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For: Ji Y, Zhou Z, Liu H, Davuluri RV. DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome. Bioinformatics 2021;37:2112-2120. [PMID: 33538820 PMCID: PMC11025658 DOI: 10.1093/bioinformatics/btab083] [Citation(s) in RCA: 340] [Impact Index Per Article: 85.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/31/2020] [Accepted: 02/01/2021] [Indexed: 12/19/2022]  Open
Number Cited by Other Article(s)
101
He Y, Zhou F, Bai J, Gao Y, Huang X, Wang Y. ViTax: adaptive hierarchical viral taxonomy classification with a taxonomy belief tree on a foundation model. Brief Bioinform 2024;26:bbaf041. [PMID: 39921398 PMCID: PMC11805961 DOI: 10.1093/bib/bbaf041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2024] [Revised: 12/18/2024] [Accepted: 01/20/2025] [Indexed: 02/10/2025]  Open
102
Lu Q, Xu J, Zhang R, Liu H, Wang M, Liu X, Yue Z, Gao Y. RiceSNP-ABST: a deep learning approach to identify abiotic stress-associated single nucleotide polymorphisms in rice. Brief Bioinform 2024;26:bbae702. [PMID: 39757606 PMCID: PMC11962596 DOI: 10.1093/bib/bbae702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2024] [Revised: 11/16/2024] [Accepted: 12/23/2024] [Indexed: 01/07/2025]  Open
103
Wang Y, Kong S, Zhou C, Wang Y, Zhang Y, Fang Y, Li G. A review of deep learning models for the prediction of chromatin interactions with DNA and epigenomic profiles. Brief Bioinform 2024;26:bbae651. [PMID: 39708837 DOI: 10.1093/bib/bbae651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2024] [Revised: 10/29/2024] [Accepted: 12/03/2024] [Indexed: 12/23/2024]  Open
104
Ding Z, Wei R, Xia J, Mu Y, Wang J, Lin Y. Exploring the potential of large language model-based chatbots in challenges of ribosome profiling data analysis: a review. Brief Bioinform 2024;26:bbae641. [PMID: 39668339 PMCID: PMC11638007 DOI: 10.1093/bib/bbae641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 11/02/2024] [Accepted: 11/27/2024] [Indexed: 12/14/2024]  Open
105
Cho HN, Jun TJ, Kim YH, Kang H, Ahn I, Gwon H, Kim Y, Seo J, Choi H, Kim M, Han J, Kee G, Park S, Ko S. Task-Specific Transformer-Based Language Models in Health Care: Scoping Review. JMIR Med Inform 2024;12:e49724. [PMID: 39556827 PMCID: PMC11612605 DOI: 10.2196/49724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/10/2023] [Accepted: 10/21/2024] [Indexed: 11/20/2024]  Open
106
Nguyen E, Poli M, Durrant MG, Kang B, Katrekar D, Li DB, Bartie LJ, Thomas AW, King SH, Brixi G, Sullivan J, Ng MY, Lewis A, Lou A, Ermon S, Baccus SA, Hernandez-Boussard T, Ré C, Hsu PD, Hie BL. Sequence modeling and design from molecular to genome scale with Evo. Science 2024;386:eado9336. [PMID: 39541441 PMCID: PMC12057570 DOI: 10.1126/science.ado9336] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 09/09/2024] [Indexed: 11/16/2024]
107
Theodoris CV. Learning the language of DNA. Science 2024;386:729-730. [PMID: 39541478 DOI: 10.1126/science.adt3007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2024]
108
Cao C, Wang C, Dai Q, Zou Q, Wang T. CRBPSA: CircRNA-RBP interaction sites identification using sequence structural attention model. BMC Biol 2024;22:260. [PMID: 39543602 PMCID: PMC11566611 DOI: 10.1186/s12915-024-02055-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2024] [Accepted: 10/30/2024] [Indexed: 11/17/2024]  Open
109
Kumar A, Dixit S, Srinivasan K, M D, Vincent PMDR. Personalized cancer vaccine design using AI-powered technologies. Front Immunol 2024;15:1357217. [PMID: 39582860 PMCID: PMC11581883 DOI: 10.3389/fimmu.2024.1357217] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 09/24/2024] [Indexed: 11/26/2024]  Open
