Arun Seetharam bio photo

Arun Seetharam

Bioinformatician

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Publications

Overview

Preprints/In-Press

  • Karthik Murugan, Arun S Seetharam, Andrew J Severin, and Dipali G Sashital. High-throughput in vitro specificity profiling of natural and high-fidelity CRISPR-Cas9 variants. bioRxiv, 2020.05.12.091991, 2020. <div class="altmetric-embed" data-badge-type="donut" data-altmetric-id="81901958"></div>

  • Urminder Singh, Jing Li, Arun S Seetharam and Eve S Wurtele. pyrpipe: a python package for rna-seq workfows. bioRxiv, page 925818, 2020.

  • Arun S Seetharam, Urminder Singh, Jing Li, Priyanka Bhandary, Zebulun Arendsee, and Eve Syrkin Wurtele. Maximizing prediction of orphan genes in assembled genomes. bioRxiv, 2019.

  • David E Hufnagel, Matthew B Hufford, and Arun S Seetharam. SequelTools: A suite of tools for working with PacBio Sequel raw sequence data. bioRxiv, page 611814, 2019.

2020

  • Jianing Liu, Arun S Seetharam, Kapeel Chougule, Shujun Ou, Kyle W. Swentowsky, Jonathan I. Gent, Victor Llaca, Margaret R. Woodhouse, Nancy Manchanda, Gernot G. Presting, David A. Kudrna, Magdy Alabady, Candice N. Hirsch, Kevin A. Fengler, Doreen Ware, Todd P. Michael, Matthew B. Hufford and R. Kelly Dawe, Gapless assembly of maize chromosomes using long read technologies. Genome Biology, (21) 121, 2020.

  • Shujun Ou, Jianing Liu, Kapeel M. Chougule, Arkarachai Fungtammasan, Arun Seetharam, Joshua Stein, Victor Llaca, Nancy Manchanda, Amanda M. Gilbert, Xuehong Wei, Chen-Shan Chin, David E. Hufnagel, Sarah Pedersen, Samantha Snodgrass, Kevin Fengler, Margaret Woodhouse, Brian P. Walenz, Sergey Koren, Adam M. Phillippy, Brett Hannigan, R. Kelly Dawe, Candice N. Hirsch, Matthew B. Hufford, Doreen Ware. Effect of sequence depth and length in long-read assembly of the maize inbred NC358. Nature Communications 11(2288), 2020

  • Karthik Murugan, Arun S Seetharam, Andrew J Severin, and Dipali G Sashital. CRISPR-Cas12a has widespread off-target and dsDNA-nicking effects. Journal of Biological Chemistry, jbc-RA120, 2020.

  • Nancy Manchanda, John L Portwood, Margaret R Woodhouse, Arun S Seetharam, Carolyn J Lawrence-Dill, Carson M Andorf, and Matthew B Hufford. GenomeQC: A quality assessment tool for genome assemblies and gene structure annotations BMC Genomics 21(193), 2020.

  • Abdelnaser M Elashry, Samer S Habash, Paramasivan Vijayapalani, Nahal Brocke-Ahmadinejad, Roman Blümel, Arun Seetharam, Heiko Schoof, and Florian MW Grundler. Transcriptome and parasitome analysis of Beet Cyst Nematode Heterodera schachtii. Scientific Reports, 10(1):1–12, 2020.

2019

  • Rick E Masonbrink, Catherine M Purcell, Sara E Boles, Andrew Whitehead, John R Hyde, Arun S Seetharam, and Andrew J Severin. An annotated genome for Haliotis rufescens (red abalone) and resequenced green, pink, pinto, black, and white abalone species. Genome biology and evolution, 11(2):431–438, 2019.

  • Rick E Masonbrink, Tom R. Maier, Usha Muppirala, Arun S. Seetharam, Etienne Lord, Parijat S. Juvale, Jeremy Schmutz, Nathan T. Johnson, Dmitry Korkin, Melissa G. Mitchum, Benjamin Mimee, Sebastian Eves-van den Akker, Matthew Hudson, Andrew J. Severin and Thomas J. Baum . The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes. BMC genomics, 20(1):119, 2019.

  • Stacey N Barnes, Rick E Masonbrink, Thomas R Maier, Arun Seetharam, Anoop S Sindhu, Andrew J Severin, and Thomas J Baum. Heterodera glycines utilizes promiscuous spliced leaders and demonstrates a unique preference for a species-specific spliced leader over C. elegans SL1. Scientific reports, 9(1):1–11, 2019.

  • Morgan M Sommer-Lassa, James Reecy, Andrew Severin, Arun Somwarpet-Seetharam, and Mary Sue Mayes. The effects of feeding a novel Saccharomyces cerevisiae feed additive on the prevalence and abundance of anti-microbial resistance genes in the microbiome (s) of receiving beef calves. Journal of Animal Science, 97(Supplement_2):40–41, 2019.

  • Zebulun Arendsee, Jing Li, Urminder Singh, Priyanka Bhandary, Arun Seetharam, and Eve Syrkin Wurtele. fagin: synteny-based phylostratigraphy and finer classification of young genes. BMC bioinformatics, 20(1):1–14, 2019.

  • Zebulun Arendsee, Jing Li, Urminder Singh, Arun Seetharam, Karin Dorman, and Eve Syrkin Wurtele. phylostratr: A framework for phylostratigraphy. Bioinformatics, 35(19):3617–3627, 2019.

