Computational and Structural Biotechnology Journal

Computational and Structural Biotechnology Journal (CSBJ), a Science Partner Journal published in collaboration with AAAS, is inviting submissions for its upcoming special issue:

“𝐂𝐨𝐦𝐩𝐮𝐭𝐚𝐭𝐢𝐨𝐧𝐚𝐥 𝐒𝐩𝐚𝐭𝐢𝐚𝐥 𝐎𝐦𝐢𝐜𝐬: 𝐌𝐮𝐥𝐭𝐢𝐦𝐨𝐝𝐚𝐥 𝐒𝐭𝐫𝐚𝐭𝐞𝐠𝐢𝐞𝐬 𝐟𝐨𝐫 𝐒𝐲𝐬𝐭𝐞𝐦𝐬 𝐁𝐢𝐨𝐥𝐨𝐠𝐲 𝐚𝐧𝐝 𝐁𝐢𝐨𝐦𝐞𝐝𝐢𝐜𝐚𝐥 𝐃𝐢𝐬𝐜𝐨𝐯𝐞𝐫𝐲”

📌 Topics include (but are not limited to):
• Spatial transcriptomics analysis pipelines (MERFISH, seqFISH+, Xenium, Visium HD, Stereo-seq)
• Spatial proteomics and tissue architecture analysis (IMC, MIBI, CODEX, t-CyCIF, IBEX)
• Spatial metabolomics and lipidomics using MALDI-MSI, DESI-MSI, SIMS-MSI
• Spatial genomics and epigenomics workflows (Spatial-ATAC-seq, Slide-DNA-seq, Spatial-CUT&Tag)
• Cross-platform and multimodal spatial omics integration
• Graph neural networks and transformer-based spatial analysis
• Cell-neighbourhood analysis and spatial domain identification
• 3D tissue reconstruction and spatial biomarker discovery
• AI-assisted digital pathology integrating imaging and spatial omics
• Clinical and translational applications across major diseases

⏳ Submission Deadline: 31 December 2026

🔗 For more info about the Call for Papers, please visit: https://spj.science.org/journal/csbj/si/computational-spatial-omics

🧠 Guest Editors:
• Sakda Khoomrung, Mahidol University, Thailand
• Intawat Nookaew, UAMS - University of Arkansas for Medical Sciences, United States

Computational and Structural Biotechnology Journal, Science Partner Journals, AAAS - The American Association for the Advancement of Science,

🦠 Could decoding bacterial regulatory proteins help us stay ahead of drug resistance?

This study uncovers conserved sequence motifs in TetR family regulators (TFRs), one of the largest groups of bacterial transcription factors involved in antibiotic resistance, multidrug resistance, metabolism, and cellular adaptation. By identifying hidden molecular signatures within ligand-binding domains, the researchers provide new tools to predict bacterial regulatory functions and support antimicrobial drug discovery.

📝 Maria Kepa, Maciej Nielipinski, Estera Widawska, Jakub Filipek, Natalia Kazmierczak, Julia Sosnowska, Krystyna Baca, Maja Nastarowicz, Marcelina Rupp, Mieszko Goslawski-Zeligowski, Julia Mokrzycka, Dominika Nielipinska, Bartosz Sekula, Agnieszka J. Pietrzyk-Brzezinska

🔗 Conserved Motifs in the Ligand-Binding Domain of TetR Family Regulators: Identification and Analysis. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0100

📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj

Politechnika Łódzka, Computational and Structural Biotechnology Journal, Science Partner Journals, AAAS - The American Association for the Advancement of Science

🧠 What if missing data is not a flaw, but one of the most informative parts of a complex system?

This study introduces a graph-theoretic framework called NIMAA (NomInal data Mining AnAlysis) that changes how we think about missing data. Instead of treating missing values as errors to remove or impute, the authors show that the 𝘴𝘵𝘳𝘶𝘤𝘵𝘶𝘳𝘦 𝘰𝘧 𝘮𝘪𝘴𝘴𝘪𝘯𝘨𝘯𝘦𝘴𝘴 𝘪𝘵𝘴𝘦𝘭𝘧 can reveal hidden biological, ecological, and social patterns across complex datasets.

📝 Ehsan Zangene, Veit Schwämmle, Mohieddin Jafari

🔗 Informative Missingness in Nominal Data: A Graph-Theoretic Approach to Revealing Hidden Structure. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0099

📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj

University of Helsinki, Tampere University, Syddansk Universitet – University of Southern Denmark, Computational and Structural Biotechnology Journal, Science Partner Journals, AAAS - The American Association for the Advancement of Science

Special Issues This issue aims to bring together cutting-edge research and integrative reviews at the intersection of metabolomics, microbiome science, and computational biology to advance the One Health agenda.

🔬 A breakthrough for spatial biology? This ultrafast 3D imaging method enables deep whole-organ visualization faster than ever before.

This study introduces an ultrafast 3D immunolabeling and tissue-clearing workflow that enables whole-organ imaging in just 2 to 2.5 days, representing a major advancement in high-resolution biological imaging and quantitative tissue analysis. The method combines rapid immunostaining, optimized tissue clearing, and light sheet microscopy to visualize intact murine and human tissues with remarkable speed and precision.

