{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,13]],"date-time":"2026-03-13T08:24:06Z","timestamp":1773390246544,"version":"3.50.1"},"publisher-location":"Cham","reference-count":20,"publisher":"Springer International Publishing","isbn-type":[{"value":"9783031047480","type":"print"},{"value":"9783031047497","type":"electronic"}],"license":[{"start":{"date-parts":[[2022,1,1]],"date-time":"2022-01-01T00:00:00Z","timestamp":1640995200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2022,1,1]],"date-time":"2022-01-01T00:00:00Z","timestamp":1640995200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022]]},"DOI":"10.1007\/978-3-031-04749-7_4","type":"book-chapter","created":{"date-parts":[[2022,5,11]],"date-time":"2022-05-11T16:13:24Z","timestamp":1652285604000},"page":"52-69","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["DeepMinimizer: A Differentiable Framework for\u00a0Optimizing Sequence-Specific Minimizer Schemes"],"prefix":"10.1007","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1053-6744","authenticated-orcid":false,"given":"Minh","family":"Hoang","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7668-2090","authenticated-orcid":false,"given":"Hongyu","family":"Zheng","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0118-5516","authenticated-orcid":false,"given":"Carl","family":"Kingsford","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2022,4,29]]},"reference":[{"issue":"12","key":"4_CR1","doi-asserted-by":"publisher","first-page":"i201","DOI":"10.1093\/bioinformatics\/btw279","volume":"32","author":"R Chikhi","year":"2016","unstructured":"Chikhi, R., Limasset, A., Medvedev, P.: Compacting de Bruijn graphs from sequencing data quickly and in low memory. Bioinformatics 32(12), i201\u2013i208 (2016)","journal-title":"Bioinformatics"},{"key":"4_CR2","doi-asserted-by":"crossref","unstructured":"DeBlasio, D., Gbosibo, F., Kingsford, C., Mar\u00e7ais, G.: Practical universal k-mer sets for minimizer schemes. In: Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, BCB 2019, pp. 167\u2013176. Association for Computing Machinery, New York (2019)","DOI":"10.1145\/3307339.3342144"},{"issue":"10","key":"4_CR3","doi-asserted-by":"publisher","first-page":"1569","DOI":"10.1093\/bioinformatics\/btv022","volume":"31","author":"S Deorowicz","year":"2015","unstructured":"Deorowicz, S., Kokot, M., Grabowski, S., Debudaj-Grabysz, A.: KMC 2: fast and resource-frugal k-mer counting. Bioinformatics 31(10), 1569\u20131576 (2015)","journal-title":"Bioinformatics"},{"key":"4_CR4","doi-asserted-by":"crossref","unstructured":"Ekim, B., Berger, B., Orenstein, Y.: A randomized parallel algorithm for efficiently finding near-optimal universal hitting sets. bioRxiv (2020)","DOI":"10.1101\/2020.01.17.910513"},{"issue":"1","key":"4_CR5","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13015-017-0097-9","volume":"12","author":"M Erbert","year":"2017","unstructured":"Erbert, M., Rechner, S., M\u00fcller-Hannemann, M.: Gerbil: a fast and memory-efficient k-mer counter with GPU-support. Algorithms Mol. Biol. 12(1), 1\u201312 (2017)","journal-title":"Algorithms Mol. Biol."},{"issue":"5","key":"4_CR6","doi-asserted-by":"publisher","first-page":"496","DOI":"10.1016\/j.devcel.2014.08.016","volume":"30","author":"T Fukagawa","year":"2014","unstructured":"Fukagawa, T., Earnshaw, W.C.: The centromere: chromatin foundation for the kinetochore machinery. Dev. Cell 30(5), 496\u2013508 (2014)","journal-title":"Dev. Cell"},{"key":"4_CR7","doi-asserted-by":"crossref","unstructured":"Jain, C., Rhie, A., Hansen, N., Koren, S., Phillippy, A.M.: A long read mapping method for highly repetitive reference sequences. bioRxiv (2020)","DOI":"10.1101\/2020.11.01.363887"},{"key":"4_CR8","doi-asserted-by":"crossref","unstructured":"Jain, C., Rhie, A., Zhang, H., Chu, C., Walenz, B.P., Koren, S., Phillippy, A.M.: Weighted minimizer sampling improves long read mapping. Bioinformatics 36(Suppl._1), i111\u2013i118 (2020)","DOI":"10.1093\/bioinformatics\/btaa435"},{"key":"4_CR9","unstructured":"Kingma, D.P., Ba, J.: ADAM: a method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014)"},{"issue":"18","key":"4_CR10","doi-asserted-by":"publisher","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","volume":"34","author":"H Li","year":"2018","unstructured":"Li, H.: Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34(18), 3094\u20133100 (2018)","journal-title":"Bioinformatics"},{"issue":"13","key":"4_CR11","doi-asserted-by":"publisher","first-page":"i13","DOI":"10.1093\/bioinformatics\/bty258","volume":"34","author":"G Mar\u00e7ais","year":"2018","unstructured":"Mar\u00e7ais, G., DeBlasio, D., Kingsford, C.: Asymptotically optimal minimizers schemes. Bioinformatics 34(13), i13\u2013i22 (2018)","journal-title":"Bioinformatics"},{"issue":"14","key":"4_CR12","doi-asserted-by":"publisher","first-page":"i110","DOI":"10.1093\/bioinformatics\/btx235","volume":"33","author":"G Mar\u00e7ais","year":"2017","unstructured":"Mar\u00e7ais, G., Pellow, D., Bork, D., Orenstein, Y., Shamir, R., Kingsford, C.: Improving the performance of minimizers and winnowing schemes. Bioinformatics 33(14), i110\u2013i117 (2017)","journal-title":"Bioinformatics"},{"issue":"7823","key":"4_CR13","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1038\/s41586-020-2547-7","volume":"585","author":"KH Miga","year":"2020","unstructured":"Miga, K.H., et al.: Telomere-to-telomere