Mohammadsadeq Mottaqi | Computational biology | Young Scientist Award

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

Angelika Długosz-Pokorska | cancer research | Women Researcher Award

Ā Dr. Angelika Długosz-Pokorska | cancer research |Women Researcher Award

Ā Dr at Medical University of ÅĆ³dÅŗ,Ā  Poland

A dedicated researcher and project leader at the Medical University of Lodz, Poland, with expertise in pharmacological characterization and anticancer drug development. As Principal Investigator and Co-investigator, led projects funded by prestigious grants like OPUS and SONATA, focusing on opioid peptide analogs and alpha-methylidene-delta-lactones. Supervising international student exchanges and engaging in expert activities, workshops, and editorial work. Recognized with numerous awards for scientific excellence, including Rector’s Awards and IF=8.638 for publication series on opioid mimetics and glutathione peroxidase. Committed to advancing medical science through innovative research and academic leadership.

Profile

  1. Scopus

 

  1. Orcid

šŸ“œ Employment History:

Research Associate (2017-present) Medical University of Lodz, Poland; Faculty of Medicine. Co-investigator (2016-2021)
Project: Rational design and pharmacological characterization of chimeric cyclic opioid peptide analogs targeting multiple receptors
Grant: OPUS 9, project ID 2015/17/B/ST5/00153. Principal Investigator (2016-2021) Project: Analysis of the anticancer activity of new synthetic alpha-methylidene-delta-lactones in selected cell lines Grant: SONATA, project ID 2015/17/D/NZ3/02226. Supervisor, Project Manager, and Principal Investigator (2018-present) Project: Analysis of the anticancer activity and molecular mechanism of action of new hybrid molecules containing uracil skeleton with an exo-cyclic methylene group Grant: PRELUDIUM13, project ID UMO-2017/25/N/NZ3/01039

šŸ“š Short Research Training:

University of Rouen, France (2014) Laboratoire de Neuropsychopharmacologie ExpƩrimentale

šŸŒ Activities:

  • Expert Activity/Reviewer (2024)
    Platform: Qeios
  • International Student Exchanges and ERASMUS Supervision (2024)
    Engaging in initiatives and participating in European Union programs, overseeing ERASMUS students.
  • Participation in Scientific Workshops and Research Teams (2024)
    Engaging in workshops aimed at exchanging experiences, self-improvement, and organization.
  • Editorial Work (2023-present)
    Journal: Reviewer for Breast Cancer-Tokyo, ISSN 1340-6868, eISSN 1880-4233.

šŸ† Awards and Distinctions:

2022: First-level Special Award for Outstanding Didactic Work by Academic Teachers Medical University of Lodz.

2020: Team Distinction from the Faculty of Chemistry Nicolaus Copernicus University in Toruń Rector’s Award Medical University of Lodz Second-degree scientific award for a series of publications titled: ‘Investigation of the Anticancer Properties of Synthetic Analogues of Compounds Isolated from Plants’. (Impact Factor – 8.034). Polish Intelligent Development Award – Nomination.

2019: Investigation of Anticancer Activity of Synthetic Analogues of Methylenolactones”, IF=4.026PTBioch Bursary Scholarship 44th FEBS Congress “From Molecules to Living Systems”. Rector’s Award Medical University of Lodz Second Prize for Publication: ‘Synthetic Analogues of Coumarin as Novel Agents with Anticancer Activity’. (Impact Factor = 4.173). Rector’s Award Medical University of Lodz Team Second award for Publication Series:

2017: Rector’s Award Medical University of Lodz First Prize for Publication Series: “Synthesis and Investigation of Biological Activity of Opioid Mimetics and Glutathione Peroxidase”. (IF=8.638). Rector’s Award Medical University of Lodz Team First Prize for Publication Series: “Anticancer Properties of Novel Synthetic Dicoumarins”. (IF=6.221) “Investigation of Anticancer Activity of Sesquiterpene Lactones”. (IF=4.994)

2016: Rector’s Award Medical University of Lodz First Prize for Publication Series: “Anticancer Properties of Novel Synthetic Lactones in Combination with Known Anticancer Drugs”. (IF = 8.835)

Publications Top Notes šŸ“

  • Title: Synthesis of New Chiral Ī²-Carbonyl Selenides with Antioxidant and Anticancer Activity Evaluation-Part I
    • Authors: Laskowska, A., Pacuła-Miszewska, A.J., Obieziurska-Fabisiak, M., et al.
    • Journal: Materials
    • Year: 2024
    • Volume: 17
    • Pages: 1ā€“15
    • Summary: This study focuses on the synthesis of new chiral Ī²-carbonyl selenides and evaluates their antioxidant and anticancer activities, providing valuable insights into potential therapeutic agents.

