{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,16]],"date-time":"2025-10-16T20:53:39Z","timestamp":1760648019120,"version":"3.40.3"},"publisher-location":"Cham","reference-count":36,"publisher":"Springer Nature Switzerland","isbn-type":[{"type":"print","value":"9781071639887"},{"type":"electronic","value":"9781071639894"}],"license":[{"start":{"date-parts":[[2024,1,1]],"date-time":"2024-01-01T00:00:00Z","timestamp":1704067200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2024,1,1]],"date-time":"2024-01-01T00:00:00Z","timestamp":1704067200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024]]},"DOI":"10.1007\/978-1-0716-3989-4_7","type":"book-chapter","created":{"date-parts":[[2024,5,16]],"date-time":"2024-05-16T08:02:38Z","timestamp":1715846558000},"page":"99-114","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["ImputeCC Enhances Integrative Hi-C-Based Metagenomic Binning Through Constrained Random-Walk-Based Imputation"],"prefix":"10.1007","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0568-3838","authenticated-orcid":false,"given":"Yuxuan","family":"Du","sequence":"first","affiliation":[]},{"given":"Wenxuan","family":"Zuo","sequence":"additional","affiliation":[]},{"given":"Fengzhu","family":"Sun","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2024,5,17]]},"reference":[{"issue":"6","key":"7_CR1","doi-asserted-by":"publisher","first-page":"533","DOI":"10.1038\/nbt.2579","volume":"31","author":"M Albertsen","year":"2013","unstructured":"Albertsen, M., Hugenholtz, P., Skarshewski, A., Nielsen, K.L., Tyson, G.W., Nielsen, P.H.: Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat. Biotechnol. 31(6), 533\u2013538 (2013)","journal-title":"Nat. Biotechnol."},{"key":"7_CR2","doi-asserted-by":"publisher","first-page":"753","DOI":"10.3389\/fgene.2019.00753","volume":"10","author":"L Baudry","year":"2019","unstructured":"Baudry, L., Foutel-Rodier, T., Thierry, A., Koszul, R., Marbouty, M.: MetaTOR: a computational pipeline to recover high-quality metagenomic bins from mammalian gut proximity-ligation (me) libraries. Front. Genet. 10, 753 (2019)","journal-title":"Front. Genet."},{"issue":"5","key":"7_CR3","doi-asserted-by":"publisher","first-page":"711","DOI":"10.1038\/s41587-021-01130-z","volume":"40","author":"DM Bickhart","year":"2022","unstructured":"Bickhart, D.M., Kolmogorov, M., Tseng, E., Portik, D.M., Korobeynikov, A., Tolstoganov, I., Uritskiy, G., Liachko, I., Sullivan, S.T., Shin, S.B., et al.: Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities. Nat. Biotechnol. 40(5), 711\u2013719 (2022)","journal-title":"Nat. Biotechnol."},{"key":"7_CR4","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1186\/s13059-019-1760-x","volume":"20","author":"DM Bickhart","year":"2019","unstructured":"Bickhart, D.M., Watson, M., Koren, S., Panke-Buisse, K., Cersosimo, L.M., Press, M.O., Van Tassell, C.P., Van Kessel, J.A.S., Haley, B.J., Kim, S.W., et al.: Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation. Genome Biol. 20, 153 (2019)","journal-title":"Genome Biol."},{"key":"7_CR5","doi-asserted-by":"crossref","unstructured":"Burton, J.N., Liachko, I., Dunham, M.J., Shendure, J.: Species-level deconvolution of metagenome assemblies with Hi-C\u2013based contact probability maps. G3 (Bethesda) 4(7), 1339\u20131346 (2014)","DOI":"10.1534\/g3.114.011825"},{"key":"7_CR6","unstructured":"Bushnell, B.: BBMap: a fast, accurate, splice-aware aligner. Tech. rep., Lawrence Berkeley National Lab.