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Thiruvarangan Ramaraj, Ph.D. - Publications

Affiliations: 
2010 Computer Science Montana State University, Bozeman, MT 
Area:
Computer Science, Bioinformatics Biology
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32 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Ramaraj T, Grover CE, Mendoza AC, Arick MA, Jareczek JJ, Leach AG, Peterson DG, Wendel JF, Udall JA. The Gossypium herbaceum L. Wagad genome as a resource for understanding cotton domestication. G3 (Bethesda, Md.). PMID 36454094 DOI: 10.1093/g3journal/jkac308  0.381
2019 Udall JA, Long E, Ramaraj T, Conover JL, Yuan D, Grover CE, Gong L, Arick MA, Masonbrink RE, Peterson DG, Wendel JF. The Genome Sequence of Illustrates a Descending Dysploidy in Plants. Frontiers in Plant Science. 10: 1541. PMID 31827481 DOI: 10.3389/Fpls.2019.01541  0.363
2019 Dieser M, Smith HJ, Ramaraj T, Foreman CM. CG23_2: Comparative Genome Analysis Reveals Enhanced Environmental Sensing and Transcriptional Regulation for Adaptation to Life in an Antarctic Supraglacial Stream. Microorganisms. 7. PMID 31618878 DOI: 10.3390/microorganisms7100454  0.352
2019 Udall JA, Long E, Hanson C, Yuan D, Ramaraj T, Conover JL, Gong L, Arick MA, Grover CE, Peterson DG, Wendel JF. Genome Sequence Assemblies of and . G3 (Bethesda, Md.). PMID 31462444 DOI: 10.1534/G3.119.400392  0.401
2018 Sun X, Chen W, Ivanov S, MacLean AM, Wight H, Ramaraj T, Mudge J, Harrison MJ, Fei Z. Genome and evolution of the arbuscular mycorrhizal fungus Diversispora epigaea (formerly Glomus versiforme) and its bacterial endosymbionts. The New Phytologist. PMID 30368822 DOI: 10.1111/Nph.15472  0.451
2018 Cleary A, Ramaraj T, Kahanda I, Mudge J, Mumey B. Exploring Frequented Regions in Pan-Genomic Graphs. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 30106690 DOI: 10.1109/Tcbb.2018.2864564  0.599
2018 Tran HTM, Ramaraj T, Furtado A, Lee LS, Henry RJ. Use of a draft genome of coffee (Coffea arabica) to identify SNPs associated with caffeine content. Plant Biotechnology Journal. PMID 29509991 DOI: 10.1111/Pbi.12912  0.47
2017 Grover CE, Arick MA, Conover JL, Thrash A, Hu G, Sanders WS, Hsu CY, Naqvi RZ, Farooq M, Li X, Gong L, Mudge J, Ramaraj T, Udall JA, Peterson DG, et al. Comparative Genomics of an Unusual Biogeographic Disjunction in the Cotton Tribe (Gossypieae) Yields Insights into Genome Downsizing. Genome Biology and Evolution. 9: 3328-3344. PMID 29194487 DOI: 10.1093/Gbe/Evx248  0.481
2017 Lightfoot DJ, Jarvis DE, Ramaraj T, Lee R, Jellen EN, Maughan PJ. Single-molecule sequencing and Hi-C-based proximity-guided assembly of amaranth (Amaranthus hypochondriacus) chromosomes provide insights into genome evolution. Bmc Biology. 15: 74. PMID 28854926 DOI: 10.1186/S12915-017-0412-4  0.378
2017 Moll KM, Zhou P, Ramaraj T, Fajardo D, Devitt NP, Sadowsky MJ, Stupar RM, Tiffin P, Miller JR, Young ND, Silverstein KAT, Mudge J. Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula. Bmc Genomics. 18: 578. PMID 28778149 DOI: 10.1186/S12864-017-3971-4  0.444
