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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)
251
Zhang J, Liu B, Wu J, Wang Z, Li J. DeepCAC: a deep learning approach on DNA transcription factors classification based on multi-head self-attention and concatenate convolutional neural network. BMC Bioinformatics 2023;24:345. [PMID: 37723425 PMCID: PMC10506269 DOI: 10.1186/s12859-023-05469-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/06/2023] [Indexed: 09/20/2023]  Open
252
Chatterjee S, Bhattacharya M, Lee SS, Chakraborty C. Can artificial intelligence-strengthened ChatGPT or other large language models transform nucleic acid research? MOLECULAR THERAPY. NUCLEIC ACIDS 2023;33:205-207. [PMID: 37727444 PMCID: PMC10505907 DOI: 10.1016/j.omtn.2023.06.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
253
Gündüz HA, Binder M, To XY, Mreches R, Bischl B, McHardy AC, Münch PC, Rezaei M. A self-supervised deep learning method for data-efficient training in genomics. Commun Biol 2023;6:928. [PMID: 37696966 PMCID: PMC10495322 DOI: 10.1038/s42003-023-05310-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 09/01/2023] [Indexed: 09/13/2023]  Open
254
Tan W, Shen Y. Multimodal learning of noncoding variant effects using genome sequence and chromatin structure. Bioinformatics 2023;39:btad541. [PMID: 37669132 PMCID: PMC10502240 DOI: 10.1093/bioinformatics/btad541] [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: 12/22/2022] [Revised: 08/28/2023] [Accepted: 09/04/2023] [Indexed: 09/07/2023]  Open
255
Lentzen M, Linden T, Veeranki S, Madan S, Kramer D, Leodolter W, Frohlich H. A Transformer-Based Model Trained on Large Scale Claims Data for Prediction of Severe COVID-19 Disease Progression. IEEE J Biomed Health Inform 2023;27:4548-4558. [PMID: 37347632 DOI: 10.1109/jbhi.2023.3288768] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2023]
256
Li Z, Jin J, Long W, Wei L. PLPMpro: Enhancing promoter sequence prediction with prompt-learning based pre-trained language model. Comput Biol Med 2023;164:107260. [PMID: 37557052 DOI: 10.1016/j.compbiomed.2023.107260] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/27/2023] [Accepted: 07/16/2023] [Indexed: 08/11/2023]
257
Zhang Y, Ge F, Li F, Yang X, Song J, Yu DJ. Prediction of Multiple Types of RNA Modifications via Biological Language Model. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:3205-3214. [PMID: 37289599 DOI: 10.1109/tcbb.2023.3283985] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
258
Liang S, Zhao Y, Jin J, Qiao J, Wang D, Wang Y, Wei L. Rm-LR: A long-range-based deep learning model for predicting multiple types of RNA modifications. Comput Biol Med 2023;164:107238. [PMID: 37515874 DOI: 10.1016/j.compbiomed.2023.107238] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/16/2023] [Accepted: 07/07/2023] [Indexed: 07/31/2023]
259
Wichmann A, Buschong E, Müller A, Jünger D, Hildebrandt A, Hankeln T, Schmidt B. MetaTransformer: deep metagenomic sequencing read classification using self-attention models. NAR Genom Bioinform 2023;5:lqad082. [PMID: 37705831 PMCID: PMC10495543 DOI: 10.1093/nargab/lqad082] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 07/14/2023] [Accepted: 08/30/2023] [Indexed: 09/15/2023]  Open
260
Strutt JPB, Natarajan M, Lee E, Teo DBL, Sin WX, Cheung KW, Chew M, Thazin K, Barone PW, Wolfrum JM, Williams RBH, Rice SA, Springs SL. Machine learning-based detection of adventitious microbes in T-cell therapy cultures using long-read sequencing. Microbiol Spectr 2023;11:e0135023. [PMID: 37646508 PMCID: PMC10580871 DOI: 10.1128/spectrum.01350-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/03/2023] [Indexed: 09/01/2023]  Open
261
Tang X, Shang J, Ji Y, Sun Y. PLASMe: a tool to identify PLASMid contigs from short-read assemblies using transformer. Nucleic Acids Res 2023;51:e83. [PMID: 37427782 PMCID: PMC10450166 DOI: 10.1093/nar/gkad578] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 06/19/2023] [Accepted: 06/26/2023] [Indexed: 07/11/2023]  Open
