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Research in Computational Molecular Biology

29th International Conference, RECOMB 2025, Seoul, South Korea, April 26–29, 2025, Proceedings

  • Conference proceedings
  • © 2025

Overview

Editors:
  1. Sriram Sankararaman

    1. University of California, Los Angeles, USA

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Part of the book series: Lecture Notes in Computer Science (LNCS, volume 15647)

Part of the book sub series: Lecture Notes in Bioinformatics (LNBI)

Included in the following conference series:

Conference proceedings info: RECOMB 2025.

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About this book

This book constitutes the proceedings of the 29th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2025, held in Seoul, South Korea, during April 26–29, 2025.

The 14 full papers and 41 short papers were carefully reviewed and selected from 339 submissions. They focus on advances in computational biology and applications in molecular biology and medicine. The conference aims at bridging the computational, mathematical, statistical, and biological sciences, and bringing together researchers, professionals, students and industrial practitioners from all over the world for interaction and exchange of new developments in all areas of bioinformatics and computational biology. 

Keywords

Table of contents (55 papers)

  1. Front Matter

    Pages i-xxiv
    Download chapter PDF

  2. Orientation-Aware Networks for Protein Structure Representation Learning

    • Jiahan Li, Shitong Luo, Congyue Deng, Chaoran Cheng, Jiaqi Guan, Leonidas Guibas et al.
    Pages 1-16

  3. Active Learning for Protein Structure Prediction

    • Zexin Xue, Michael Bailey, Abhinav Gupta, Ruijiang Li, Alejandro Corrochano-Navarro, Sizhen Li et al.
    Pages 17-33

  4. Sequence-Based TCR-Peptide Representations Using Cross-Epitope Contrastive Fine-Tuning of Protein Language Models

    • Chiho Im, Ryan Zhao, Scott D. Boyd, Anshul Kundaje
    Pages 34-48

  5. DualGOFiller: A Dual-Channel Graph Neural Network with Contrastive Learning for Enhancing Function Prediction in Partially Annotated Proteins

    • Shaojun Wang, Hancheng Liu, Weiqi Zhai, Shanfeng Zhu
    Pages 49-67

  6. Detecting Antimicrobial Resistance Through MALDI-TOF Mass Spectrometry with Statistical Guarantees Using Conformal Prediction

    • Nina Corvelo Benz, Lucas Miranda, Dexiong Chen, Janko Sattler, Karsten Borgwardt
    Pages 68-85

  7. Hierarchical Spatio-Temporal State-Space Modeling for fMRI Analysis

    • Yuxiang Wei, Anees Abrol, Vince D. Calhoun
    Pages 86-98

  8. A Phylogenetic Approach to Genomic Language Modeling

    • Carlos Albors, Jianan Canal Li, Gonzalo Benegas, Chengzhong Ye, Yun S. Song
    Pages 99-117

  9. Dynamic Programming Algorithms for Fast and Accurate Cell Lineage Tree Reconstruction from CRISPR-Based Lineage Tracing Data

    • Junyan Dai, Erin K. Molloy
    Pages 118-133

  10. Old Dog, New Tricks: Exact Seeding Strategy Improves RNA Design Performances

    • Théo Boury, Leonhard Sidl, Ivo L. Hofacker, Yann Ponty, Hua-Ting Yao
    Pages 134-152

  11. Scalable and Interpretable Identification of Minimal Undesignable RNA Structure Motifs with Rotational Invariance

    • Tianshuo Zhou, Apoorv Malik, Wei Yu Tang, David H. Mathews, Liang Huang
    Pages 153-174

  12. An Exact and Fast SAT Formulation for the DCJ Distance

    • Aaryan M. Sarnaik, Ke Chen, Austin Diaz, Mingfu Shao
    Pages 175-189

  13. Improved Pangenomic Classification Accuracy with Chain Statistics

    • Nathaniel K. Brown, Vikram S. Shivakumar, Ben Langmead
    Pages 190-208

  14. Dynamic \(\mu \)-PBWT: Dynamic Run-Length Compressed PBWT for Biobank Scale Data

    • Pramesh Shakya, Ahsan Sanaullah, Degui Zhi, Shaojie Zhang
    Pages 209-226

  15. Prokrustean Graph: A Substring Index for Rapid K-Mer Size Analysis

    • Adam Park, David Koslicki
    Pages 227-249

  16. Rag2Mol: Structure-Based Drug Design Based on Retrieval Augmented Generation

    • Peidong Zhang, Xingang Peng, Rong Han, Ting Chen, Jianzhu Ma
    Pages 250-254

  17. Rewiring Protein Sequence and Structure Generative Models to Enhance Protein Stability Prediction

    • Ziang Li, Yunan Luo
    Pages 255-259

  18. Learning a CoNCISE Language for Small-Molecule Binding

    • Mert Erden, Kapil Devkota, Lia Varghese, Lenore Cowen, Rohit Singh
    Pages 260-263

  19. An Adversarial Scheme for Integrating Multi-modal Data on Protein Function

    • Rami Nasser, Leah V. Schaffer, Trey Ideker, Roded Sharan
    Pages 264-267

  20. Decoding the Functional Interactome of Non-model Organisms with PHILHARMONIC

    • Sam Sledzieski, Charlotte Versavel, Rohit Singh, Faith Ocitti, Kapil Devkota, Lokender Kumar et al.
    Pages 268-272
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Other volumes

  1. Research in Computational Molecular Biology

Editors and Affiliations

  • University of California, Los Angeles, USA

    Sriram Sankararaman

Bibliographic Information

  • Book Title: Research in Computational Molecular Biology

  • Book Subtitle: 29th International Conference, RECOMB 2025, Seoul, South Korea, April 26–29, 2025, Proceedings

  • Editors: Sriram Sankararaman

  • Series Title: Lecture Notes in Computer Science

  • DOI: https://doi.org/10.1007/978-3-031-90252-9

  • Publisher: Springer Cham

  • eBook Packages: Computer Science, Computer Science (R0)

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Switzerland AG 2025

  • Softcover ISBN: 978-3-031-90251-2Published: 25 April 2025

  • eBook ISBN: 978-3-031-90252-9Published: 24 April 2025

  • Series ISSN: 0302-9743

  • Series E-ISSN: 1611-3349

  • Edition Number: 1

  • Number of Pages: XXIV, 440

  • Number of Illustrations: 6 b/w illustrations, 107 illustrations in colour

  • Topics: Bioinformatics, Mathematical and Computational Biology, Statistics and Computing/Statistics Programs

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