud’s research primarily focuses on neurological disorders and human genetic diseases, specifically identifying the genetic basis of neurodevelopmental disorders. He employs advanced techniques such as next-generation sequencing and molecular biology methods to analyze candidate genes. His recent studies aim to elucidate the cellular mechanisms behind disease-causing mutations, contributing to the broader understanding of genetic disorders. Dr. Ben Mahmoud’s work is instrumental in developing targeted therapeutic strategies, enhancing the potential for personalized medicine in treating complex genetic conditions.

Conclusion šŸ“

Dr. Afif Ben Mahmoud exemplifies excellence in research through his substantial contributions to the field of neurological disorders and human genetics. His extensive experience, technical expertise, and commitment to mentorship position him as a strong candidate for the Excellence in Research Award. By addressing potential areas for improvement, such as broadening his research focus and enhancing public engagement, Dr. Ben Mahmoud could further amplify his impact within the scientific community and beyond. His ongoing work promises to advance our understanding of complex genetic diseases, making him a valuable asset to the field.

Publications Top Notes

  • Antagonist effects of Bacillus spp. strains against Fusarium graminearum for protection of durum wheat (Triticum turgidum L. subsp. durum)
    • Authors: I Zalila-Kolsi, AB Mahmoud, H Ali, S Sellami, Z Nasfi, S Tounsi, …
    • Journal: Microbiological Research, 2016
    • Pages: 148-158

 

  • Mitochondrial DNA mutations and polymorphisms in asthenospermic infertile men
    • Authors: S Baklouti-Gargouri, M Ghorbel, A Ben Mahmoud, E Mkaouar-Rebai, …
    • Journal: Molecular Biology Reports, 2013
    • Volume/Pages: 40, 4705-4712

 

  • A novel mutation MT-COIII m.9267G>C and MT-COI m.5913G>A mutation in mitochondrial genes in a Tunisian family with maternally inherited diabetes and deafness (MIDD)
    • Authors: M Tabebi, E Mkaouar-Rebai, M Mnif, F Kallabi, AB Mahmoud, WB Saad, …
    • Journal: Biochemical and Biophysical Research Communications, 2015
    • Volume/Pages: 459(3), 353-360

 

  • Genetics of hypogonadotropic hypogonadismā€”Human and mouse genes, inheritance, oligogenicity, and genetic counseling
    • Authors: ED Louden, A Poch, HG Kim, A Ben-Mahmoud, SH Kim, LC Layman
    • Journal: Molecular and Cellular Endocrinology, 2021
    • Volume: 534, 111334

 

  • Identification of a novel m.9588G>A missense mutation in the mitochondrial COIII gene in asthenozoospermic Tunisian infertile men
    • Authors: S Baklouti-Gargouri, M Ghorbel, A Ben Mahmoud, E Mkaouar-Rebai, …
    • Journal: Journal of Assisted Reproduction and Genetics, 2014
    • Volume/Pages: 31, 595-600

 

  • A novel aberrant splice site mutation in COL27A1 is responsible for Steel syndrome and extension of the phenotype to include hearing loss
    • Authors: N Gariballa, A Ben-Mahoud, M Komara, AM Al-Shamsi, …
    • Journal: American Journal of Medical Genetics Part A, 2017
    • Volume/Pages: 173(5), 1257-1263

 

  • Whole mitochondrial genome screening of a family with maternally inherited diabetes and deafness (MIDD) associated with retinopathy: A putative haplotype associated to MIDD and its phenotypic implications
    • Authors: M Tabebi, N Charfi, F Kallabi, O Alila-Fersi, AB Mahmoud, A Tlili, …
    • Journal: Journal of Diabetes and its Complications, 2017
    • Volume/Pages: 31(1), 253-259

 

  • Two novel mutations in COII and tRNAHis mitochondrial genes in asthenozoospermic infertiles men
    • Authors: BG Siwar, G Myriam, BM Afif, MR Emna, C Nozha, S Afifa, F Faiza, …
    • Journal: Biochemical and Biophysical Research Communications, 2014
    • Volume/Pages: 450(1), 610-615

 

