{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,8]],"date-time":"2025-12-08T22:43:50Z","timestamp":1765233830333,"version":"3.41.0"},"publisher-location":"New York, NY, USA","reference-count":35,"publisher":"ACM","license":[{"start":{"date-parts":[[2024,1,26]],"date-time":"2024-01-26T00:00:00Z","timestamp":1706227200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.acm.org\/publications\/policies\/copyright_policy#Background"}],"content-domain":{"domain":["dl.acm.org"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2024,1,26]]},"DOI":"10.1145\/3665689.3665761","type":"proceedings-article","created":{"date-parts":[[2024,6,28]],"date-time":"2024-06-28T17:02:34Z","timestamp":1719594154000},"page":"430-436","update-policy":"https:\/\/doi.org\/10.1145\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["DeepSipred: A deep-learning-based approach on siRNA inhibition prediction"],"prefix":"10.1145","author":[{"ORCID":"https:\/\/orcid.org\/0009-0005-0197-6675","authenticated-orcid":false,"given":"Bin","family":"Liu","sequence":"first","affiliation":[{"name":"Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-7204-1467","authenticated-orcid":false,"given":"Huiya","family":"Huang","sequence":"additional","affiliation":[{"name":"Syngentech Inc., Zhongguancun Life Science Park, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-4527-5968","authenticated-orcid":false,"given":"Weixi","family":"Liao","sequence":"additional","affiliation":[{"name":"Syngentech Inc., Zhongguancun Life Science Park, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5010-464X","authenticated-orcid":false,"given":"Xiaoyong","family":"Pan","sequence":"additional","affiliation":[{"name":"Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-7579-0035","authenticated-orcid":false,"given":"Cheng","family":"Jin","sequence":"additional","affiliation":[{"name":"Medical Robot Research Institute, School of Biomedical Engineering, Shanghai Jiao Tong University, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4270-8002","authenticated-orcid":false,"given":"Ye","family":"Yuan","sequence":"additional","affiliation":[{"name":"Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"320","published-online":{"date-parts":[[2024,6,28]]},"reference":[{"key":"e_1_3_2_1_1_1","volume-title":"RNA interference. Nature","author":"Hannon G.J.","year":"2002","unstructured":"Hannon, G.J., RNA interference. Nature, 2002. 418(6894): p. 244-251."},{"key":"e_1_3_2_1_2_1","first-page":"127","volume":"200","author":"Sontheimer E.J.","unstructured":"Sontheimer, E.J., Assembly and function of RNA silencing complexes. Nature Reviews Molecular Cell Biology, 2005. 6(2): p. 127-138.","journal-title":"Nature Reviews Molecular Cell Biology"},{"key":"e_1_3_2_1_3_1","first-page":"494","volume-title":"Nature","author":"Elbashir S.M.","year":"2001","unstructured":"Elbashir, S.M., , Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature, 2001. 411(6836): p. 494-498."},{"key":"e_1_3_2_1_4_1","first-page":"15","volume":"200","author":"Lewis B.P.","unstructured":"Lewis, B.P., C.B. Burge, and D.P. Bartel, Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell, 2005. 120(1): p. 15-20.","journal-title":"Cell"},{"key":"e_1_3_2_1_5_1","first-page":"6407","volume":"202","author":"Humphreys S.C.","unstructured":"Humphreys, S.C., , Emerging siRNA Design Principles and Consequences for Biotransformation and Disposition in Drug Development. Journal of Medicinal Chemistry, 2020. 63(12): p. 6407-6422.","journal-title":"Medicinal Chemistry"},{"key":"e_1_3_2_1_6_1","first-page":"464","volume":"200","author":"Pai S.I.","unstructured":"Pai, S.I., , Prospects of RNA interference therapy for cancer. Gene Therapy, 2006. 13(6): p. 464-477.","journal-title":"Gene Therapy"},{"key":"e_1_3_2_1_7_1","first-page":"816","volume":"200","author":"Xia H.","unstructured":"Xia, H., , RNAi suppresses polyglutamine-induced neurodegeneration in a model of spinocerebellar ataxia. Nature Medicine, 2004. 