A guide to machine learning for biologists
Open accessThe claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Compared with traditional methods, machine learning excels in handling larger datasets and delivering accurate predictive outcomes more efficiently, with reduced bias.
“Compared with traditional methods, ML excels in handling larger datasets and delivering accurate predictive outcomes more efficiently, with reduced bias [10].”
From Machine learning with the body roundness index and associated indicators: a new approach to predicting metabolic syndrome (2025) · cites this paper as [10]
The Introduction (page not supplied) says machine learning is useful for datasets too large or complex for human analysis and can make analysis reproducible and time-efficient. It does not establish that ML generally produces more accurate predictions or reduces bias compared with traditional methods. The Traditional machine learning section also cautions that deep learning can take more time and computation than traditional ML methods. (LLM, conf=0.86)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
LeCun, Y., Bengio, Y., & Hinton, G. (2015) · Nature · doi:10.1038/nature14539 · Cited by 84,126 · see citing works
Regression shrinkage and selection via the lasso
Tibshirani, R. (1996) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1996.tb02080.x · Cited by 51,482 · see citing works
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works
The Elements of Statistical Learning
Hastie, T., Tibshirani, R., & Friedman, J. (2009) · Springer Series in Statistics · doi:10.1007/978-0-387-84858-7 · Cited by 25,970 · see citing works
Dermatologist-level classification of skin cancer with deep neural networks
Esteva, A., Kuprel, B., Novoa, R. A., Ko, J., Swetter, S. M., Blau, H. M., & Thrun, S. (2017) · Nature · doi:10.1038/nature21056 · Cited by 14,362 · see citing works
Dropout as a bayesian approximation: Representing model uncertainty in deep learning
Gal, Y., & Ghahramani, Z. (2015) · arXiv · doi:10.48550/arxiv.1506.02142 · Cited by 6,471 · see citing works
The relation between the divergence of sequence and structure in proteins.
Chothia, C., & Lesk, A. M. (1986) · The EMBO Journal · doi:10.1002/j.1460-2075.1986.tb04288.x · Cited by 2,458 · see citing works
Practical Recommendations for Gradient-Based Training of Deep Architectures
Bengio, Y. (2012) · Lecture Notes in Computer Science · doi:10.1007/978-3-642-35289-8_26 · Cited by 2,259 · see citing works
Shortcut learning in deep neural networks
Geirhos, R., Jacobsen, J.-H., Michaelis, C., Zemel, R., Brendel, W., Bethge, M., & Wichmann, F. A. (2020) · Nature Machine Intelligence · doi:10.1038/s42256-020-00257-z · Cited by 2,224 · see citing works
A universal SNP and small-indel variant caller using deep neural networks
Poplin, R., Chang, P.-C., Alexander, D., Schwartz, S., Colthurst, T., Ku, A., Newburger, D., Dijamco, J., Nguyen, N., Afshar, P. T., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4235 · Cited by 1,840 · see citing works
Zech, J. R., Badgeley, M. A., Liu, M., Costa, A. B., Titano, J. J., & Oermann, E. K. (2018) · PLOS Medicine · doi:10.1371/journal.pmed.1002683 · Cited by 1,719 · see citing works
Deep learning enables rapid identification of potent DDR1 kinase inhibitors
Zhavoronkov, A., Ivanenkov, Y. A., Aliper, A., Veselov, M. S., Aladinskiy, V. A., Aladinskaya, A. V., Terentiev, V. A., Polykovskiy, D. A., Kuznetsov, M. D., Asadulaev, A., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0224-x · Cited by 1,573 · see citing works
Unified rational protein engineering with sequence-based deep representation learning
Alley, E. C., Khimulya, G., Biswas, S., AlQuraishi, M., & Church, G. M. (2019) · Nature Methods · doi:10.1038/s41592-019-0598-1 · Cited by 1,131 · cited 2× · see citing works
“biological sequences Protein engineering [68] Variable input size Long training times”
BackgroundDeepTox: toxicity prediction using deep learning