2017 Miller JR, Zhou P, Mudge J, Gurtowski J, Lee H, Ramaraj T, Walenz BP, Liu J, Stupar RM, Denny R, Song L, Singh N, Maron LG, McCouch SR, McCombie WR, et al. Hybrid assembly with long and short reads improves discovery of gene family expansions. Bmc Genomics. 18: 541. PMID 28724409 DOI: 10.1186/S12864-017-3927-8  0.442
2017 Zhou P, Silverstein KA, Ramaraj T, Guhlin J, Denny R, Liu J, Farmer AD, Steele KP, Stupar RM, Miller JR, Tiffin P, Mudge J, Young ND. Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes. Bmc Genomics. 18: 261. PMID 28347275 DOI: 10.1186/S12864-017-3654-1  0.468
2016 Clouse JW, Adhikary D, Page JT, Ramaraj T, Deyholos MK, Udall JA, Fairbanks DJ, Jellen EN, Maughan PJ. The Amaranth Genome: Genome, Transcriptome, and Physical Map Assembly. The Plant Genome. 9. PMID 27898770 DOI: 10.3835/Plantgenome2015.07.0062  0.458
2016 Sundararajan A, Dukowic-Schulze S, Kwicklis M, Engstrom K, Garcia N, Oviedo OJ, Ramaraj T, Gonzales MD, He Y, Wang M, Sun Q, Pillardy J, Kianian SF, Pawlowski WP, Chen C, et al. Gene Evolutionary Trajectories and GC Patterns Driven by Recombination in Zea mays. Frontiers in Plant Science. 7: 1433. PMID 27713757 DOI: 10.3389/Fpls.2016.01433  0.353
2016 Chaney L, Mangelson R, Ramaraj T, Jellen EN, Maughan PJ. The complete chloroplast genome sequences for four Amaranthus species (Amaranthaceae). Applications in Plant Sciences. 4. PMID 27672525 DOI: 10.3732/Apps.1600063  0.428
2016 Vishwanathan N, Bandyopadhyay AA, Fu HY, Sharma M, Johnson KC, Mudge J, Ramaraj T, Onsongo G, Silverstein KA, Jacob NM, Le H, Karypis G, Hu WS. Augmenting Chinese hamster genome assembly by identifying regions of high confidence. Biotechnology Journal. PMID 27374913 DOI: 10.1002/Biot.201500455  0.47
2016 Deschamps S, Mudge J, Cameron C, Ramaraj T, Anand A, Fengler K, Hayes K, Llaca V, Jones TJ, May G. Characterization, correction and de novo assembly of an Oxford Nanopore genomic dataset from Agrobacterium tumefaciens. Scientific Reports. 6: 28625. PMID 27350167 DOI: 10.1038/Srep28625  0.405
2016 Horn RL, Ramaraj T, Devitt NP, Schilkey FD, Cowley DE. De novo assembly of a tadpole shrimp (Triops newberryi) transcriptome and preliminary differential gene expression analysis. Molecular Ecology Resources. PMID 27292122 DOI: 10.1111/1755-0998.12555  0.426
2016 He J, Sundararajan A, Devitt NP, Schilkey FD, Ramaraj T, Melançon CE. Complete Genome Sequence of Streptomyces venezuelae ATCC 15439, Producer of the Methymycin/Pikromycin Family of Macrolide Antibiotics, Using PacBio Technology. Genome Announcements. 4. PMID 27151802 DOI: 10.1128/Genomea.00337-16  0.446
2016 Smith HJ, Foreman CM, Akiyama T, Franklin MJ, Devitt NP, Ramaraj T. Genome Sequence of Janthinobacterium sp. CG23_2, a Violacein-Producing Isolate from an Antarctic Supraglacial Stream. Genome Announcements. 4. PMID 26823573 DOI: 10.1128/Genomea.01468-15  0.474
2016 Clouse JW, Adhikary D, Page JT, Ramaraj T, Deyholos MK, Udall JA, Fairbanks DJ, Jellen EN, Maughan PJ. The amaranth genome: Genome, transcriptome, and physical map assembly Plant Genome. 9. DOI: 10.3835/plantgenome2015.07.0062  0.363
2015 Ogasawara Y, Torrez-Martinez N, Aragon AD, Yackley BJ, Weber JA, Sundararajan A, Ramaraj T, Edwards JS, Melançon CE. High-Quality Draft Genome Sequence of Actinobacterium Kibdelosporangium sp. MJ126-NF4, Producer of Type II Polyketide Azicemicins, Using Illumina and PacBio Technologies. Genome Announcements. 3. PMID 25838474 DOI: 10.1128/Genomea.00114-15  0.431