  • A novel m.6307A>G mutation in the mitochondrial COXI gene in asthenozoospermic infertile men
    • Authors: S Baklouti-Gargouri, M Ghorbel, A Ben Mahmoud, E Mkaouar-Rebai, …
    • Journal: Molecular Reproduction and Development, 2013
    • Volume/Pages: 80(7), 581-587

 

  • Bacillus amyloliquefaciens: Harnessing Its Potential for Industrial, Medical, and Agricultural Applicationsā€”A Comprehensive Review
    • Authors: I Zalila-Kolsi, A Ben-Mahmoud, R Al-Barazie
    • Journal: Microorganisms, 2023
    • Volume/Pages: 11(9), 2215

 

  • Novel cases of Tunisian patients with mutations in the gene encoding 17Ī²-hydroxysteroid dehydrogenase type 3 and a founder effect
    • Authors: BB Rhouma, F Kallabi, N Mahfoudh, AB Mahmoud, RT Engeli, H Kamoun, …
    • Journal: The Journal of Steroid Biochemistry and Molecular Biology, 2017
    • Volume/Pages: 165, 86-94

 

  • Eif2b3 mutants recapitulate phenotypes of vanishing white matter disease and validate novel disease alleles in zebrafish
    • Authors: YR Lee, SH Kim, A Ben-Mahmoud, OH Kim, TI Choi, KH Lee, B Ku, J Eum, …
    • Journal: Human Molecular Genetics, 2021
    • Volume/Pages: 30(5), 331-342

 

Mohammadsadeq Mottaqi | Computational biology | Young Scientist Award

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Mr. Mohammadsadeq Mottaqi | Computational biology | Young Scientist Award

MohammadSadeq Mottaqi is a dedicated Ph.D. candidate in Biochemistry at the City University of New York, with a strong foundation in Biotechnology from the University of Tehran. He possesses a robust skill set in Python, R, and various bioinformatics tools. His research focuses on machine learning-based drug action prediction, molecular dynamics simulations, and protein-ligand interactions. He has contributed significantly to research projects at Hunter College and Weill Cornell Medicine, and has industry experience as an R&D intern. MohammadSadeq is a published author, with works in journals like the Journal of Environmental Management and Informatics in Medicine Unlocked.

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EducationšŸŽ“

City University of New York, the Graduate Center, New York, NY PhD in Biochemistry, Computer Science Department
Aug 2022 – Present. University of Tehran, Tehran, Iran B.Sc. in Biotechnology, GPA: 3.8 (top 15%) Sep 2017 – March 2022

Ā Technical SkillsšŸ’»

Programming Languages: Python, R, Bioinformatics Tools and Libraries: PyMol, MOE, Gromacs, Spss, Unity, Scikit-learn, Data Analysis: Transcriptomics data analysis, Statistical analysis, Data Visualization, Operating Systems: Linux, Unix, Others: High-performance computing

Ā Relevant Experience šŸŒŸ

Machine learning-based prediction methods for drug actions
Prof. Lei Xie lab, Hunter College and Weill Cornell Medicine
June 2023 – Present
Thesis: Deep learning models for chemical-induced differential gene expression and cell viability predictions for de novo drugs and cell lines

  • Resolve challenges in predictive modeling using algorithmic approaches
  • Design pre-processing pipelines for Transcriptomics datasets
  • Integrate disparate Transcriptomics datasets (80 cell-lines) using Python
  • Incorporate multiple diverse labeled and unlabeled OMICS data
  • Contribute to writing manuscript

Molecular dynamics simulations of mutated HER2 protein
Research assistant – Dr. Mateusz Marianski lab, Hunter College
April 2023 – June 2023

  • Investigated coupling reactions and residue interactions in several mutated HER2 proteins
  • Performed molecular dynamics (MD) simulations employing Gromacs
  • Analyzed the data of the MD simulations
  • Presented the interpreted results

Protein-Ligand interactions in docking
Research assistant – Prof. Tom Kurtzman lab, Lehman College
Nov 2022 – Jan 2023

  • Identified the potential molecular interactions between protein pharmacophores and ligands
  • Wrote Python scripts in PyMOL for detection of potential H-bonds and Van der Waals forces

Aral Teb CO. Ltd., Tehran, Iran
R&D Intern
May 2020 – Oct 2020

  • Designed and executed experiments for a bacterial diagnostic kit
  • Converted 3D MRI data into a format compatible with 3D bioprinter
  • Served as a key researcher in the clean room

