Weekly BioML Digest [February 02, 2026]

Machine Learning × Computational Biology paper compilation

Hey! It's your weekly digest of machine learning papers in CompBio and Drug Discovery.

Feedback? Email me at biomldigest@gmail.com.

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

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

• Advancing regulatory variant effect prediction with AlphaGenome
  Avsec, Žiga, Latysheva, Natasha, Cheng, Jun, Novati, Guido, Taylor, Kyle R., Ward, Tom, Bycroft, Clare, Nicolaisen, Lauren, Arvaniti, Eirini, Pan, Joshua, Thomas, Raina, Dutordoir, Vincent, Perino, Matteo, De, Soham, Karollus, Alexander, Gayoso, Adam, Sargeant, Toby, Mottram, Anne, Wong, Lai Hong, Drotár, Pavol, Kosiorek, Adam, Senior, Andrew, Tanburn, Richard, Applebaum, Taylor, Basu, Souradeep, Hassabis, Demis, Kohli, Pushmeet — Nature, 2026-01-29
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• De novo design of potent CRISPR–Cas13 inhibitors
  Taveneau, Cyntia, Chai, Her Xiang, D’Silva, Jovita, Bamert, Rebecca S., Chen, Honglin, Hayes, Brooke K., Calvert, Roland W., Purcell, Jacob, Curwen, Daniel J., Munder, Fabian, Martin, Lisandra L., Barr, Jeremy J., Rosenbluh, Joseph, Fareh, Mohamed, Grinter, Rhys, Knott, Gavin J. — Nature Chemical Biology, 2026-01-26
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• An adaptive, continuous-learning framework for clinical decision-making from proteome-wide biofluid data
  Müller-Reif, Johannes B., Albrecht, Vincent, Brennsteiner, Vincenth, Bader, Jakob M., Treit, Peter V., Wewer Albrechtsen, Nicolai J., Pangratz-Führer, Susanne, Mann, Matthias — Nature Communications, 2026-01-27
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• Aligned cross-modal integration and regulatory heterogeneity characterization of single-cell multiomic data with deep contrastive learning
  Cheng, Yue, Su, Yanchi, Fan, Yi, Yang, Yuning, Chen, Xingjian, Wang, Fuzhou, Wong, Ka-Chun, Li, Xiangtao — Genome Medicine, 2026-01-26
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• stGCL: a versatile cross-modality fusion method based on multi-modal graph contrastive learning for spatial transcriptomics
  Yu, Na, Zhang, Daoliang, Zhang, Wei, Liu, Zhiping, Qiao, Xu, Wang, Chuanyuan, Zhao, Miaoqing, Yue, Weiming, Li, Wei, Marinis, Yang, Gao, Rui — Genome Biology, 2026-01-28
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• DualPG-DTA: A Large Language Model-Powered Graph Neural Network Framework for Enhanced Drug-Target Affinity Prediction and Discovery of Novel CDK9 Inhibitors Exhibiting in Vivo Anti-Leukemia Activity.
  Yihao Chen, Jindi Huang, Cong Liu, Shipeng Zhang, Xinze Li, Zhang Zhang, Tie-Gen Chen, Ling Wang — Advanced science, 2026-01-27
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• Trustworthy prediction of enzyme commission numbers using a hierarchical interpretable transformer
  Dumontet, Louis, Han, So-Ra, Lee, Jun Hyuck, Oh, Tae-Jin, Kang, Mingon — Nature Communications, 2026-01-30
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• PLMCA: A General Multimodal Protein-Ligand Cross-Attention Framework for Pocket Identification and Binding Affinity Prediction.
  Yi He, Minghao Liu, Haohao Wang, Lu Han, Weiwei Han — Journal of medicinal chemistry, 2026-01-30
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• Chemical genomics language model toward reliable and explainable compound-protein interaction exploration
  Koyama, Takuto, Tsumura, Hayato, Okita, Ryunosuke, Yamazaki, Kimihiro, Hasegawa, Aki, Imamura, Keiko, Kato, Takashi, Iwata, Hiroaki, Kojima, Ryosuke, Inoue, Haruhisa, Matsumoto, Shigeyuki, Okuno, Yasushi — Journal of Cheminformatics, 2026-01-30
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• Lipid Nanoparticle Database towards structure-function modeling and data-driven design for nucleic acid delivery
