Table of Contents

• DeepSSETracer 2.0: Improved Deep Learning Model Performance for Protein Secondary Structure Segmentation from Cryo-EM MapsBryan Hawickhorst, Thu Nguyen, Willy Wriggers, Jiangwen Sun, Jing He 0002. [doi]
• A Molecular Dynamics Study of Polyacrylamide Conformational Changes in Ca2+ and Mg2+ SolutionsGideon K. Gogovi, Lorcan Cheng. [doi]
• Improving Antimicrobial Resistance (AMR) Phenotype Prediction for Unseen Bacteria through Data Augmentation and Machine LearningYeojin Jung, Namkyeong Kim, Donghoon Kim. [doi]
• ConSOLAE: Learning Smooth and Generalizable Representations for Protein Fold RecognitionShraddha Patre, Riya Kanani, Aarnav Tare, Pranavh Vallabhaneni, Fardina Fathmiul Alam. [doi]
• Evaluating GNN Inference on Edge ComputersLuca Barillaro, Chiara Zucco, Marianna Milano, Giuseppe Agapito, Mario Cannataro. [doi]
• PRIMRose: Insights into the Per-Residue Energy Metrics of Proteins with Double InDel Mutations using Deep LearningStella Brown, Nicolas Preisig, Autumn Davis, Brian Hutchinson, Filip Jagodzinski. [doi]
• Optimizing the Variant Calling Pipeline Execution on Human Genomes Using GPU-Enabled MachinesAjay Kumar, Praveen Rao 0001, Peter Sanders 0001. [doi]
• Identifying Physiochemical Variables important to LLM Prediction of Coliform Bacteria PresenceHamza Shahrukh Kiyani, Kristina Yoo, Hyunwoo Yoo, Gail Rosen, Hunter Quon, Alyssa Rosenbaum, Charles Gerba, Kelly Bright, Natalie Brassill, Channah Rock, Kerry Hamilton. [doi]
• Uncertainty-Aware Fine-Tuning in Genomic Language ModelsGavin L. A. Hearne, Gail Rosen. [doi]
• Computational Structural Bioinformatics Workshop (CSBW): EditorialSalim Sazzed, Brian Chen. [doi]
• 14th Workshop on Parallel and AI-based Bioinformatics and Biomedicine (ParBio): EditorialGiuseppe Agapito, Mario Cannataro, Wes J. Lloyd, Chiara Zucco. [doi]
• Promises and Pitfalls of Large Language Models use to interpret Healthcare GuidelinesRaghav Awasthi, Shreya Mishra, Ashish Atreja, Charumathi Raghu Subramanian, Moises Auron, Nishant Singh, Jacek B. Cywinski, Francis A. Papay, Kamal Maheshwari, Ashish K. Khanna, Piyush Mathur. [doi]
• Systematic evaluation of 566 sequence-based features for predicting protein stability changes induced by mutations using machine learningQiaobin Yao, Junyan Li, Dongxiao Liu, Krish Wahi, Shaolei Teng. [doi]
• Physics-Guided Active Learning for New Ligand DiscoveryNikhil Dhiman, Dikshant Sagar, Negin Forouzesh. [doi]
• Graph Neural Network with Pretrained Embeddings for Cancer and miRNA Regulator DiscoverySa Li, Jonah Shader, Abhijeet Bhattacharya, Tianle Ma. [doi]
• Using Diffusion Models as Cell Fate Reprogramming PlannersShiv Shankar. [doi]
• Benchmarking and Consensus Ranking of Inverse Folding Models for Protein-Ligand Interface DesignYao Wei, Uliano Guerrini, Ivano Eberini. [doi]
• Translating the Language of LifeChaz Allegra, Robi Polikar, Gail Rosen. [doi]
• Structural Impacts of Insertion Mutations on Protein-Protein InterfacesJames Tessmer, Logan Nicholas Day, Bogdan Trigubov, Emilia Galant, Filip Jagodzinski. [doi]
• Large Language Models for Molecular Biology (LLMBio): EditorialGavin L. A. Hearne, Glen Rogers, Chaz Allegra, Robi Polikar, Gail Rosen. [doi]
• PRiVDIS: A Pathway-Based Risk-Informed Variant Dosage Integration Score Framework for Machine Learning-Based Discovery of Disease-Specific Molecular PathwaysSanghyun Shon, Younhee Ko, Hojin Yoon, Kyeongmin Kwak, HwaMin Lee. [doi]
• From Contrast to Control: Domain Conditioned Masking for Small Molecule Generation of Quaternary Ammonium CompoundsShiva Ghaemi, Rehenuma Tasmin Rodoshi, Shahana Shultana, Amarda Shehu, Daniel Barbará. [doi]
• Red Teaming Generative Proteins with Unsupervised Toxin-Based Risk EmbeddingsTia Pope, Ahmad Patooghy. [doi]
• DyVarMap: An Interpretable, Dynamics-Aware Framework for Missense Variant ClassificationYiyang Lian, Amarda Shehu. [doi]
• Multimodal Dementia Prediction with LLMs: Cross-Attention over Text, Audio, and ImageFelix Agbavor, Hualou Liang. [doi]
• Fast and Scalable Gene Embedding Search: A Comparative Study of FAISS and ScaNNMohammadsaleh Refahi, Gavin L. A. Hearne, Harrison Muller, Kieran Lynch, Bahrad A. Sokhansanj, James R. Brown, Gail Rosen. [doi]