Chandan Shivamalli | Life Sciences | Excellence in Research

Assoc Prof Dr. Chandan Shivamalli | Life Sciences | Excellence in Research

 

Assoc Prof Dr at JSS Academy of Higher Education and Research India

Assoc Prof Dr Chandan S is an accomplished academic and researcher specializing in Biotechnology and Bioinformatics. He holds a Ph.D. from the University of Mysore and currently serves as an Assistant Professor and Coordinator at Jagadguru Sri Shivarathreeshwara University. Assoc Prof Dr. Chandan has extensive research experience, having worked on projects funded by prestigious agencies like DST-SERB and ICMR. He has led various projects, including studies on anti-mucosal inflammatory effects, Alzheimer’s disease therapy, and leptospiral peptidomimetics. Assoc Prof Dr. Chandan’s contributions to the field have earned him awards such as the DST-SERB Young Scientist Award and the ICMR Senior Research Fellowship.

profile

Scholar

📚 Educational Qualification

Bachelor of Science (B.Sc) University / College: University of Mysore, JSS College, Mysore Period: 2002-2005. M.Sc University / College: University of Mysore, JSS College, Mysore Period: 2005-2007 . Master of Philosophy (M.Phil) University / College: Vinayaka Missions University (Deemed), Vinayaka Missions University Period: 2007-2008 . Ph.D University / College: University of Mysore, University of Mysore Period: 2010-2013

💼 Work Experience

1. Project Directorate on Animal Disease Monitoring and Surveillance, ICAR Designation / Department: Post Graduate Research Assistant Period: June 02, 2007 – March 31, 2010 Duration: 2 Years 9 Months. 2. Department of Studies in Biotechnology Designation / Department: Project Fellow Period: May 17, 2010 – May 21, 2011 Duration: 1 Year 0 Months. 3. Indian Council for Medical Research Designation / Department: Senior Research Fellow Period: May 21, 2011 – December 13, 2013 Duration: 2 Years 7 Months. 4. Jagadguru Sri Shivarathreeshwara University Designation / Department: Lecturer, Biotechnology & Bioinformatics Period: December 13, 2013 – January 31, 2016 Duration: 2 Years 1 Month 5. Jagadguru Sri Shivarathreeshwara University Designation / Department: Assistant Professor & Coordinator, Biotechnology & Bioinformatics Period: February 01, 2016 – Till Date Duration: 5 Years 9 Months

🏆 Awards

1. DST-SERB Young Scientist Awarding Agency: DST-SERB, Purpose of Award: Sanction of Project, Award Type: National, Award Date: June 1, 2016 2. Senior Research Fellow Awarding Agency: ICMR, Purpose of Award: To pursue PhD, Award Type: National, Award Date: May 21, 2011

🔬 Projects

1. Evaluation of anti-mucosal inflammatory effect of Acacia fernesiana using Zebra fish as model organism Principal Investigator: Dr. Chandan S Duration: 1 Year(s) Institute: School of Life Sciences – Mysuru Department: Biotechnology & Bioinformatics 2. A prospective study of synergistic effect of combination therapy of FDA approved drugs and in silico characterization against Alzheimer’s disease Principal Investigator: Dr. Chandan S Duration: 2 Year(s) Institute: School of Life Sciences – Mysuru Department: Biotechnology & Bioinformatics 3. Genomic and proteomic analysis of outer membrane vesicles from clinical isolates of Leptospira and development of antileptospiral peptidomimetics Principal Investigator: Dr. Chandan SDuration: 3 Year(s) Institute: Faculty of Life Sciences [FLS] Department: Bioinformatics [BIOINFO]

Publications Top Notes📝

 

  • Title: A systematic review on ethnopharmacology, phytochemistry and pharmacological aspects of Thymus vulgaris Linn.
    Authors: SM Patil, R Ramu, PS Shirahatti, C Shivamallu, RG Amachawadi
    Year: 2021
    Journal: Heliyon
    Volume and Issue: 7(5)
    Article Number: 134

 

  • Title: Antiviral and immunomodulatory activity of curcumin: A case for prophylactic therapy for COVID-19
    Authors: RK Thimmulappa, KK Mudnakudu-Nagaraju, C Shivamallu, …
    Year: 2021
    Journal: Heliyon
    Volume and Issue: 7(2)
    Article Number: 133

 

  • Title: Bioactive compounds effective against type 2 diabetes mellitus: a systematic review
    Authors: C Egbuna, CG Awuchi, G Kushwaha, M Rudrapal, …
    Year: 2021
    Journal: Current Topics in Medicinal Chemistry
    Volume and Issue: 21(12)
    Pages: 1067-1095

 