  Collins, Evan, Ji, Jungyong, Kim, Sung-Gwang, Witten, Jacob, Kim, Seonghoon, Zhu, Richard, Park, Peter, Jung, Minjun, Park, Aron, Manan, Rajith S., Rudra, Arnab, Keum, Gyochang, Bang, Eun-Kyoung, Jin, Jun-O, Jeang, William J., Langer, Robert, Anderson, Daniel G., Im, Wonpil — Nature Communications, 2026-01-28
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• Mapping targetable sites on the human surfaceome for the design of novel binders.
  Petra E. M. Balbi, Ahmed Sadek, Anthony Marchand, Ta-Yi Yu, Jovan Damjanovic, S. Georgeon, Joseph Schmidt, Simone Fulle, Che Yang, Hammed Khakzad, Bruno E. Correia — Proceedings of the National Academy of Sciences of the United States of America, 2026-01-28
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• Augmenting Large Language Models for Automated Discovery of F-Element Extractants.
  Baosen Zhang, Thomas J. Summers, L. Augustine, Michael G Taylor, Andreas Geist, Rebecca Li, Enrique R. Batista, D. Perez, Ping Yang, Joshua Schrier — Journal of the American Chemical Society, 2026-01-29
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• Evaluation of a machine learning system for genomic antimicrobial susceptibility determination on a clinically representative test set
  Jason D. Wittenbach, A. Conwill, Hayden Sansum, Alison Gassett, Adam Gardner, Allison Brookhart, Talia Hollowell, Paul Knysh, Nicholas B. Worley, Nicole Billings, Ian C. Herriott, Julie A. Shimabukuro, K. Quan, Keith M. Madey, Susan S. Huang, M. Sater, Cassiana E. Bittencourt, Miriam H. Huntley — Microbiology Spectrum, 2026-01-27
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• AI-Guided Design and Predictive Modeling of Synthetic Escherichia coli Promoters through Comprehensive -10/-35 Box Engineering.
  Xuan Zhou, Nana Ding, Shenghu Zhou, Yu Deng — ACS synthetic biology, 2026-01-27
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• A quantitative, multimodal wearable bioelectronic device for comprehensive stress assessment and sub-classification
  Pei, Xiaochang, Ghandehari, Anita, Chakoma, Shingirirai, Rajendran, Jerome, Tavares-Negrete, Jorge Alfonso, Esfandyarpour, Rahim — Nature Communications, 2026-01-29
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• Ultrasensitive MicroRNA Detection Combining Reduced Graphene Oxide Electrolyte-Gated Transistors and Machine Learning.
  Ana Vitória Ferreira Deleigo, Gabrielle Coelho Lelis, M. Braunger, Stefano Casalini, Yasmin Watanabe, G. R. Schleder, Wilson Tiago Fonseca, R. F. de Oliveira — Small, 2026-01-29
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• Harnessing deep statistical potential for biophysical scoring of protein-peptide interactions
  Jiang, De-jun, Zhao, Hui-feng, Du, Hong-yan, Kang, Yu, Pan, Pei-chen, Wu, Zhen-xing, Zeng, Yun-dian, Zhang, O-din, Wang, Xiao-rui, Wang, Ji-ke, Huang, Yuan-sheng, Zhao, Yi-hao, Hsieh, Chang-Yu, Cao, Dong-sheng, Sun, Hui-yong, Hou, Ting-jun — Acta Pharmacologica Sinica, 2026-02-01
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• AI-Guided Conformational Dynamics of p53 L1 Loop Reveal an Allosteric Switch Regulating DNA Binding and Cancer Hotspots.
  Pablo Navarro Acero, Ming-Hong Hao, Karan Kapoor — Journal of chemical information and modeling, 2026-01-29
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• PAM-CDR: Property-Aware Multi-Modal Drug Representation Learning for Accurate Cancer Drug Response Prediction.
  Yang Li, Chang Liu, Haijie Cui, Jianli Ma — IEEE journal of biomedical and health informatics, 2026-01-27
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• Leveraging cfDNA fragmentomic features for the early detection of colorectal cancer
  Lina Shan, Dengyong Xu, Jie Chen, Wenjia Liu, Ji Lin, Juhang Bao, Jianfei Huang, Hanqing Zhang, Hanchen Zhao, Wei Xue, Ziao Lin, Bingjun Bai — Frontiers in Immunology, 2026-01-28
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🧬 Section 2: Preprints (arXiv + bioRxiv)