10(8): p. 816-820.","journal-title":"Nature Medicine"},{"key":"e_1_3_2_1_8_1","first-page":"329","volume":"201","author":"Davidson B.L.","unstructured":"Davidson, B.L. and P.B. McCray, Current prospects for RNA interference-based therapies. Nature Reviews Genetics, 2011. 12(5): p. 329-340.","journal-title":"Nature Reviews Genetics"},{"key":"e_1_3_2_1_9_1","first-page":"343","volume-title":"Nature","author":"Meister G.","year":"2004","unstructured":"Meister, G. and T. Tuschl, Mechanisms of gene silencing by double-stranded RNA. Nature, 2004. 431(7006): p. 343-9."},{"key":"e_1_3_2_1_10_1","first-page":"9742","volume":"200","author":"Caplen N.J.","unstructured":"Caplen, N.J., , Specific inhibition of gene expression by small double-stranded RNAs in invertebrate and vertebrate systems. Proceedings of the National Academy of Sciences, 2001. 98(17): p. 9742-9747.","journal-title":"Sciences"},{"key":"e_1_3_2_1_11_1","first-page":"209","volume":"200","author":"Khvorova A.","unstructured":"Khvorova, A., A. Reynolds, and S.D. Jayasena, Functional siRNAs and miRNAs Exhibit Strand Bias. Cell, 2003. 115(2): p. 209-216.","journal-title":"RNAs Exhibit Strand Bias. Cell"},{"key":"e_1_3_2_1_12_1","first-page":"7108","volume":"200","author":"Vickers T.A.","unstructured":"Vickers, T.A., , Efficient Reduction of Target RNAs by Small Interfering RNA and RNase H-dependent Antisense Agents: A COMPARATIVE ANALYSIS *. Journal of Biological Chemistry, 2003. 278(9): p. 7108-7118.","journal-title":"Biological Chemistry"},{"key":"e_1_3_2_1_13_1","first-page":"883","volume":"200","author":"Schubert S.","unstructured":"Schubert, S., , Local RNA Target Structure Influences siRNA Efficacy: Systematic Analysis of Intentionally Designed Binding Regions. Journal of Molecular Biology, 2005. 348(4): p. 883-893.","journal-title":"Molecular Biology"},{"key":"e_1_3_2_1_14_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gni026"},{"key":"e_1_3_2_1_15_1","first-page":"1050","volume":"200","author":"Amarzguioui M.","unstructured":"Amarzguioui, M. and H. Prydz, An algorithm for selection of functional siRNA sequences. Biochemical and Biophysical Research Communications, 2004. 316(4): p. 1050-1058.","journal-title":"Biophysical Research Communications"},{"key":"e_1_3_2_1_16_1","first-page":"247","volume":"200","author":"Saetrom P.","unstructured":"Saetrom, P. and O. Sn\u00f8ve, Jr., A comparison of siRNA efficacy predictors. Biochem Biophys Res Commun, 2004. 321(1): p. 247-53.","journal-title":"Biochem Biophys Res Commun"},{"key":"e_1_3_2_1_17_1","first-page":"995","volume":"200","author":"Huesken D.","unstructured":"Huesken, D., , Design of a genome-wide siRNA library using an artificial neural network. Nature Biotechnology, 2005. 23(8): p. 995-1001.","journal-title":"Nature Biotechnology"},{"key":"e_1_3_2_1_18_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-7-520"},{"key":"e_1_3_2_1_19_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-018-5028-8"},{"key":"e_1_3_2_1_20_1","first-page":"1515","volume":"202","author":"Muzio G.","unstructured":"Muzio, G., L. O'Bray, and K. Borgwardt, Biological network analysis with deep learning. Brief Bioinform, 2021. 22(2): p. 1515-1530.","journal-title":"Brief Bioinform"},{"key":"e_1_3_2_1_21_1","first-page":"14211","volume-title":"International Journal of Molecular Sciences","author":"La Rosa M.","year":"2022","unstructured":"La Rosa, M., , A Graph Neural Network Approach for the Analysis of siRNA-Target Biological Networks. International Journal of Molecular Sciences, 2022. 23(22): p. 14211."},{"key":"e_1_3_2_1_22_1","volume-title":"Interpretable RNA Foundation Model from Unannotated Data for Highly Accurate RNA Structure and Function Predictions. bioRxiv","author":"Chen J.","year":"2022","unstructured":"Chen, J., , Interpretable RNA Foundation Model from Unannotated Data for Highly Accurate RNA Structure and Function Predictions. bioRxiv, 2022: p. 2022.08.06.503062."},{"key":"e_1_3_2_1_23_1","first-page":"326","volume":"200","author":"Reynolds A.","unstructured":"Reynolds, A., , Rational siRNA design for RNA interference. Nat Biotechnol, 2004. 