Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity von 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.

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Long read isoform sequencing reveals hidden transcriptional complexity between cattle subspecies von Ren, Yan, Tseng, Elizabeth, Smith, Timothy P L, Hiendleder, Stefan, Williams, John L, Low, Wai Yee

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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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Genome wide analysis of fertility and production traits in Italian Holstein cattle von Minozzi, Giulietta, Nicolazzi, Ezequiel L, Stella, Alessandra, Biffani, Stefano, Negrini, Riccardo, Lazzari, Barbara, Ajmone-Marsan, Paolo, Williams, John L

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Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle von 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.

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Responses of Bovine Innate Immunity to Mycobacterium avium subsp. paratuberculosis Infection Revealed by Changes in Gene Expression and Levels of MicroRNA von Malvisi, Michela, Palazzo, Fiorentina, Morandi, Nicola, Lazzari, Barbara, Williams, John L, Pagnacco, Giulio, Minozzi, Giulietta

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Analysis of immune-related microRNAs in cows and newborn calves von Hue, Do T., Petrovski, Kiro, Chen, Tong, Williams, John L., Bottema, Cynthia D.K.

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Whole genome analysis of water buffalo and global cattle breeds highlights convergent signatures of domestication von Dutta, Prasun, Talenti, Andrea, Young, Rachel, Jayaraman, Siddharth, Callaby, Rebecca, Jadhav, Santosh Kumar, Dhanikachalam, Velu, Manikandan, Mayakannan, Biswa, Bhim B., Low, Wai Y., Williams, John L., Cook, Elizabeth, Toye, Phil, Wall, Eileen, Djikeng, Appolinaire, Marshall, Karen, Archibald, Alan L., Gokhale, Suresh, Kumar, Satish, Hume, David A., Prendergast, James G. D.

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Study of whole genome linkage disequilibrium patterns of Iranian water buffalo breeds using the Axiom Buffalo Genotyping 90K Array von Mokhber, Mahdi, Shahrbabak, Mohammad Moradi, Sadeghi, Mostafa, Shahrbabak, Hossein Moradi, Stella, Alessandra, Nicolzzi, Ezequiel, Williams, John L

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RNA-sequence analysis of gene expression from honeybees (Apis mellifera) infected with Nosema ceranae von Badaoui, Bouabid, Fougeroux, André, Petit, Fabien, Anselmo, Anna, Gorni, Chiara, Cucurachi, Marco, Cersini, Antonella, Granato, Anna, Cardeti, Giusy, Formato, Giovanni, Mutinelli, Franco, Giuffra, Elisabetta, Williams, John L, Botti, Sara

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A genome-wide scan for signatures of selection in Azeri and Khuzestani buffalo breeds von Mokhber, Mahdi, Moradi-Shahrbabak, Mohammad, Sadeghi, Mostafa, Moradi-Shahrbabak, Hossein, Stella, Alessandra, Nicolzzi, Ezequiel, Rahmaninia, Javad, Williams, John L

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Distinctive gene expression patterns and imprinting signatures revealed in reciprocal crosses between cattle sub-species von Liu, Ruijie, Tearle, Rick, Low, Wai Yee, Chen, Tong, Thomsen, Dana, Smith, Timothy P L, Hiendleder, Stefan, Williams, John L

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Regional variations in growth plate chondrocyte deformation as predicted by three-dimensional multi-scale simulations von Gao, Jie, Roan, Esra, Williams, John L

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AffyPipe: an open-source pipeline for Affymetrix Axiom genotyping workflow von Nicolazzi, Ezequiel L, Iamartino, Daniela, Williams, John L

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New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes von 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

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Linkage Disequilibrium and Effective Population Size of Buffalo Populations of Iran, Turkey, Pakistan, and Egypt Using a Medium Density SNP Array von Rahimmadar, Shirin, Ghaffari, Mokhtar, Mokhber, Mahdi, Williams, John L

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Maternal peri-conceptional undernourishment perturbs offspring sperm methylome von Toschi, Paola, Capra, Emanuele, Anzalone, Debora A, Lazzari, Barbara, Turri, Federica, Pizzi, Flavia, Scapolo, Pier A, Stella, Alessandra, Williams, John L, Ajmone Marsan, Paolo, Loi, Pasqualino

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The distribution of runs of homozygosity in the genome of river and swamp buffaloes reveals a history of adaptation, migration and crossbred events von Macciotta, Nicolo P P, Colli, Licia, Cesarani, Alberto, Ajmone-Marsan, Paolo, Low, Wai Y, Tearle, Rick, Williams, John L

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Integrative analysis of methylomic and transcriptomic data in fetal sheep muscle tissues in response to maternal diet during pregnancy von Namous, Hadjer, Peñagaricano, Francisco, Del Corvo, Marcello, Capra, Emanuele, Thomas, David L, Stella, Alessandra, Williams, John L, Marsan, Paolo Ajmone, Khatib, Hasan

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A genetically unique Chinese cattle population shows evidence of common ancestry with wild species when analysed with a reduced ascertainment bias SNP panel von Barbato, Mario, Reichel, Michael P, Passamonti, Matilde, Low, Wai Yee, Colli, Licia, Tearle, Rick, Williams, John L, Ajmone Marsan, Paolo

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