Weekly BioML Digest [March 09, 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.

📚 Peer-Reviewed Journals (Top 20)

604 matched filters -> 20 selected after LLM relevance + novelty ranking.

• Genome modelling and design across all domains of life with Evo 2
  Brixi, Garyk, Durrant, Matthew G., Ku, Jerome, Naghipourfar, Mohsen, Poli, Michael, Sun, Gwanggyu, Brockman, Greg, Chang, Daniel, Fanton, Alison, Gonzalez, Gabriel A., King, Samuel H., Li, David B., Merchant, Aditi T., Nguyen, Eric, Ricci-Tam, Chiara, Romero, David W., Schmok, Jonathan C., Taghibakhshi, Ali, Vorontsov, Anton, Yang, Brandon, Deng, Myra, Gorton, Liv, Nguyen, Nam, Wang, Nicholas K., Pearce, Michael T., Simon, Elana, Adams, Etowah, Amador, Zachary J., Ashley, Euan A., Baccus, Stephen A., Dai, Haoyu, Dillmann, Steven, Ermon, Stefano, Guo, Daniel, Herschl, Michael H., Ilango, Rajesh, Janik, Ken, Lu, Amy X., Mehta, Reshma, Mofrad, Mohammad R. K., Ng, Madelena Y., Pannu, Jaspreet, Ré, Christopher, John, John, Sullivan, Jeremy, Tey, Joseph, Viggiano, Ben, Zhu, Kevin, Zynda, Greg, Balsam, Daniel, Collison, Patrick, Costa, Anthony B., Hernandez-Boussard, Tina, Ho, Eric, Liu, Ming-Yu, McGrath, Thomas, Powell, Kimberly, Pinglay, Sudarshan, Burke, Dave P., Goodarzi, Hani, Hsu, Patrick D., Hie, Brian L. — Nature, 2026-03-04
  abs

• Cell-free chromatin state tracing reveals disease origin and therapy responses
  Chen, Xubin, Meng, Xiaoxuan, Zhang, Weilong, Zhang, Xiawei, Zhang, Yaping, Yang, Ping, Liu, Yan, Bao, Fang, Li, Sen, Wang, Jing, Yan, Changjian, Li, Chunyuan, Zhang, Lingke, Hao, Xiaoyu, Liu, Jia, Sun, Jing, Wang, Zhengting, Tian, Yu, Zhu, Liqing, Hou, Yan, Liu, Zongchao, Li, Wenqing, Mi, Lan, Qi, Xinyu, Yue, Yanzhu, Du, Peng, Chen, Guoqiang, Zheng, Junke, Dou, Liping, Jing, Hongmei, He, Aibin — Nature, 2026-03-04
  abs

• Language model-guided anticipation and discovery of mammalian metabolites
  Qiang, Hantao, Wang, Fei, Lu, Wenyun, Xing, Xi, Kim, Hahn, Mérette, Sandrine A. M., Ayres, Lucas B., Oler, Eponine, AbuSalim, Jenna E., Roichman, Asael, Neinast, Michael, Cordova, Ricardo A., Lee, Won Dong, Herbst, Ehud, Gupta, Vishu, Neff, Samuel L., Hiebert-Giesbrecht, Mickel, Young, Adamo, Gautam, Vasuk, Tian, Siyang, Wang, Bo, Röst, Hannes, Baidwan, Jatinder, Greiner, Russell, Chen, Li, Johnston, Chad W., Foster, Leonard J., Shapiro, Aaron M., Wishart, David S., Rabinowitz, Joshua D., Skinnider, Michael A. — Nature, 2026-03-05
  abs

• A scalable and quantum-accurate foundation model for biomolecular force fields via linearly tensorized quadrangle attention
  Su, Qun, Zhu, Kai, Gou, Qiaolin, Zhang, Jintu, Hu, Renling, Li, Yurong, Wang, Yongze, Zhang, Hui, You, Ziyi, Jiang, Linlong, Kang, Yu, Wang, Jike, Hsieh, Chang-Yu, Hou, Tingjun — Nature Communications, 2026-03-07
  abs

• De novo design of GPCR exoframe modulators
  Cheng, Shizhuo, Guo, Jia, Zhou, Yun-li, Luo, Xumei, Zhang, Gufang, Zhang, Ya-zhi, Yang, Yixin, Xie, Jiannan, Xu, Ping, Shen, Dan-dan, Zang, Shaokun, Yang, Huicui, Zhen, Xuechu, Zhang, Min, Zhang, Yan — Nature, 2026-03-05
  abs