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

• 📄 From Human Labels to Literature: Semi-Supervised Learning of NMR Chemical Shifts at Scale
  Yongqi Jin, Yecheng Wang, Jun-jie Wang, Rong Zhu, Guolin Ke, Weinan E — arXiv, 2026-01-26
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• 🧬 BEACON: predicting side effects and therapeutics outcomes to drugs by Bridging knowlEdge grAph with CONtextual language model
  Xu, C.; Xu, J.; Bulusu, K.; Pan, H.; Elemento, O. — bioRxiv, 2026-01-30
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• 📄 Purely Agentic Black-Box Optimization for Biological Design
  Natalie Maus, Yimeng Zeng, Haydn Thomas Jones, Yining Huang, Gaurav Ng Goel, Alden Rose, Kyurae Kim, Hyun-Su Lee, Marcelo Der Torossian Torres, Fangping Wan, Cesar de la Fuente-Nunez, Mark Yatskar, Osbert Bastani, Jacob R. Gardner — arXiv, 2026-01-29
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• 🧬 An AI-Native Biofoundry for Autonomous Enzyme Engineering: Integrating Active Learning with Automated Experimentation
  Zhang, C.; Yang, L.; Qin, Y.; Li, D.; Dong, S.; Yang, M. — bioRxiv, 2026-02-01
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• 🧬 De novo design of phosphotyrosine peptide binders
  Bauer, M. S.; Zhang, J. Z.; Wu, K.; Lee, G. R.; Coventry, B.; Silvestri, I. M.; Klupt, K. A.; Shi, J.; Brent, R. I.; Li, X.; Moller, C.; Roullier, N.; Vafeados, D. K.; Kalvet, I.; Skotheim, R. K.; Zhu, S.; Motmaen, A.; Herrmann, L. C.; Sturmfels, P.; Tischer, D.; Altae-Tran, H.; Juergens, D.; Krishna, R.; Ahern, W.; Yim, J.; Bera, A. K.; Kang, A.; Joyce, E.; Lu, A.; Stewart, L.; DiMaio, F.; Mudumbi, K. C.; Baker, D. — bioRxiv, 2026-01-28
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• 📄 GPCR-Filter: a deep learning framework for efficient and precise GPCR modulator discovery
  Jingjie Ning, Xiangzhen Shen, Li Hou, Shiyi Shen, Jiahao Yang, Junrui Li, Hong Shan, Sanan Wu, Sihan Gao, Huaqiang Eric Xu, Xinheng He — arXiv, 2026-01-27
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• 📄 EnzyPGM: Pocket-conditioned Generative Model for Substrate-specific Enzyme Design
  Zefeng Lin, Zhihang Zhang, Weirong Zhu, Tongchang Han, Xianyong Fang, Tianfan Fu, Xiaohua Xu — arXiv, 2026-01-27
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• 🧬 MolSpecFlow: Mass-Constrained Hybrid Flow Matching for Joint Molecular-Spectral Analysis
  Wang, Y.; Yang, F.; Xu, K.; Yuan, L.; Zhu, J.; Zhang, J.; Tang, Z.; Bian, Y.; Chang, C.; Tian, Y.; Yao, J. — bioRxiv, 2026-02-01
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• 🧬 Distance-Restraint-Guided Diffusion Models for Sampling Protein Conformational Changes and Ligand Dissociation Pathways
  Hori, T.; Moriwaki, Y.; Ishitani, R. — bioRxiv, 2026-01-31
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• 🧬 ProChoreo: De novo Binder Design from Conformational Ensembles with Generative Deep Learning
  Ding, S.; Zhang, Y. — bioRxiv, 2026-01-26
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• 🧬 cellGeometry: ultra-fast single-cell deconvolution of bulk RNA-Seq using a geometric solution
  Lau, R.; Cubuk, C.; Spiliopoulou, A.; Martinez-Paz, P.; Surace, A. E. A.; Fossati-Jimack, L.; Raychaudhuri, S.; Pitzalis, C.; Lewis, M. J. — bioRxiv, 2026-01-26
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• 🧬 Dual-channel graph learning reveals similarity and complementarity in protein-protein interaction networks
  Tang, T.; Shen, T.; Li, W.; Chen, Y.; Yuan, S.; Liu, Y.; Yang, X.; Luo, X. — bioRxiv, 2026-01-27
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• 🧬 HYALINE: Geometric Deep Learning for Accurate Prediction of G Protein-Coupled Receptor Activation States from Structure
  Khaleq, A.; Kabodha, H. — bioRxiv, 2026-01-26
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• 🧬 Context-Aware Protein Representations Using Protein Language Models and Optimal Transport
  Patel, S. S.; NaderiAlizadeh, N. — bioRxiv, 2026-01-26
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• 🧬 Exploring protein conformational ensembles using evolutionary conditional diffusion
  cui, X.; Ge, L.; Yang, X.; Li, X.; Hou, D.; Zhou, X.; Zhang, G. — bioRxiv, 2026-01-30
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• 🧬 Enhancing interpretability of cryo-EM maps with hybrid attention Transformers
  Lin, J.; Zhang, Z.; Zhang, Y.; Wang, C.; Zhang, G.; Zhou, X. — bioRxiv, 2026-01-27
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• 🧬 LocAlign: Local Protein Structural Alignment with Geometric Deep Learning
  Ravid, H.; Tubiana, J.; Wolfson, H. J. — bioRxiv, 2026-01-26
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• 🧬 UdonPred: Untangling Protein Intrinsic Disorder Prediction
  Schlensok, J.; Wagemann, D.; Senoner, T.; Haak, M.; Rost, B. — bioRxiv, 2026-01-27
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• 🧬 clinTALL: machine learning-driven multimodal subtypeclassification and treatment outcome prediction in pediatric T-ALL
  Stoiber, L.; Antic, Z.; Rebellato, S.; Fazio, G.; Rademacher, A.; Lenk, L.; Locatelli, F.; Balduzzi, A.; Cario, G.; Rizzari, C.; Cazzaniga, G.; Yu, J.; Bergmann, A. K. — bioRxiv, 2026-01-30
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• 🧬 ProMeta: A meta-learning framework for robust disease diagnosis and prediction from plasma proteomics
  Li, H.; Gu, H.; Hu, L.; Zhang, Z.; Lv, Y.; Gao, P.; Cooper-Knock, J.; Min, Y.; Zeng, J.; Zhang, S. — bioRxiv, 2026-01-30
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