Weekly BioML Digest - more Journals added! [December 15, 2025]

🧠 Machine Learning × Computational Biology Digest

Hey! Here’s your weekly digest with some exciting updates to share:

🔍 What’s New?

• Expanded coverage: now includes most peer-reviewed journals like Nature Group, Science, Cell, PNAS etc.
• Two sections:
  1. Peer-Reviewed Journals
  2. Preprints (arXiv + bioRxiv)

Feedback? Email me at biomldigest@gmail.com.

📚 Section 1: Peer-Reviewed Journals (Top 20)

623 papers matched filters → 20 selected after LLM relevance + novelty ranking.

• Bottom-up design of Ca^2+ channels from defined selectivity filter geometry
  Liu, Yulai, Weidle, Connor, Mihaljević, Ljubica, Watson, Joseph L., Li, Zhe, Yu, Le Tracy, Majumder, Sagardip, Borst, Andrew J., Carr, Kenneth D., Kibler, Ryan D., Gamal El-Din, Tamer M., Catterall, William A., Baker, David — Nature, 2025-12-11
  abs

• Protein-nucleic acid language model-assisted design of precise and compact adenine base editor
  Ren, Jingxuan, Yao, Jiawei, Cao, Qiuyu, Li, Yinuo, Li, Yang, Zhang, Ziyi, Ge, Xiyu, Wang, Shengfang, Zhang, Yang, Wang, Xiaogang, Zhang, Xiaohui — Nature Communications, 2025-12-13
  abs

• Deciphering RNA–ligand binding specificity with GerNA-Bind
  Xia, Yunpeng, Li, Jiayi, Chu, Yi-Ting, Rao, Jiahua, Chen, Jing, Hua, Chenqing, Yu, Dong-Jun, Chen, Xiu-Cai, Zheng, Shuangjia — Nature Machine Intelligence, 2025-12-12
  abs

• Semi-inductive dataset construction and framework optimization for practical drug target interaction prediction with ScopeDTI
  Chen, Yigang, Ji, Xiang, Zhang, Ziyue, Zhu, Zihao, Zhou, Yuming, Su, Chang, Lin, Yang-Chi-Dung, Huang, Hsi-Yuan, Wei, Kangping, Lai, Yi, Chen, Ke, Lin, Xingqiao, Zhang, Yangyi, Fu, Jiehui, Huang, Yixian, Cui, Shidong, Yen, Shih-Chung, Zhang, Tao, Warshel, Arieh, Huang, Hsien-Da — Nature Communications, 2025-12-13
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• PhenoProfiler: advancing phenotypic learning for image-based drug discovery
  Li, Bo, Zhang, Bob, Zhang, Chengyang, Zhou, Minghao, Huang, Weiliang, Wang, Shihang, Wang, Qing, Li, Mengran, Zhang, Yong, Song, Qianqian — Nature Communications, 2025-12-14
  abs

• SGEDiff: a subgraph-enriched diffusion model for structure-based 3D molecular generation
  Gong, Changda, Fang, Jiaojiao, Tang, Yan, Liu, Guixia, Tang, Yun, Li, Weihua — Journal of Cheminformatics, 2025-12-08
  abs

• Nativeness-constrained diffusion framework for nanobody design
  Yinghan Zhang, Tao Jiang, Cheuk Shuen Li — Briefings in Bioinformatics, 2025-12-12
  abs

• Medt5-bi: bidirectional translation between drug indications and molecular structures using a chemically-aware transformer
  Pahari, Soham, Srinivas, M. — Journal of Computer-Aided Molecular Design, 2025-12-13
  abs

• Biophysical simulation enables segmentation and nervous system atlas mapping for image first spatial omics
  Ali, Lina Mohammed, Yim, Aldrin Kay Yuen, Gerbi, Emanuel, Nguyen, Thien, Tu, Nicholas, Ikede, Faith, Sampaleanu, Remi, Grigore, Diana, Waligorski, Jason, Kremitzki, Colin, Yuan, Liya, Dong, Wendy, Mitra, Robi, Milbrandt, Jeffrey, Buchser, William — npj Systems Biology and Applications, 2025-12-14
  abs

• A morphology-based machine learning model for scoring epithelial-mesenchymal plasticity using organelle dynamics
  Slager, Justin, Gatto, Francesca, Frey, Benjamin, Shi, Wenyang, Porebski, Bartlomiej, Carreras-Puigvert, Jordi, Parniewska, Malgorzata Maria, Fuxe, Jonas — Communications Biology, 2025-12-10
  abs

• Function-aware biosecurity screening: datasets, benchmarks, and detection systems for next-generation pathogen identification
  Emilin M. Mathew — Briefings in Bioinformatics, 2025-12-12
  abs