Mayr, A., Klambauer, G., Unterthiner, T., & Hochreiter, S. (2016) · Frontiers in Environmental Science · doi:10.3389/fenvs.2015.00080 · Cited by 1,081 · see citing works
Visualizing structure and transitions in high-dimensional biological data
Moon, K. R., van Dijk, D., Wang, Z., Gigante, S., Burkhardt, D. B., Chen, W. S., Yim, K., Elzen, A. V. D., Hirn, M. J., Coifman, R. R., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0336-3 · Cited by 1,065 · see citing works
Roberts, M., Driggs, D., Thorpe, M., Gilbey, J., Yeung, M., Ursprung, S., Aviles-Rivero, A. I., Etmann, C., McCague, C., Beer, L., et al. (2021) · Nature Machine Intelligence · doi:10.1038/s42256-021-00307-0 · Cited by 1,044 · see citing works
Mutation effects predicted from sequence co-variation
Hopf, T. A., Ingraham, J. B., Poelwijk, F. J., Schärfe, C. P. I., Springer, M., Sander, C., & Marks, D. S. (2017) · Nature Biotechnology · doi:10.1038/nbt.3769 · Cited by 775 · see citing works
Evaluating Protein Transfer Learning with TAPE
Rao, R., Bhattacharya, N., Thomas, N., Duan, Y., Chen, X., Canny, J., Abbeel, P., & Song, Y. S. (2019) · doi:10.1101/676825 · Cited by 719 · see citing works
De novo protein design by deep network hallucination
Anishchenko, I., Chidyausiku, T. M., Ovchinnikov, S., Pellock, S. J., & Baker, D. (2020) · doi:10.1101/2020.07.22.211482 · Cited by 629 · see citing works
ECOD: an evolutionary classification of protein domains
Cheng, H., Schaeffer, R. D., Liao, Y., Kinch, L. N., Pei, J., Shi, S., Kim, B.-H., & Grishin, N. V. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003926 · Cited by 426 · see citing works
End-to-End Differentiable Learning of Protein Structure
AlQuraishi, M. (2019) · Cell Systems · doi:10.1016/j.cels.2019.03.006 · Cited by 371 · see citing works
Data-driven advice for applying machine learning to bioinformatics problems
Olson, R. S., Cava, W. L., Mustahsan, Z., Varik, A., & Moore, J. H. (2018) · Biocomputing 2018 · doi:10.1142/9789813235533_0018 · Cited by 287 · see citing works
FFPred 3: feature-based function prediction for all Gene Ontology domains
Cozzetto, D., Minneci, F., Currant, H., & Jones, D. T. (2016) · Scientific Reports · doi:10.1038/srep31865 · Cited by 127 · see citing works
Self-citationPrediction of enhancer-promoter interactions via natural language processing
Zeng, W., Wu, M., & Jiang, R. (2018) · BMC Genomics · doi:10.1186/s12864-018-4459-6 · Cited by 96 · cited 3× · see citing works
“Another class of robust non-linear methods are ensemble-based models like random forests [39] and XGBoost [40,41].”
BackgroundMethodEnvironmental conditions shape the nature of a minimal bacterial genome
Antczak, M., Michaelis, M., & Wass, M. N. (2019) · Nature Communications · doi:10.1038/s41467-019-10837-2 · Cited by 55 · see citing works
Flagged first, then by citations
Research works printed but not linked: 101
- Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, et al. Opportunities and obstacles for deep learning in biology and medicine. J R Soc Interface. 2018;15. A thorough review of applications of deep learning to biology and medicine including many references to the literature.
- Mitchell TM. Machine Learning. McGraw Hill; 1997.
- Goodfellow I, Bengio Y, Courville A. Deep Learning. MIT Press; 2016.
- Libbrecht MW, Noble WS. Machine learning applications in genetics and genomics. Nat Rev Genet. 2015;16: 321-332.
- Zou J, Huss M, Abid A, Mohammadi P, Torkamani A, Telenti A. A primer on deep learning in genomics. Nat Genet. 2019;51: 12-18.
- Myszczynska MA, Ojamies PN, Lacoste AMB, Neil D, Saffari A, Mead R, et al. Applications of machine learning to diagnosis and treatment of neurodegenerative diseases. Nat Rev Neurol. 2020;16: 440-456.
- Yang KK, Wu Z, Arnold FH. Machine-learning-guided directed evolution for protein engineering. Nature Methods. 2019;16: 687-694.
- Tarca AL, Carey VJ, Chen X-W, Romero R, Drăghici S. Machine learning and its applications to biology. PLoS Comput Biol. 2007;3: e116. An introduction to machine learning concepts and applications in biology with a focus on traditional machine learning methods.