  • Title: In silico evaluation of flavonoids as effective antiviral agents on the spike glycoprotein of SARS-CoV-2
    Authors: AS Jain, P Sushma, C Dharmashekar, MS Beelagi, SK Prasad, …
    Year: 2021
    Journal: Saudi Journal of Biological Sciences
    Volume and Issue: 28(1)
    Pages: 1040-1051

 

  • Title: Genetic typing of recent classical swine fever isolates from India
    Authors: SS Patil, D Hemadri, BP Shankar, AG Raghavendra, H Veeresh, …
    Year: 2010
    Journal: Veterinary Microbiology
    Volume and Issue: 141(3-4)
    Pages: 367-373

 

  • Title: Genistein: a potent anti-breast cancer agent
    Authors: SS Bhat, SK Prasad, C Shivamallu, KS Prasad, A Syed, P Reddy, CA Cull, …
    Year: 2021
    Journal: Current Issues in Molecular Biology
    Volume and Issue: 43(3)
    Pages: 1502-1517

 

  • Title: Palladium (II) complexes as biologically potent metallo-drugs: Synthesis, spectral characterization, DNA interaction studies and antibacterial activity
    Authors: KS Prasad, LS Kumar, S Chandan, RMN Kumar, HD Revanasiddappa
    Year: 2013
    Journal: Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy
    Volume: 107
    Pages: 108-116

 

  • Title: Aqueous Extract of Saraca indica Leaves in the Synthesis of Copper Oxide Nanoparticles: Finding a Way towards Going Green
    Authors: KS Prasad, A Patra, G Shruthi, S Chandan
    Year: 2017
    Journal: Journal of Nanotechnology
    Volume and Issue: 2017(1)
    Article Number: 7502610

 

  • Title: Quinazolinones linked amino acids derivatives as a new class of promising antimicrobial, antioxidant and anti-inflammatory agents
    Authors: KP Rakesh, S Ramesh, HMM Kumar, S Chandan, DC Gowda
    Year: 2015
    Journal: European Journal of Chemistry
    Volume and Issue: 6(3)
    Pages: 254-260

 

  • Title: Diorganotin(IV) complexes of biologically potent 4(3H)-quinazolinone derived Schiff bases: Synthesis, spectroscopic characterization, DNA interaction studies and …
    Authors: KS Prasad, LS Kumar, S Chandan, B Jayalakshmi, HD Revanasiddappa
    Year: 2011
    Journal: Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy
    Volume and Issue: 81(1)

 

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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Education🎓

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

 Technical Skills💻

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

 Relevant Experience 🌟

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, Iran’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 📝

  • 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

Hyun Suk Shin | Molecular Biology | Best Researcher Award

 Dr. Hyun Suk Shin | Molecular Biology | Best Researcher Award

 Dr. University of Las Palmas de Gran Canaria,  Spain

👩‍🔬 Hyun Suk Shin is a Marine Biotechnology expert with a rich academic background. She holds a B.Sc., M.Sc., and Ph.D. from Korea Maritime and Ocean University, where she delved into various aspects of aquaculture, molecular biology, and biochemistry. With extensive research experience, including international collaborations, she has contributed significantly to the field, resulting in numerous publications and patents. As a postdoctoral researcher, she continued her impactful work at institutions like the National Fisheries Research and Development Institute of Korea and the Fundación Canaria Parque Científico Tecnológico de la Universidad de Las Palmas de Gran Canaria. Recognized for her excellence, she received prestigious scholarships and awards, demonstrating her dedication to advancing aquaculture research.

 

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Scholar

Education 📚

  1. Higher Degree
    • Name of Qualification: M.S. Science
    • Degree Awarding Entity: Korea Maritime and Ocean University
    • Date of Qualification: 28/02/2010
  2. Higher Degree
    • Name of Qualification: B.S. Science, Marine Biotechnology
    • Degree Awarding Entity: Korea Maritime and Ocean University
    • Date of Qualification: 28/02/2008

Doctorates

  • PhD Science
    • Degree Awarding Entity: Korea Maritime and Ocean University
    • Date of Degree: 28/02/2014

Teaching Experience📊

Experience Supervising Doctoral Theses and/or Final Year Projects: Project Title: Analysis of Skeletal Deformities in Gilthead Sea Bream Entity: Universidad de las Palmas de Gran Canaria Type of Entity: University Student: Alvaro Lorenzo Felipe Date of Reading: 05/07/2022Project Title: Programa Mejora Genética en Camarón Entity: Universidad de las Palmas de Gran Canaria Type of Entity: University

 