110
Liu J, Shen H, Yang Y, Yang M, Zhang Q, Chen K, Li X. Transformer-based representation learning and multiple-instance learning for cancer diagnosis exclusively from raw sequencing fragments of bisulfite-treated plasma cell-free DNA. Mol Oncol 2024;18:2755-2769. [PMID: 39380154 PMCID: PMC11547222 DOI: 10.1002/1878-0261.13745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 07/31/2024] [Accepted: 09/24/2024] [Indexed: 10/10/2024]  Open
111
Romeijn L, Bernatavicius A, Vu D. MycoAI: Fast and accurate taxonomic classification for fungal ITS sequences. Mol Ecol Resour 2024;24:e14006. [PMID: 39152642 DOI: 10.1111/1755-0998.14006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 07/12/2024] [Accepted: 08/06/2024] [Indexed: 08/19/2024]
112
Song T, Song H, Pan Z, Gao Y, Dai H, Wang X. DeepDualEnhancer: A Dual-Feature Input DNABert Based Deep Learning Method for Enhancer Recognition. Int J Mol Sci 2024;25:11744. [PMID: 39519295 PMCID: PMC11546905 DOI: 10.3390/ijms252111744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2024] [Revised: 10/23/2024] [Accepted: 10/28/2024] [Indexed: 11/16/2024]  Open
113
Xu R, Li D, Yang W, Wang G, Li Y. Improving ncRNA family prediction using multi-modal contrastive learning of sequence and structure. Bioinformatics 2024;40:btae640. [PMID: 39460948 PMCID: PMC11639665 DOI: 10.1093/bioinformatics/btae640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 10/15/2024] [Accepted: 10/22/2024] [Indexed: 10/28/2024]  Open
114
Li C, Wang H, Wen Y, Yin R, Zeng X, Li K. GenoM7GNet: An Efficient N7-Methylguanosine Site Prediction Approach Based on a Nucleotide Language Model. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024;21:2258-2268. [PMID: 39302806 DOI: 10.1109/tcbb.2024.3459870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
115
Yu Z, Zhang Y. Foundation model for comprehensive transcriptional regulation analysis. Natl Sci Rev 2024;11:nwae355. [PMID: 39555104 PMCID: PMC11565239 DOI: 10.1093/nsr/nwae355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 09/22/2024] [Accepted: 10/11/2024] [Indexed: 11/19/2024]  Open
116
Yu X, Yani C, Wang Z, Long H, Zeng R, Liu X, Anas B, Ren J. iDNA-ITLM: An interpretable and transferable learning model for identifying DNA methylation. PLoS One 2024;19:e0301791. [PMID: 39480834 PMCID: PMC11527195 DOI: 10.1371/journal.pone.0301791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 03/20/2024] [Indexed: 11/02/2024]  Open
117
Jyoti, Ritu, Gupta S, Shankar R. Comprehensive analysis of computational approaches in plant transcription factors binding regions discovery. Heliyon 2024;10:e39140. [PMID: 39640721 PMCID: PMC11620080 DOI: 10.1016/j.heliyon.2024.e39140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 08/23/2024] [Accepted: 10/08/2024] [Indexed: 12/07/2024]  Open
118
Shao B, Yan J. A long-context language model for deciphering and generating bacteriophage genomes. Nat Commun 2024;15:9392. [PMID: 39477977 PMCID: PMC11525655 DOI: 10.1038/s41467-024-53759-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 10/22/2024] [Indexed: 11/02/2024]  Open
119
Nahali S, Safari L, Khanteymoori A, Huang J. StructmRNA a BERT based model with dual level and conditional masking for mRNA representation. Sci Rep 2024;14:26043. [PMID: 39472486 PMCID: PMC11522565 DOI: 10.1038/s41598-024-77172-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Accepted: 10/21/2024] [Indexed: 11/02/2024]  Open
120