- Silva JCF, Teixeira RM, Silva FF, Brommonschenkel SH, Fontes EPB. Machine learning approaches and their current application in plant molecular biology: A systematic review. Plant Sci. 2019;284: 37-47.
- Kandoi G, Acencio ML, Lemke N. Prediction of Druggable Proteins Using Machine Learning and Systems Biology: A Mini-Review. Front Physiol. 2015;6: 366.
- Marblestone AH, Wayne G, Kording KP. Toward an Integration of Deep Learning and Neuroscience. Front Comput Neurosci. 2016;10: 94.
- Jiménez-Luna J, Grisoni F, Schneider G. Drug discovery with explainable artificial intelligence. Nature Machine Intelligence. 2020;2: 573-584.
- Buchan DWA, Jones DT. The PSIPRED Protein Analysis Workbench: 20 years on. Nucleic Acids Res. 2019;47: W402-W407.
- Kelley DR, Snoek J, Rinn JL. Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks. Genome Res. 2016;26: 990-999.
- Altman N, Krzywinski M. Clustering. Nat Methods. 2017;14: 545-546.
- Zhang Z, Wang L, Gao Y, Zhang J, Zhenirovskyy M, Alexov E. Predicting folding free energy changes upon single point mutations. Bioinformatics. 2012;28: 664-671.
- Pedregosa F, Varoquaux G, Gramfort A, Michel V, Thirion B, Grisel O, et al. Scikit-learn: Machine Learning in Python. J Mach Learn Res. 2011;12: 2825-2830.
- Kuhn M. Building Predictive Models in R Using the caret Package. Journal of Statistical Software. 2008;28: 1- 26.
- Blaom AD, Kiraly F, Lienart T, Simillides Y, Arenas D, Vollmer SJ. MLJ: A Julia package for composable machine learning. Journal of Open Source Software. 2020;5: 2704.
- Jones DT. Setting the standards for machine learning in biology. Nat Rev Mol Cell Biol. 2019;20: 659-660.
- Alipanahi B, Delong A, Weirauch MT, Frey BJ. Predicting the sequence specificities of DNA-and RNA- binding proteins by deep learning. Nat Biotechnol. 2015;33: 831-838.
- Senior AW, Evans R, Jumper J, Kirkpatrick J, Sifre L, Green T, et al. Improved protein structure prediction using potentials from deep learning. Nature. 2020;577: 706-710.
- Tegunov D, Cramer P. Real-time cryo-electron microscopy data preprocessing with Warp. Nat Methods. 2019;16: 1146-1152.
- A review of deep learning by some of the major figures in the deep learning revolution.
- Adebayo J, Gilmer J, Muelly M, Goodfellow I, Hardt M, Kim B. Sanity Checks for Saliency Maps. NeurIPS. 2018. Available: https://arxiv.org/abs/1810.03292 · arXiv
- Smith AM, Walsh JR, Long J, Davis CB, Henstock P, Hodge MR, et al. Standard machine learning approaches outperform deep representation learning on phenotype prediction from transcriptomics data. BMC Bioinformatics. 2020;21: 119.
- Zou H, Hastie T. Regularization and variable selection via the elastic net. J R Stat Soc Series B. 2005;67: 301- 320.
- Noble WS. What is a support vector machine? Nat Biotechnol. 2006;24: 1565-1567.
- Ben-Hur A, Ong CS, Sonnenburg S, Schölkopf B, Rätsch G. Support Vector Machines and Kernels for Computational Biology. PLoS Computational Biology. 2008;4: e1000173. An introduction to support vector machines with a focus on biological data and prediction tasks.
- Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014;46: 310-315.
- Driscoll MK, Welf ES, Jamieson AR, Dean KM, Isogai T, Fiolka R, et al. Robust and automated detection of subcellular morphological motifs in 3D microscopy images. Nat Methods. 2019;16: 1037-1044.
- Bzdok D, Krzywinski M, Altman N. Machine learning: supervised methods. Nat Methods. 2018;15: 5-6.
- Wang C, Zhang Y. Improving scoring-docking-screening powers of protein-ligand scoring functions using random forest. J Comput Chem. 2017;38: 169-177.
- Rappoport N, Shamir R. Multi-omic and multi-view clustering algorithms: review and cancer benchmark. Nucleic Acids Res. 2019;47: 1044.
