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ArticlesPeer ReviewedFull Text
Linking the resistome and plasmidome to the microbiome
Author / Creator:Stalder, Thibault ; Press, Maximilian O. ; Sullivan, Shawn ; Liachko, Ivan ; Top, Eva M.
Publisher:London: Nature Publishing Group UK
Journal title:The ISME Journal, 2019-10, Vol.13 (10), p.2437-2446
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Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C
Author / Creator:Kronenberg, Zev N. ; Rhie, Arang ; Koren, Sergey ; Concepcion, Gregory T. ; Peluso, Paul ; Munson, Katherine M. ; Porubsky, David ; Kuhn, Kristen ; Mueller, Kathryn A. ; Low, Wai Yee ; Hiendleder, Stefan ; Fedrigo, Olivier ; Liachko, Ivan ; Hall, Richard J. ; Phillippy, Adam M. ; Eichler, Evan E. ; Williams, John L. ; Smith, Timothy P. L. ; Jarvis, Erich D. ; Sullivan, Shawn T. ; Kingan, Sarah B.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2021-04, Vol.12 (1), p.1935-1935, Article 1935
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Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen
Author / Creator:Stewart, Robert D. ; Auffret, Marc D. ; Warr, Amanda ; Wiser, Andrew H. ; Press, Maximilian O. ; Langford, Kyle W. ; Liachko, Ivan ; Snelling, Timothy J. ; Dewhurst, Richard J. ; Walker, Alan W. ; Roehe, Rainer ; Watson, Mick
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2018-02, Vol.9 (1), p.870-11, Article 870
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Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities
Author / Creator:Bickhart, Derek M. ; Kolmogorov, Mikhail ; Tseng, Elizabeth ; Portik, Daniel M. ; Korobeynikov, Anton ; Tolstoganov, Ivan ; Uritskiy, Gherman ; Liachko, Ivan ; Sullivan, Shawn T. ; Shin, Sung Bong ; Zorea, Alvah ; Andreu, Victòria Pascal ; Panke-Buisse, Kevin ; Medema, Marnix H. ; Mizrahi, Itzhak ; Pevzner, Pavel A. ; Smith, Timothy P. L.
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2022-05, Vol.40 (5), p.711-719
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Repeat elements organise 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae
Author / Creator:Winter, David J. ; Ganley, Austen R. D. ; Young, Carolyn A. ; Liachko, Ivan ; Schardl, Christopher L. ; Dupont, Pierre-Yves ; Berry, Daniel ; Ram, Arvina ; Scott, Barry ; Cox, Murray P.
Publisher:United States: Public Library of Science
Journal title:PLoS genetics, 2018-10, Vol.14 (10), p.e1007467-e1007467
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Proximity ligation strategy for the genomic reconstruction of microbial communities associated with the ectoparasite Caligus rogercresseyi
Author / Creator:Valenzuela-Miranda, Diego ; Gonçalves, Ana Teresa ; Valenzuela-Muñoz, Valentina ; Nuñez-Acuña, Gustavo ; Liachko, Ivan ; Nelson, Bradley ; Gallardo-Escarate, Cristian
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2022-01, Vol.12 (1), p.783-10, Article 783
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Author Correction: Proximity ligation strategy for the genomic reconstruction of microbial communities associated with the ectoparasite Caligus rogercresseyi
Author / Creator:Valenzuela-Miranda, Diego ; Gonçalves, Ana Teresa ; Valenzuela-Muñoz, Valentina ; Nuñez-Acuña, Gustavo ; Liachko, Ivan ; Nelson, Bradley ; Gallardo-Escarate, Cristian
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2022-05, Vol.12 (1), p.7530-7530, Article 7530
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Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation
Author / Creator:Bickhart, Derek M. ; Watson, Mick ; Koren, Sergey ; Panke-Buisse, Kevin ; Cersosimo, Laura M. ; Press, Maximilian O. ; Van Tassell, Curtis P. ; Van Kessel, Jo Ann S. ; Haley, Bradd J. ; Kim, Seon Woo ; Heiner, Cheryl ; Suen, Garret ; Bakshy, Kiranmayee ; Liachko, Ivan ; Sullivan, Shawn T. ; Myer, Phillip R. ; Ghurye, Jay ; Pop, Mihai ; Weimer, Paul J. ; Phillippy, Adam M. ; Smith, Timothy P. L.
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2019-08, Vol.20 (1), p.153-153, Article 153
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Evolution of protein phosphorylation across 18 fungal species
Author / Creator:Studer, Romain A. ; Rodriguez-Mias, Ricard A. ; Haas, Kelsey M. ; Hsu, Joanne I. ; Viéitez, Cristina ; Solé, Carme ; Swaney, Danielle L. ; Stanford, Lindsay B. ; Liachko, Ivan ; Böttcher, René ; Dunham, Maitreya J. ; de Nadal, Eulàlia ; Posas, Francesc ; Beltrao, Pedro ; Villén, Judit
Publisher:United States: American Association for the Advancement of Science
Journal title:Science (American Association for the Advancement of Science), 2016-10, Vol.354 (6309), p.229-232
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ArticlesPeer ReviewedFull Text
autonomously replicating sequence for use in a wide range of budding yeasts
Author / Creator:Liachko, Ivan ; Dunham, Maitreya J
Publisher:Oxford, UK: Published by Elsevier Science B.V. on behalf of the Federation of European Microbiological Societies