(LBNL), Berkeley, CA (United States) (2014)"},{"issue":"23","key":"7_CR7","doi-asserted-by":"publisher","first-page":"5315","DOI":"10.1093\/bioinformatics\/btac672","volume":"38","author":"PA Chaumeil","year":"2022","unstructured":"Chaumeil, P.A., Mussig, A.J., Hugenholtz, P., Parks, D.H.: GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics 38(23), 5315\u20135316 (2022)","journal-title":"Bioinformatics"},{"key":"7_CR8","doi-asserted-by":"publisher","first-page":"5398","DOI":"10.1038\/s41467-021-25678-1","volume":"12","author":"Y Chen","year":"2021","unstructured":"Chen, Y., Wang, Y., Paez-Espino, D., Polz, M.F., Zhang, T.: Prokaryotic viruses impact functional microorganisms in nutrient removal and carbon cycle in wastewater treatment plants. Nat. Commun. 12, 5398 (2021)","journal-title":"Nat. Commun."},{"key":"7_CR9","doi-asserted-by":"publisher","first-page":"1203","DOI":"10.1038\/s41592-023-01940-w","volume":"20","author":"A Chklovski","year":"2023","unstructured":"Chklovski, A., Parks, D.H., Woodcroft, B.J., Tyson, G.W.: CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nat. Methods 20, 1203\u20131212 (2023)","journal-title":"Nat. Methods"},{"key":"7_CR10","doi-asserted-by":"crossref","unstructured":"DeMaere, M.Z., Darling, A.E.: Sim3C: simulation of Hi-C and Meta3C proximity ligation sequencing technologies. GigaScience 7(2), gix103 (2018)","DOI":"10.1093\/gigascience\/gix103"},{"key":"7_CR11","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1186\/s13059-019-1643-1","volume":"20","author":"MZ DeMaere","year":"2019","unstructured":"DeMaere, M.Z., Darling, A.E.: bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes. Genome Biol. 20, 46 (2019)","journal-title":"Genome Biol."},{"key":"7_CR12","doi-asserted-by":"publisher","first-page":"502","DOI":"10.1038\/s41467-023-35945-y","volume":"14","author":"Y Du","year":"2023","unstructured":"Du, Y., Fuhrman, J.A., Sun, F.: ViralCC retrieves complete viral genomes and virus-host pairs from metagenomic Hi-C data. Nat. Commun. 14, 502 (2023)","journal-title":"Nat. Commun."},{"key":"7_CR13","doi-asserted-by":"publisher","first-page":"106","DOI":"10.1089\/cmb.2021.0439","volume":"29","author":"Y Du","year":"2022","unstructured":"Du, Y., Laperriere, S.M., Fuhrman, J., Sun, F.: Normalizing Metagenomic Hi-C Data and Detecting Spurious Contacts Using Zero-Inflated Negative Binomial Regression. J. Comput. Biol. 29, 106\u2013120 (2022)","journal-title":"J. Comput. Biol."},{"key":"7_CR14","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1186\/s13059-022-02626-w","volume":"23","author":"Y Du","year":"2022","unstructured":"Du, Y., Sun, F.: HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps. Genome Biol. 23, 63 (2022)","journal-title":"Genome Biol."},{"key":"7_CR15","doi-asserted-by":"publisher","first-page":"6231","DOI":"10.1038\/s41467-023-41209-6","volume":"14","author":"Y Du","year":"2023","unstructured":"Du, Y., Sun, F.: MetaCC allows scalable and integrative analyses of both long-read and short-read metagenomic Hi-C data. Nat. Commun. 14, 6231 (2023)","journal-title":"Nat. Commun."},{"key":"7_CR16","doi-asserted-by":"crossref","unstructured":"Finn, R.D., Clements, J., Eddy, S.R.: HMMER web server: interactive sequence similarity searching. Nucl Acids Res 39(suppl_2), W29\u2013W37 (2011)","DOI":"10.1093\/nar\/gkr367"},{"issue":"4","key":"7_CR17","doi-asserted-by":"publisher","first-page":"669","DOI":"10.1128\/MMBR.68.4.669-685.2004","volume":"68","author":"J Handelsman","year":"2004","unstructured":"Handelsman, J.: Metagenomics: application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev. 68(4), 669\u2013685 (2004)","journal-title":"Microbiol. Mol. Biol. Rev."