- Steinegger M, Söding J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat Biotechnol. 2017;35: 1026-1028.
- Jain AK. Data clustering: 50 years beyond K-means. Pattern Recognition Letters. 2010;31: 651-666.
- Ester M, Kriegel H-P, Sander J, Xu X. A density-based algorithm for discovering clusters in large spatial databases with noise. KDD'96: Proceedings of the Second International Conference on Knowledge Discovery and Data Mining. 1996;96: 226-231.
- Nguyen LH, Holmes S. Ten quick tips for effective dimensionality reduction. PLoS Comput Biol. 2019;15: e1006907.
- van der Maaten L, Hinton G. Visualizing Data using t-SNE. J Mach Learn Res. 2008;9: 2579-2605.
- Kobak D, Berens P. The art of using t-SNE for single-cell transcriptomics. Nat Commun. 2019;10: 5416. Discussion and tips for using t-SNE as a dimensionality reduction technique on single-cell transcriptomics data.
- Crick F. The recent excitement about neural networks. Nature. 1989;337: 129-132.
- Qian N, Sejnowski TJ. Predicting the secondary structure of globular proteins using neural network models. J Mol Biol. 1988;202: 865-884.
- deFigueiredo RJ, Shankle WR, Maccato A, Dick MB, Mundkur P, Mena I, et al. Neural-network-based classification of cognitively normal, demented, Alzheimer disease and vascular dementia from single photon emission with computed tomography image data from brain. Proc Natl Acad Sci U S A. 1995;92: 5530-5534.
- Yang J, Anishchenko I, Park H, Peng Z, Ovchinnikov S, Baker D. Improved protein structure prediction using predicted interresidue orientations. Proc Natl Acad Sci U S A. 2020;117: 1496-1503.
- Xu J, Mcpartlon M, Li J. Improved protein structure prediction by deep learning irrespective of co-evolution information. bioRxiv. 2020. Available: https://www.biorxiv.org/content/10.1101/2020.10.12.336859v1 · DOI
- Fudenberg G, Kelley DR, Pollard KS. Predicting 3D genome folding from DNA sequence with Akita. Nat Methods. 2020;17: 1111-1117.
- Zeng H, Edwards MD, Liu G, Gifford DK. Convolutional neural network architectures for predicting DNA- protein binding. Bioinformatics. 2016;32: i121-i127.
- Yao R, Qian J, Huang Q. Deep-learning with synthetic data enables automated picking of cryo-EM particle images of biological macromolecules. Bioinformatics. 2020;36: 1252-1259.
- Si D, Moritz SA, Pfab J, Hou J, Cao R, Wang L, et al. Deep Learning to Predict Protein Backbone Structure from High-Resolution Cryo-EM Density Maps. Sci Rep. 2020;10: 4282.
- Poplin R, Varadarajan AV, Blumer K, Liu Y, McConnell MV, Corrado GS, et al. Prediction of cardiovascular risk factors from retinal fundus photographs via deep learning. Nat Biomed Eng. 2018;2: 158-164.
- Heffernan R, Yang Y, Paliwal K, Zhou Y. Capturing non-local interactions by long short-term memory bidirectional recurrent neural networks for improving prediction of protein secondary structure, backbone angles, contact numbers and solvent accessibility. Bioinformatics. 2017;33: 2842-2849.
- Müller AT, Hiss JA, Schneider G. Recurrent Neural Network Model for Constructive Peptide Design. J Chem Inf Model. 2018;58: 472-479.
- Choi E, Bahadori MT, Schuetz A, Stewart WF, Sun J. Doctor AI: Predicting Clinical Events via Recurrent Neural Networks. JMLR Workshop Conf Proc. 2016;56: 301-318.
- Quang D, Xie X. DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences. Nucleic Acids Res. 2016;44: e107.
- Vaswani A, Shazeer N, Parmar N, Uszkoreit J, Jones L, Gomez AN, et al. Attention Is All You Need. arXiv. 2017;1706.03762.
