Machine learning on alignment features for parent-of-origin classification of simulated hybrid RNA-seq

Autor: Jason R. Miller, Donald A. Adjeroh

Publikováno v: BMC Bioinformatics, Vol 25, Iss 1, Pp 1-21 (2024)

Abstract Background Parent-of-origin allele-specific gene expression (ASE) can be detected in interspecies hybrids by virtue of RNA sequence variants between the parental haplotypes. ASE is detectable by differential expression analysis (DEA) applied

Externí odkaz: https://doaj.org/article/2266bf46cc5c4b97997a999d75b8c3cc

Predicting the functional effect of amino acid substitutions and indels.

Autor: Yongwook Choi, Gregory E Sims, Sean Murphy, Jason R Miller, Agnes P Chan

Publikováno v: PLoS ONE, Vol 7, Iss 10, p e46688 (2012)

As next-generation sequencing projects generate massive genome-wide sequence variation data, bioinformatics tools are being developed to provide computational predictions on the functional effects of sequence variations and narrow down the search of

Externí odkaz: https://doaj.org/article/c2ceb4a084d04415961af97935940f5d

Radiographic evaluation of naviculo-cuneiform sag deformity following triplane bunion correction via first tarsometatarsal joint arthrodesis

Autor: Jason R. Miller, DPM, FACFAS, FAPWCA, Mark J. Capuzzi, DPM, AACFAS, Tymoteusz Siwy, DPM, Alexandra Parish, DPM, Marcus Duvall, DPM

Publikováno v: Foot & Ankle Surgery: Techniques, Reports & Cases, Vol 2, Iss 3, Pp 100215- (2022)

Purpose: To evaluate naviculo-cuneiform joint sag after first tarsometatarsal joint arthrodesis and the possible correlation between the presence of NC sag, loss of anatomic correction, and other radiographic angle measurements such as Calcaneal incl

Externí odkaz: https://doaj.org/article/7a95befb0d054c4bbb7e60219f8bbb98

Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes

Autor: Peng Zhou, Kevin A. T. Silverstein, Thiruvarangan Ramaraj, Joseph Guhlin, Roxanne Denny, Junqi Liu, Andrew D. Farmer, Kelly P. Steele, Robert M. Stupar, Jason R. Miller, Peter Tiffin, Joann Mudge, Nevin D. Young

Publikováno v: BMC Genomics, Vol 18, Iss 1, Pp 1-14 (2017)

Abstract Background Previous studies exploring sequence variation in the model legume, Medicago truncatula, relied on mapping short reads to a single reference. However, read-mapping approaches are inadequate to examine large, diverse gene families o

Externí odkaz: https://doaj.org/article/a9a67f3494e34291aab3f13dd93751b8

Genomic insights into the Ixodes scapularis tick vector of Lyme disease

Autor: Monika Gulia-Nuss, Andrew B. Nuss, Jason M. Meyer, Daniel E. Sonenshine, R. Michael Roe, Robert M. Waterhouse, David B. Sattelle, José de la Fuente, Jose M. Ribeiro, Karine Megy, Jyothi Thimmapuram, Jason R. Miller, Brian P. Walenz, Sergey Koren, Jessica B. Hostetler, Mathangi Thiagarajan, Vinita S. Joardar, Linda I. Hannick, Shelby Bidwell, Martin P. Hammond, Sarah Young, Qiandong Zeng, Jenica L. Abrudan, Francisca C. Almeida, Nieves Ayllón, Ketaki Bhide, Brooke W. Bissinger, Elena Bonzon-Kulichenko, Steven D. Buckingham, Daniel R. Caffrey, Melissa J. Caimano, Vincent Croset, Timothy Driscoll, Don Gilbert, Joseph J. Gillespie, Gloria I. Giraldo-Calderón, Jeffrey M. Grabowski, David Jiang, Sayed M. S. Khalil, Donghun Kim, Katherine M. Kocan, Juraj Koči, Richard J. Kuhn, Timothy J. Kurtti, Kristin Lees, Emma G. Lang, Ryan C. Kennedy, Hyeogsun Kwon, Rushika Perera, Yumin Qi, Justin D. Radolf, Joyce M. Sakamoto, Alejandro Sánchez-Gracia, Maiara S. Severo, Neal Silverman, Ladislav Šimo, Marta Tojo, Cristian Tornador, Janice P. Van Zee, Jesús Vázquez, Filipe G. Vieira, Margarita Villar, Adam R. Wespiser, Yunlong Yang, Jiwei Zhu, Peter Arensburger, Patricia V. Pietrantonio, Stephen C. Barker, Renfu Shao, Evgeny M. Zdobnov, Frank Hauser, Cornelis J. P. Grimmelikhuijzen, Yoonseong Park, Julio Rozas, Richard Benton, Joao H. F. Pedra, David R. Nelson, Maria F. Unger, Jose M. C. Tubio, Zhijian Tu, Hugh M. Robertson, Martin Shumway, Granger Sutton, Jennifer R. Wortman, Daniel Lawson, Stephen K. Wikel, Vishvanath M. Nene, Claire M. Fraser, Frank H. Collins, Bruce Birren, Karen E. Nelson, Elisabet Caler, Catherine A. Hill

Publikováno v: Nature Communications, Vol 7, Iss 1, Pp 1-13 (2016)

Ticks transmit a large number of pathogens that cause human diseases. Here, the authors sequence the genome of the tick Ixodes scapularisand uncover expansion of genes associated with parasitic processes unique to ticks and tick-host interactions.

Externí odkaz: https://doaj.org/article/fa4043b3779c4d0db50b094e385f7e3b