Arun Seetharam bio photo

Arun Seetharam

Bioinformatician

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Publications

Overview

Preprints/In-Press

  • Jonathan Cahn, Michael Regulski, Jason Lynn, Evan Ernst, Cristiane de Santis Alves, Srividya Ramakrishnan, Kapeel Chougule, Sharon Wei, Zhenyuan Lu, Xiaosa Xu, Jorg Drenkow, Melissa Kramer, Arun S. Seetharam, Matthew B. Hufford, W. Richard McCombie, Doreen Ware, David Jackson, Michael C. Schatz, Thomas R. Gingeras, and Robert A. Martienssen. MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication. bioRxiv, 10.1101/2024.02.22.581585, 2024

  • Carson M. Andorf, Jeffrey Ross-Ibarra, Arun S. Seetharam, Matthew B. Hufford, and Margaret R. Woodhouse, A unified VCF data set from nearly 1,500 diverse maize accessions and resources to explore the genomic landscape of maize, bioRxiv, 10.1101/2024.04.30.591904, 2024

  • Julia Engelhorn, Samantha J. Snodgrass, Amelie Kok, Arun S. Seetharam, Michael Schneider, Tatjana Kiwit, Ayush Singh, Michael Banf, Merritt Khaipho-Burch, Daniel E. Runcie, Victor Sánchez Camargo, J. Vladimir Torres-Rodriguez, Guangchao Sun, Maike Stam, Fabio Fiorani, James C. Schnable, Hank W. Bass, Matthew B. Hufford, Benjamin Stich, Wolf B. Frommer, Jeffrey Ross-Ibarra, and Thomas Hartwig. Genetic variation at transcription factor binding sites largely explains phenotypic heritability in maize. bioRxiv, 10.1101/2023.08.08.551183, 2023

  • Aimee J Schulz, Jingjing Zhai, Taylor AuBuchon-Elder, Mohamed El-Walid, Taylor H Ferebee, Elizabeth H Gilmore, Matthew B Hufford, Lynn C Johnson, Elizabeth A Kellogg, Thuy La, Evan Long, Zachary R Miller, M Cinta Romay, Arun S. Seetharam, Michelle C Stitzer, Travis Wrightsman, Edward S Buckler, Brandon Monier, Sheng-Kai Hsu. Fishing for a reelGene: evaluating gene models with evolution and machine learning. bioRxiv, 10.1101/2023.09.19.558246, 2023

  • Travis Wrightsman, Taylor H. Ferebee, M. Cinta Romay, Arun S. Seetharam, Taylor AuBuchon-Elder, Alyssa R. Phillips, Michael Syring, Matthew B. Hufford, Elizabeth A. Kellogg, and Edward S. Buckler, Current genomic deep learning architectures generalize across grass species but not alleles. bioRxiv, 10.1101/2024.04.11.589024, 2024,

  • Urminder Singh, Jeffrey A. Haltom, Joseph W. Guarnieri, Jing Li, Arun Seetharam, Afshin Beheshti, Bruce Aronow, and Eve Syrkin Wurtele A pan-tissue, pan-disease compendium of human orphan genes bioRxiv, 10.1101/2024.02.21.581488, 2024

2024

  • Shujun Ou, Tyler Collins, Yinjie Qiu, Arun S. Seetharam, Claire C. Menard, Nancy Manchanda, Jonathan I Gent, Michael C. Schatz, Sarah. N. Anderson, Matthew B Hufford, and Candice N Hirsch. Differences in activity and stability drive transposable element variation in tropical and temperate maize. Genome Research, 34(8) 10.1101/gr.278131.123, 2024

  • Jessica A. Kinkade, Arun S. Seetharam, Shrikesh Sachdev, Nathan J. Bivens, Brett S. Phinney, Gabriela Grigorean, R Michael Roberts, Geetu Tuteja, Cheryl S. Rosenfeld, Extracellular vesicles from mouse trophoblast cells: effects on neural progenitor cells and potential participants in the placenta-brain Axis, Biology of Reproduction, ioad146, 2023.

  • Foster Tyler L., Monika Kloiber-Maitz, Laurine Gilles, Ursula K. Frei, Sarah Pfeffer, Yu-Ru Chen, Somak Dutta, Arun S. Seetharam, Matthew B. Hufford, and Thomas Lübberstedt, Fine mapping of major QTL qshgd1 for spontaneous haploid genome doubling in maize (Zea mays L.). Theoretical and Applied Genetics 137, no. 5 10.1007/s00122-024-04615-y

2023

  • Silas Tittes, Anne Lorant, Sean McGinty, James B. Holland, Jose de Jesus Sánchez-González, Arun S. Seetharam, Maud Tenaillon, and Jeffrey Ross-Ibarra, Not so local: the population genetics of convergent adaptation in maize and teosinte, eLife, 12:RP92405 10.7554/eLife.92405.1.sa2, 2023

  • Thomas Hartwig, Michael Banf, Gisele Passaia Prietsch, Jia-Ying Zhu, Isabel Mora-Ramírez, Jos H. M. Schippers, Samantha J. Snodgrass, Arun S. Seetharam, Bruno Huettel, Judith M. Kolkman, Jinliang Yang, Julia Engelhorn, Zhi-Yong Wang, Hybrid allele-specific ChIP-seq analysis identifies variation in brassinosteroid-responsive transcription factor binding linked to traits in maize Genome Biology 24(108) 2023.

