Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome
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
Published in Nature genetics (01.04.2017)
Published in Nature genetics (01.04.2017)
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Journal Article
Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity
Low, Wai Yee, Tearle, Rick, Bickhart, Derek M., Rosen, Benjamin D., Kingan, Sarah B., Swale, Thomas, Thibaud-Nissen, Françoise, Murphy, Terence D., Young, Rachel, Lefevre, Lucas, Hume, David A., Collins, Andrew, Ajmone-Marsan, Paolo, Smith, Timothy P. L., Williams, John L.
Published in Nature communications (16.01.2019)
Published in Nature communications (16.01.2019)
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Journal Article
MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs
Zhai, Jixian, Jeong, Dong-Hoon, De Paoli, Emanuele, Park, Sunhee, Rosen, Benjamin D, Li, Yupeng, González, Alvaro J, Yan, Zhe, Kitto, Sherry L, Grusak, Michael A, Jackson, Scott A, Stacey, Gary, Cook, Douglas R, Green, Pamela J, Sherrier, D Janine, Meyers, Blake C
Published in Genes & development (01.12.2011)
Published in Genes & development (01.12.2011)
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Journal Article
Araport: the Arabidopsis information portal
Krishnakumar, Vivek, Hanlon, Matthew R, Contrino, Sergio, Ferlanti, Erik S, Karamycheva, Svetlana, Kim, Maria, Rosen, Benjamin D, Cheng, Chia-Yi, Moreira, Walter, Mock, Stephen A, Stubbs, Joseph, Sullivan, Julie M, Krampis, Konstantinos, Miller, Jason R, Micklem, Gos, Vaughn, Matthew, Town, Christopher D
Published in Nucleic acids research (28.01.2015)
Published in Nucleic acids research (28.01.2015)
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Journal Article
Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle
Low, Wai Yee, Tearle, Rick, Liu, Ruijie, Koren, Sergey, Rhie, Arang, Bickhart, Derek M., Rosen, Benjamin D., Kronenberg, Zev N., Kingan, Sarah B., Tseng, Elizabeth, Thibaud-Nissen, Françoise, Martin, Fergal J., Billis, Konstantinos, Ghurye, Jay, Hastie, Alex R., Lee, Joyce, Pang, Andy W. C., Heaton, Michael P., Phillippy, Adam M., Hiendleder, Stefan, Smith, Timothy P. L., Williams, John L.
Published in Nature communications (29.04.2020)
Published in Nature communications (29.04.2020)
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Journal Article
Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies
Leonard, Alexander S., Crysnanto, Danang, Fang, Zih-Hua, Heaton, Michael P., Vander Ley, Brian L., Herrera, Carolina, Bollwein, Heinrich, Bickhart, Derek M., Kuhn, Kristen L., Smith, Timothy P. L., Rosen, Benjamin D., Pausch, Hubert
Published in Nature communications (31.05.2022)
Published in Nature communications (31.05.2022)
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Journal Article
Signatures of selection and environmental adaptation across the goat genome post-domestication
Bertolini, Francesca, Servin, Bertrand, Talenti, Andrea, Rochat, Estelle, Kim, Eui Soo, Oget, Claire, Palhière, Isabelle, Crisà, Alessandra, Catillo, Gennaro, Steri, Roberto, Amills, Marcel, Colli, Licia, Marras, Gabriele, Milanesi, Marco, Nicolazzi, Ezequiel, Rosen, Benjamin D, Van Tassell, Curtis P, Guldbrandtsen, Bernt, Sonstegard, Tad S, Tosser-Klopp, Gwenola, Stella, Alessandra, Rothschild, Max F, Joost, Stéphane, Crepaldi, Paola
Published in Genetics selection evolution (Paris) (19.11.2018)
Published in Genetics selection evolution (Paris) (19.11.2018)
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Journal Article
Genome-wide SNP profiling of worldwide goat populations reveals strong partitioning of diversity and highlights post-domestication migration routes
Colli, Licia, Milanesi, Marco, Talenti, Andrea, Bertolini, Francesca, Chen, Minhui, Crisà, Alessandra, Daly, Kevin Gerard, Del Corvo, Marcello, Guldbrandtsen, Bernt, Lenstra, Johannes A, Rosen, Benjamin D, Vajana, Elia, Catillo, Gennaro, Joost, Stéphane, Nicolazzi, Ezequiel Luis, Rochat, Estelle, Rothschild, Max F, Servin, Bertrand, Sonstegard, Tad S, Steri, Roberto, Van Tassell, Curtis P, Ajmone-Marsan, Paolo, Crepaldi, Paola, Stella, Alessandra
Published in Genetics selection evolution (Paris) (19.11.2018)
Published in Genetics selection evolution (Paris) (19.11.2018)
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Journal Article
The Bovine Pangenome Consortium: democratizing production and accessibility of genome assemblies for global cattle breeds and other bovine species
Smith, Timothy P L, Bickhart, Derek M, Boichard, Didier, Chamberlain, Amanda J, Djikeng, Appolinaire, Jiang, Yu, Low, Wai Y, Pausch, Hubert, Demyda-Peyrás, Sebastian, Prendergast, James, Schnabel, Robert D, Rosen, Benjamin D
Published in Genome Biology (19.06.2023)
Published in Genome Biology (19.06.2023)
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Journal Article
Investigation of ancestral alleles in the Bovinae subfamily
Naji, Maulana M, Utsunomiya, Yuri T, Sölkner, Johann, Rosen, Benjamin D, Mészáros, Gábor
Published in BMC genomics (08.02.2021)
Published in BMC genomics (08.02.2021)
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Journal Article
Comparative whole genome DNA methylation profiling across cattle tissues reveals global and tissue-specific methylation patterns
Zhou, Yang, Liu, Shuli, Hu, Yan, Fang, Lingzhao, Gao, Yahui, Xia, Han, Schroeder, Steven G, Rosen, Benjamin D, Connor, Erin E, Li, Cong-Jun, Baldwin, Ransom L, Cole, John B, Van Tassell, Curtis P, Yang, Liguo, Ma, Li, Liu, George E
Published in BMC biology (06.07.2020)
Published in BMC biology (06.07.2020)
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Journal Article
Telomere-to-telomere assemblies of cattle and sheep Y-chromosomes uncover divergent structure and gene content
Olagunju, Temitayo A., Rosen, Benjamin D., Neibergs, Holly L., Becker, Gabrielle M., Davenport, Kimberly M., Elsik, Christine G., Hadfield, Tracy S., Koren, Sergey, Kuhn, Kristen L., Rhie, Arang, Shira, Katie A., Skibiel, Amy L., Stegemiller, Morgan R., Thorne, Jacob W., Villamediana, Patricia, Cockett, Noelle E., Murdoch, Brenda M., Smith, Timothy P. L.