  • Rick Masonbrink, Tom R Maier, Arun S Seetharam, Parijat S Juvale, Levi Baber, Thomas J Baum, and Andrew J Severin. SCNbase: a genomics portal for the Soybean Cyst Nematode (Heterodera glycines). Database, 2019(1):baz111, 2019.

2018

  • Priyanka Bhandary, Arun S Seetharam, Zebulun W Arendsee, Manhoi Hur, and Eve Syrkin Wurtele. Raising orphans from a metadata morass: A researcher’s guide to re-use of public’omics data. Plant science, 267:32–47, 2018.

  • Catherine M. Purcell, Arun S. Seetharam, Owyn Snodgrass, Sofia Ortega-García, John R. Hyde, and Andrew J. Severin. Insights into teleost sex determination from the Seriola dorsalis genome assembly. BMC Genomics, 19(31), 2018.

  • Joshua T Trujillo, Arun S Seetharam, Matthew B Hufford, Mark A Beilstein, and Rebecca A Mosher. Evidence for a unique DNA-dependent RNA polymerase in cereal crops. Molecular biology and evolution, 35(10):2454–2462, 2018.

2017

  • Mingfeng Cao, Meirong Gao, Carmen Lorena Lopez-Garcia, Yutong Wu, Arun Somwarpet Seetharam, Andrew Josef Severin, and Zengyi Shao. Centromeric DNA facilitates nonconventional yeast genetic engineering. ACS synthetic biology, 6(8):1545–1553, 2017.

  • J. N. Cullen, A. Lithio, A. S. Seetharam, Y. Zheng, G. Li, D. Nettleton, and A.M. O’Connor. Microbial community sequencing analysis of the calf eye microbiota and relationship to infectious bovine kerato-conjunctivitis. Veterinary Microbiology, 207(2017):267–279, 2017.

  • Mingfeng Cao, Arun Somwarpet Seetharam, Andrew Josef Severin, and Zengyi Shao. Rapid isolation of centromeres from Scheffersomyces stipitis. ACS synthetic biology, 6(11):2028–2034, 2017.

  • Rick E Masonbrink, Andrew J Severin, and Arun S Seetharam. Comparative genomics of soybean and other legumes. In The Soybean Genome, pages 83–93. Springer, 2017.

2016

  • Basudev Chowdhury, Arun Seetharam, Zhiping Wang, Yunlong Liu, Amy C. Lossie, Jyothi Thimmapuram, and Joseph Irudayaraj. A study of alterations in dna epigenetic modifications (5mc and 5hmc) and gene expression influenced by simulated microgravity in human lymphoblastoid cells. PLoS ONE, 11(1):e0147514, 2016.

2015

  • Arun S Seetharam, Emily Kawaler, Zhi-Qiang Du, Max F Rothschild, and Andrew J Severin. Microbiome analyses of pacific white shrimp (Litopenaeus vannamei) collected from disparate geographical locations. Genomics data, 6:67, 2015.

  • Chaoyou Xue, Arun S Seetharam, Olga Musharova, Konstantin Severinov, Stan J J. Brouns, Andrew J Severin, and Dipali G Sashital. CRISPR interference and priming varies with individual spacer sequences. Nucleic acids research, 43(22):10831–10847, 2015.

  • Arun Seetharam, Antonio Gomez, Catherine M Purcell, John R Hyde, Philip D Blood, and Andrew J Severin. NCBI-BLAST programs optimization on XSEDE resources for sustainable aquaculture. In Proceedings of the 2015 XSEDE Conference: Scientific Advancements Enabled by Enhanced Cyberinfrastructure, pages 1–5, 2015.

Ph.D/Masters

  • Arun S Seetharam and Gary W Stuart. Whole genome phylogeny for 21 Drosophila species using predicted 2b-RAD fragments. PeerJ, 1:e226, 2013.

  • Arun Seetharam and Gary W Stuart. A study on the distribution of 37 well conserved families of C2H2 zinc finger genes in eukaryotes. Bmc Genomics, 14(1):420, 2013.

  • Rajkumar, B. Fakrudin, S. P. Kavil, Y. Girma, S. S. Arun, D. Dadakhalandar, B. H. Gurusiddesh, A. M. Patil, M. Thudi, S. B. Bhairappanavar. Molecular mapping of genomic regions harbouring QTLs for root and yield traits in sorghum (Sorghum bicolor L. Moench). Physiology and Molecular Biology of Plants, 19(3):409–419, 2013.

  • Arun Seetharam and Gary W Stuart. Whole genome phylogenies for multiple Drosophila species. BMC research notes, 5(1):670, 2012.

  • Arun Seetharam, Yang Bai, and Gary W Stuart. A survey of well conserved families of C2H2 zinc-finger genes in Daphnia. BMC genomics, 11(1):276, 2010.

  • P. Srinivasa Reddy, B. Fakrudin, Rajkumar, S. M. Punnuri, S. S. Arun, M. S. Kuruvinashetti, I. K. Das, and N. Seetharama. Molecular mapping of genomic regions harboring QTLs for stalk rot resistance in sorghum. Euphytica, 159(1–2):191–198, 2007.

Thesis/Dissertation

  • Arun Somwarpet Seetharam. Phylogenomics: Molecular Evolution in the Genomics Era. PhD thesis, 2012.

  • SS Arun. In Silico Est Datamining for Elucidation of Repeats Biology and Functional Annotation in Sorghum [Sorghum bicolor (L.) Moench.]. Masters thesis, UAS, Dharwad, 2006.