Kabir A, Bhattarai M, Peterson S, Najman-Licht Y, Rasmussen K, Shehu A, Bishop A, Alexandrov B, Usheva A. DNA breathing integration with deep learning foundational model advances genome-wide binding prediction of human transcription factors. Nucleic Acids Res 2024;52:e91. [PMID: 39271116 PMCID: PMC11514457 DOI: 10.1093/nar/gkae783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 08/21/2024] [Accepted: 08/29/2024] [Indexed: 09/15/2024]  Open
121
Zhao H, Song G. Antiviral Peptide-Generative Pre-Trained Transformer (AVP-GPT): A Deep Learning-Powered Model for Antiviral Peptide Design with High-Throughput Discovery and Exceptional Potency. Viruses 2024;16:1673. [PMID: 39599788 PMCID: PMC11599114 DOI: 10.3390/v16111673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Revised: 10/20/2024] [Accepted: 10/23/2024] [Indexed: 11/29/2024]  Open
122
La Fleur A, Shi Y, Seelig G. Decoding biology with massively parallel reporter assays and machine learning. Genes Dev 2024;38:843-865. [PMID: 39362779 PMCID: PMC11535156 DOI: 10.1101/gad.351800.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2024]
123
Chiliński M, Plewczynski D. HiCDiffusion - diffusion-enhanced, transformer-based prediction of chromatin interactions from DNA sequences. BMC Genomics 2024;25:964. [PMID: 39407104 PMCID: PMC11481779 DOI: 10.1186/s12864-024-10885-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2024] [Accepted: 10/09/2024] [Indexed: 10/19/2024]  Open
124
Bunne C, Roohani Y, Rosen Y, Gupta A, Zhang X, Roed M, Alexandrov T, AlQuraishi M, Brennan P, Burkhardt DB, Califano A, Cool J, Dernburg AF, Ewing K, Fox EB, Haury M, Herr AE, Horvitz E, Hsu PD, Jain V, Johnson GR, Kalil T, Kelley DR, Kelley SO, Kreshuk A, Mitchison T, Otte S, Shendure J, Sofroniew NJ, Theis F, Theodoris CV, Upadhyayula S, Valer M, Wang B, Xing E, Yeung-Levy S, Zitnik M, Karaletsos T, Regev A, Lundberg E, Leskovec J, Quake SR. How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities. ARXIV 2024:arXiv:2409.11654v2. [PMID: 39398201 PMCID: PMC11468656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 10/15/2024]
125
Naghipourfar M, Chen S, Howard MK, Macdonald CB, Saberi A, Hagen T, Mofrad MRK, Coyote-Maestas W, Goodarzi H. A Suite of Foundation Models Captures the Contextual Interplay Between Codons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.10.617568. [PMID: 39416097 PMCID: PMC11482952 DOI: 10.1101/2024.10.10.617568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
126
Lal A, Garfield D, Biancalani T, Eraslan G. Designing realistic regulatory DNA with autoregressive language models. Genome Res 2024;34:1411-1420. [PMID: 39322281 PMCID: PMC11529870 DOI: 10.1101/gr.279142.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 08/19/2024] [Indexed: 09/27/2024]
127
Zhang G, Xie H, Dai X. DeepIndel: An Interpretable Deep Learning Approach for Predicting CRISPR/Cas9-Mediated Editing Outcomes. Int J Mol Sci 2024;25:10928. [PMID: 39456711 PMCID: PMC11507043 DOI: 10.3390/ijms252010928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2024] [Revised: 10/01/2024] [Accepted: 10/08/2024] [Indexed: 10/28/2024]  Open
128
Rafi AM, Nogina D, Penzar D, Lee D, Lee D, Kim N, Kim S, Kim D, Shin Y, Kwak IY, Meshcheryakov G, Lando A, Zinkevich A, Kim BC, Lee J, Kang T, Vaishnav ED, Yadollahpour P, Kim S, Albrecht J, Regev A, Gong W, Kulakovskiy IV, Meyer P, de Boer CG. A community effort to optimize sequence-based deep learning models of gene regulation. Nat Biotechnol 2024:10.1038/s41587-024-02414-w. [PMID: 39394483 DOI: 10.1038/s41587-024-02414-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 08/29/2024] [Indexed: 10/13/2024]
129
Wang J. Deep Learning in Hematology: From Molecules to Patients. Clin Hematol Int 2024;6:19-42. [PMID: 39417017 PMCID: PMC11477942 DOI: 10.46989/001c.124131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 06/29/2024] [Indexed: 10/19/2024]  Open