- Elnaggar A, Heinzinger M, Dallago C, Rihawi G, Wang Y, Jones L, et al. ProtTrans: Towards Cracking the Language of Life's Code Through Self-Supervised Deep Learning and High Performance Computing. bioRxiv. 2020. Available: https://www.biorxiv.org/content/10.1101/2020.07.12.199554v1 · DOI
- Battaglia PW, Hamrick JB, Bapst V, Sanchez-Gonzalez A, Zambaldi V, Malinowski M, et al. Relational inductive biases, deep learning, and graph networks. arXiv. 2018;1806.01261. Available: https://arxiv.org/abs/1806.01261 · arXiv
- Stokes JM, Yang K, Swanson K, Jin W, Cubillos-Ruiz A, Donghia NM, et al. A Deep Learning Approach to Antibiotic Discovery. Cell. 2020;181: 475-483.
- Gainza P, Sverrisson F, Monti F, Rodolà E, Boscaini D, Bronstein MM, et al. Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning. Nat Methods. 2020;17: 184-192.
- Strokach A, Becerra D, Corbi-Verge C, Perez-Riba A, Kim PM. Fast and Flexible Protein Design Using Deep Graph Neural Networks. Cell Syst. 2020;11: 402-411.e4.
- Gligorijevic V, Douglas Renfrew P, Kosciolek T, Leman JK, Cho K, Vatanen T, et al. Structure-Based Function Prediction using Graph Convolutional Networks. bioRxiv. 2019. Available: https://www.biorxiv.org/content/10.1101/786236v1 · DOI
- Zitnik M, Agrawal M, Leskovec J. Modeling polypharmacy side effects with graph convolutional networks. Bioinformatics. 2018;34: i457-i466.
- Veselkov K, Gonzalez G, Aljifri S, Galea D, Mirnezami R, Youssef J, et al. HyperFoods: Machine intelligent mapping of cancer-beating molecules in foods. Sci Rep. 2019;9: 9237.
- Fey M, Lenssen JE. Fast Graph Representation Learning with PyTorch Geometric. ICLR. 2019. Available: https://arxiv.org/abs/1903.02428 · arXiv
- Wang Y, Liu T, Xu D, Shi H, Zhang C, Mo Y-Y, et al. Predicting DNA Methylation State of CpG Dinucleotide Using Genome Topological Features and Deep Networks. Scientific Reports. 2016;6: 19598.
- Linder J, Bogard N, Rosenberg AB, Seelig G. A Generative Neural Network for Maximizing Fitness and Diversity of Synthetic DNA and Protein Sequences. Cell Syst. 2020;11: 49-62.e16.
- Greener JG, Moffat L, Jones DT. Design of metalloproteins and novel protein folds using variational autoencoders. Sci Rep. 2018;8: 16189.
- Wang J, Ma A, Chang Y, Gong J, Jiang Y, Qi R, et al. scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses. Nat Commun. 2021;12: 1882.
- Abadi M, Barham P, Chen J, Chen Z, Davis A, Dean J, et al. Tensorflow: A system for large-scale machine learning. 12th USENIX Symposium on Operating Systems Design and Implementation. 2016; 265-283.
- Wei Q, Dunbrack RL Jr. The role of balanced training and testing data sets for binary classifiers in bioinformatics. PLoS One. 2013;8: e67863.
- Walsh I, Pollastri G, Tosatto SCE. Correct machine learning on protein sequences: a peer-reviewing perspective. Brief Bioinform. 2016;17: 831-840.
- Söding J, Remmert M. Protein sequence comparison and fold recognition: progress and good-practice benchmarking. Curr Opin Struct Biol. 2011;21: 404-411.
- Steinegger M, Meier M, Mirdita M, Vöhringer H, Haunsberger SJ, Söding J. HH-suite3 for fast remote homology detection and deep protein annotation. BMC Bioinformatics. 2019;20: 473.
- Sillitoe I, Dawson N, Lewis TE, Das S, Lees JG, Ashford P, et al. CATH: expanding the horizons of structure- based functional annotations for genome sequences. Nucleic Acids Res. 2019;47: D280-D284.
- Li Y, Yang J. Structural and Sequence Similarity Makes a Significant Impact on Machine-Learning-Based Scoring Functions for Protein-Ligand Interactions. J Chem Inf Model. 2017;57: 1007-1012.
- Szegedy C, Zaremba W, Sutskever I, Bruna J, Erhan D, Goodfellow I, et al. Intriguing properties of neural networks. ICLR. 2014. Available: https://arxiv.org/abs/1312.6199 · arXiv
- Hie B, Cho H, Berger B. Realizing private and practical pharmacological collaboration. Science. 2018;362: 347-350.
