Mapping and Dynamics of Regulatory DNA and Transcription Factor Networks in A. thaliana von Sullivan, Alessandra M., Arsovski, Andrej A., Lempe, Janne, Bubb, Kerry L., Weirauch, Matthew T., Sabo, Peter J., Sandstrom, Richard, Thurman, Robert E., Neph, Shane, Reynolds, Alex P., Stergachis, Andrew B., Vernot, Benjamin, Johnson, Audra K., Haugen, Eric, Sullivan, Shawn T., Thompson, Agnieszka, Neri, Fidencio V., Weaver, Molly, Diegel, Morgan, Mnaimneh, Sanie, Yang, Ally, Hughes, Timothy R., Nemhauser, Jennifer L., Queitsch, Christine, Stamatoyannopoulos, John A.

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Linking the resistome and plasmidome to the microbiome von Stalder, Thibault, Press, Maximilian O., Sullivan, Shawn, Liachko, Ivan, Top, Eva M.

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

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

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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 von 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

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Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome von Bickhart, Derek M, Rosen, Benjamin D, Koren, Sergey, Sayre, Brian L, Hastie, Alex R, Chan, Saki, Lee, Joyce, Lam, Ernest T, Liachko, Ivan, Sullivan, Shawn T, Burton, Joshua N, Huson, Heather J, Nystrom, John C, Kelley, Christy M, Hutchison, Jana L, Zhou, Yang, Sun, Jiajie, Crisà, Alessandra, Ponce de León, F Abel, Schwartz, John C, Hammond, John A, Waldbieser, Geoffrey C, Schroeder, Steven G, Liu, George E, Dunham, Maitreya J, Shendure, Jay, Sonstegard, Tad S, Phillippy, Adam M, Van Tassell, Curtis P, Smith, Timothy P L

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Improvement of the Threespine Stickleback Genome Using a Hi-C-Based Proximity-Guided Assembly von Peichel, Catherine L, Sullivan, Shawn T, Liachko, Ivan, White, Michael A

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Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise von Peona, Valentina, Blom, Mozes P. K., Xu, Luohao, Burri, Reto, Sullivan, Shawn, Bunikis, Ignas, Liachko, Ivan, Haryoko, Tri, Jønsson, Knud A., Zhou, Qi, Irestedt, Martin, Suh, Alexander

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Degradation of Recalcitrant Polyurethane and Xenobiotic Additives by a Selected Landfill Microbial Community and Its Biodegradative Potential Revealed by Proximity Ligation-Based M... von Gaytan, Itzel, Sanchez-Reyes, Ayixon, Burelo, Manuel, Vargas-Suarez, Martin, Liachko, Ivan, Press, Maximilian, Sullivan, Shawn, Cruz-Gomez, M. Javier, Loza-Tavera, Herminia

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Gaur genome reveals expansion of sperm odorant receptors in domesticated cattle von Low, Wai Yee, Rosen, Benjamin D, Ren, Yan, Bickhart, Derek M, To, Thu-Hien, Martin, Fergal J, Billis, Konstantinos, Sonstegard, Tad S, Sullivan, Shawn T, Hiendleder, Stefan, Williams, John L, Heaton, Michael P, Smith, Timothy P L

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

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Genomic Resources to Guide Improvement of the Shea Tree von Hale, Iago, Ma, Xiao, Melo, Arthur T. O., Padi, Francis Kwame, Hendre, Prasad S., Kingan, Sarah B., Sullivan, Shawn T., Chen, Shiyu, Boffa, Jean-Marc, Muchugi, Alice, Danquah, Agyemang, Barnor, Michael Teye, Jamnadass, Ramni, Van de Peer, Yves, Van Deynze, Allen

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

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Mapping and Dynamics of Regulatory DNA in Maturing Arabidopsis thaliana Siliques von Sullivan, Alessandra M., Arsovski, Andrej A., Thompson, Agnieszka, Sandstrom, Richard, Thurman, Robert E., Neph, Shane, Johnson, Audra K., Sullivan, Shawn T., Sabo, Peter J., Neri, Fidencio V., Weaver, Molly, Diegel, Morgan, Nemhauser, Jennifer L., Stamatoyannopoulos, John A., Bubb, Kerry L., Queitsch, Christine

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Divergent evolutionary trajectories following speciation in two ectoparasitic honey bee mites von 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.

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From transcriptome analysis to therapeutic anti-CD40L treatment in the SOD1 model of amyotrophic lateral sclerosis von Vieira, Fernando G, Levine, Beth A, Moreno, Andrew, Thompson, Kenneth, Sanchez, Ricardo, Lincecum, John M, Wang, Monica Z, Gill, Alan, Perrin, Steven, Al-Nakhala, Bashar M, De Zutter, Gerald S, Kidd, Joshua, Carrion, Isarelis J, Sullivan, Shawn M

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Quantitative characterization of catalyst layer degradation in PEM fuel cells by X-ray photoelectron spectroscopy von Zhang, Feng-Yuan, Advani, Suresh G., Prasad, Ajay K., Boggs, Mary E., Sullivan, Shawn P., Beebe, Thomas P.

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Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum von Olarte, Rodrigo A, Menke, Jon, Zhang, Ying, Sullivan, Shawn, Slot, Jason C, Huang, Yinyin, Badalamenti, Jonathan P, Quandt, Alisha C, Spatafora, Joseph W, Bushley, Kathryn E

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Growth and chemical modification of silicon nanostructures templated in molecule corrals: Parallels with the surface chemistry of single crystalline silicon von Sullivan, Shawn P., Leftwich, Timothy R., Goodwin, Christopher M., Ni, Chaoying, Teplyakov, Andrew V., Beebe, Thomas P.

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Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data von Jibran, Rubina, Dzierzon, Helge, Bassil, Nahla, Bushakra, Jill M., Edger, Patrick P., Sullivan, Shawn, Finn, Chad E., Dossett, Michael, Vining, Kelly J., VanBuren, Robert, Mockler, Todd C., Liachko, Ivan, Davies, Kevin M., Foster, Toshi M., Chagné, David

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