📝 Junyu Chen, Zhangfan Ding, Lincoln Biswas, Jessica De Angelis, Alexandros Chatzis, Anjali P. Kusumbe

🔗 Rapid 3D Immunolabeling and Light Sheet Microscopy for Quantitative Analysis of Intact Tissues. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0121

📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj

Computational and Structural Biotechnology Journal, Science Partner Journals, AAAS - The American Association for the Advancement of Science, Sichuan University, MIA Portugal, Nanyang Technological University, Singapore

📢 We are pleased to announce that authors can now submit manuscripts directly from bioRxiv to the 𝘊𝘰𝘮𝘱𝘶𝘵𝘢𝘵𝘪𝘰𝘯𝘢𝘭 𝘢𝘯𝘥 𝘚𝘵𝘳𝘶𝘤𝘵𝘶𝘳𝘢𝘭 𝘉𝘪𝘰𝘵𝘦𝘤𝘩𝘯𝘰𝘭𝘰𝘨𝘺 𝘑𝘰𝘶𝘳𝘯𝘢𝘭 (CSBJ) through the 𝗯𝗶𝗼𝗥𝘅𝗶𝘃-𝘁𝗼-𝗝𝗼𝘂𝗿𝗻𝗮𝗹 (B2J) transfer service.

🔄 This integration enables authors to seamlessly transfer their preprint manuscripts, metadata, and author information from bioRxiv directly to CSBJ, saving valuable time by eliminating the need to re-upload files and re-enter submission details during the manuscript submission process.

🙏 We sincerely thank Cold Spring Harbor Laboratory (CSHL) for integrating CSBJ into the 𝗕𝟮𝗝 transfer service and for their continued contributions to advancing scientific communication and open science.

Detailed instructions for submission can be found in the 𝘎𝘶𝘪𝘥𝘦𝘭𝘪𝘯𝘦𝘴 𝘧𝘰𝘳 𝘈𝘶𝘵𝘩𝘰𝘳𝘴: https://spj.science.org/page/csbj/for-authors

📩 For inquiries regarding submissions or the submission process, please contact: [email protected]

We look forward to receiving your submissions and advancing the rapid dissemination of open science.

Computational and Structural Biotechnology Journal, Science Partner Journals, AAAS - The American Association for the Advancement of Science

🐶🩸 Could a routine blood sample unlock earlier detection of breast cancer in dogs?

A new pilot study explores how blood based DNA methylation profiling could transform the diagnosis and prognosis of canine mammary gland tumors (cMGTs), one of the most common cancers in female dogs. The research demonstrates that peripheral blood samples may capture tumor associated epigenetic changes, opening the door to less invasive cancer monitoring and earlier detection strategies.

📝 Keunhwan Jang, Geunwoo Jeon, Jungwoo Han, Seung-Bum Cho, Suyeon Kim, Songju Oh, Ha-Jung Kim

🔗 DNA Methylation in Blood Samples from Malignant Mammary Tumors of Companion Dogs: A Pilot Study. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0104

📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj

Computational and Structural Biotechnology Journal, Science Partner Journals, AAAS - The American Association for the Advancement of Science

⚛️ What if randomness inside cells isn’t noise — but biology’s hidden operating system?

This study introduces a hybrid Physics-Informed Neural Network (PINN) and Bayesian modeling framework to analyze how single nanoparticles adhere to living cells under different cytoskeletal perturbations — offering a major advancement for nanomedicine, drug delivery, and mechanobiology. The framework combines classical viscoelastic physics with AI-driven learning to accurately model complex and noisy biological interactions.

📝 Houari Bettahar, Hélder A. Santos, Quan Zhou

🔗 Hybrid Physics-Informed and Bayesian Modeling of Single-Nanoparticle–Cell Adhesion Kinetics under Cytoskeletal Perturbation. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0077

📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj

Aalto University, University of Helsinki, UMCG - Universitair Medisch Centrum Groningen, University of Groningen, Computational and Structural Biotechnology Journal, Science Partner Journals, AAAS - The American Association for the Advancement of Science

⚛️ Can spherical voxelization improve how AI interprets protein chemistry and interactions?

Artificial intelligence is transforming structural biology, but the quality of AI predictions depends heavily on how proteins are represented computationally. This study introduces SpheronizaTor, a novel residue-centered spherical voxelization framework that enables more interpretable and chemically aware modeling of protein microenvironments.

📝 Jose Cleydson Ferreira Silva, Matthew Richardson, José D. D. Cediel-Becerra, Layla Schuster, Raquel Dias

🔗 SpheronizaTor: Spherical Voxelization for Interpretable Protein Microenvironment Modeling. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0076

📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj

UF Microbiology and Cell Science & ASM Gators, UF Department of Chemical Engineering, University of Florida, Computational and Structural Biotechnology Journal, Science Partner Journals, AAAS - The American Association for the Advancement of Science

CSBJ Smart Hospital (https://spj.science.org/journal/csbj/smarthospital), is inviting submissions for its upcoming special issue:

“Data Orchestration in Smart Health: From Raw Biomedical Data to AI-Ready Frameworks”

📌 Topics include (but are not limited to):
• Wearable physiological signal preprocessing (EEG, ECG, PPG, EMG, EDA, accelerometry)
• Medical imaging pipelines for AI (MRI, CT, ultrasound, histopathology)
• Multi-omics integration and AI-readiness
• EHR extraction, normalization, and clinical NLP
• FAIR data principles and benchmark dataset construction
• Annotation frameworks and weak supervision
• Federated learning, privacy-preserving AI, GDPR/HIPAA compliance
• Bias mitigation and reproducibility in biomedical AI
• Cloud-native biomedical AI workflows and clinical deployment pipelines

⏳ Submission Deadline: 30 December 2026

🔗 For more info about the Call for Papers, please visit: https://spj.science.org/journal/csbj/si/data-orchestration

🧠 Guest Editors:
• Eleni Kaldoudi, Δημοκρίτειο Πανεπιστήμιο Θράκης/Democritus University of Thrace, Greece
• Vaidotas Marozas, KTU Kauno technologijos universitetas/Kaunas University of Technology, Lithuania
• Antti Vehkaoja, Tampere University, Finland

Computational and Structural Biotechnology Journal, Science Partner Journals, AAAS - The American Association for the Advancement of Science