Virtual reality (VR) project, Iranā€™s National Elites Foundation
Nov 2020 – Aug 2021

  • Devised 7 biotechnological experiments in VR environments employing Unity software
  • Collaborated with 9 computer scientists and 4 biologists

Publications Top Notes šŸ“

  • Iman Kianian, Mohammad Sadeq Mottaqi, et al. Automated identification of toxigenic cyanobacterial genera for water quality control purposes, Journal of Environmental Management

 

  • Mohammad Sadeq Mottaqi, et al. Contribution of machine learning approaches in response to SARS-CoV-2 infection, Informatics in Medicine Unlocked, 2021

Annesha Chakraborty| Bioinformatics | Women Researcher Award

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Ā Dr. Annesha Chakraborty | Bioinformatics | Women Researcher Award

Ā Dr. SASTRA DEEMED UNIVERSITY

šŸ‘©ā€šŸ”¬ A highly motivated Ph.D. candidate at SASTRA Deemed University, specializing in Bioinformatics and Biomolecular Crystallography, with hands-on experience in molecular docking, dynamics, and laboratory techniques. Possessing an M.Sc. in Microbiology and B.Sc. (Hons.) in Microbiology, Chemistry, and Botany, I excel in research and academic achievements. As a Research Intern at MEAB LAB and Lab Tech. Intern at Suraksha Diagnostic Pvt. Ltd., I contributed to multiple publications and gained expertise in DNA/RNA extraction and PCR. Currently engaged in molecular dynamics studies on COVID Mpro, biomass production, and A.baumanniiā€™s efflux pump research. Passionate about advancing scientific knowledge and addressing real-world challenges.šŸŒŸ

 

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šŸŽ“ Education

Doctor of Philosophy (2023-Ongoing) SASTRA Deemed University, India Bioinformatics Center and Biomolecular Crystallography Lab, under the supervision of Dr. S. Thamotharan and co-supervision of Dr. Vigneshwer R. Currently pursuing research funded by DBT-govt. of India. M.Sc in Microbiology (2020-2022) Grade: A+ (80%) [Ranked 4th] B.Sc (Hons.) in Microbiology (2017-2020) Optional subjects: Chemistry and Botany Grade: B+ 12th (High School) (2015-2017) Science stream

šŸ”¬ Key Skills

  • Molecular Docking
  • Molecular Dynamics
  • Schrodinger
  • Pymol
  • MegaAUTODOCK
  • Agarose Gel Electrophoresis
  • ELISA
  • qPCR
  • RT-PCR
  • Flow Cytometry
  • Online tools for nucleic acid or protein sequence-based analysis (Expasy, Clustal Omega, NCBI)

šŸ’¼ Work Experience

Research Intern at MEAB LAB (08/2021-09/2022) JIS University (Hybrid mode) Responsibilities: Worked on current research projects with PhD scholars as a Project Associate Intern. Co-authored 3 review articles and 1 book chapter, and contributed to 3 research projects. Previously worked here for Master’s thesis paper. Lab Tech Intern at Suraksha Diagnostic Pvt. Ltd. (12.08.2022-24.08.2022) Responsibilities: Conducted DNA and RNA extraction for PCR to detect HLA, hepatitis B, hepatitis C, and Covid-19 virus. Performed RT-PCR and real-time PCR to detect RNA and DNA viruses.

Publications Top Notes šŸ“

  1. Title: Lignocellulolytic Microbial Systems and its Importance in Dye Decolourization: A Review

 

  1. Title: Microbial electrolysis cells for effective biohydrogen biogenesis from biowastes

 

  1. Title: Algae educed industrial enzymes production: a sustainable way forward?
    • Book: Industrial Microbiology
    • ISBN: 978-93-5461-997-7
    • Publisher: Astral International Pvt. Ltd. (Scopus)

Yubo ZHANG | Genomics Award | Best Researcher Award

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Prof. Yubo ZHANG | Genomics Award | Best Researcher Award

šŸ‘Øā€šŸ«Profile Summary

As a senior genomic scientist with over a decade of experience specializing in 3D genome research, I have a proven track record of leveraging cutting-edge technologies to investigate the dynamic functions of transcription factors (TFs) and genes within intricate genomes. My work has significantly contributed to enhancing our understanding of enhancer-promoter interactions and gene expression regulation. Currently, I am seeking a role where I can utilize my expertise in translational applications, particularly in identifying novel drug targets and optimizing therapeutic approaches in areas such as cancer and stem cell research.