Scientific or Technological Activities 🔬

R&D Projects Funded Through Competitive Calls of Public or Private Entities

  1. Project Name: AquaIMPACT: Genomic and Nutritional Innovation for Genetically Superior Farmed Fish

Keywords: Molecular markers and recognition; Genetics transcription; Genetics expression of regulations; Epigenetics; Genetic drift; Population geneticsType of Project: Research and development, including transferGeographical Area: European UnionDegree of Contribution: ResearcherEntity: Universidad de las Palmas de Gran CanariaType of Entity: UniversityCity of Entity: Las Palmas de Gran Canaria, Canary Islands, SpainPrincipal Investigators: Daniel Montero Vítorres; Marisol Izquierdo Lopez; Juan Manuel Afonso Lopez; Maria Jesus Zamorano Serrano; Silvia Torrecillas Burriel; Hyun Suk Shin; Cathaysa Pérez GarcíaNumber of Researchers: 72Number of People/Year: 14Type of Participation: Team memberProgramme Name: Horizon 2020 Research and InnovationCode: 818367Start-End Date: 01/01/2018 – 02/01/2023Duration: 5 yearsParticipating Entities: [List of entities involved]Total Amount: €6,100,000Sub-Project Amount: €702,913Percentage as Grant: 100%Relevant Results: Determining the additive genetic components of immune system traits of sea bream and sea bass populations under genetic selection pressure for growth.Dedication Regime: Part-timeApplicant’s Contribution: In this project, my contribution is assigned within the WP2: Nutritional Innovation: Precision nutrition for superior genotypes, through the following tasks:Evaluation and divergent selection of sea bream breeders for growth and absence of skeletal deformities.Breeding, marking, fattening, and characterization of offspring and breeders using microsatellite markers “SMsa-1/ SMsa-2”.Study of genetic parameters of immune system traits.

Project Name: PerformFISH – Consumer Driven Production: Integrating Innovative Approaches for Competitive and Sustainable Performance across the Mediterranean Aquaculture Value Chain

Keywords: Genetics expression of regulations; Genetic drift; Population geneticsType of Project: Research and development, including transferGeographical Area: European Union[Include any additional information about the project here]

Publications Top Notes 📝

  • Effects of LED light spectra on oxidative stress and the protective role of melatonin in relation to the daily rhythm of the yellowtail clownfish, Amphiprion clarkii
    • Authors: HS Shin, J Lee, CY Choi
    • Journal: Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology
    • Year: 2011

 

  • Effect of LED light spectra on starvation-induced oxidative stress in the cinnamon clownfish Amphiprion melanopus
    • Authors: CY Choi, HS Shin, YJ Choi, NN Kim, J Lee, GS Kil
    • Journal: Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology
    • Year: 2012

 

  • Kisspeptin regulates the hypothalamus–pituitary–gonad axis gene expression during sexual maturation in the cinnamon clownfish, Amphiprion melanopus
    • Authors: NN Kim, HS Shin, YJ Choi, CY Choi
    • Journal: Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology
    • Year: 2014

 

  • Effects of LED light spectra on the growth of the yellowtail clownfish Amphiprion clarkii
    • Authors: HS Shin, J Lee, CY Choi
    • Journal: Fisheries Science
    • Year: 2012

 

  • Profiles of antioxidant gene expression and physiological changes by thermal and hypoosmotic stresses in black porgy (Acanthopagrus schlegeli)
    • Authors: KW An, NN Kim, HS Shin, GS Kil, CY Choi
    • Journal: Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology
    • Year: 2010

 

  • The effects of quercetin on physiological characteristics and oxidative stress resistance in olive flounder, Paralichthys olivaceus
    • Authors: HS Shin, JH Yoo, TS Min, KY Lee, CY Choi
    • Journal: Asian-Australasian Journal of Animal Sciences
    • Year: 2010

 

  • Selection for growth is associated in gilthead sea bream (Sparus aurata) with diet flexibility, changes in growth patterns and higher intestine plasticity
    • Authors: E Perera, P Simó-Mirabet, HS Shin, E Rosell-Moll, F Naya-Catalá, …
    • Journal: Aquaculture
    • Year: 2019

 

  • Quantitative mRNA expression of sox3 and DMRT1 during sex reversal, and expression profiles after GnRHa administration in black porgy, Acanthopagrus schlegeli
    • Authors: HS Shin, KW An, MS Park, MH Jeong, CY Choi
    • Journal: Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology
    • Year: 2009

 

Annesha Chakraborty| Bioinformatics | Women Researcher Award

 Dr. Annesha Chakraborty | Bioinformatics | Women Researcher Award

 Dr. SASTRA DEEMED UNIVERSITY

👩‍🔬 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.baumannii’s efflux pump research. Passionate about advancing scientific knowledge and addressing real-world challenges.🌟

 

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🎓 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

🔬 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)

💼 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 📝

  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

Prof. Yubo ZHANG | Genomics Award | Best Researcher Award

👨‍🏫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.

🌐 Professional Profiles

Education🎓

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.

🔬 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 🏆

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

📝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

🎖️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, “Pearl River Talents Plan” Leading Talents, 2017GC010063, 2017.05-2021.12, 0.81 million CNY. (Competitive Project)

📚Top 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