},{"issue":"7212","key":"7_CR18","first-page":"481","volume":"455","author":"P Hugenholtz","year":"2008","unstructured":"Hugenholtz, P., Tyson, G.W.: Metagenomics. Nature 455(7212), 481\u2013483 (2008)","journal-title":"Metagenomics. Nature"},{"key":"7_CR19","doi-asserted-by":"publisher","first-page":"279","DOI":"10.1186\/s13059-015-0834-7","volume":"16","author":"LW Hugerth","year":"2015","unstructured":"Hugerth, L.W., Larsson, J., Alneberg, J., Lindh, M.V., Legrand, C., Pinhassi, J., Andersson, A.F.: Metagenome-assembled genomes uncover a global brackish microbiome. Genome Biol. 16, 279 (2015)","journal-title":"Genome Biol."},{"issue":"2","key":"7_CR20","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1002\/net.3230100205","volume":"10","author":"RM Karp","year":"1980","unstructured":"Karp, R.M.: An algorithm to solve the m$$\\times $$ n assignment problem in expected time O (mn log n). Networks 10(2), 143\u2013152 (1980)","journal-title":"Networks"},{"key":"7_CR21","unstructured":"Li, H.: Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv (2013). 10.48550\/arXiv.1303.3997"},{"key":"7_CR22","doi-asserted-by":"crossref","unstructured":"Marbouty, M., Cournac, A., Flot, J.F., Marie-Nelly, H., Mozziconacci, J., Koszul, R.: Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms. eLife 3, e03318 (2014)","DOI":"10.7554\/eLife.03318"},{"issue":"1","key":"7_CR23","doi-asserted-by":"publisher","first-page":"694","DOI":"10.1038\/s41597-022-01762-z","volume":"9","author":"V Meslier","year":"2022","unstructured":"Meslier, V., Quinquis, B., Da Silva, K., Plaza O\u00f1ate, F., Pons, N., Roume, H., Podar, M., Almeida, M.: Benchmarking second and third-generation sequencing platforms for microbial metagenomics. Sci Data 9(1), 694 (2022)","journal-title":"Sci Data"},{"key":"7_CR24","doi-asserted-by":"publisher","first-page":"555","DOI":"10.1038\/s41587-020-00777-4","volume":"39","author":"JN Nissen","year":"2021","unstructured":"Nissen, J.N., Johansen, J., Alles\u00f8e, R.L., S\u00f8nderby, C.K., Armenteros, J.J.A., Gr\u00f8nbech, C.H., Jensen, L.J., Nielsen, H.B., Petersen, T.N., Winther, O., et al.: Improved metagenome binning and assembly using deep variational autoencoders. Nat. Biotechnol. 39, 555\u2013560 (2021)","journal-title":"Nat. Biotechnol."},{"key":"7_CR25","doi-asserted-by":"publisher","first-page":"132","DOI":"10.1186\/s13059-016-0997-x","volume":"17","author":"BD Ondov","year":"2016","unstructured":"Ondov, B.D., Treangen, T.J., Melsted, P., Mallonee, A.B., Bergman, N.H., Koren, S., Phillippy, A.M.: Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 17, 132 (2016)","journal-title":"Genome Biol."},{"issue":"7","key":"7_CR26","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1101\/gr.186072.114","volume":"25","author":"DH Parks","year":"2015","unstructured":"Parks, D.H., Imelfort, M., Skennerton, C.T., Hugenholtz, P., Tyson, G.W.: CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25(7), 1043\u20131055 (2015)","journal-title":"Genome Res."},{"key":"7_CR27","doi-asserted-by":"crossref","unstructured":"Press, M.O., Wiser, A.H., Kronenberg, Z.N., Langford, K.W., Shakya, M., Lo, C.C., Mueller, K.A., Sullivan, S.T., Chain, P.S., Liachko, I.: Hi-C deconvolution of a human gut microbiome yields high-quality draft genomes and reveals plasmid-genome interactions. bioRxiv (2017). 10.1101\/198713","DOI":"10.1101\/198713"},{"issue":"7","key":"7_CR28","doi-asserted-by":"publisher","first-page":"1665","DOI":"10.1016\/j.cell.2014.11.021","volume":"159","author":"SS Rao","year":"2014","unstructured":"Rao, S.S., Huntley, M.H., Durand, N.C., Stamenova, E.K., Bochkov, I.D., Robinson, J.T., Sanborn, A.L., Machol, I., Omer, A.D., Lander, E.S., et al.: A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159(7), 1665\u20131680 (2014)","journal-title":"Cell"},{"issue":"1","key":"7_CR29","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevE.74.016110","volume":"74","author":"J