assembly of a complete human X chromosome. Nature 585(7823), 79\u201384 (2020)","journal-title":"Nature"},{"key":"4_CR14","doi-asserted-by":"crossref","unstructured":"Orenstein, Y., Pellow, D., Marcais, G., Shamir, R., Kingsford, C.: Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing. PLOS Comput. Biol. 13, e1005777 (2017)","DOI":"10.1371\/journal.pcbi.1005777"},{"key":"4_CR15","doi-asserted-by":"publisher","first-page":"3363","DOI":"10.1093\/bioinformatics\/bth408","volume":"20","author":"M Roberts","year":"2005","unstructured":"Roberts, M., Hayes, W., Hunt, B., Mount, S., Yorke, J.: Reducing storage requirements for biological sequence comparison. Bioinformatics 20, 3363\u20139 (2005)","journal-title":"Bioinformatics"},{"key":"4_CR16","doi-asserted-by":"crossref","unstructured":"Schleimer, S., Wilkerson, D., Aiken, A.: Winnowing: local algorithms for document fingerprinting. In: Proceedings of the ACM SIGMOD International Conference on Management of Data 10 (2003)","DOI":"10.1145\/872757.872770"},{"key":"4_CR17","doi-asserted-by":"crossref","unstructured":"Ye, C., Ma, Z.S., Cannon, C.H., Pop, M., Douglas, W.Y.: Exploiting sparseness in de novo genome assembly. In: BMC Bioinformatics, vol. 13, pp. 1\u20138. BioMed Central (2012)","DOI":"10.1186\/1471-2105-13-S6-S1"},{"issue":"6","key":"4_CR18","doi-asserted-by":"publisher","first-page":"787","DOI":"10.1101\/gr.5573107","volume":"17","author":"ZD Zhang","year":"2007","unstructured":"Zhang, Z.D., et al.: Statistical analysis of the genomic distribution and correlation of regulatory elements in the encode regions. Genome Res. 17(6), 787\u2013797 (2007)","journal-title":"Genome Res."},{"key":"4_CR19","doi-asserted-by":"crossref","unstructured":"Zheng, H., Kingsford, C., Mar\u00e7ais, G.: Improved design and analysis of practical minimizers. Bioinformatics 36(Suppl._1), i119\u2013i127 (2020)","DOI":"10.1093\/bioinformatics\/btaa472"},{"key":"4_CR20","doi-asserted-by":"crossref","unstructured":"Zheng, H., Kingsford, C., Mar\u00e7ais, G.: Sequence-specific minimizers via polar sets. Bioinformatics 37, i187\u2013i195 (2021)","DOI":"10.1093\/bioinformatics\/btab313"}],"container-title":["Lecture Notes in Computer Science","Research in Computational Molecular Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-031-04749-7_4","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,5,11]],"date-time":"2022-05-11T23:04:09Z","timestamp":1652310249000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-3-031-04749-7_4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022]]},"ISBN":["9783031047480","9783031047497"],"references-count":20,"URL":"https:\/\/doi.org\/10.1007\/978-3-031-04749-7_4","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"value":"0302-9743","type":"print"},{"value":"1611-3349","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022]]},"assertion":[{"value":"29 April 2022","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"RECOMB","order":1,"name":"conference_acronym","label":"Conference Acronym","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"International Conference on Research in Computational Molecular Biology","order":2,"name":"conference_name","label":"Conference Name","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"San Diego, CA","order":3,"name":"conference_city","label":"Conference City","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"USA","order":4,"name":"conference_country","label":"Conference Country","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2022","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"22 May 2022","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"25 May 2022","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"26","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"recomb2022","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"https:\/\/recomb2022.net\/","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Single-blind","order":1,"name":"type","label":"Type","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"EasyChair","order":2,"name":"conference_management_system","label":"Conference Management System","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"188","order":3,"name":"number_of_submissions_sent_for_review","label":"Number of Submissions Sent for Review","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"17","order":4,"name":"number_of_full_papers_accepted","label":"Number of Full Papers Accepted","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"23","order":5,"name":"number_of_short_papers_accepted","label":"Number of Short Papers Accepted","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"9% - The value is computed by the equation \"Number of Full Papers Accepted \/ Number of Submissions Sent for Review * 100\" and then rounded to a whole number.","order":6,"name":"acceptance_rate_of_full_papers","label":"Acceptance Rate of Full Papers","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"3.2","order":7,"name":"average_number_of_reviews_per_paper","label":"Average Number of Reviews per Paper","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"6.5","order":8,"name":"average_number_of_papers_per_reviewer","label":"Average Number of Papers per Reviewer","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"Yes","order":9,"name":"external_reviewers_involved","label":"External Reviewers Involved","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}}]}}