Journal title:FEMS yeast research, 2014-03, Vol.14 (2), p.364-367
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The Fitness Consequences of Aneuploidy Are Driven by Condition-Dependent Gene Effects
Author / Creator:Sunshine, Anna B. ; Payen, Celia ; Ong, Giang T. ; Liachko, Ivan ; Tan, Kean Ming ; Dunham, Maitreya J.
Publisher:United States: Public Library of Science
Journal title:PLoS biology, 2015-05, Vol.13 (5), p.e1002155
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The dynamic three-dimensional organization of the diploid yeast genome
Author / Creator:Kim, Seungsoo ; Liachko, Ivan ; Brickner, Donna G ; Cook, Kate ; Noble, William S ; Brickner, Jason H ; Shendure, Jay ; Dunham, Maitreya J
Publisher:England: eLife Science Publications, Ltd
Journal title:eLife, 2017-05, Vol.6
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A high-resolution haplotype collection uncovers somatic hybridization, recombination and intercontinental movement in oat crown rust
Author / Creator:Henningsen, Eva C. ; Lewis, David ; Nazareno, Eric S. ; Mangelson, Hayley ; Sanchez, Monica ; Langford, Kyle ; Huang, Yung-Fen ; Steffenson, Brian J. ; Boesen, Brendan ; Kianian, Shahryar F. ; Liachko, Ivan ; Stone, Eric ; Dodds, Peter N. ; Sperschneider, Jana ; Figueroa, Melania
Publisher:United States: Public Library of Science
Journal title:PLoS genetics, 2024-11, Vol.20 (11), p.e1011493
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Shotgun and Hi-C Sequencing Datasets for Binning Wheat Rhizosphere Microbiome
Author / Creator:Regmi, Roshan ; Anderson, Jonathan ; Burgess, Lauren ; Mangelson, Hayley ; Liachko, Ivan ; Vadakattu, Gupta
Publisher:London: Nature Publishing Group UK
Journal title:Scientific data, 2025-03, Vol.12 (1), p.367-9, Article 367
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Divergent evolutionary trajectories following speciation in two ectoparasitic honey bee mites
Author / Creator:Techer, Maeva A. ; Rane, Rahul V. ; Grau, Miguel L. ; Roberts, John M. K. ; Sullivan, Shawn T. ; Liachko, Ivan ; Childers, Anna K. ; Evans, Jay D. ; Mikheyev, Alexander S.
Publisher:London: Nature Publishing Group UK
Journal title:Communications biology, 2019-10, Vol.2 (1), p.357-357, Article 357
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Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis
Author / Creator:Gallardo-Escárate, Cristian ; Valenzuela-Muñoz, Valentina ; Nuñez-Acuña, Gustavo ; Valenzuela-Miranda, Diego ; Gonçalves, Ana Teresa ; Escobar-Sepulveda, Hugo ; Liachko, Ivan ; Nelson, Bradley ; Roberts, Steven ; Warren, Wesley
Publisher:London: Nature Publishing Group UK
Journal title:Scientific data, 2021-02, Vol.8 (1), p.60-60, Article 60
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underlying mechanism for the increased mutagenesis of lagging-strand genes in Bacillus subtilis
Author / Creator:Million-Weaver, Samuel ; Samadpour, Ariana N. ; Moreno-Habel, Daniela A. ; Nugent, Patrick ; Brittnacher, Mitchell J. ; Weiss, Eli ; Hayden, Hillary S. ; Miller, Samuel I. ; Liachko, Ivan ; Merrikh, Houra
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2015-03, Vol.112 (10), p.E1096-E1105
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Integration of multi-omics data reveals cis-regulatory variants that are associated with phenotypic differentiation of eastern from western pigs
Author / Creator:Liu, Yuwen ; Fu, Yang ; Yang, Yalan ; Yi, Guoqiang ; Lian, Jinmin ; Xie, Bingkun ; Yao, Yilong ; Chen, Muya ; Niu, Yongchao ; Liu, Lei ; Wang, Liyuan ; Zhang, Yongsheng ; Fan, Xinhao ; Tang, Yijie ; Yuan, Pengxiang ; Zhu, Min ; Li, Qiaowei ; Zhang, Song ; Chen, Yun ; Wang, Binhu ; He, Jieyu ; Lu, Dan ; Liachko, Ivan ; Sullivan, Shawn T. ; Pang, Bin ; Chen, Yaoqing ; He, Xin ; Li, Kui ; Tang, Zhonglin
Publisher:London: BioMed Central Ltd
Journal title:Genetics selection evolution (Paris), 2022-09, Vol.54 (1), p.62-62, Article 62
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Integrating chromatin conformation information in a self-supervised learning model improves metagenome binning
Author / Creator:Ho, Harrison ; Chovatia, Mansi ; Egan, Rob ; He, Guifen ; Yoshinaga, Yuko ; Liachko, Ivan ; O’Malley, Ronan ; Wang, Zhong
Publisher:United States: PeerJ. Ltd
Journal title:PeerJ (San Francisco, CA), 2023-09, Vol.11, p.e16129-e16129, Article e16129
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ArticlesPeer ReviewedFull Text
Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities
Author / Creator:Bickhart, Derek M. ; Kolmogorov, Mikhail ; Tseng, Elizabeth ; Portik, Daniel M. ; Korobeynikov, Anton ; Tolstoganov, Ivan ; Uritskiy, Gherman ; Liachko, Ivan ; Sullivan, Shawn T. ; Shin, Sung Bong ; Zorea, Alvah ; Andreu, Victòria Pascal ; Panke-Buisse, Kevin ; Medema, Marnix H. ; Mizrahi, Itzhak ; Pevzner, Pavel A. ; Smith, Timothy P. L.
Journal title:Nature biotechnology, 2022-05, Vol.40 (5), p.711-719
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Showing 1 to 20 of 63 results