262
Ju H, Bai J, Jiang J, Che Y, Chen X. Comparative evaluation and analysis of DNA N4-methylcytosine methylation sites using deep learning. Front Genet 2023;14:1254827. [PMID: 37671040 PMCID: PMC10476523 DOI: 10.3389/fgene.2023.1254827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 07/31/2023] [Indexed: 09/07/2023]  Open
263
Yelmen B, Jay F. An Overview of Deep Generative Models in Functional and Evolutionary Genomics. Annu Rev Biomed Data Sci 2023;6:173-189. [PMID: 37137168 DOI: 10.1146/annurev-biodatasci-020722-115651] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
264
Aspromonte MC, Conte AD, Zhu S, Tan W, Shen Y, Zhang Y, Li Q, Wang MH, Babbi G, Bovo S, Martelli PL, Casadio R, Althagafi A, Toonsi S, Kulmanov M, Hoehndorf R, Katsonis P, Williams A, Lichtarge O, Xian S, Surento W, Pejaver V, Mooney SD, Sunderam U, Srinivasan R, Murgia A, Piovesan D, Tosatto SCE, Leonardi E. CAGI6 ID-Challenge: Assessment of phenotype and variant predictions in 415 children with Neurodevelopmental Disorders (NDDs). RESEARCH SQUARE 2023:rs.3.rs-3209168. [PMID: 37577579 PMCID: PMC10418555 DOI: 10.21203/rs.3.rs-3209168/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
265
Myronov A, Mazzocco G, Król P, Plewczynski D. BERTrand-peptide:TCR binding prediction using Bidirectional Encoder Representations from Transformers augmented with random TCR pairing. Bioinformatics 2023;39:btad468. [PMID: 37535685 PMCID: PMC10444968 DOI: 10.1093/bioinformatics/btad468] [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: 01/04/2023] [Revised: 06/28/2023] [Accepted: 08/01/2023] [Indexed: 08/05/2023]  Open
266
Li L, Xue Z, Du X. ASCRB: Multi-view based attentional feature selection for CircRNA-binding site prediction. Comput Biol Med 2023;162:107077. [PMID: 37290390 DOI: 10.1016/j.compbiomed.2023.107077] [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: 02/23/2023] [Revised: 05/15/2023] [Accepted: 05/27/2023] [Indexed: 06/10/2023]
267
Chao KH, Mao A, Salzberg SL, Pertea M. Splam: a deep-learning-based splice site predictor that improves spliced alignments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.27.550754. [PMID: 37546880 PMCID: PMC10402160 DOI: 10.1101/2023.07.27.550754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
268
Zhu C, Baumgarten N, Wu M, Wang Y, Das AP, Kaur J, Ardakani FB, Duong TT, Pham MD, Duda M, Dimmeler S, Yuan T, Schulz MH, Krishnan J. CVD-associated SNPs with regulatory potential reveal novel non-coding disease genes. Hum Genomics 2023;17:69. [PMID: 37491351 PMCID: PMC10369730 DOI: 10.1186/s40246-023-00513-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 07/12/2023] [Indexed: 07/27/2023]  Open
269
Li H, He X, Kurowski L, Zhang R, Zhao D, Zeng J. Improving comparative analyses of Hi-C data via contrastive self-supervised learning. Brief Bioinform 2023;24:bbad193. [PMID: 37287135 DOI: 10.1093/bib/bbad193] [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: 02/06/2023] [Revised: 04/12/2023] [Accepted: 04/27/2023] [Indexed: 06/09/2023]  Open
270
Prakash A, Banerjee M. An interpretable block-attention network for identifying regulatory feature interactions. Brief Bioinform 2023;24:bbad250. [PMID: 37401370 DOI: 10.1093/bib/bbad250] [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: 12/28/2022] [Revised: 05/15/2023] [Accepted: 06/16/2023] [Indexed: 07/05/2023]  Open
271
Wu KE, Zou JY, Chang H. Machine learning modeling of RNA structures: methods, challenges and future perspectives. Brief Bioinform 2023;24:bbad210. [PMID: 37280185 DOI: 10.1093/bib/bbad210] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 05/12/2023] [Accepted: 05/17/2023] [Indexed: 06/08/2023]  Open
272