22(3): p. 326-30.","journal-title":"Nat Biotechnol"},{"key":"e_1_3_2_1_24_1","first-page":"83","volume":"200","author":"Harborth J.","unstructured":"Harborth, J., , Sequence, chemical, and structural variation of small interfering RNAs and short hairpin RNAs and the effect on mammalian gene silencing. Antisense Nucleic Acid Drug Dev, 2003. 13(2): p. 83-105.","journal-title":"Antisense Nucleic Acid Drug Dev"},{"key":"e_1_3_2_1_25_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkm699"},{"key":"e_1_3_2_1_26_1","first-page":"936","volume":"200","author":"Ui-Tei K.","unstructured":"Ui-Tei, K., , Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference. Nucleic Acids Res, 2004. 32(3): p. 936-48.","journal-title":"Nucleic Acids Res"},{"key":"e_1_3_2_1_27_1","first-page":"215","volume":"201","author":"Liu L.","unstructured":"Liu, L., , The effect of regions flanking target site on siRNA potency. Genomics, 2013. 102(4): p. 215-22.","journal-title":"Genomics"},{"key":"e_1_3_2_1_28_1","first-page":"199","volume":"200","author":"Schwarz D.S.","unstructured":"Schwarz, D.S., , Asymmetry in the Assembly of the RNAi Enzyme Complex. Cell, 2003. 115(2): p. 199-208.","journal-title":"RNAi Enzyme Complex. Cell"},{"key":"e_1_3_2_1_29_1","first-page":"674","volume":"200","author":"Vermeulen A.","unstructured":"Vermeulen, A., , The contributions of dsRNA structure to Dicer specificity and efficiency. Rna, 2005. 11(5): p. 674-82.","journal-title":"Rna"},{"key":"e_1_3_2_1_30_1","volume":"200","author":"Teramoto R.","unstructured":"Teramoto, R., , Prediction of siRNA functionality using generalized string kernel and support vector machine. FEBS Letters, 2005. 579(13): p. 2878-2882.","journal-title":"FEBS Letters"},{"key":"e_1_3_2_1_31_1","first-page":"1440","volume":"200","author":"Patzel V.","unstructured":"Patzel, V., , Design of siRNAs producing unstructured guide-RNAs results in improved RNA interference efficiency. Nat Biotechnol, 2005. 23(11): p. 1440-4.","journal-title":"Nat Biotechnol"},{"key":"e_1_3_2_1_32_1","first-page":"133","volume":"198","author":"Zuker M.","unstructured":"Zuker, M. and P. Stiegler, Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res, 1981. 9(1): p. 133-48.","journal-title":"Nucleic Acids Res"},{"key":"e_1_3_2_1_33_1","first-page":"1343","volume":"201","author":"Das S.","unstructured":"Das, S., , An siRNA designing tool with a unique functional off-target filtering approach. J Biomol Struct Dyn, 2013. 31(11): p. 1343-57.","journal-title":"J Biomol Struct Dyn"},{"key":"e_1_3_2_1_34_1","volume-title":"International Journal of Molecular Sciences","author":"La Rosa M.","year":"2022","unstructured":"La Rosa, M., , A Graph Neural Network Approach for the Analysis of siRNA-Target Biological Networks. International Journal of Molecular Sciences, 2022. 23(22)."},{"key":"e_1_3_2_1_35_1","first-page":"65","volume":"202","author":"Ahmed F.","unstructured":"Ahmed, F., , pssRNAit: A Web Server for Designing Effective and Specific Plant siRNAs with Genome-Wide Off-Target Assessment Plant Physiology, 2020. 184(1): p. 65-81.","journal-title":"Genome-Wide Off-Target Assessment Plant Physiology"}],"event":{"name":"BIC 2024: 2024 4th International Conference on Bioinformatics and Intelligent Computing","acronym":"BIC 2024","location":"Beijing China"},"container-title":["Proceedings of the 2024 4th International Conference on Bioinformatics and Intelligent Computing"],"original-title":[],"link":[{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/3665689.3665761","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/dl.acm.org\/doi\/pdf\/10.1145\/3665689.3665761","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,18]],"date-time":"2025-06-18T23:44:27Z","timestamp":1750290267000},"score":1,"resource":{"primary":{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/3665689.3665761"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,1,26]]},"references-count":35,"alternative-id":["10.1145\/3665689.3665761","10.1145\/3665689"],"URL":"https:\/\/doi.org\/10.1145\/3665689.3665761","relation":{},"subject":[],"published":{"date-parts":[[2024,1,26]]},"assertion":[{"value":"2024-06-28","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}