130
Crombie TA, Rajaei M, Saxena AS, Johnson LM, Saber S, Tanny RE, Ponciano JM, Andersen EC, Zhou J, Baer CF. Direct inference of the distribution of fitness effects of spontaneous mutations from recombinant inbred Caenorhabditis elegans mutation accumulation lines. Genetics 2024;228:iyae136. [PMID: 39139098 PMCID: PMC12098947 DOI: 10.1093/genetics/iyae136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 07/30/2024] [Accepted: 08/02/2024] [Indexed: 08/15/2024]  Open
131
Yang Y, Li G, Pang K, Cao W, Zhang Z, Li X. Deciphering 3'UTR Mediated Gene Regulation Using Interpretable Deep Representation Learning. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024;11:e2407013. [PMID: 39159140 PMCID: PMC11497048 DOI: 10.1002/advs.202407013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/23/2024] [Indexed: 08/21/2024]
132
Lam HYI, Ong XE, Mutwil M. Large language models in plant biology. TRENDS IN PLANT SCIENCE 2024;29:1145-1155. [PMID: 38797656 DOI: 10.1016/j.tplants.2024.04.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 05/29/2024]
133
Zhang Y, Mao M, Zhang R, Liao YT, Wu VCH. DeepPL: A deep-learning-based tool for the prediction of bacteriophage lifecycle. PLoS Comput Biol 2024;20:e1012525. [PMID: 39418300 PMCID: PMC11521287 DOI: 10.1371/journal.pcbi.1012525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 10/29/2024] [Accepted: 09/30/2024] [Indexed: 10/19/2024]  Open
134
Hou A, Luo H, Liu H, Luo L, Ding P. Multi-scale DNA language model improves 6 mA binding sites prediction. Comput Biol Chem 2024;112:108129. [PMID: 39067351 DOI: 10.1016/j.compbiolchem.2024.108129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 06/05/2024] [Accepted: 06/10/2024] [Indexed: 07/30/2024]
135
Kumar Halder A, Agarwal A, Jodkowska K, Plewczynski D. A systematic analyses of different bioinformatics pipelines for genomic data and its impact on deep learning models for chromatin loop prediction. Brief Funct Genomics 2024;23:538-548. [PMID: 38555493 DOI: 10.1093/bfgp/elae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/07/2024] [Accepted: 03/04/2024] [Indexed: 04/02/2024]  Open
136
İhtiyar MN, Özgür A. Generative language models on nucleotide sequences of human genes. Sci Rep 2024;14:22204. [PMID: 39333252 PMCID: PMC11437190 DOI: 10.1038/s41598-024-72512-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 09/09/2024] [Indexed: 09/29/2024]  Open
137
AlSaad R, Abd-Alrazaq A, Boughorbel S, Ahmed A, Renault MA, Damseh R, Sheikh J. Multimodal Large Language Models in Health Care: Applications, Challenges, and Future Outlook. J Med Internet Res 2024;26:e59505. [PMID: 39321458 PMCID: PMC11464944 DOI: 10.2196/59505] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 08/07/2024] [Accepted: 08/20/2024] [Indexed: 09/27/2024]  Open
138
Yang K, Islas N, Jewell S, Jha A, Radens CM, Pleiss JA, Lynch KW, Barash Y, Choi PS. Machine learning-optimized targeted detection of alternative splicing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.20.614162. [PMID: 39386495 PMCID: PMC11463589 DOI: 10.1101/2024.09.20.614162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
139
Fu L, Shi J, Huang B. Binning Metagenomic Contigs Using Contig Embedding and Decomposed Tetranucleotide Frequency. BIOLOGY 2024;13:755. [PMID: 39452065 PMCID: PMC11505167 DOI: 10.3390/biology13100755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Revised: 09/15/2024] [Accepted: 09/23/2024] [Indexed: 10/26/2024]
140