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Linking the resistome and plasmidome to the microbiome

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Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C

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Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen

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Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities

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Repeat elements organise 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae

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Proximity ligation strategy for the genomic reconstruction of microbial communities associated with the ectoparasite Caligus rogercresseyi

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Author Correction: Proximity ligation strategy for the genomic reconstruction of microbial communities associated with the ectoparasite Caligus rogercresseyi

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Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

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Evolution of protein phosphorylation across 18 fungal species

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autonomously replicating sequence for use in a wide range of budding yeasts

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The Fitness Consequences of Aneuploidy Are Driven by Condition-Dependent Gene Effects

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The dynamic three-dimensional organization of the diploid yeast genome

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A high-resolution haplotype collection uncovers somatic hybridization, recombination and intercontinental movement in oat crown rust

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Shotgun and Hi-C Sequencing Datasets for Binning Wheat Rhizosphere Microbiome

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Divergent evolutionary trajectories following speciation in two ectoparasitic honey bee mites

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Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis

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underlying mechanism for the increased mutagenesis of lagging-strand genes in Bacillus subtilis

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Integration of multi-omics data reveals cis-regulatory variants that are associated with phenotypic differentiation of eastern from western pigs

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Integrating chromatin conformation information in a self-supervised learning model improves metagenome binning

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Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities

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