Reichardt","year":"2006","unstructured":"Reichardt, J., Bornholdt, S.: Statistical mechanics of community detection. Phys. Rev. E 74(1), 016110 (2006)","journal-title":"Phys. Rev. E"},{"issue":"20","key":"7_CR30","doi-asserted-by":"publisher","first-page":"e191","DOI":"10.1093\/nar\/gkq747","volume":"38","author":"M Rho","year":"2010","unstructured":"Rho, M., Tang, H., Ye, Y.: FragGeneScan: predicting genes in short and error-prone reads. Nucl Acids Res 38(20), e191\u2013e191 (2010)","journal-title":"Nucl Acids Res"},{"key":"7_CR31","doi-asserted-by":"publisher","first-page":"382","DOI":"10.1038\/s41571-018-0006-2","volume":"15","author":"B Routy","year":"2018","unstructured":"Routy, B., Gopalakrishnan, V., Daill\u00e8re, R., Zitvogel, L., Wargo, J.A., Kroemer, G.: The gut microbiota influences anticancer immunosurveillance and general health. Nat. Rev. Clin. Oncol. 15, 382\u2013396 (2018)","journal-title":"Nat. Rev. Clin. Oncol."},{"issue":"10","key":"7_CR32","doi-asserted-by":"publisher","first-page":"2437","DOI":"10.1038\/s41396-019-0446-4","volume":"13","author":"T Stalder","year":"2019","unstructured":"Stalder, T., Press, M.O., Sullivan, S., Liachko, I., Top, E.M.: Linking the resistome and plasmidome to the microbiome. ISME J. 13(10), 2437\u20132446 (2019)","journal-title":"ISME J."},{"key":"7_CR33","doi-asserted-by":"publisher","first-page":"5233","DOI":"10.1038\/s41598-019-41695-z","volume":"9","author":"VA Traag","year":"2019","unstructured":"Traag, V.A., Waltman, L., Van Eck, N.J.: From Louvain to Leiden: guaranteeing well-connected communities. Sci. Rep. 9, 5233 (2019)","journal-title":"Sci. Rep."},{"key":"7_CR34","doi-asserted-by":"crossref","unstructured":"Wu, Y.W., Tang, Y.H., Tringe, S.G., Simmons, B.A., Singer, S.W.: MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. Microbiome 2(26) (2014)","DOI":"10.1186\/2049-2618-2-26"},{"issue":"2","key":"7_CR35","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1038\/s41564-019-0625-0","volume":"5","author":"E Yaffe","year":"2020","unstructured":"Yaffe, E., Relman, D.A.: Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation. Nat. Microbiol. 5(2), 343\u2013353 (2020)","journal-title":"Nat. Microbiol."},{"key":"7_CR36","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1038\/nature11053","volume":"486","author":"T Yatsunenko","year":"2012","unstructured":"Yatsunenko, T., Rey, F.E., Manary, M.J., Trehan, I., Dominguez-Bello, M.G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R.N., Anokhin, A.P., et al.: Human gut microbiome viewed across age and geography. Nature 486, 222\u2013227 (2012)","journal-title":"Nature"}],"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\/978-1-0716-3989-4_7","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,16]],"date-time":"2024-05-16T08:03:33Z","timestamp":1715846613000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-1-0716-3989-4_7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024]]},"ISBN":["9781071639887","9781071639894"],"references-count":36,"URL":"https:\/\/doi.org\/10.1007\/978-1-0716-3989-4_7","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2024]]},"assertion":[{"value":"17 May 2024","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":"Cambridge, MA","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":"2024","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"29 April 2024","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2 May 2024","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"28","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"recomb2024","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"https:\/\/recomb.org\/recomb2024\/","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}}]}}