Liu R, Hu YF, Huang JD, Fan X. A Bayesian approach to estimate MHC-peptide binding threshold. Brief Bioinform 2023;24:bbad208. [PMID: 37279464 DOI: 10.1093/bib/bbad208] [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: 03/22/2023] [Revised: 05/08/2023] [Accepted: 05/16/2023] [Indexed: 06/08/2023]  Open
273
Zhang Z, Feng F, Qiu Y, Liu J. A generalizable framework to comprehensively predict epigenome, chromatin organization, and transcriptome. Nucleic Acids Res 2023;51:5931-5947. [PMID: 37224527 PMCID: PMC10325920 DOI: 10.1093/nar/gkad436] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 03/31/2023] [Accepted: 05/09/2023] [Indexed: 05/26/2023]  Open
274
Umerenkov D, Herbert A, Konovalov D, Danilova A, Beknazarov N, Kokh V, Fedorov A, Poptsova M. Z-flipon variants reveal the many roles of Z-DNA and Z-RNA in health and disease. Life Sci Alliance 2023;6:e202301962. [PMID: 37164635 PMCID: PMC10172764 DOI: 10.26508/lsa.202301962] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 05/12/2023]  Open
275
Biharie K, Michielsen L, Reinders MJT, Mahfouz A. Cell type matching across species using protein embeddings and transfer learning. Bioinformatics 2023;39:i404-i412. [PMID: 37387141 PMCID: PMC10311290 DOI: 10.1093/bioinformatics/btad248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]  Open
276
Valeri JA, Soenksen LR, Collins KM, Ramesh P, Cai G, Powers R, Angenent-Mari NM, Camacho DM, Wong F, Lu TK, Collins JJ. BioAutoMATED: An end-to-end automated machine learning tool for explanation and design of biological sequences. Cell Syst 2023;14:525-542.e9. [PMID: 37348466 PMCID: PMC10700034 DOI: 10.1016/j.cels.2023.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 02/17/2023] [Accepted: 05/22/2023] [Indexed: 06/24/2023]
277
Luo H, Li Y, Liu H, Ding P, Yu Y, Luo L. SENet: A deep learning framework for discriminating super- and typical enhancers by sequence information. Comput Biol Chem 2023;105:107905. [PMID: 37348298 DOI: 10.1016/j.compbiolchem.2023.107905] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 05/08/2023] [Accepted: 06/09/2023] [Indexed: 06/24/2023]
278
Zhu H, Liu T, Wang Z. scHiMe: predicting single-cell DNA methylation levels based on single-cell Hi-C data. Brief Bioinform 2023:7193585. [PMID: 37302805 PMCID: PMC10359091 DOI: 10.1093/bib/bbad223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 05/10/2023] [Accepted: 05/23/2023] [Indexed: 06/13/2023]  Open
279
Yang R, Das A, Gao VR, Karbalayghareh A, Noble WS, Bilmes JA, Leslie CS. Epiphany: predicting Hi-C contact maps from 1D epigenomic signals. Genome Biol 2023;24:134. [PMID: 37280678 PMCID: PMC10242996 DOI: 10.1186/s13059-023-02934-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 04/06/2023] [Indexed: 06/08/2023]  Open
280
Zhou M, Zhang H, Baii Z, Mann-Krzisnik D, Wang F, Li Y. Single-cell multi-omic topic embedding reveals cell-type-specific and COVID-19 severity-related immune signatures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.31.526312. [PMID: 36778483 PMCID: PMC9915637 DOI: 10.1101/2023.01.31.526312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
281
Cao C, Yang S, Li M, Li C. CircSSNN: circRNA-binding site prediction via sequence self-attention neural networks with pre-normalization. BMC Bioinformatics 2023;24:220. [PMID: 37254080 DOI: 10.1186/s12859-023-05352-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 05/25/2023] [Indexed: 06/01/2023]  Open
282
Shen L, Feng H, Qiu Y, Wei GW. SVSBI: sequence-based virtual screening of biomolecular interactions. Commun Biol 2023;6:536. [PMID: 37202415 PMCID: PMC10195826 DOI: 10.1038/s42003-023-04866-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 04/24/2023] [Indexed: 05/20/2023]  Open
283
Smith GD, Ching WH, Cornejo-Páramo P, Wong ES. Decoding enhancer complexity with machine learning and high-throughput discovery. Genome Biol 2023;24:116. [PMID: 37173718 PMCID: PMC10176946 DOI: 10.1186/s13059-023-02955-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 04/28/2023] [Indexed: 05/15/2023]  Open
284