  • Alyssa R. Phillips, Arun S. Seetharam, Taylor AuBuchon-Elder, Edward S. Buckler, Lynn J. Gillespie, Matthew B. Hufford, Victor Llaca, M. Cinta Romay, Robert J. Soreng, Elizabeth A. Kellogg, Jeffrey Ross-Ibarra. A happy accident: a novel turfgrass reference genome, G3, 10.1101/2022.03.08.483531, 2023

2022

  • Arun S. Seetharam, Ha T.H. Vu, Sehee Choi, Teka Khan, Megan A. Sheridan, Toshihiko Ezashi, R. Michael Roberts, Geetu Tuteja, The product of BMP-directed differentiation protocols for human primed pluripotent stem cells is placental trophoblast and not amnion, Stem Cell Reports, 17(6) p1289-1302, 2022.

2021

  • Jing Li, Urminder Singh, Priyanka Bhandary, Jacqueline Campbell, Zebulun Arendsee, Arun S. Seetharam, Eve Syrkin Wurtele.Foster thy young: Enhanced prediction of orphan genes in assembled genomes, Nucleic Acids Research, gkab1238_, 2021.

  • Arun Seetharam†, Yunqing Yu†, Sébastien Belanger, Lynn G. Clark, Blake C. Meyers, Elizabeth A. Kellogg, Matthew B. Hufford. The Streptochaeta genome and the evolution of the grasses. Frontiers in Plant Science, vol. 12, p2165, 2021.

  • Matthew B Hufford, Arun S Seetharam, Margaret R Woodhouse, Kapeel M. Chougule, Shujun Ou, Jianing Liu, William A Ricci, Tingting Guo, Andrew Olson, Yinjie Qiu, Rafael Della Coletta, Silas Tittes, Asher I Hudson, Alexandre P. Marand, Sharon Wei, Zhenyuan Lu, Bo Wang, Marcela K Tello-Ruiz, Rebecca D Piri, Na Wang, Dong won Kim, Yibing Zeng, Christine H O’Connor, Xianran Li, Amanda M Gilbert, Erin Baggs, Ksenia V Krasileva, John L Portwood II, Ethalinda KS Cannon, Carson M Andorf, Nancy Manchanda, Samantha J Snodgrass, David E Hufnagel, Qiuhan Jiang, Sarah Pedersen, Michael L Syring, David A Kudrna, Victor Llaca, Kevin Fengler, Robert J. Schmitz, Jeffrey Ross-Ibarra, Jianming Yu, Jonathan I Gent, Candice N Hirsch, Doreen Ware, R Kelly Dawe. De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science, Vol. 373, Issue 6555, pp. 655-662, 2021.

  • Teka Khan†, Arun S. Seetharam†, Jie Zhou, Nathan J. Bivens, Danny J. Schust, Toshihiko Ezashi, Geetu Tuteja and R M. Roberts. Single nucleus RNA sequence (snRNAseq) analysis of the spectrum of trophoblast lineages generated from human pluripotent stem cells in vitro. Frontiers in Cell and Developmental Biology, vol. 9, p1881, 2021.

  • Nolan Bornowski, Kathryn J. Michel, John P. Hamilton, Shujun Ou, Arun S. Seetharam, Jerry Jenkins, Jane Grimwood, Chris Plott, Shengqiang Shu, Jayson Talag, Megan Kennedy, Hope Hundley, Vasanth R. Singan, Kerrie Barry, Chris Daum, Yuko Yoshinaga, Jeremy Schmutz, Candice N. Hirsch, Matthew B. Hufford, Natalia de Leon, Shawn M. Kaeppler, C. Robin Buell. Genomic variation within the maize Stiff Stalk heterotic germplasm pool. The Plant Genome, e20114, 2021.

  • Urminder Singh, Jing Li, Arun S Seetharam and Eve S Wurtele. pyrpipe: a Python package for RNA-Seq workfows. NAR Genomics and Bioinformatics, 3(2) lqab04, 2021.

  • Wyatt A. Shell, Michael A. Steffen, Hannah K. Pare, Arun S. Seetharam, Andrew J. Severin, Amy L. Toth and Sandra M. Rehan. Sociality sculpts similar patterns of molecular evolution in two independently evolved lineages of eusocial bees. Communications Biology (4) 253, 2021

  • Karthik Murugan, Shravanti Suresh, Arun S Seetharam, Andrew J Severin, and Dipali G Sashital. Systematic in vitro specificity profiling reveals nicking defects in natural and engineered CRISPR-Cas9 variants. Nucleic Acids Research, gkab163, 2021.

2020

  • David E Hufnagel, Matthew B Hufford, and Arun S Seetharam. SequelTools: a suite of tools for working with PacBio Sequel raw sequence data. BMC Bioinformatics, (21) 429, 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.

  • 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 S. 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 S. Seetharam, Andrew J. 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.

† shared first authors