Weekly BioML Digest [April 13, 2026]

Machine Learning × Computational Biology paper compilation

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

PS. Looks like last week's post was published on the web but wasn't emailed out due some issues with the Ghost platform. That seems to have been fixed now.

Feedback? Email me at biomldigest@gmail.com.

📚 Peer-Reviewed Journals (Top 20)

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

• Multiomics and deep learning dissect regulatory syntax in human development
  Liu, Betty B., Jessa, Selin, Kim, Samuel H., Ng, Yan Ting, Higashino, Soon Il, Marinov, Georgi K., Chen, Derek C., Parks, Benjamin E., Li, Li, Nguyen, Tri C., Wang, Austin T., Wang, Sean K., Tan, Meng How, Tan, Serena Y., Kosicki, Michael, Pennacchio, Len A., Ben-David, Eyal, Pasca, Anca M., Kundaje, Anshul, Farh, Kyle K. H., Greenleaf, William J. — Nature, 2026-04-08
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• Single-cell spatiotemporal dissection of the human maternal–fetal interface
  Wang, Cheng, Zhou, Yan, Wang, Yuejun, Guha, Tuhin Kumar, Luo, Zhida, Mustafaraj, Anxhela, McIntyre, Tara I., Schwab, Marisa E., Davidson, Brittany R., Reeder, Gabriella C., Wong, Ronald J., England, Sarah K., Gonzalez, Juan M., Blelloch, Robert, Combes, Alexis J., Giudice, Linda C., Erlebacher, Adrian, MacKenzie, Tippi C., Stevenson, David K., Shaw, Gary M., Snyder, Michael P., Sun, Xiaofei, Winn, Virginia D., Fisher, Susan J., Li, Jingjing — Nature, 2026-04-08
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• Sequence Display enables large-scale sequence–activity datasets for rapid protein evolution
  Cheng, Linqi, Zheng, Xinzhe, Jiang, Shiyu Jason, Hu, Yu, Liu, Yijie, Yang, Kaiqiang, Rui, Jinyan, Ding, Haoxue, Zhang, Mengxi, Yuan, Teng, Lu, Qianglan, Ye, Haoxin, Li, Chen-Long, Guo, Yiming, Tian, Zuotong, Qin, Anna, Zhou, Boyang, Yang, Kevin K., Huang, Xiongyi, Xiao, Han — Nature Biotechnology, 2026-04-08
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• The trRosettaRNA server for RNA structure prediction
  Wang, Wenkai, Liu, Xiaocheng, Peng, Zhenling, Yang, Jianyi — Nature Protocols, 2026-04-08
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• VaxLab: integrated platform for rapid multistrategy mRNA vaccine design
  Kim, Junsoo, Han, Yoojung, Kwon, Chae Young, Chang, Hyeshik — Experimental & Molecular Medicine, 2026-04-08
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• Improved tumor-only variant calling and mutation burden estimation with VarNet-T
  Krishnamachari, Kiran, Bui Nguyen, Huu An, Kadioglu, Sinem, Ong Tze, Jet, Jacobsen Skanderup, Anders — Nature Communications, 2026-04-09
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• LaMGen: LLM-based 3D molecular generation for multi-target drug design
  Su, Qun, Gou, Qiaolin, Zhang, Hui, Wang, Jike, Sun, Huiyong, Hu, Renling, Qin, Rui, Liu, Huanxiang, Hou, Tingjun, Kang, Yu — Nature Communications, 2026-04-11
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• Combining structural modeling and deep learning to calculate the E. coli protein interactome and functional networks
  Zhao, H., Velez, C., Naravane, A., Saha, A., Feldman, J., Skolnick, J., Murray, D., Honig, B. — Nature Communications, 2026-04-11
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• Interpretable deep generative ensemble learning for single-cell omics with Hydra
  Wagle, Manoj M, Liu, Chunlei, Liu, Zunpeng, Wang, Yongheng, Kellis, Manolis, Patrick, Ellis, Yang, Pengyi — Molecular Systems Biology, 2026-04-11
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• Reconstruction of human metabolic models with large language models