 

  • Title: New Uracil Analog with Exocyclic Methylidene Group Can Reverse Resistance to Taxol in MCF7 Cancer Cells
    • Authors: Długosz-Pokorska, A., Perlikowska, R., Janecki, T., et al.
    • Journal: Biologics: Targets and Therapy
    • Year: 2023
    • Volume: 17
    • Pages: 69ā€“83
    • Summary: This article presents a novel uracil analog with potential to reverse resistance to Taxol in MCF7 cancer cells, indicating its promising role as an anticancer agent.

 

  • Title: New Uracil Analog- U-359 can Reverse Resistance to Taxol in MCF-7 cancer cells
    • Authors: Długosz-Pokorska, A., Perlikowska, R., Janecki, T., et al.
    • Journal: Acta Biochimica Polonica
    • Year: 2023
    • Volume: 70
    • Pages: 56
    • Summary: This study explores another uracil analog’s potential to reverse resistance to Taxol in MCF-7 cancer cells, indicating a promising avenue for further research.

 

  • Title: The Influence of Long Carbon Chains on the Antioxidant and Anticancer Properties of N-Substituted Benzisoselenazolones and Corresponding Diselenides
    • Authors: Pacuła-Miszewska, A.J., Obieziurska-Fabisiak, M., Jastrzębska, A., et al.
    • Journal: Pharmaceuticals
    • Year: 2023
    • Volume: 16
    • Pages: 1ā€“11
    • Summary: This research investigates the impact of long carbon chains on the antioxidant and anticancer properties of N-substituted benzisoselenazolones and corresponding diselenides, providing valuable insights into structure-activity relationships.

 

  • Title: Attachment of Chiral Functional Groups to Modify the Activity of New GPx Mimetics
    • Authors: Laskowska, A., Pacuła-Miszewska, A., Długosz-Pokorska, A., et al.
    • Journal: Materials
    • Year: 2022
    • Volume: 16
    • Pages: 1ā€“14
    • Summary: This study explores the modification of GPx mimetics’ activity through the attachment of chiral functional groups, offering potential strategies for enhancing therapeutic effects.

 

Annesha Chakraborty| Bioinformatics | Women Researcher Award

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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Scholar

 

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)

Somayeh Hashemi Sheikhshabani | Human Genetics | Best Researcher Award

Dr. Somayeh Hashemi Sheikhshabani | Human Genetics | Best Researcher Award

šŸ‘Øā€šŸ«Profile Summary

I am a highly skilled researcher specializing in Medical Genetics with a focus on Cancer Biology, Cancer Drug Resistance, Noncoding RNAs, Computational Biology, and Genetics of Rare Diseases. With a Ph.D. from Shahid Beheshti University of Medical Sciences, Tehran, Iran, and a strong background in Cellular and Molecular Biology, I’ve conducted extensive research on genetic analysis of male infertility, identification of genes involved in various cancers, and prediction of regulatory networks using bioinformatics tools. Proficient in a wide range of experimental techniques and software applications, I am dedicated to advancing knowledge in genetics and contributing to the development of innovative therapies.

 

šŸŒ Professional Profiles

Education šŸ“š

PhD in Medical Genetics Shahid Beheshti University of Medical Sciences, Tehran, Iran September 23, 2019 ā€“ October 7, 2023 PhD Thesis: Genetic investigation of non-obstructive azoospermia families with cytogenetic and molecular genetic tests, and determining the relationship between genetic and clinical findings of patients.M.Sc. in Cellular and Molecular Biology National Institute of Genetic Engineering and Biotechnology, Tehran, Iran September 23, 2010 ā€“ October 27, 2012 Master Thesis: Alkaloid extract of Peganum harmala L. seed on the expression of Bax and Bcl-2 genes involved in mitochondrial apoptosis pathway in cancer cells.B.Sc. in Molecular Genetics Shahrekord University, Shahrekord, Iran September 23, 2005 ā€“ October 7, 2009

Research Interests šŸ”¬

  • Cancer Biology
  • Cancer Drug Resistance
  • Noncoding RNAs
  • Computational Biology
  • Genetics of Rare Diseases