• Collective intelligence for AI-assisted chemical synthesis
  Li, Haote, Sarkar, Sumon, Lu, Wenxin, Loftus, Patrick O., Qiu, Tianyin, Shee, Yu, Cuomo, Abbigayle E., Webster, John-Paul, Kelly, H. Ray, Manee, Vidhyadhar, Sreekumar, Sanil, Buono, Frederic G., Crabtree, Robert H., Newhouse, Timothy R., Batista, Victor S. — Nature, 2026-03-05
  abs

• Reinforcement learning-based design of sequential drug treatment targeting the evolving tumour landscape with SequenTx
  Chen, Xiaohan, Deng, Yue, Yang, Xingbo, Zhang, Ying, Huang, Yuting, Li, Shuxian, Yang, Hong, Shi, Qiongyu, Wu, Siqi, Chen, Shaoqi, Jin, Xuan, Xing, Feiyang, Zhang, Chen, Gao, Yicheng, Yang, Degang, Chuai, Guohui, Ding, Jian, Huang, Xun, Liu, Qi — Nature Machine Intelligence, 2026-03-04
  abs

• Dissecting spatial patterning and signaling with directional diffusion in spatial multi-omics.
  Haiyun Wang, Zhiyuan Yuan, Yansen Su, Chun-Hou Zheng, Xiaoqiang Sun — Proceedings of the National Academy of Sciences of the United States of America, 2026-03-05
  abs

• Cross-species gene redesign leveraging ortholog information and generative modeling
  Akiyama, Manato, Tashiro, Motohiko, Huang, Ying, Uehara, Mika, Kanzaki, Taiki, Itaya, Mitsuhiro, Kataoka, Masakazu, Miyamoto, Kenji, Sakakibara, Yasubumi — Nature Communications, 2026-03-03
  abs

• Uncovering evolutionarily remote and highly potent antimicrobial peptides with protein language models
  Yu, Qinze, Liu, Hongbin, Shi, Haimei, Abdrakhmanov, Yerzhan, Shen, Junbo, Zhang, Chunhe, Dong, Zhihang, Zong, Licheng, Si, Longlong, Dai, Lei, Li, Yu — Nature Biomedical Engineering, 2026-03-03
  abs

• Interaction-constrained 3D molecular generation using a diffusion model enables structure-based pharmacophore modeling for drug design
  Sako, Masami, Yasuo, Nobuaki, Sekijima, Masakazu — npj Drug Discovery, 2026-03-02
  abs

• Unified protein-small molecule graph neural networks for binding site prediction.
  Jian Wang, Nikolay V. Dokholyan — Proceedings of the National Academy of Sciences of the United States of America, 2026-03-03
  abs

• TANGO: direct optimization of constrained synthesizability for generative molecular design
  Guo, Jeff, Schwaller, Philippe — Nature Computational Science, 2026-03-03
  abs

• AMR-GNN: a multi-representation graph neural network framework to enable genomic antimicrobial resistance prediction
  Nguyen, Hoai-An, Peleg, Anton Y., Wisniewski, Jessica A., Wang, Xiaoyu, Wang, Zhikang, Blakeway, Luke V., Badoordeen, Gnei Z., Theegala, Ravali, Doan, Nhu Quynh, Parker, Matthew H., Green, Anna G., Song, Jiangning, Dowe, David L., Macesic, Nenad — Nature Communications, 2026-03-06
  abs

• DiNovo enables high-coverage and high-confidence de novo peptide sequencing via mirror proteases and deep learning
  Cao, Zixuan, Peng, Xueli, Zhang, Di, Zhou, Piyu, Kang, Li, Chi, Hao, Wu, Ruitao, Cheng, Zhiyuan, Zhang, Yao, Dai, Jiaxing, Li, Yanchang, Yao, Lijin, Li, Xinming, He, Yaoyu, Yang, Jinghan, Wang, Haipeng, Xu, Ping, Fu, Yan — Nature Communications, 2026-03-05
  abs

• Generative modeling enables molecular structure retrieval from Coulomb explosion imaging
  Li, Xiang, Jahnke, Till, Boll, Rebecca, Han, Jiaqi, Xu, Minkai, Meyer, Michael, Piancastelli, Maria Novella, Rolles, Daniel, Rudenko, Artem, Trinter, Florian, Wolf, Thomas J. A., Thayer, Jana B., Cryan, James P., Ermon, Stefano, Ho, Phay J. — Nature Communications, 2026-03-03
  abs