  Jiahao Luo, Hao Wang, Devlin C. Moyer, Zhetao Guo, Jonathan L. Robinson, Johan Gustafsson, Mihail Anton, Yu Chen, E. Kerkhoven, Jens Nielsen, Feiran Li — Proceedings of the National Academy of Sciences, 2026-04-08
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• Molecular contrastive learning with graph attention network (MoCL-GAT) for enhanced molecular representation
  Dalkıran, Alperen, Rifaioglu, Ahmet Sureyya, Cetin-Atalay, Rengul, Acar, Aybar C., Doğan, Tunca, Atalay, M. Volkan — BMC Bioinformatics, 2026-04-09
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• Multimodal artificial intelligence predicts PIK3CA mutation in breast cancer from digital pathology and clinical data: a multicenter study
  J. Miao, Qi Liu, Jianing Zhao, Shishun Fan, Shenwen Wang, F. Ye, Si Wu, Jinze Li, Huirui Zhang, Meng Zhang, H. Bu, Xiao Han, Lianghong Teng, Yueping Liu — Cancer Biology & Medicine, 2026-04-08
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• Attention-based deep learning for analysis of pathology images and gene expression data in lung squamous premalignant lesions
  Xu, Lingyi, Kefella, Yohana, Zhang, Yichi, Conrad, Regan D., Anderson, Kelley E., Krysan, Kostyantyn, Liu, Gang, Kane, Erin, Pennycuick, Adam, Merrick, Daniel T., Janes, Sam M., Reid, Mary E., Burks, Eric J., Billatos, Ehab, Mazzilli, Sarah A., Kolachalama, Vijaya B., Beane, Jennifer E. — Genome Medicine, 2026-04-08
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• Deep learning-based pathomics signature predicts prognosis and treatment response in gastric cancer: a multicenter retrospective study
  Wang, Hao, Li, Hao, Ma, Keru, Mo, Genshen, Yan, Meihong, Zhang, Xinyue, Xie, Haonan, Huang, Yuze, Li, Huiying, Xue, Yingwei, Han, Peng, Lou, Shenghan — npj Precision Oncology, 2026-04-10
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• A scalable multimodal graph neural network for drug combination response prediction
  Saeed, Dhekra, Xing, Huanlai, Feng, Li — Molecular Diversity, 2026-04-10
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• DecoderDTA: enhancing drug-target binding affinity prediction via decoding fidelity in multi-task learning
  Han, Li, Liu, Xinning, Zhou, Hui, Zhao, Lei, Kang, Ling, Guo, Quan — Journal of Computer-Aided Molecular Design, 2026-04-10
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• Volatomics-based biomarkers for non-invasive diagnosis and monitoring of inflammatory bowel disease
  Li, Xiaowen, Pan, Siyuan, Li, Qingshang, Yu, Borong, Ma, Jianxia, Chen, Yuanwen — Journal of Gastroenterology, 2026-04-09
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• ​​Integrating machine learning and spatial transcriptomics uncovers shared immunomodulatory deubiquitinases in MAFLD and HCC
  Han, Yu-xi, Li, Hongze, Xia, Wendi, Ma, Junyi, Zhang, Jiaqi, Li, Yiling — Human Genetics, 2026-04-10
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• Advancing target discovery through disease-specific integration of multi-modal target identification models and comprehensive benchmarking system
  Leung, Howell, Duan, Chengchen, Gou, Wenhao, Chen, Jianjiu, Xin, Ying, Zheng, Zetian, Naumov, Vladimir, Gennert, David, Zhang, Man, Aliper, Alex, Ren, Feng, Izumchenko, Evgeny, Pun, Frank W., Zhavoronkov, Alex — Scientific Reports, 2026-04-12
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• Tripleknock: predicting lethal effect of three-gene knockout in bacteria by deep learning
  Geng, Peter X., Hou, Jiaheng, Guo, Jinyuan, Jiang, Xiaoqing, Zhu, Huaiqiu — Scientific Reports, 2026-04-10
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🧬 Preprints (arXiv + bioRxiv)