Research Projects šŸ§¬

Genetic analysis of male infertility in a family using Whole Exome Sequencing. (Student Research Committee, Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran; 2024)In silico prediction of non-coding RNA-gene regulatory network in primary gonad failure defects. (Student Research Committee, Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran; 2024)In silico identification of functional single nucleotide polymorphisms of azoospermia genes. (Student Research Committee, Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran; 2024)In silico prediction of coagulation system functional polymorphisms. (Student Research Committee, Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran; 2024)Identification of genes involved in Imatinib resistance in chronic myeloid leukemia (CML). (Student Research Committee, Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran; 2024)Genetic analysis of families with non-obstructive azoospermia by Whole Exome Sequencing. (Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran; 2024)Genetic investigation of infertility in an Iranian family with infertility in both sexes. (Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran; 2023)Prediction of tissue-specific inflammatory LncRNAs in COVID-19 patients. (Student Research Committee, Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran; 2021-2024)Identification of inflammatory miRNAs associated with COVID-19 and determination of their potential target genes using bioinformatics tools. (Student Research Committee, Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran; 2021-2023)Identification of genes involved in the development of chemotherapy resistance in lung cancer. (Student Research Committee, Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran; 2021-2024)Identification of common polymorphisms in the host antioxidant pathway against viruses and prediction of their effects. (Student Research Committee, Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran; 2021-2024)Identification of genes involved in the development of chemotherapy resistance in ovarian cancer. (Student Research Committee, Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran; 2021-2023)Investigation of the effect of oleuropein on miR-125b and miR-34a expression in ovarian cancer cell lines. (Cellular and Molecular Research Center, Shahrekord University of Medical Sciences; 2019-2020)Investigation of the effect of oleuropein on miR-181b and miR-21 expression in breast cancer cell line. (Cellular and Molecular Research Center, Shahrekord University of Medical Sciences; 2019-2020)Investigation of the effect of oleuropein on the expression of genes involved in apoptosis in cisplatin-resistant ovarian cell line. (Cellular and Molecular Research Center, Shahrekord University of Medical Sciences; 2019-2020)Study of the effect of nanoparticles containing altretiamine and arstin on ferroptosis in ovarian cancer cell line. (Cellular and Molecular Research Center, Shahrekord University of Medical Sciences; 2016-2020)Study of the effect of nanoparticles containing altretamine on ferroptosis-apoptosis in ovarian cancer cell line. (Cellular and Molecular Research Center, Shahrekord University of Medical Sciences; 2018-2019)Genetic etiology determination of non-syndromic hearing loss families using Whole Exome Sequencing. (Cellular and Molecular Research Center, Shahrekord University of Medical Sciences; 2018-2019)

Skills šŸ› ļø

A. Experimental Techniques:Human cell cultureMTT assay (Drugs, Natural products, Nanoparticles)DNA and RNA extractionApoptosis assayROS assayElectrophoresisQuantitative PCRConventional PCRSonicationNanodropKaryotypingSanger sequencingWhole exome sequencingB. Software Ability:Various microRNA databases (TargetScan, miRBase, miRWalk, etc.)Various lncRNA databases (starBase, LncBase, etc.)Pathway databases (KEGG, WikiPathways, Reactome)Variant prediction tools (SIFT, Mutation Taster, Polyphen, CADD, etc.)Genome browsers (NCBI, Ensembl, UCSC)Primer design software and tools (AlleleID, Primer3, Oligo 7, etc.)Sequence analysis software (QIAGEN CLC Genomics Workbench, Mutation Surveyor, FinchTV, etc.)STRINGDBCytoscapeGene RunnerGenome expression databases (GEO, GTEx, etc.)

Workshops šŸ“š

 

  • Various workshops covering topics such as predicting LncRNAs, the role of biological systems in cancer, electronic resource investigation, Next Generation sequencing, molecular techniques, article writing, PCR, and bioinformatics.

šŸ“šTop Noted Publication

  1. Title: The effect of oleuropein on apoptotic pathway regulators in breast cancer cells
    • Journal: European Journal of Pharmacology
    • Year: 2020
    • Volume: 886
    • Pages: 173509
    • Citations: 43

 

  1. Title: Peganum harmala L.ā€™s anti-growth effect on a breast cancer cell line
    • Journal: Biotechnology reports
    • Year: 2015
    • Volume: 8
    • Pages: 138-143
    • Citations: 39

 

  1. Title: Oleuropein reduces cisplatin resistance in ovarian cancer by targeting apoptotic pathway regulators
    • Journal: Life Sciences
    • Year: 2021
    • Volume: 278
    • Pages: 119525
    • Citations: 26

 

  1. Title: Growth inhibitory impact of Peganum harmala L. on two breast cancer cell lines
    • Journal: Iranian journal of biotechnology
    • Year: 2014
    • Volume: 12
    • Issue: 1
    • Pages: 8-14
    • Citations: 23

 

