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