Published in Nature communications (27.09.2024)
Published in Nature communications (27.09.2024)
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Journal Article
Systemic interindividual DNA methylation variants in cattle share major hallmarks with those in humans
Chang, Wen-Jou, Baker, Maria S, Laritsky, Eleonora, Gunasekara, Chathura J, Maduranga, Uditha, Galliou, Justine C, McFadden, Joseph W, Waltemyer, Jessica R, Berggren-Thomas, Bruce, Tate, Brianna N, Zhang, Hanxue, Rosen, Benjamin D, Van Tassell, Curtis P, Liu, George E, Coarfa, Cristian, Ren, Yi Athena, Waterland, Robert A
Published in Genome Biology (15.07.2024)
Published in Genome Biology (15.07.2024)
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Journal Article
New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes
Liu, Ruijie, Low, Wai Yee, Tearle, Rick, Koren, Sergey, Ghurye, Jay, Rhie, Arang, Phillippy, Adam M, Rosen, Benjamin D, Bickhart, Derek M, Smith, Timothy P L, Hiendleder, Stefan, Williams, John L
Published in BMC genomics (19.12.2019)
Published in BMC genomics (19.12.2019)
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Journal Article
MTGD: The Medicago truncatula genome database
Krishnakumar, Vivek, Kim, Maria, Rosen, Benjamin D, Karamycheva, Svetlana, Bidwell, Shelby L, Tang, Haibao, Town, Christopher D
Published in Plant and cell physiology (01.01.2015)
Published in Plant and cell physiology (01.01.2015)
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Journal Article
Assessing Bos taurus introgression in the UOA Bos indicus assembly
Naji, Maulana M, Utsunomiya, Yuri T, Sölkner, Johann, Rosen, Benjamin D, Mészáros, Gábor
Published in Genetics selection evolution (Paris) (18.12.2021)
Published in Genetics selection evolution (Paris) (18.12.2021)
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Journal Article
Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome
Edwards, Richard J, Field, Matt A, Ferguson, James M, Dudchenko, Olga, Keilwagen, Jens, Rosen, Benjamin D, Johnson, Gary S, Rice, Edward S, Hillier, La Deanna, Hammond, Jillian M, Towarnicki, Samuel G, Omer, Arina, Khan, Ruqayya, Skvortsova, Ksenia, Bogdanovic, Ozren, Zammit, Robert A, Aiden, Erez Lieberman, Warren, Wesley C, Ballard, J William O
Published in BMC genomics (16.03.2021)
Published in BMC genomics (16.03.2021)
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Journal Article
Detection of copy number variants in African goats using whole genome sequence data
Nandolo, Wilson, Mészáros, Gábor, Wurzinger, Maria, Banda, Liveness J, Gondwe, Timothy N, Mulindwa, Henry A, Nakimbugwe, Helen N, Clark, Emily L, Woodward-Greene, M. Jennifer, Liu, Mei, Liu, George E, Van Tassell, Curtis P, Rosen, Benjamin D, Sölkner, Johann
Published in BMC genomics (29.05.2021)
Published in BMC genomics (29.05.2021)
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Journal Article
Gaur genome reveals expansion of sperm odorant receptors in domesticated cattle
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
Published in BMC genomics (04.05.2022)
Published in BMC genomics (04.05.2022)
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Journal Article
Towards the detection of copy number variation from single sperm sequencing in cattle
Yang, Liu, Gao, Yahui, Oswalt, Adam, Fang, Lingzhao, Boschiero, Clarissa, Neupane, Mahesh, Sattler, Charles G, Li, Cong-Jun, Seroussi, Eyal, Xu, Lingyang, Yang, Lv, Li, Li, Zhang, Hongping, Rosen, Benjamin D, Van Tassell, Curtis P, Zhou, Yang, Ma, Li, Liu, George E
Published in BMC genomics (17.03.2022)
Published in BMC genomics (17.03.2022)
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