• Integrative analysis of hi-C variance and multi-contact data identifies enhancer–promoter hub structures
  HidekiTanizawa, Claire Yik-Lok Chung, Ken-ichi Noma — Briefings in Bioinformatics, 2025-12-12
  abs

• DeepSAHF: deep learning-based detection of senescence-associated chromatin features reveals nuclear heterogeneity
  Claire Yik-Lok Chung, Shinya Ohta, HidekiTanizawa, Ken-ichi Noma — Briefings in Bioinformatics, 2025-12-12
  abs

• CoSMIM: a covariance-based multi-scale framework for integrated spatial microenvironment analysis
  Bairui Du, H. Kiryu — Briefings in Bioinformatics, 2025-12-12
  abs

• CellSigFlow: a flow-based optimization framework for realistic single-cell and spatial inference of intercellular communication
  Menghan Wang, Junya Yang, Jiaxing Chen — Briefings in Bioinformatics, 2025-12-12
  abs

• CellTypeHGCN: a heterogeneous graph convolutional network for cell typing on single-cell RNA-seq data with reference TRN
  Yongyu Long, Wenhao Zhang, Lan Cao, Xiaobing Huang, Ying Wang — Briefings in Bioinformatics, 2025-12-12
  abs

• Discovery and optimization of antimicrobial peptides from extreme environments on global scale
  Zixin Kang, Haohong Zhang, Kang Ning — Briefings in Bioinformatics, 2025-12-12
  abs

• MMETHANE: interpretable AI for predicting host status from microbial composition and metabolomics data
  Dawkins, Jennifer J., Gerber, Georg K. — Microbiome, 2025-12-08
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• CACLENS: A Multitask Deep Learning System for Enzyme Discovery.
  Xilong Yi, Yingzhu Tan, Huikang Lin, Guoqing Zhang, Ye Tian, Aibo Wu — Advanced science, 2025-12-09
  abs

• RNA regulation mechanisms study using physics-informed machine learning
  Liu, Haoquan, Zhu, Yanan, Gao, Jiaming, Zhuo, Chen, Zeng, Chengwei, Zhao, Yunjie — Communications Physics, 2025-12-09
  abs

📚 Section 2: Preprints (arXiv + bioRxiv)

136 papers matched filters → 20 selected after LLM relevance + novelty ranking.

• 🧬 Query-driven generative AI synthesizes multi-modal spatial omics from histology
  Pang, M.; Roy, T. K.; Wu, X.; Tan, K. — bioRxiv, 2025-12-13
  abs

• 🧬 Modeling patient tissues at molecular resolution with Eva
  Liu, Y.; Sharma, R.; Bieniosek, M.; Kang, A.; Wu, E.; Chou, P.; Li, I.; Rahim, M.; Bauer, E.; Ji, R.; Duan, W.; Qian, L.; Luo, R.; Sharma, P.; Dhanasekaran, R.; Schürch, C. M.; Charville, G.; Mayer, A.; Zou, J.; Trevino, A. E.; Wu, Z. — bioRxiv, 2025-12-12
  abs

• 🧬 Unimeth: A unified transformer framework for accurate DNA methylation detection from nanopore reads
  Wang, S.; Xiao, Y.; Tao, S.; Huang, N.; Shu, Y.; Zhai, J.; Luo, F.; Ni, P. — bioRxiv, 2025-12-09
  abs

• 🧬 Protein Diffusion Models as Statistical Potentials
  Roney, J.; Ou, C.; Ovchinnikov, S. — bioRxiv, 2025-12-09
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• 📄 De novo generation of functional terpene synthases using TpsGPT
  Hamsini Ramanathan, Roman Bushuiev, Matouš Soldát, Jirí Kohout, Téo Hebra, Joshua David Smith, Josef Sivic, Tomáš Pluskal — arXiv, 2025-12-09
  abs

• 🧬 CryoDDM: CryoEM denoising diffusion model for heterogeneous conformational reconstruction
  Li, F.; Chen, Y.; Dong, H.; Ji, C.; Wang, X.; Zhang, C.; Wang, Z.; Bin, H.; Zhang, F.; Wan, X. — bioRxiv, 2025-12-12
  abs