šŸŒ Professional Profiles

EducationšŸŽ“

Certification in Intro + Intermediate Python, CyberWeb Consulting, USA (2012): Enhanced computational skills for genomic data analysis and bioinformatics. Ph.D. in Hydrobiology, Institute of Hydrobiology (IHB), Chinese Academy of Sciences (CAS), China (2007): Conducted research on aquatic ecosystems, providing a solid foundation in biological sciences. M.S. in Molecular Biology and Animal Breeding, Huazhong Agricultural University, China (2004): Specialized in molecular biology techniques and genetic breeding strategies. B.S. in Animal Husbandry, Huazhong Agricultural University, China (2000): Acquired fundamental knowledge in animal science and husbandry practices.

šŸ”¬ Researcher Experience

Principal Investigator, Agricultural Genomics Institute at ShenZhen, CAAS, China (2016/05-2023/12): Led research projects focusing on elucidating the mechanisms underlying 3D genome organization and function. Director, NGS Facility, Agricultural Genomics Institute at ShenZhen, CAAS, China (2016/10-2023/12): Oversaw the operations of the Next-Generation Sequencing (NGS) facility, ensuring high-quality genomic data generation and analysis. Research Fellow, National Institutes of Health, USA (2013/04-2016/05): Conducted research on transcriptional regulation and chromatin architecture, contributing to advancements in understanding gene regulation networks. Post-doctoral Fellow, Lawrence Berkeley National Laboratory, USA (2011/01-2013/03): Investigated the role of chromatin remodeling complexes in gene expression control, utilizing state-of-the-art genomic techniques. Post-doctoral Fellow, Genome Institute of Singapore, Singapore (2008/01-2011/01): Explored the epigenetic regulation of stem cell differentiation pathways, with a focus on chromatin modifications.

Awards šŸ†

The Elite Leading Scientists of CAAS, Category B, China, 2017, The Thousand Talents Plan, Youth, China, 2017, Distinguish Scientist Award, NIH-CAAS, USA, 2016, Overseas High-Caliber Personnel, Level B, ShenZhen, China, 2016, National-Level Talent, ShenZhen, China, 2015, Youth Talent Program, Category A, CAAS, China, 2015, Special Award, Genome Institute of Singapore, Singapore, 2010, Special Award, Genome Institute of Singapore, Singapore, 2009

šŸ“Membership in Societies and Editorial Boards:

Committee, China Anti-Cancer Association (CACA), 2021-present, Editorial Board Member, Pathology and Laboratory Medicine, 2021-present, Editorial Board Member, Chinese Journal of Biochemistry and Molecular Biology, 2021-present, Editorial Board Member, Chinese Journal of Herbivores, 2019-present, Member, The Chinese Society of Biochemistry & Molecular Biology, 2019-present, Advanced Member, Chinese Association of Animal Science and Veterinary Medicine, CAAV, 2018-present, Committee, National Yak Industry Quality Improvement and Efficiency Technology Innovation, 2018-present, Committee, National Special Economic Animal Science and Efficiency Technology Innovation, 2018-present, Deputy Editor-in-Chief/Editorial Board Member, Global Journal of Animal Sciences and Medicine, 2018-present, Committee, National Agricultural Genomics Innovation, 2017-present, Editorial Board Member, Animal Models and Experimental Medicine, 2017-presen

šŸŽ–ļøResearch Grants Awarded:

Principal Investigator, Study on the regulation of Sox2 gene in embryonic stem cells by different long-distance gene interactions, National Natural Science Foundation of China, 31970592, 2020.01-2023.12, 0.58 million CNY. (Competitive Project), Principal Investigator, Research and application of key technologies for yak genetic modification and efficient breeding in Taxian County, Shenzhen Science and Technology Program, KCXFZ20201221173205015, 2021.01-2023.12, 4.00 million CNY. (Competitive Project), Principal Investigator, Analysis of synthetic pathways and heterologous expression of active natural products such as anti-tumor and anti-infection (sub-project). National Key Research and Development Program of China, SQ2018YFA090005, 2019.07-2014.06, 1.28 million CNY. (Competitive Project), Principal Investigator, Construction of cross-species three-dimensional genomics platform, Basic scientific research business fund of CAAS, Y2019PT18-02, 2019.01-2019.12, 0.20 million CNY. (Institute Funding), Principal Investigator, ā€œPearl River Talents Planā€ Leading Talents, 2017GC010063, 2017.05-2021.12, 0.81 million CNY. (Competitive Project)

šŸ“šTop Noted Publication

  1. Distinct enhancer-promoter modes determine Sox2 regulation in mouse pluripotent cells
    • Source: Genes & Diseases
    • Publication Date: 2024-01
    • DOI: 10.1016/j.gendis.2022.11.019
    • Contributors: Lei Huang; Xiusheng Zhu; Qing Li; Dashuai Kong; Qitong Huang; Jing Luo; Siyuan Kong; Yanling Peng; Yubo Zhang

 

  1. MAE-seq refines regulatory elements across the genome
    • Source: Nucleic Acids Research
    • Publication Date: 2023-11-10
    • DOI: 10.1093/nar/gkad1129
    • Contributors: Yubo Zhang; Xiusheng Zhu; Qitong Huang; Lei, Huang; Jing Luo; Qing` Li; Dashuai Kong; Yi Gu; Xueyan Wang; Chenying Li et al.

 

  1. Exploring the Role of Enhancer-Mediated Transcriptional Regulation in Precision Biology
    • Source: International Journal of Molecular Sciences
    • Publication Date: 2023-06-29
    • DOI: 10.3390/ijms241310843
    • Contributors: Xueyan Wang; Danli Liu; Jing Luo; Dashuai Kong; Yubo Zhang

 

  1. Genome-wide identification of silencers in human cells
    • Source: Preprint
    • Publication Date: 2023-06-23
    • DOI: 10.1101/2023.06.20.545673
    • Contributors: Xiusheng Zhu; Chao Wang; Dashuai Kong; Jing Luo; Biao Deng; Yi Gu; Siyuan Kong; Lei Huang; Yuwen Liu; Yubo Zhang

 

  1. Nucleosome-Omics: A Perspective on the Epigenetic Code and 3D Genome Landscape
    • Source: Genes
    • Publication Date: 2022-06-22
    • DOI: 10.3390/genes13071114
    • Contributors: Siyuan Kong; Yuhui Lu; Shuhao Tan; Rongrong Li; Yan Gao; Kui Li; Yubo Zhang

 

  1. Baiting out a full length sequence from unmapped RNA-seq data
    • Source: BMC Genomics
    • Publication Date: 2021-12
    • DOI: 10.1186/s12864-021-08146-4
    • Contributors: Dongwei Li; Qitong Huang; Lei Huang; Jikai Wen; Jing Luo; Qing Li; Yanling Peng; Yubo Zhang

 

  1. A single-cell genomic strategy for alternative transcript start sites identification
    • Source: Preprint
    • Publication Date: 2021-12-10
    • DOI: 10.1101/2021.12.09.472038
    • Contributors: Yanling Peng; Qitong Huang; Rui Kamada; Keiko Ozato; Yubo Zhang; Jun Zhu

 

  1. Induce Pluripotency via Specific distal enhancer-promoter associations
    • Source: Other
    • Publication Date: 2021-06-10
    • DOI: 10.1101/2021.06.09.447809
    • Contributors: Xiusheng Zhu; Lei Huang; Dongwei Li; Jing Luo; Qitong Huang; Xueyan Wang; Yubo Zhang

 

  1. Comparative Analysis of Super-enhancers Across Mammals Reveals Their High Function Conservation
    • Source: Other
    • Publication Date: 2020-12-08
    • DOI: 10.21203/rs.3.rs-121951/v1
    • Contributors: Yanling Peng; Yubo Zhang

 

  1. Exonuclease combinations reduce noises in 3D genomics technologies
    • Source: Nucleic Acids Research
    • Publication Date: 2020-03-04
    • DOI: 10.1093/nar/gkaa106
    • Contributors: Yubo Zhang