- Beaulieu-Jones BK, Wu ZS, Williams C, Lee R, Bhavnani SP, Byrd JB, et al. Privacy-Preserving Generative Deep Neural Networks Support Clinical Data Sharing. Circ Cardiovasc Qual Outcomes. 2019;12: e005122.
- Konečný J, Brendan McMahan H, Ramage D, Richtárik P. Federated Optimization: Distributed Machine Learning for On-Device Intelligence. arXiv. 2016;1610.02527. Available: https://arxiv.org/abs/1610.02527 100. · arXiv
- Pérez A, Martínez-Rosell G, De Fabritiis G. Simulations meet machine learning in structural biology. Curr Opin Struct Biol. 2018;49: 139-144. 101.
- Noé F, Olsson S, Köhler J, Wu H. Boltzmann generators: Sampling equilibrium states of many-body systems with deep learning. Science. 2019;365: 6457. 102.
- Shrikumar A, Greenside P, Kundaje A. Reverse-complement parameter sharing improves deep learning models for genomics. bioRxiv. 2017. Available: https://www.biorxiv.org/content/10.1101/103663v1 103. · DOI
- Lopez R, Gayoso A, Yosef N. Enhancing scientific discoveries in molecular biology with deep generative models. Mol Syst Biol. 2020;16: e9198. 104.
- Innes M, Edelman A, Fischer K, Rackauckas C, Saba E, Shah VB, et al. A differentiable programming system to bridge machine learning and scientific computing. arXiv. 2019;1907.07587. Available: https://arxiv.org/abs/1907.07587 106. · arXiv
- Ingraham J, Riesselman AJ, Sander C, Marks DS. Learning Protein Structure with a Differentiable Simulator. ICLR. 2019. Available: https://openreview.net/forum?id=Byg3y3C9Km 107.
- Jumper JM, Faruk NF, Freed KF, Sosnick TR. Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours. PLoS Comput Biol. 2018;14: e1006578. 108.
- Wang Y, Fass J, Chodera JD. End-to-End Differentiable Molecular Mechanics Force Field Construction. arXiv. 2020;2010.01196. Available: http://arxiv.org/abs/2010.01196 109. · arXiv
- Chen KM, Cofer EM, Zhou J, Troyanskaya OG. Selene: a PyTorch-based deep learning library for sequence data. Nat Methods. 2019;16: 315-318.
- Kopp W, Monti R, Tamburrini A, Ohler U, Akalin A. Deep learning for genomics using Janggu. Nat Commun. 2020;11: 3488. 112. Schoenholz SS, Cubuk ED. JAX, M.D.: End-to-End Differentiable, Hardware Accelerated, Molecular Dynamics in Pure Python. arXiv. 2019;1912.04232. Available: https://arxiv.org/abs/1912.04232 113. · arXiv
- Avsec Ž, Kreuzhuber R, Israeli J, Xu N, Cheng J, Shrikumar A, et al. The Kipoi repository accelerates community exchange and reuse of predictive models for genomics. Nature Biotechnol. 2019;37: 592-600. 114. Isensee F, Jaeger PF, Kohl SAA, Petersen J, Maier-Hein KH. nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation. Nat Methods. 2020. 115. Livesey BJ, Marsh JA. Using deep mutational scanning to benchmark variant effect predictors and identify disease mutations. Mol Syst Biol. 2020;16: e9380. 116. AlQuraishi M. ProteinNet: a standardized data set for machine learning of protein structure. BMC Bioinformatics. 2019;20: 311. 117. Townshend RJL, Vögele M, Suriana P, Derry A, Powers A, Laloudakis Y, et al. ATOM3D: Tasks On Molecules in Three Dimensions. arXiv. 2020;2012.04035. 118
- Kryshtafovych A, Schwede T, Topf M, Fidelis K, Moult J. Critical assessment of methods of protein structure prediction (CASP)-Round XIII. Proteins: Structure, Function, and Bioinformatics. 2019;87: 1011- 1020. 120
- Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, et al. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biol. 2019;20: 244. 121.
- Munro D, Singh M. DeMaSk: a deep mutational scanning substitution matrix and its use for variant impact prediction. Bioinformatics. 2020;36: 5322-5329. 122. Haario H, Taavitsainen V-M. Combining soft and hard modelling in chemical kinetic models. Chemometrics Intellig Lab Syst. 1998;44: 77-98. 123.