Mourad R. Semi-supervised learning improves regulatory sequence prediction with unlabeled sequences. BMC Bioinformatics 2023;24:186. [PMID: 37147561 PMCID: PMC10163727 DOI: 10.1186/s12859-023-05303-2] [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: 12/08/2022] [Accepted: 04/25/2023] [Indexed: 05/07/2023]  Open
285
Grešová K, Martinek V, Čechák D, Šimeček P, Alexiou P. Genomic benchmarks: a collection of datasets for genomic sequence classification. BMC Genom Data 2023;24:25. [PMID: 37127596 PMCID: PMC10150520 DOI: 10.1186/s12863-023-01123-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 03/31/2023] [Indexed: 05/03/2023]  Open
286
Rios-Martinez C, Bhattacharya N, Amini AP, Crawford L, Yang KK. Deep self-supervised learning for biosynthetic gene cluster detection and product classification. PLoS Comput Biol 2023;19:e1011162. [PMID: 37220151 PMCID: PMC10241353 DOI: 10.1371/journal.pcbi.1011162] [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: 07/24/2022] [Revised: 06/05/2023] [Accepted: 05/07/2023] [Indexed: 05/25/2023]  Open
287
Soylu NN, Sefer E. BERT2OME: Prediction of 2'-O-Methylation Modifications From RNA Sequence by Transformer Architecture Based on BERT. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:2177-2189. [PMID: 37819796 DOI: 10.1109/tcbb.2023.3237769] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
288
Nikolados EM, Oyarzún DA. Deep learning for optimization of protein expression. Curr Opin Biotechnol 2023;81:102941. [PMID: 37087839 DOI: 10.1016/j.copbio.2023.102941] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/02/2023] [Accepted: 03/17/2023] [Indexed: 04/25/2023]
289
Kravchuk EV, Ashniev GA, Gladkova MG, Orlov AV, Vasileva AV, Boldyreva AV, Burenin AG, Skirda AM, Nikitin PI, Orlova NN. Experimental Validation and Prediction of Super-Enhancers: Advances and Challenges. Cells 2023;12:cells12081191. [PMID: 37190100 DOI: 10.3390/cells12081191] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/07/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023]  Open
290
Barbero-Aparicio JA, Olivares-Gil A, Díez-Pastor JF, García-Osorio C. Deep learning and support vector machines for transcription start site identification. PeerJ Comput Sci 2023;9:e1340. [PMID: 37346545 PMCID: PMC10280436 DOI: 10.7717/peerj-cs.1340] [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: 10/26/2022] [Accepted: 03/21/2023] [Indexed: 06/23/2023]
291
Joiret M, Leclercq M, Lambrechts G, Rapino F, Close P, Louppe G, Geris L. Cracking the genetic code with neural networks. Front Artif Intell 2023;6:1128153. [PMID: 37091301 PMCID: PMC10117997 DOI: 10.3389/frai.2023.1128153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/21/2023] [Indexed: 04/09/2023]  Open
292
Rozowsky J, Gao J, Borsari B, Yang YT, Galeev T, Gürsoy G, Epstein CB, Xiong K, Xu J, Li T, Liu J, Yu K, Berthel A, Chen Z, Navarro F, Sun MS, Wright J, Chang J, Cameron CJF, Shoresh N, Gaskell E, Drenkow J, Adrian J, Aganezov S, Aguet F, Balderrama-Gutierrez G, Banskota S, Corona GB, Chee S, Chhetri SB, Cortez Martins GC, Danyko C, Davis CA, Farid D, Farrell NP, Gabdank I, Gofin Y, Gorkin DU, Gu M, Hecht V, Hitz BC, Issner R, Jiang Y, Kirsche M, Kong X, Lam BR, Li S, Li B, Li X, Lin KZ, Luo R, Mackiewicz M, Meng R, Moore JE, Mudge J, Nelson N, Nusbaum C, Popov I, Pratt HE, Qiu Y, Ramakrishnan S, Raymond J, Salichos L, Scavelli A, Schreiber JM, Sedlazeck FJ, See LH, Sherman RM, Shi X, Shi M, Sloan CA, Strattan JS, Tan Z, Tanaka FY, Vlasova A, Wang J, Werner J, Williams B, Xu M, Yan C, Yu L, Zaleski C, Zhang J, Ardlie K, Cherry JM, Mendenhall EM, Noble WS, Weng Z, Levine ME, Dobin A, Wold B, Mortazavi A, Ren B, Gillis J, Myers RM, Snyder MP, Choudhary J, Milosavljevic A, Schatz MC, Bernstein BE, et alRozowsky J, Gao J, Borsari B, Yang YT, Galeev T, Gürsoy G, Epstein CB, Xiong K, Xu J, Li T, Liu J, Yu K, Berthel A, Chen Z, Navarro F, Sun MS, Wright J, Chang J, Cameron CJF, Shoresh N, Gaskell E, Drenkow J, Adrian J, Aganezov S, Aguet