Todhunter ME, Jubair S, Verma R, Saqe R, Shen K, Duffy B. Artificial intelligence and machine learning applications for cultured meat. Front Artif Intell 2024;7:1424012. [PMID: 39381621 PMCID: PMC11460582 DOI: 10.3389/frai.2024.1424012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 08/21/2024] [Indexed: 10/10/2024]  Open
141
Phan H, Brouard C, Mourad R. Semi-supervised learning with pseudo-labeling compares favorably with large language models for regulatory sequence prediction. Brief Bioinform 2024;25:bbae560. [PMID: 39489607 PMCID: PMC11531863 DOI: 10.1093/bib/bbae560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 09/13/2024] [Accepted: 10/17/2024] [Indexed: 11/05/2024]  Open
142
Li Q, Hu Z, Wang Y, Li L, Fan Y, King I, Jia G, Wang S, Song L, Li Y. Progress and opportunities of foundation models in bioinformatics. Brief Bioinform 2024;25:bbae548. [PMID: 39461902 PMCID: PMC11512649 DOI: 10.1093/bib/bbae548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 08/20/2024] [Accepted: 10/12/2024] [Indexed: 10/29/2024]  Open
143
Xu J, Gao Y, Lu Q, Zhang R, Gui J, Liu X, Yue Z. RiceSNP-BST: a deep learning framework for predicting biotic stress-associated SNPs in rice. Brief Bioinform 2024;25:bbae599. [PMID: 39562160 PMCID: PMC11576077 DOI: 10.1093/bib/bbae599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2024] [Revised: 10/07/2024] [Accepted: 11/04/2024] [Indexed: 11/21/2024]  Open
144
Benegas G, Ye C, Albors C, Li JC, Song YS. Genomic Language Models: Opportunities and Challenges. ARXIV 2024:arXiv:2407.11435v2. [PMID: 39070037 PMCID: PMC11275703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
145
Chao KH, Mao A, Salzberg SL, Pertea M. Splam: a deep-learning-based splice site predictor that improves spliced alignments. Genome Biol 2024;25:243. [PMID: 39285451 PMCID: PMC11406845 DOI: 10.1186/s13059-024-03379-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 08/28/2024] [Indexed: 09/19/2024]  Open
146
Sanabria M, Hirsch J, Poetsch AR. Distinguishing word identity and sequence context in DNA language models. BMC Bioinformatics 2024;25:301. [PMID: 39272021 PMCID: PMC11395559 DOI: 10.1186/s12859-024-05869-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 07/12/2024] [Indexed: 09/15/2024]  Open
147
Bhattacharya M, Pal S, Chatterjee S, Lee SS, Chakraborty C. Large language model to multimodal large language model: A journey to shape the biological macromolecules to biological sciences and medicine. MOLECULAR THERAPY. NUCLEIC ACIDS 2024;35:102255. [PMID: 39377065 PMCID: PMC11456558 DOI: 10.1016/j.omtn.2024.102255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/09/2024]
148
Sereshki S, Lonardi S. Predicting Differentially Methylated Cytosines in TET and DNMT3 Knockout Mutants via a Large Language Model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.02.592257. [PMID: 39282350 PMCID: PMC11398415 DOI: 10.1101/2024.05.02.592257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
149
Yu CQ, Wang XF, Li LP, You ZH, Ren ZH, Chu P, Guo F, Wang ZY. RBNE-CMI: An Efficient Method for Predicting circRNA-miRNA Interactions via Multiattribute Incomplete Heterogeneous Network Embedding. J Chem Inf Model 2024. [PMID: 39231016 DOI: 10.1021/acs.jcim.4c01118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
150
Boshar S, Trop E, de Almeida BP, Copoiu L, Pierrot T. Are genomic language models all you need? Exploring genomic language models on protein downstream tasks. BIOINFORMATICS (OXFORD, ENGLAND) 2024;40:btae529. [PMID: 39212609 PMCID: PMC11399231 DOI: 10.1093/bioinformatics/btae529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 08/20/2024] [Accepted: 08/28/2024] [Indexed: 09/04/2024]
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