- Nugent T, Jones DT. Transmembrane protein topology prediction using support vector machines. BMC Bioinformatics. 2009;10: 159. 125. Bao L, Zhou M, Cui Y. nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms. Nucleic Acids Res. 2005;33: W480-2. 126. Li W, Yin Y, Quan X, Zhang H. Gene Expression Value Prediction Based on XGBoost Algorithm. Front Genet. 2019;10: 1077. 127. Zhang Y, Skolnick J. SPICKER: a clustering approach to identify near-native protein folds. J Comput Chem. 2004;25: 865-871. 128. Teodoro ML, Phillips GN Jr, Kavraki LE. Understanding protein flexibility through dimensionality reduction. J Comput Biol. 2003;10: 617-634. 129. Schlichtkrull M, Kipf TN, Bloem P, van den Berg R, Titov I, Welling M. Modeling Relational Data with Graph Convolutional Networks. The Semantic Web. Springer International Publishing; 2018. pp. 593-607. 130. Pandarinath C, O'Shea DJ, Collins J, Jozefowicz R, Stavisky SD, Kao JC, et al. Inferring single-trial neural population dynamics using sequential auto-encoders. Nat Methods. 2018;15: 805-815. 131.
- Sun T, Zhou B, Lai L, Pei J. Sequence-based prediction of protein protein interaction using a deep-learning algorithm. BMC Bioinformatics. 2017;18: 277. 133.
- Hiranuma N, Park H, Baek M, Anishchenko I, Dauparas J, Baker D. Improved protein structure refinement guided by deep learning based accuracy estimation. Nat Commun. 2021;12: 1340. 134. Pagès G, Charmettant B, Grudinin S. Protein model quality assessment using 3D oriented convolutional neural networks. Bioinformatics. 2019;35: 3313-3319. 135. Pires DEV, Ascher DB, Blundell TL. DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach. Nucleic Acids Research. 2014;42: W314-W319. 136.
- Yuan Y, Bar-Joseph Z. Deep learning for inferring gene relationships from single-cell expression data. Proc Natl Acad Sci U S A. 2019;116: 27151-27158. 137
- Kantz ED, Tiwari S, Watrous JD, Cheng S, Jain M. Deep Neural Networks for Classification of LC-MS Spectral Peaks. Anal Chem. 2019;91: 12407-12413. 139
- Dührkop K, Fleischauer M, Ludwig M, Aksenov AA, Melnik AV, Meusel M, et al. SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information. Nat Methods. 2019;16: 299-302. 140. Liebal UW, Phan ANT, Sudhakar M, Raman K, Blank LM. Machine Learning Applications for Mass Spectrometry-Based Metabolomics. Metabolites. 2020;10: 243. 141. Zhong ED, Bepler T, Berger B, Davis JH. CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks. Nat Methods. 2021;18: 176-185. 142.
- Schmauch B, Romagnoni A, Pronier E, Saillard C, Maillé P, Calderaro J, et al. A deep learning model to predict RNA-Seq expression of tumours from whole slide images. Nat Commun. 2020;11: 3877. 143. Das P, Sercu T, Wadhawan K, Padhi I, Gehrmann S, Cipcigan F, et al. Accelerated antimicrobial discovery via deep generative models and molecular dynamics simulations. Nat Biomed Eng. 2021. 144.
- List M, Ebert P, Albrecht F. Ten Simple Rules for Developing Usable Software in Computational Biology. PLoS Comput Biol. 2017;13: e1005265. 149. Sonnenburg SÃ, Braun ML, Ong CS, Bengio S. The need for open source software in machine learning. Journal of Machine Learning Research. 2007;8: 2443-2466.