F, Balderrama-Gutierrez G, Banskota S, Corona GB, Chee S, Chhetri SB, Cortez Martins GC, Danyko C, Davis CA, Farid D, Farrell NP, Gabdank I, Gofin Y, Gorkin DU, Gu M, Hecht V, Hitz BC, Issner R, Jiang Y, Kirsche M, Kong X, Lam BR, Li S, Li B, Li X, Lin KZ, Luo R, Mackiewicz M, Meng R, Moore JE, Mudge J, Nelson N, Nusbaum C, Popov I, Pratt HE, Qiu Y, Ramakrishnan S, Raymond J, Salichos L, Scavelli A, Schreiber JM, Sedlazeck FJ, See LH, Sherman RM, Shi X, Shi M, Sloan CA, Strattan JS, Tan Z, Tanaka FY, Vlasova A, Wang J, Werner J, Williams B, Xu M, Yan C, Yu L, Zaleski C, Zhang J, Ardlie K, Cherry JM, Mendenhall EM, Noble WS, Weng Z, Levine ME, Dobin A, Wold B, Mortazavi A, Ren B, Gillis J, Myers RM, Snyder MP, Choudhary J, Milosavljevic A, Schatz MC, Bernstein BE, Guigó R, Gingeras TR, Gerstein M. The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. Cell 2023;186:1493-1511.e40. [PMID: 37001506 PMCID: PMC10074325 DOI: 10.1016/j.cell.2023.02.018] [Show More Authors] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 10/16/2022] [Accepted: 02/10/2023] [Indexed: 04/03/2023]
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Wang L, Sun J, Ma S, Xia J, Li X. PredDSMC: A predictor for driver synonymous mutations in human cancers. Front Genet 2023;14:1164593. [PMID: 37051593 PMCID: PMC10083435 DOI: 10.3389/fgene.2023.1164593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 03/09/2023] [Indexed: 03/29/2023]  Open
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Huang Z, Wang J, Lu X, Mohd Zain A, Yu G. scGGAN: single-cell RNA-seq imputation by graph-based generative adversarial network. Brief Bioinform 2023;24:7024714. [PMID: 36733262 DOI: 10.1093/bib/bbad040] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/21/2022] [Accepted: 01/18/2023] [Indexed: 02/04/2023]  Open
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M6A-BERT-Stacking: A Tissue-Specific Predictor for Identifying RNA N6-Methyladenosine Sites Based on BERT and Stacking Strategy. Symmetry (Basel) 2023. [DOI: 10.3390/sym15030731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]  Open
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Luo H, Shan W, Chen C, Ding P, Luo L. Improving language model of human genome for DNA-protein binding prediction based on task-specific pre-training. Interdiscip Sci 2023;15:32-43. [PMID: 36136096 DOI: 10.1007/s12539-022-00537-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 08/30/2022] [Accepted: 09/07/2022] [Indexed: 11/27/2022]
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Wang X, Zhang M, Long C, Yao L, Zhu M. Self-Attention Based Neural Network for Predicting RNA-Protein Binding Sites. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:1469-1479. [PMID: 36067103 DOI: 10.1109/tcbb.2022.3204661] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
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Hwang H, Chang HR, Baek D. Determinants of Functional MicroRNA Targeting. Mol Cells 2023;46:21-32. [PMID: 36697234 PMCID: PMC9880601 DOI: 10.14348/molcells.2023.2157] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/09/2022] [Accepted: 11/15/2022] [Indexed: 01/27/2023]  Open
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Jonnakuti VS, Wagner EJ, Maletić-Savatić M, Liu Z, Yalamanchili HK. PolyAMiner-Bulk: A Machine Learning Based Bioinformatics Algorithm to Infer and Decode Alternative Polyadenylation Dynamics from bulk RNA-seq data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.23.523471. [PMID: 36747700 PMCID: PMC9900750 DOI: 10.1101/2023.01.23.523471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Li Z, Gao E, Zhou J, Han W, Xu X, Gao X. Applications of deep learning in understanding gene regulation. CELL REPORTS METHODS 2023;3:100384. [PMID: 36814848 PMCID: PMC9939384 DOI: 10.1016/j.crmeth.2022.100384] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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