MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery von Wang, Kai, Singh, Darshan, Zeng, Zheng, Coleman, Stephen J, Huang, Yan, Savich, Gleb L, He, Xiaping, Mieczkowski, Piotr, Grimm, Sara A, Perou, Charles M, MacLeod, James N, Chiang, Derek Y, Prins, Jan F, Liu, Jinze

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iMapSplice: Alleviating reference bias through personalized RNA-seq alignment von Liu, Xinan, MacLeod, James N, Liu, Jinze

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Improved reference genome for the domestic horse increases assembly contiguity and composition von Kalbfleisch, Theodore S., Rice, Edward S., DePriest, Michael S., Walenz, Brian P., Hestand, Matthew S., Vermeesch, Joris R., O′Connell, Brendan L., Fiddes, Ian T., Vershinina, Alisa O., Saremi, Nedda F., Petersen, Jessica L., Finno, Carrie J., Bellone, Rebecca R., McCue, Molly E., Brooks, Samantha A., Bailey, Ernest, Orlando, Ludovic, Green, Richard E., Miller, Donald C., Antczak, Douglas F., MacLeod, James N.

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Annotation of the Protein Coding Regions of the Equine Genome von Hestand, Matthew S, Kalbfleisch, Theodore S, Coleman, Stephen J, Zeng, Zheng, Liu, Jinze, Orlando, Ludovic, MacLeod, James N

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Cellular Proliferation of Equine Bone Marrow- and Adipose Tissue-Derived Mesenchymal Stem Cells Decline With Increasing Donor Age von Bagge, Jasmin, MacLeod, James N., Berg, Lise C.

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"Adopt-a-Tissue" Initiative Advances Efforts to Identify Tissue-Specific Histone Marks in the Mare von Kingsley, N. B., Hamilton, Natasha A., Lindgren, Gabriella, Orlando, Ludovic, Bailey, Ernie, Brooks, Samantha, McCue, Molly, Kalbfleisch, T. S., MacLeod, James N., Petersen, Jessica L., Finno, Carrie J., Bellone, Rebecca R.

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Tissue Restricted Splice Junctions Originate Not Only from Tissue-Specific Gene Loci, but Gene Loci with a Broad Pattern of Expression von Hestand, Matthew S, Zeng, Zheng, Coleman, Stephen J, Liu, Jinze, MacLeod, James N

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Analysis of unannotated equine transcripts identified by mRNA sequencing von Coleman, Stephen J, Zeng, Zheng, Hestand, Matthew S, Liu, Jinze, Macleod, James N

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Transcriptional adaptations following exercise in thoroughbred horse skeletal muscle highlights molecular mechanisms that lead to muscle hypertrophy von McGivney, Beatrice A, Eivers, Suzanne S, MacHugh, David E, MacLeod, James N, O'Gorman, Grace M, Park, Stephen D E, Katz, Lisa M, Hill, Emmeline W

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Comparison of Poly-A+ Selection and rRNA Depletion in Detection of lncRNA in Two Equine Tissues Using RNA-seq von Dahlgren, Anna R., Scott, Erica Y., Mansour, Tamer, Hales, Erin N., Ross, Pablo J., Kalbfleisch, Theodore S., MacLeod, James N., Petersen, Jessica L., Bellone, Rebecca R., Finno, Carrie J.

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Correction: Analysis of Unannotated Equine Transcripts Identified by mRNA Sequencing von Coleman, Stephen J., Zeng, Zheng, Hestand, Matthew S., Liu, Jinze, Macleod, James N.

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Changes in the appendicular skeleton during metamorphosis in the axolotl salamander (Ambystoma mexicanum) von Thampi, Parvathy, Liu, Jinpeng, Zeng, Zheng, MacLeod, James N.

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Inflamed synovial fluid induces a homeostatic response in bone marrow mononuclear cells in vitro: Implications for joint therapy von Menarim, Bruno C., Gillis, Kiersten H., Oliver, Andrea, Mason, Caitlin, Werre, Stephen R., Luo, Xin, Byron, Christopher R., Kalbfleisch, Theodore S., MacLeod, James N., Dahlgren, Linda A.

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Production of Calcium Maintenance Factor Stanniocalcin-1 (STC1) by the Equine Endometrium During the Early Pregnant Period von KIKUCHI, Masato, NAKANO, Yasuko, NAMBO, Yasuo, HANEDA, Shingo, MATSUI, Motozumi, MIYAKE, Yoichi, MACLEOD, James N., NAGAOKA, Kentaro, IMAKAWA, Kazuhiko

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Transcriptional profiling differences for articular cartilage and repair tissue in equine joint surface lesions von Mienaltowski, Michael J, Huang, Liping, Frisbie, David D, McIlwraith, C Wayne, Stromberg, Arnold J, Bathke, Arne C, Macleod, James N

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Chondrogenic differentiation potential of adult and fetal equine cell types von Adam, Emma N., Janes, Jennifer, Lowney, Rachael, Lambert, Joshua, Thampi, Parvathy, Stromberg, Arnold, MacLeod, James N.

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Bone marrow mononuclear cells for joint therapy: The role of macrophages in inflammation resolution and tissue repair von Menarim, Bruno C., MacLeod, James N., Dahlgren, Linda A.

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Functionally Annotating Regulatory Elements in the Equine Genome Using Histone Mark ChIP-Seq von Kingsley, N. B., Kern, Colin, Creppe, Catherine, Hales, Erin N., Zhou, Huaijun, Kalbfleisch, T. S., MacLeod, James N., Petersen, Jessica L., Finno, Carrie J., Bellone, Rebecca R.

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Effect of Skeletal Paracrine Signals on the Proliferation of Interzone Cells von Thampi, Parvathy, Dubey, Rashmi, Lowney, Rachael, Adam, Emma N., Janse, Sarah, Wood, Constance L., MacLeod, James N.

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Corticosteroids alter the differentiated phenotype of articular chondrocytes von Fubini, Susan L, Todhunter, Rory J, Burton-Wurster, Nancy, Vernier-Singer, Margaret, MacLeod, James N

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