• 🧬 Programmatic design and editing of cis-regulatory elements
  Schreiber, J.; Lorbeer, F. K.; Heinzl, M.; Reiter, F.; Rafanel, B.; Lu, Y.; Stark, A.; Noble, W. S. — bioRxiv, 2025-12-08
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• 📄 Toward Closed-loop Molecular Discovery via Language Model, Property Alignment and Strategic Search
  Junkai Ji, Zhangfan Yang, Dong Xu, Ruibin Bai, Jianqiang Li, Tingjun Hou, Zexuan Zhu — arXiv, 2025-12-10
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• 📄 UNAAGI: Atom-Level Diffusion for Generating Non-Canonical Amino Acid Substitutions
  Han Tang, Wouter Boomsma — arXiv, 2025-12-11
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• 🧬 SynPROTAC: synthesizable PROTACs design through synthesis constrained generative model and reinforcement learning
  Xu, M.; Deng, Q.; Zhang, H.; Qiao, A.; Wang, Z.; Hsieh, C.-Y.; Chen, H.; lei, j. — bioRxiv, 2025-12-12
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• 📄 Fused Gromov-Wasserstein Contrastive Learning for Effective Enzyme-Reaction Screening
  Gengmo Zhou, Feng Yu, Wenda Wang, Zhifeng Gao, Guolin Ke, Zhewei Wei, Zhen Wang — arXiv, 2025-12-09
  abs

• 🧬 Uncovering the Genomic Manifold via Scalable Learning from the Global Microbiome
  Wu, W.; Zhou, Z.; Riley, R.; Abdulqader, M.; Song, X.; Kautsar, S.; Egan, R.; Hofmeyr, S.; Liu, G.; Goldhaber-Gordon, S.; Yu, M.; Ho, H.; Liu, Y.; Steindorff, A. S.; Liu, F.; Chen, F.; Morgan-Kiss, R.; Shi, L.; Liu, H.; Wang, Z. — bioRxiv, 2025-12-09
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• 🧬 scProtoTransformer: Scalable Reference Mapping Across Molecules, Cells and Donors
  Tang, Z.; He, H.; Chen, S.; Zhu, J.; Lv, T.; Zhou, J.; Huang, J.; Chen, G.; You, L.; Chen, C. Y.-C. — bioRxiv, 2025-12-09
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• 🧬 SPARK: deciphering tumor-specific signaling networks through an integrative predictive model
  Chen, D.; Zhang, A.; Li, J. — bioRxiv, 2025-12-10
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• 🧬 PhaLP 2.0: extending the community-oriented phage lysin database with a SUBLYME pipeline for metagenomic discovery
  Boulay, A.; Nemeth, V.; Criel, B.; Stock, M.; De Baets, B.; Galiez, C.; Rousseau, E.; Briers, Y.; Vazquez, R. — bioRxiv, 2025-12-10
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• 🧬 A Corporative Language Model for Protein-Protein Interaction, Binding Affinity, and Interface Contact Prediction
  Liu, J.; Chen, H.; Zhang, Y. — bioRxiv, 2025-12-10
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• 🧬 AI recognizes convergent somatic hypermutation signatures to allow the discovery of variant-resilient broadly neutralizing antibodies
  Yan, Q.; Huang, X.; Liu, B.; Yao, Y.; Zheng, H.; Song, Y.; Wu, F.; He, Z.; Li, S.; Chen, F.; Niu, C.; Li, Z.; Yuan, H.; Lin, Y.; Chen, L.; Zang, N.; Xiao, J.; Wang, T.; Chen, C.; Bai, H.; Li, J.; Wu, M.; Zhao, J.; Yao, J.; Yang, Y.; Zhu, A.; Zhao, J. — bioRxiv, 2025-12-10
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• 🧬 Spatially distinct chromatin compaction states predict neoadjuvant chemotherapy resistance in Triple Negative Breast Cancer
  Mealem, R.; Phillips, T. A.; Rose, L. A.; Marcotti, S.; Parsons, M.; Zaritsky, A. — bioRxiv, 2025-12-08
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• 🧬 RamanOmics Decodes Spatial Vibrational-Molecular Architecture and Rewiring in Aging and Repair
  Zhang, K.; Chen, X.; Monticolo, F.; Sorrentino, S.; Huang, H.; Callahan, C.; Qiao, Y.; Zhou, J.; Brodowska, S.; Sapantzi, S.; Qi, J.; Wu, Y.; Dang, T. N. S.; Viggiani, F.; Ho, C.-K.; Xu, Y.; J. Kobayashi-Kirschvink, K.; Mung, T.; Phatnani, H.; Dou, Z.; Kang, J. W.; So, P. T. C.; Shu, J. — bioRxiv, 2025-12-08
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• 🧬 Subtype-Specific Dependencies and Drug Vulnerabilities Enable Precision Therapeutics in Head and Neck Cancer
  Vaz, J. M.; Zhu, S.; Useche, M.; Shih, L.; Marchiano, E.; Beronja, S.; Clurman, B. E.; Rodriguez, C.; Barber, B.; Chan, M.; Gujral, T. S. — bioRxiv, 2025-12-09
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