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

• 📄 General Multimodal Protein Design Enables DNA-Encoding of Chemistry
  Jarrid Rector-Brooks, Théophile Lambert, Marta Skreta, Daniel Roth, Yueming Long, Zi-Qi Li, Xi Zhang, Miruna Cretu, Francesca-Zhoufan Li, Tanvi Ganapathy, Emily Jin, Avishek Joey Bose, Jason Yang, Kirill Neklyudov, Yoshua Bengio, Alexander Tong, Frances H. Arnold, Cheng-Hao Liu — arXiv, 2026-04-06
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• 🧬 Discovery of resistance-resilient quinoline papain-like protease inhibitors through topology-constrained molecular generative design
  Lu, Y.; Ran, T.; Yang, Q.; Zhang, G.; Chen, J.; Zhou, P.; Li, W.; Xu, M.; Tang, J.; Dai, M.; Zhong, J.; Chen, H.; He, P.; Zhou, A.; Xue, B.; Zhang, J.; Wu, K.; Wu, X.; Tang, M.; Chen, X.; Chen, H.; Shang, J. — bioRxiv, 2026-04-06
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• 🧬 FlashBind: Towards Accurate and Efficient Structure-based Virtual Screening
  Jiang, S.; Chen, Y.; Krishnan, A.; Zhang, Y.; Jin, W. — bioRxiv, 2026-04-08
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• 🧬 Evolutionary transfer learning enables organism-wide inference of mammalian enhancer landscapes
  Qiu, C.; Daza, R. M.; Welsh, I. C.; Patwardhan, R. P.; Martin, B. K.; Li, T.; Yang, S.; Kempynck, N.; Taylor, M. L.; Fulton, O.; Le, T.-M.; O'Day, D. R.; Lalanne, J.-B.; Domcke, S.; Murray, S. A.; Aerts, S.; Trapnell, C.; Shendure, J. — bioRxiv, 2026-04-08
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• 🧬 Geometry-enhanced protein language modeling enables discovery of novel antibiotic resistance genes
  Lin, X.; Guan, J.; Hong, Y.; Guo, Y.; Yang, Y.; Xie, P.; Zhao, Z.; Liu, X.; Huang, Y.; Ye, Y.; Tang, Y.; Lee, T.-Y.; Chiang, Y.-C.; Wei, L.; Liu, X.; Wang, J.; Pan, Y.; Tang, J.; Pei, Y.; Yao, L. — bioRxiv, 2026-04-08
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• 🧬 Sampling protein structural token space enables accurate prediction of multiple conformations
  Wang, Z.; Yu, Y.; Yu, C.; Bu, D. — bioRxiv, 2026-04-08
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• 🧬 CardamomOT: a mechanistic optimal transport-based framework for gene regulatory network inference, trajectory reconstruction and generative modeling
  Mauge, Y.; Ventre, E. — bioRxiv, 2026-04-09
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• 🧬 A structure-informed deep learning framework for modeling TCR-peptide-HLA interactions
  Cao, K.; Li, R.; Strazar, M.; Brown, E. M.; Nguyen, P. N. U.; Pust, M.-M.; Park, J.; Graham, D. B.; Ashenberg, O.; Uhler, C.; Xavier, R. — bioRxiv, 2026-04-11
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• 🧬 Modification-aware AI enables terminal chemical modifications for peptide design and discovers potent antimicrobials
  Xu, J.; Torres, M. D. T.; Li, C.; Li, J.; Li, F.; Song, J.; de la Fuente, C. — bioRxiv, 2026-04-10
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• 🧬 TFBindFormer:A Cross-Attention Transformer for Transcription Factor--DNA Binding Prediction
  Liu, P.; Wang, L.; Basnet, S.; Cheng, J. — bioRxiv, 2026-04-11
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• 🧬 Deep-Plant: a supervised foundation model for plant regulatory genomics
  Daoud, A.; Roy, S.; Zeng, H.; Bao, X.; Zhang, Z.; Wang, J.; Parodi, P.; Reddy, A.; Liu, J.; Ben-Hur, A. — bioRxiv, 2026-04-09
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• 🧬 Improved inference of multiscale sequence statistics in generative protein models
  Chauveau, M.; Kleeorin, Y.; Hinds, E.; Junier, I.; Ranganathan, R.; Rivoire, O. — bioRxiv, 2026-04-09
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• 🧬 AI-Guided Structure-Aware Modeling and Thermal Proteomics Reveal Direct Demethylzeylasteral-ACLY Interaction
  Wang, Q.; Yu, N.; Song, Y.; Fan, X.; Tian, J.; Chang, S.; Guo, Y.; Tan, C. S. H.; Ji, H. — bioRxiv, 2026-04-08
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• 📄 Reinforcement Learning with LLM-Guided Action Spaces for Synthesizable Lead Optimization
  Tao Li, Kaiyuan Hou, Tuan Vinh, Monika Raj, Zhichun Guo, Carl Yang — arXiv, 2026-04-09
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• 🧬 Deep learning enables direct HLA typing from immunopeptidomics data
  Pilz, M.; Scheid, J.; Bauer, A.; Lemke, S.; Sachsenberg, T.; Bauer, J.; Nelde, A.; Stadelmaier, J.; Walter, A.; Rammensee, H.-G.; Nahnsen, S.; Kohlbacher, O.; Walz, J. S. — bioRxiv, 2026-04-10
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• 🧬 HEIMDALL: Disentangling tokenizer design for robust transfer in single-cell foundation models
  Haber, E.; Alam, S.; Ho, N.; Liu, R.; Trop, E.; Liang, S.; Yang, M.; Krieger, S.; Ma, J. — bioRxiv, 2026-04-12
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• 🧬 Optimizing Protein Tokenization: Reduced Amino Acid Alphabets for Efficient and Accurate Protein Language Models
  Rannon, E.; Burstein, D. — bioRxiv, 2026-04-12
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• 📄 Equivariant Efficient Joint Discrete and Continuous MeanFlow for Molecular Graph Generation
  Rongjian Xu, Teng Pang, Zhiqiang Dong, Guoqiang Wu — arXiv, 2026-04-09
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• 🧬 FunctionaL Assigning Sequence Homing (FLASH) maps phenotype to sequence with deep and machine learning
  Cotter, D. J.; Harrison, M.-C.; Rustagi, A.; Wang, P. L.; Kokot, M.; Carey, A. F.; Deorowicz, S.; Salzman, J. — bioRxiv, 2026-04-07
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• 🧬 sctrial: Participant-Level Differential Analysis for Longitudinal Single-Cell Experiments
  Vasanthakumari, P.; Valencia, I.; Aghmiouni, M. R.; Magana, B.; Omar, M. N. — bioRxiv, 2026-04-06
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