  1. Title: The impact of oleuropein on miRNAs regulating cell death signaling pathway in human cervical cancer cells
    • Journal: Biotechnology and Applied Biochemistry
    • Year: 2024
    • Volume: 71
    • Issue: 1
    • Pages: 61-71
    • Citations: 1

 

  1. Title: In Silico Prediction of Functional SNPs Interrupting Antioxidant Defense Genes in Relation to COVID-19 Progression
    • Journal: Biochemical Genetics
    • Year: 2024
    • Pages: 1-27

 

  1. Title: Meta-analysis of microarray data to determine gene indicators involved in the cisplatin resistance in ovarian cancer
    • Journal: Cancer Reports
    • Year: 2023
    • Volume: 6
    • Issue: 12
    • Pages: e1884

Mi Rim Lee |cancer science Award | Young Scientist Award

Ms. Mi Rim Lee| Genomics Award | Young Scientist Award

šŸ‘Øā€šŸ«Profile Summary

John Doe is a dedicated Ph.D. candidate in Cancer Biomedical Science at the National Cancer Center Graduate School of Cancer Science and Policy. With a solid academic background in Biomaterials, he obtained both his Master’s and Bachelor’s degrees from Pusan National University. John’s achievements include prestigious scholarships and poster awards from esteemed institutions like the Korean Society of Laboratory Animal Science and the Korean Cancer Association. His research interests lie at the intersection of cancer biology and biomaterials, aiming to contribute novel insights into cancer treatment and therapy development. John’s academic excellence and commitment to cancer research mark him as a promising young scientist in the field.

šŸŒ Professional Profiles

EducationšŸŽ“

2019.09~present: National Cancer Center Graduate School of Cancer Science and Policy Major: Cancer Biomedical Science Degree: Ph.D. candidate, 2017.03~2019.02: Pusan National University Major: Biomaterial Degree: MS. 2011.03~2017.02: Pusan National University Major: Biomaterial Degree: BA.

Awards šŸ†

2018.02: Title: Scholarship Student Institution: Korean Society of Laboratory Animal Science 2018.07: Title: Poster Award Institution: Korean Society of Laboratory Animal Science 2019.01: Title: Academic Award Institution: College of Life and Resources Sciences, Pusan National University 2021.06: Title: Poster Award Institution: Korean Cancer Associati

šŸ“šTop Noted Publication

  1. Title: New Function Annotation of PROSER2 in Pancreatic Ductal Adenocarcinoma
    • Authors: Lee, Y.-S., Im, J., Yang, Y., … Hwang, H., Kim, Y.-H.
    • Journal: Journal of Proteome Research
    • Publication Year: 2024
    • Volume: 23
    • Issue: 3
    • Pages: 905ā€“915

 

  1. Title: Application of plasma circulating KRAS mutations as a predictive biomarker for targeted treatment of pancreatic cancer
    • Authors: Lee, M.R., Woo, S.M., Kim, M.K., … Kim, Y.-H., Kong, S.-Y.
    • Journal: Cancer Science
    • Publication Year: 2024

 

  1. Title: Complexation of drug and hapten-conjugated aptamer with universal hapten antibody for pancreatic cancer treatment
    • Authors: Choi, S.I., Lee, Y.-S., Lee, Y.M., … Kim, Y.-H., Kim, I.-H.
    • Journal: Journal of Controlled Release
    • Publication Year: 2023
    • Volume: 360
    • Pages: 940ā€“952

 

  1. Title: Refining Classification of Cholangiocarcinoma Subtypes via Proteogenomic Integration Reveals New Therapeutic Prospects
    • Authors: Cho, S.Y., Hwang, H., Kim, Y.-H., … Park, S.-J., Woo, S.M.
    • Journal: Gastroenterology
    • Publication Year: 2023
    • Volume: 164
    • Issue: 7
    • Pages: 1293ā€“1309

 

  1. Title: Establishment of Patient-Derived Organoids Using Ascitic or Pleural Fluid from Cancer Patients
    • Authors: Choi, W., Kim, Y.-H., Woo, S.M., … Lee, K.S., Kong, S.-Y.
    • Journal: Cancer Research and Treatment
    • Publication Year: 2023
    • Volume: 55
    • Issue: 4
    • Pages: 1077ā€“1086

 

  1. Title: Establishment of Patient-derived Preclinical Models for Invasive Papillary Cholangiocarcinoma
    • Authors: Mwesige, B., Lee, M.R., Lee, Y.-S., … Woo, S.M., Kim, Y.-H.
    • Journal: Anticancer Research
    • Publication Year: 2022
    • Volume: 42
    • Issue: 1
    • Pages: 599ā€“608

Yubo ZHANG | Genomics Award | Best Researcher Award

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