Publications
Submissions from 2020
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Comprehensive Analysis of Non Redundant Protein Database, Bagheri, Hamid, Dyer, Robert, Severin, Andrew J., Rajan, Hridesh
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CRISPR-Cas12a has widespread off-target and dsDNA-nicking effects, Murugan, Karthik, Seetharam, Arun S., Severin, Andrew J., Sashital, Dipali G.
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pyrpipe: a python package for RNA-Seq workflows, Singh, Urminder, Li, Jing, Seetharam, Arun, Wurtele, Eve Syrkin
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Transcriptome and Parasitome Analysis of Beet Cyst Nematode Heterodera schachtii, Elashry, Abdelnaser M., Habash, Samer S., Vijayapalani, Paramasivan, Brocke-Ahmadinejad, Nahal, Blümel, Roman, Seetharam, Arun, Schoof, Heiko, Grundler, Florian M. W.
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A genetic toolbox for metabolic engineering of Issatchenkia orientalis, Cao, Mingfeng, Fatma, Zia, Song, Xiaofei, Hsieh, Ping-Hung, Tran, Vinh G., Lyon, William L., Sayadi, Maryam, Shao, Zengyi, Yoshikuni, Yasuo, Zhao, Huimin
Submissions from 2019
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The Genome Sequence of Gossypioides kirkii Illustrates a Descending Dysploidy in Plants, Udall, Joshua A., Long, Evan, Ramaraj, Thiruvarangan, Conover, Justin L., Yuan, Daojun, Grover, Corrinne E., Gong, Lei, Arick, Mark A., II, Masonbrink, Rick E., Peterson, Daniel G., Wendel, Jonathan F.
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An Annotated Genome for Haliotis rufescens (Red Abalone) and Resequenced Green, Pink, Pinto, Black and White Abalone Species, Masonbrink, Rick E., Purcell, Catherine, Boles, Sara, Whitehead, Andrew, Hyde, John, Seetharam, Arun S., Severin, Andrew J.
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The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes, Masonbrink, Rick E., Maier, Tom R., Muppirala, Usha, Seetharam, Arun S., Lord, Etienne, Juvale, Parijat S., Schmutz, Jeremy, Johnson, Nathan T., Korkin, Dmitry, Mitchum, Melissa G., Mimee, Benjamin, Eves-van den Akker, Sebastian, Hudson, Matthew, Severin, Andrew J., Baum, Thomas J.
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fagin: synteny-based phylostratigraphy and finer classification of young genes, Arendsee, Zebulun, Li, Jing, Singh, Urminder, Bhandary, Priyanka, Seetharam, Arun, Wurtele, Eve Syrkin
Submissions from 2018
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Response to Persistent ER Stress in Plants: a Multiphasic Process that Transitions Cells from Prosurvival Activities to Cell Death, Srivastava, Renu, Li, Zhaoxia, Russo, Giulia, Tang, Jie, Bi, Ran, Muppirala, Usha, Chudalayandi, Sivanandan, Severin, Andrew J., He, Mingze, Vaitkevicius, Samuel I., Lawrence-Dill, Carolyn J., Liu, Peng, Stapleton, Ann E., Bassham, Diane C., Brandizzi, Federica, Howell, Stephen H.
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Evidence for a unique DNA-dependent RNA polymerase in cereal crops, Trujillo, Joshua T., Seetharam, Arun S., Hufford, Matthew B., Beilstein, Mark A., Mosher, Rebecca A.
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Insights into teleost sex determination from the Seriola dorsalis genome assembly, Purcell, Catherine M., Seetharam, Arun S., Snodgrass, Owyn, Ortega-García, Sofia, Hyde, John R., Severin, Andrew J.
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Shared Data Science Infrastructure for Genomics Data, Bagheri, Hamid, Muppirala, Usha, Severin, Andrew J., Rajan, Hridesh
Submissions from 2017
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The In-Feed Antibiotic Carbadox Induces Phage Gene Transcription in the Swine Gut Microbiome, Johnson, Timothy A., Looft, Torey, Severin, Andrew J., Bayles, Darrell O., Nasko, Daniel J., Wommack, K. Eric, Howe, Adina, Allen, Heather K.
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Vascular Endothelial Growth Factor A and Leptin Expression Associated with Ectopic Proliferation and Retinal Dysplasia in Zebrafish Optic Pathway Tumors, Schultz, Laura E., Solin, Staci L., Wierson, Welsey A., Lovan, Janna M., Syrkin-Nikolau, Judith, Lincow, Deborah E., Severin, Andrew J., Sakaguchi, Donald S., McGrail, Maura
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Transcriptomic responses to environmental temperature by turtles with temperature-dependent and genotypic sex determination assessed by RNAseq inform the genetic architecture of embryonic gonadal development, Radhakrishnan, Srihari, Literman, Robert A., Neuwald, Jennifer L., Severin, Andrew, Valenzuela, Nicole
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Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research, The Aquaculture Genomics, Genetics and Breeding Workshop, Severin, Andrew J., et al
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Raising orphans from a metadata morass: a researcher's guide to re-use of public ’omics data, Bhandary, Priyanka, Seetharam, Arun S., Arendsee, Zebulun, Hur, Manhoi, Wurtele, Eve Syrkin
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Transcriptomic responses to environmental temperature by turtles with temperature-dependent and genotypic sex determination assessed by RNAseq inform the genetic architecture of embryonic gonadal development, Radhakrishnan, Shrihari, Literman, Robert, Neuwald, Jennifer, Severin, Andrew, Valenzuela, Nicole
Submissions from 2016
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A Plasmodium‐like virulence effector of the soybean cyst nematode suppresses plant innate immunity, Noon, Jason B., Qi, Mingsheng, Sill, Danielle N., Muppirala, Usha, Eves-van den Akker, Sebastian, Maier, Thomas R., Dobbs, Drena, Mitchum, Melissa G., Hewezi, Tarek, Baum, Thomas J.
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Genome, transcriptome and methylome sequencing of a primitively eusocial wasp reveal a greatly reduced DNA methylation system in a social insect, Standage, Daniel S., Berens, Ali J., Glastad, Karl M., Severin, Andrew J., Brendel, Volker P., Toth, Amy L.
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A Study of Alterations in DNA Epigenetic Modifications (5mC and 5hmC) and Gene Expression Influenced by Simulated Microgravity in Human Lymphoblastoid Cells, Chowdhury, Basudev, Seetharam, Arun S., Wang, Zhiping, Liu, Yunlong, Lossie, Amy C., Thimmapuram, Jyothi, Irudayaraj, Joseph
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A motif-based method for predicting interfacial residues in both the RNA and protein components of protein-RNA complexes, Muppirala, Usha, Lewis, Benjamin A., Mann, Carla M., Dobbs, Drena L.
Submissions from 2015
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Transcriptome profiling of soybean (Glycine max) roots challenged with pathogenic and non-pathogenic isolates of Fusarium oxysporum, Lanubile, Alessandra, Muppirala, Usha K., Severin, Andrew J., Marocco, Adriano, Munkvold, Gary P.
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CRISPR interference and priming varies with individual spacer sequences, Xue, Chaoyou, Seetharam, Arun S., Musharova, Olga, Severinov, Konstantin, Brouns, Stan J. J., Severin, Andrew J., Sashital, Dipali G.