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Quantitative Biology (q-bio)

Wednesday, 4 November 2026: 11 new papers, 9 cross-lists and 10 replacements in all of Quantitative Biology, in arXiv's order, with full abstracts. The same papers as arXiv's own listing, set as a newspaper; every title links to arXiv.

Its categories: Biomolecules (q-bio.BM) · Cell Behavior (q-bio.CB) · Genomics (q-bio.GN) · Molecular Networks (q-bio.MN) · Neurons and Cognition (q-bio.NC) · Other Quantitative Biology (q-bio.OT) · Populations and Evolution (q-bio.PE) · Quantitative Methods (q-bio.QM) · Subcellular Processes (q-bio.SC) · Tissues and Organs (q-bio.TO)

New submissions (11)

1. BEND 2.0: Benchmarking the Capabilities Needed to Design DNA

   Andreas Bjerregaard, Rachael DeVries, Dionysia Danai Brilli, Panagiotis Antoniadis, Yan Li, Anders Krogh, Wouter Boomsma, Ole Winther, Frederikke Isa Marin · arXiv:2611.03806

2. Evolved Spiking Neural Networks for EEG Seizure Detection: Calcium Dynamics and Delay Mechanics

   Tuba Aksoy · arXiv:2611.03841

3. Fly Whiskers Meet LiDAR: Robust Navigation under Sensor Failure

   Ali Mahzarnia, Homayoun Jamshidi · arXiv:2611.03897

4. Visualization and Characterization of Gene Group Distribution Patterns Across Genomes

   Yanying Wu · arXiv:2611.04037

5. When Model Complexity Matters in Cross-Subject Naturalistic fMRI Prediction

   Junhao Zhao, Jacob Kang, Colin Kurniawan, David Simberg, Nan Xu · arXiv:2611.04041

6. GINsim 3.1: Qualitative modelling and dynamical analysis of logical regulatory networks

   Laurent Tichit, Dominique Benielli, Olivier Chabrol, Denis Thieffry, Claudine Chaouiya, Pedro T. Monteiro · arXiv:2611.04109

7. Evolving view on phylogenetic networks

   Claudia Solis-Lemus · arXiv:2611.04149

8. Predicting protein structures at any folding stage from sequence

   Lisheng Zhang, Qingsong Li, Zinan Xie, Yanting Yang, Qikui Yang, Peng Lu, Zhican Fu, Wentao Cui, Runtong Hou, Zhengwei Xie · arXiv:2611.04287

9. Basic Reproductive Numbers in Host-Parasite Systems with Demographic Bistability

   Carli Peterson, Erika Gallo, Christopher Kribs · arXiv:2611.04990

10. Ablating Design Choices for Protein Ensemble Generators Across Structural Regimes

    Eoin Quinn, Oliver Bent · arXiv:2611.05055

11. A Bayesian Optimized Biquad Filter-Burg Model for Real-Time EEG Phase Estimation

    Ivan Martinez-Kay, Tatiana Kardashina, ShiNung Ching, Eric C. Leuthardt, Benjamin T. Acland · arXiv:2611.05374

Cross-lists (9)

1. Learning Directional Randers Geometry for Latent-Space Exploration

   Th\'eau Blanchard (HeKA | U1346, GE Healthcare), St\'ephanie Allassonni\`ere (CMAP) · arXiv:2611.03675

2. El Agente F\'armaco: A Scalable AI Scientist for Drug Discovery

   Marcel M\"uller, Mohammad Ghazi Vakili, Yoshihiro Ogura, Ella Ashoori, Shimeng Wang, Alessandro S. Nascimento, Eddie Calleja, Yutong Zhao, Yimeng Liu, Ella Miray Rajaonson, Aiwei Yin, Jiaru Bai, Yunheng Zou, Abraham C. Stern, Varinia Bernales, Al\'an Aspuru-Guzik · arXiv:2611.03832

3. BEAGLE in Action: Phylogenetic Likelihoods for Very Large State Spaces

   Benjamin D Redelings, April Wright, Karthik Gangavarapu, Yucai Shao, Filippo Monti, Wu-Min Deng, Shuo Su, Andrew Rambaut, Guy Baele, Philippe Lemey, Marc A. Suchard, Xiang Ji · arXiv:2611.03873

4. ProteoCraft: Protein Design as Proposal-Verification Search

   Fang Wu, Hongbin Lin, Bingchen Duan, Yuchen Wang, Li Erran Li, Yanjie Huang, Mingxuan Cao, Yijun Ma, Yunxiang Mo, Yanchao Li, Kuan Pang, Juangui Xu, Hanqun Cao, Dongwei Jiang, Xinyue Xu, Xiangru Tang, Zehong Wang, Jian Ma, Kejun Ying, Guanlue Li, Mingran Cao, Fanjin Wang, Tianfan Fu, Shuangjia Zheng, Yao Shu, Jure Leskovec, Yejin Choi · arXiv:2611.03963

5. One Mistake, Three Layers: Persistence Rules Under Depth Correlation

   Maryam Rahimimovassagh, Michael Brown, Sanjeda Sara Jennifer, Niloofar Yousefi · arXiv:2611.03968

6. Trail systems self-organize through individual route optimization

   Brendan Wallace, Andrew Berdahl · arXiv:2611.04346

7. Curriculum unlearning in humans and neural networks

   Jirko Rubruck, Alice Zhang, Andrew Saxe, Christopher Summerfield · arXiv:2611.04565

8. Empirical Bayes Flow Matching for Continuous Cryo-EM Heterogeneity

   Daniel Aibinder, Azmi Haider, Dan Rosenbaum · arXiv:2611.05202

9. iGC: Antibody Optimization via Reinforcement Learning over a Learned Somatic Hypermutation Prior

   Thao Nguyen, Robert G. Alberstein, Ewa Nowara, Homa MohammadiPeyhani, Holly R. Steach, Sarah A. Robinson, Yuval Shechter, Donald W. Lee, Jason A. Vander Heiden, Franziska Seeger, Andrew Leaver-Fay, Richard Bonneau, Joshua Yao-Yu Lin · arXiv:2611.05270

Replacements (10)

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