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Bioinformatics
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Bioinformatics, Computational Biology & Systems Biology

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📣 Pre-Registration Now Open for the International ORCA Workshop
Interested? Please fill out this short pre-registration form:
👉 https://forms.gle/UQZgNvr26AGBSnja6
____________________________________
Are you interested in learning how to perform quantum mechanical calculations using the powerful and free ORCA software package?
We are excited to announce a potential international workshop on ORCA, a widely used program for quantum chemistry calculations. Whether you're a beginner or have basic knowledge of computational chemistry, this workshop is designed to introduce you to ORCA and help you get started with geometry optimization, frequency analysis, transition state searches, and more.
👨‍🏫 Instructor: Dr. Mehdi Irani — a recognized expert in computational chemistry
🔗 https://prof.uok.ac.ir/m.irani/index.htm
____________________________________
🧪 What is ORCA?
ORCA is a versatile and efficient quantum chemistry software developed by the Neese group. It supports a wide range of methods, including:
• Hartree–Fock
• DFT
• Post-Hartree–Fock methods
(e.g., MP2, CCSD)
• Multiscale QM/MM techniques
It is freely available for academic use and runs on Linux, macOS, and Windows platforms.
________________________________
📚 Topics to Be Covered
• Introduction to quantum mechanical methods in chemistry
• Installing and running ORCA on your system
• Preparing input files for basic and advanced calculations
• Geometry optimizations and single-point energy calculations
• Frequency calculations and reaction transition states
• Analyzing output files
• (Possibly) An introduction to QM/MM and QM1/QM2 multiscale methods using ORCA
________________________________
🎯 Who Should Attend?
This workshop is suitable for:
• Students, researchers, and faculty with elementary knowledge of quantum chemistry or molecular modeling
• Beginners looking to start using ORCA for their computational research
• Participants from any country or region interested in theoretical chemistry
________________________________
📅 Tentative Date
The workshop is planned for late August or early September 2025.
The exact date and structure will be finalized based on the number of interested participants.
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👩‍🏫 Single-Molecule & Spatial Sequencing: Methods & Applications (Spring 2025)
💥Online recorded course from Cornell University

👩‍💻 Course link
🎞 Recorded videos

📲Channel: @Bioinformatics
#video #course #sequencing #rna
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📑 Learning and teaching biological data science in the Bioconductor community

📕 Journal: PLOS Computational Biology (I.F.=3.6)
🗓Publish year: 2025

🧑‍💻Authors: Jenny Drnevich ,Frederick J. Tan ,Fabricio Almeida-Silva, ...
🏢Universities: University of Illinois Urbana-Champaign & Johns Hopkins University & , USA - Ghent University,Belgium - Universitat Pompeu Fabra, Spain - University of Limerick, Ireland

📎 Study the paper

📲Channel: @Bioinformatics
#data #bioconductor #r
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📄 Integrating artificial intelligence in drug discovery and early drug development: a transformative approach

📗 Journal: Biomarker Research (I.F.=11.5)
🗓Publish year: 2025

🧑‍💻Authors: Alberto Ocana, Atanasio Pandiella, Cristian Privat, ...
🏢Universities: Instituto de Investigación Sanitaria San Carlos (IdISSC) & Instituto de Biología Molecular y Celular del Cáncer & Universidad de Castilla La Mancha, Spain

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📲Channel: @Bioinformatics
#review #ai #drug
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📃 Transformers in Protein: A Survey

🗓Publish year: 2025

🧑‍💻Authors: Xiaowen Ling, Zhiqiang Li, Yanbin Wang, Zhuhong You
🏢Universities: Shenzhen MSU-BIT University & Northwestern Polytechnical University, China

📎 Study the paper

📲Channel: @Bioinformatics
#review #transformer #protein
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📑 Unlocking the potential of circular RNA vaccines: a bioinformatics and computational biology perspective

📔 Journal: Biomarker Research (I.F.=11.5)
🗓Publish year: 2025

🧑‍💻Authors: Xuyuan Liua,e ∙ Siqi Wanga,e ∙ Yunan Sun, ...
🏢Universities: Peking University & University of Science and Technology of China & The First Affiliated Hospital of Guangzhou Medical University, China

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📲Channel: @Bioinformatics
#review #circular_rna #vaccine
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📄 Systematic Review of Phylogenetic Analysis Techniques for RNA Viruses Using Bioinformatics

📗 Journal: International Journal of Molecular Sciences (I.F.=4.9) Q1
🗓Publish year: 2025

🧑‍💻Authors: Irena Wadas & Inês Domingues
🏢Universities: Polytechnic University of Coimbra & Research Centre of the Portuguese Institute of Oncology of Porto (CI-IPOP), Portugal

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📲Channel: @Bioinformatics
#review #Phylogenetic #rna #virus
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📃 Large language models transform biological research: from architecture to utilization

📘 Journal: Science China Information Sciences (I.F.=7.6) Q1
🗓Publish year: 2025

🧑‍💻Authors: Tao Wang & Zeyu Luo
🏢Universities: Northwestern Polytechnical University & Northeast Forestry University, China

📎 Study the paper

📲Channel: @Bioinformatics
#review #llm #ai
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📄 Biclustering in bioinformatics using big data and High Performance Computing applications: challenges and perspectives, a review

📓 Journal: Supercomputing (I.F.=2.7)
🗓Publish year: 2025

🧑‍💻Authors: Aurelio López-Fernández, Francisco A. Gomez-Vela, Domingo S. Rodriguez-Baena, ...
🏢Universities: Universidad de Sevilla, Universidad Pablo de Olavide, Universidad Pablo de Olavide, Universidade da Coruña, Spain - University of Hamburg, Germany

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📲Channel: @Bioinformatics
#review #biclustering #clustering #hpc
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📑 Computational biology and artificial intelligence in mRNA vaccine design for cancer immunotherapy

📕 Journal: Frontiers in Cellular and Infection Microbiology (I.F.=4.8)
🗓Publish year: 2025

🧑‍💻Authors: Saber Imani, Xiaoyan Li, Keyi Chen, ...
🏢Universities: Zhejiang Shuren University & Shulan International Medical College & Southwest Medical University, China - Medical University of Warsaw, Poland - Islamic Azad University, Iran

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📲Channel: @Bioinformatics
#review #vaccine #mrna #ai
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📄 Generative Artificial Intelligence in Healthcare: Applications, Implementation Challenges, and Future Directions

📔 Journal: International Journal of Molecular Sciences (I.F.=4.9) Q1
🗓Publish year: 2025

🧑‍💻Authors: Syed Arman Rabbani 1,Mohamed El-Tanani,Shrestha Sharma, ...
🏢Universities: RAK Medical and Health Sciences University, UAE - Amity University & Jagannath University & Geeta University, India

📎 Study the paper

📲Channel: @Bioinformatics
#review #ai #healthcare #chatgpt
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