Cited by
Sorted by citations
Metabolomic machine learning predictor for diagnosis and prognosis of gastric cancer
Chen, Y., Wang, B., Zhao, Y., Shao, X., Wang, M., Ma, F., Yang, L., Nie, M., Jin, P., Yao, K., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-46043-y · Cited by 244 · see citing works
Machine-learning-assisted single-vessel analysis of nanoparticle permeability in tumour vasculatures
Zhu, M., Zhuang, J., Li, Z., Liu, Q., Zhao, R., Gao, Z., Midgley, A. C., Qi, T., Tian, J., Zhang, Z., et al. (2023) · Nature Nanotechnology · doi:10.1038/s41565-023-01323-4 · Cited by 140 · see citing works
Application of machine learning for advanced material prediction and design
Chan, C. H., Sun, M., & Huang, B. (2022) · EcoMat · doi:10.1002/eom2.12194 · Cited by 123 · see citing works
Machine learning-enabled optimization of extrusion-based 3D printing
Rahmani Dabbagh, S., Ozcan, O., & Tasoglu, S. (2022) · Methods · doi:10.1016/j.ymeth.2022.08.002 · Cited by 94 · see citing works
Quantum Computing for Molecular Biology**
Baiardi, A., Christandl, M., & Reiher, M. (2023) · ChemBioChem · doi:10.1002/cbic.202300120 · Cited by 93 · see citing works
Live-cell imaging powered by computation
Shroff, H., Testa, I., Jug, F., & Manley, S. (2024) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-024-00702-6 · Cited by 75 · see citing works
Giri, N., Roy, R. S., & Cheng, J. (2023) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102536 · Cited by 59 · see citing works
Scientific novelty beyond the experiment
Hallsworth, J. E., Udaondo, Z., Pedrós‐Alió, C., Höfer, J., Benison, K. C., Lloyd, K. G., Cordero, R. J. B., de Campos, C. B. L., Yakimov, M. M., & Amils, R. (2023) · Microbial Biotechnology · doi:10.1111/1751-7915.14222 · Cited by 62 · see citing works
A review on the recent applications of deep learning in predictive drug toxicological studies
Sinha, K., Ghosh, N., & Sil, P. C. (2023) · Chemical Research in Toxicology · doi:10.1021/acs.chemrestox.2c00375 · Cited by 64 · see citing works
Han, X., Liu, Q., Li, Y., Zhang, M., Liu, K., Kwok, L.-Y., Zhang, H., & Zhang, W. (2025) · Trends in Food Science & Technology · doi:10.1016/j.tifs.2025.104938 · Cited by 64 · see citing works
Design of synthetic promoters for cyanobacteria with generative deep-learning model
Seo, E., Choi, Y.-N., Shin, Y. R., Kim, D., & Lee, J. W. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad451 · Cited by 61 · see citing works
Muse, E. D., & Topol, E. J. (2024) · Cell Metabolism · doi:10.1016/j.cmet.2024.02.002 · Cited by 50 · see citing works
Quantum computing algorithms: getting closer to critical problems in computational biology
Marchetti, L., Nifosì, R., Martelli, P. L., Da Pozzo, E., Cappello, V., Banterle, F., Trincavelli, M. L., Martini, C., & D’Elia, M. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac437 · Cited by 47 · see citing works
“These tasks can be performed on most of the biological data sets, and indeed machine learning has been demonstrated to improve the performance of most of the above-mentioned computational tasks [57].”
BackgroundHe, Y., Chen, Z., Tang, Z., Qin, Y., & Wang, F. (2025) · BMC Public Health · doi:10.1186/s12889-025-23858-y · Cited by 5 · see citing works
Arnoux, J. (2026) · Thèse de doctorat, Université Paris-Saclay / PPanGGOLiN · doi:10.70675/eee354d9zf63dz48ebz9444zd1809f8fb74d
- Authors
- Greener, J. G., Kandathil, S. M., Moffat, L., & Jones, D. T.
- Affiliations
- University College London (GB)
- Corresponding author
- Jones, David T.
- Venue
- Nature Reviews Molecular Cell Biology
- Published
- 2021-09-13
- Volume
- 23
- Issue
- 1
- Pages
- 40-55
- ISSN
- 1471-0072 (ISSN-L)
- 1471-0080
- OpenAlex
- W3200707343
- Cited by
- 2,127
- References
- 25
- Citations by year
- 2026: 382 · 2025: 611 · 2024: 551 · 2023: 380 · 2022: 195 · 2021: 6
- FWCI
- 30.05
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nature Reviews Molecular Cell Biology (publishedVersion)
- PubMed (publishedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Physical Sciences › Computer Science › Artificial Intelligence › Neural Networks and Applications
- Keywords
- machine learning, biological data analysis, deep neural network, predictive modeling
- MeSH terms
- Machine Learning, Deep Learning, Animals, Biology, Humans, Neural Networks, Computer
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review