• Fragmentomic liquid biopsy enables early breast cancer detection, molecular subtyping and lymph node assessment
  Zhu, Yuxuan, Zheng, Siwei, Shao, Yinkuan, Zhou, Jun, Gu, Xidong, Shen, Lesang, Li, Xue, Liu, Wenjia, Xue, Wei, Lu, Haiqi, Zhou, Jun, Ding, Jinghua, Deng, Haiming, Chen, Jiayin, Yu, Zhuohang, Yao, Yao, Xia, Wenjie, Chen, Wuzhen, Sun, Shanshan, Wang, Zheng, Qian, Tianyi, Yu, Xiuyan, Liu, Jian, Chen, Yiding, Lin, Ziao, Huang, Jian, Ni, Chao — Nature Communications, 2026-03-06
  abs

• Accelerated discovery of highly active enzyme nanohybrids with parallelized Bayesian optimization in hybrid space
  Liu, Yu, Hu, Haoyang, Han, Yueheng, Deon Chon, Jia Song, Lo, Chin Lee, Chen, Zhixuan, Zhang, Zheng, Yuan, Zhihong, Ge, Jun — Nature Communications, 2026-03-07
  abs

• Optimizing cross-domain transfer for universal machine learning interatomic potentials
  Kim, Jaesun, You, Jinmu, Park, Yutack, Lim, Yunsung, Kang, Yujin, Kim, Jisu, Jeon, Haekwan, Ju, Suyeon, Hong, Deokgi, Lee, Seung Yul, Choi, Saerom, Kim, Yongdeok, Lee, Jae W., Han, Seungwu — Nature Communications, 2026-03-03
  abs

• Fine-Tuning DiffDock-L for Allosteric Kinase Docking.
  Eric A. Chen, J. Green, Yingkai Zhang — Journal of chemical information and modeling, 2026-03-04
  abs

🧬 Preprints (arXiv + bioRxiv)

165 matched filters -> 20 selected after LLM relevance + novelty ranking.

• 🧬 Phenotypic Bioactivity Prediction as Open-set Biological Assay Querying
  Sun, Y.; Zhang, X.; Zheng, Q.; Li, H.; Zhang, J.; Hong, L.; Wang, Y.; Zhang, Y.; Xie, W. — bioRxiv, 2026-03-03
  abs

• 🧬 Towards building a World Model to simulate perturbation-induced cellular dynamics by AlphaCell
  Chuai, G.; Chen, X.; Yang, X.; Zhang, C.; Qu, K.; Wang, Y.; Li, W.; Yang, J.; Si, D.; Xing, F.; Gao, Y.; Wu, S.; Fu, S.; He, B.; Liu, Q. — bioRxiv, 2026-03-05
  abs

• 🧬 Automated high-throughput fabrication of patient-specific vessel-on-chips enables a generative AI digital twin--Cascade Learner of Thrombosis (CLoT) for personalized thrombosis prediction
  Wang, Z.; Zhao, Y. C.; Zhao, H.; Nasser, A.; Yap, N. A.; Liu, Y.; Sun, A.; Chen, W.; Butcher, K. S.; Ang, T.; Ju, L. A. — bioRxiv, 2026-03-05
  abs

• 🧬 What comes after de novo? Automated lead optimization of proteins with CRADLE-1
  Bixby, E.; Brunner, G.; Danciu, D.; Dela Rosa, R.; Deutschmann, N.; Ferragu, C.; Geiger, F.; Holberg, C.; Kidger, P.; Lindoulsi, A.; Lutz, N.; McColgan, T.; Milius, S.; Shah, J.; Vandeloo, M.; Vidas, P.; Ziegler, J. D.; van Rossum, H.; van der Vorm, D.; Baldi, N.; IJSpeert, C.; Monza, E.; Schriek, A. — bioRxiv, 2026-03-08
  abs

• 🧬 Ligand-guided Sequence-structure Co-design of De Novo Functional Enzymes
  Song, Z.; Liu, H.; Zhao, Y.; Yang, Y.; Li, L. — bioRxiv, 2026-03-04
  abs

• 📄 FuseDiff: Symmetry-Preserving Joint Diffusion for Dual-Target Structure-Based Drug Design
  Jianliang Wu, Anjie Qiao, Zhen Wang, Zhewei Wei, Sheng Chen — arXiv, 2026-03-05
  abs

• 🧬 Predicting how perturbations reshape cellular trajectories with PerturbGen
  Chi Hao Ly, K.; Miraki Feriz, A.; Isobe, T.; Vahidi, A.; Vaghari, D.; Rostron, A.; Quiroga Londono, M.; Mende, N.; Vijayabaskar, M.; Moullet, M.; Rose Foster, A.; Graves, E.; Torabi, F.; Admane, C.; Horsfall, D.; Basurto-Lozada, D.; Stephenson, E.; A. Botting, R.; Iskander, D.; Webb, S.; Goh, I.; Jafree, D.; H. M. Sturgess, K.; Scott, J.; Sendama, W.; Magnani, L.; Hannah, R.; Asadollahzadeh, H.; Holland, A.; Prete, M.; Simpson, J.; Roy, A.; Roberts, I.; Jardine, L.; Laurenti, E.; Trynka, G.; Wilson, N. K.; Haniffa, M.; Gottgens, B.; Lotfollahi, M. — bioRxiv, 2026-03-05
  abs

• 📄 Count Bridges enable Modeling and Deconvolving Transcriptomic Data
  Nic Fishman, Gokul Gowri, Tanush Kumar, Jiaqi Lu, Valentin de Bortoli, Jonathan S. Gootenberg, Omar Abudayyeh — arXiv, 2026-03-05
  abs

• 🧬 ProtNHF: Neural Hamiltonian Flows for Controllable Protein Sequence Generation
  Raghavan, B.; Rogers, D. M. — bioRxiv, 2026-03-06
  abs

• 🧬 Discovery of a phenazine thiol conjugase from sparse data using genome-informed machine learning
  Newman, D. K.; Shan, X.; Trindade, I. B.; Glasser, N. R.; Thalhammer, K. O.; Scurria, M.; Mora, A.; Conway, S. J. — bioRxiv, 2026-03-06
  abs

• 📄 Rigidity-Aware Geometric Pretraining for Protein Design and Conformational Ensembles
  Zhanghan Ni, Yanjing Li, Zeju Qiu, Bernhard Schölkopf, Hongyu Guo, Weiyang Liu, Shengchao Liu — arXiv, 2026-03-02
  abs

• 🧬 Sampling protein structural token space enables accurate prediction of multiple conformations
  Wang, Z.; Yu, Y.; Yu, C.; Bu, D. — bioRxiv, 2026-03-04
  abs

• 🧬 LLMsFold: Integrating Large Language Models and Biophysical Simulations for De Novo Drug Design
  Waththe Liyanage, W. W.; Bove, F.; Righelli, D.; Romano, S.; Visone, R.; Iorio, M. V.; Lio, P.; Taccioli, C. — bioRxiv, 2026-03-04
  abs

• 🧬 t2pmhc: A Structure-Informed Graph Neural Network to predict TCR-pMHC Binding
  Polster, M.; Stadelmaier, J.; Ball, E.; Scheid, J.; Bauer, J.; Nelde, A.; Claassen, M.; Dubbelaar, M. L.; Walz, J. S.; Nahnsen, S. — bioRxiv, 2026-03-02
  abs

• 🧬 Explainable AI for end-to-end pathogen target discovery and molecular design
  Polonio, A.; Perez-Garcia, A.; Fernandez-Ortuno, D.; Jimenez-Castro, L. — bioRxiv, 2026-03-02
  abs

• 🧬 GTA-5: A Unified Graph Transformer Framework for Ligands and Protein Binding Sites - Part I: Constructing the PDB Pocket and Ligand Space
  Ciambur, B. C.; Pageau, R.; Sperandio, O. — bioRxiv, 2026-03-02
  abs

• 🧬 Linear-time prediction of proteome-scale microbial protein interactions
  Cornman, A.; Tranzillo, M.; Zulaybar, N. G.; Bouzit, I.; Hwang, Y. — bioRxiv, 2026-03-02
  abs

• 🧬 Genome-wide classification of tumor-derived reads from bulk long-read sequencing
  Baker, T. M.; Matulionis, N.; Andrasz, C.; Gerke, D.; Garcia-Dutton, N.; Atkinson, D.; Chiotti, K.; Wu, S.; Lulla, S.; Oh, J.; Winata, H.; Huang, R.-R.; Lester, J.; Karlan, B. Y.; Spellman, P. T. — bioRxiv, 2026-03-05
  abs

• 🧬 FoldARE, an RNA secondary structure analysis and prediction tool via generative pseudo-SHAPE modeling
  Marino, S. M.; Husak, V.; Tebaldi, T. — bioRxiv, 2026-03-05
  abs

• 🧬 Multi-Modal Protein Representation Learning with CLASP
  Bolouri, N.; Szymborski, J.; Emad, A. — bioRxiv, 2026-03-08
  abs