2014 Smith HJ, Foreman CM, Ramaraj T. Draft Genome Sequence of a Metabolically Diverse Antarctic Supraglacial Stream Organism, Polaromonas sp. Strain CG9_12, Determined Using Pacific Biosciences Single-Molecule Real-Time Sequencing Technology. Genome Announcements. 2. PMID 25477404 DOI: 10.1128/Genomea.01242-14  0.415
2014 Ramaraj T, Matyi SA, Sundararajan A, Lindquist IE, Devitt NP, Schilkey FD, Lamichhane-Khadka R, Hoyt PR, Mudge J, Gustafson JE. Draft Genome Sequences of Vancomycin-Susceptible Staphylococcus aureus Related to Heterogeneous Vancomycin-Intermediate S. aureus. Genome Announcements. 2. PMID 25301662 DOI: 10.1128/Genomea.01033-14  0.367
2014 Matyi SA, Ramaraj T, Sundararajan A, Lindquist IE, Devitt NP, Schilkey FD, Lamichhane-Khadka R, Hoyt PR, Mudge J, Gustafson JE. Draft Genomes of Heterogeneous Vancomycin-Intermediate Staphylococcus aureus Strain MM66 and MM66 Derivatives with Altered Vancomycin Resistance Levels. Genome Announcements. 2. PMID 25013145 DOI: 10.1128/Genomea.00688-14  0.332
2014 Ramaraj T, Sundararajan A, Schilkey FD, Delvecchio VG, Donlon M, Ziemer C, Mudge J. Improved Hybrid Genome Assemblies of Two Strains of Bacteroides xylanisolvens, SD_CC_1b and SD_CC_2a, Obtained Using Illumina and 454 Sequencing Technologies. Genome Announcements. 2. PMID 24699955 DOI: 10.1128/Genomea.00237-14  0.386
2014 Dukowic-Schulze S, Sundararajan A, Ramaraj T, Mudge J, Chen C. Sequencing-based large-scale genomics approaches with small numbers of isolated maize meiocytes. Frontiers in Plant Science. 5: 57. PMID 24611068 DOI: 10.3389/Fpls.2014.00057  0.396
2014 Schleiss MR, McAllister S, Armién AG, Hernandez-Alvarado N, Fernández-Alarcón C, Zabeli JC, Ramaraj T, Crow JA, McVoy MA. Molecular and biological characterization of a new isolate of guinea pig cytomegalovirus. Viruses. 6: 448-75. PMID 24473341 DOI: 10.3390/V6020448  0.311
2013 Schleiss MR, Hernandez-Alvarado N, Ramaraj T, Crow JA. Genome Sequence of a Novel, Newly Identified Isolate of Guinea Pig Cytomegalovirus, the CIDMTR Strain. Genome Announcements. 1. PMID 24371200 DOI: 10.1128/Genomea.01052-13  0.439
2013 Francis F, Kim J, Ramaraj T, Farmer A, Rush MC, Ham JH. Comparative genomic analysis of two Burkholderia glumae strains from different geographic origins reveals a high degree of plasticity in genome structure associated with genomic islands. Molecular Genetics and Genomics : Mgg. 288: 195-203. PMID 23563926 DOI: 10.1007/S00438-013-0744-X  0.419
2012 Ramaraj T, Angel T, Dratz EA, Jesaitis AJ, Mumey B. Antigen-antibody interface properties: composition, residue interactions, and features of 53 non-redundant structures. Biochimica Et Biophysica Acta. 1824: 520-32. PMID 22246133 DOI: 10.1016/J.Bbapap.2011.12.007  0.524
2010 Baranzini SE, Mudge J, van Velkinburgh JC, Khankhanian P, Khrebtukova I, Miller NA, Zhang L, Farmer AD, Bell CJ, Kim RW, May GD, Woodward JE, Caillier SJ, McElroy JP, Gomez R, ... ... Ramaraj T, et al. Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis. Nature. 464: 1351-6. PMID 20428171 DOI: 10.1038/Nature08990  0.363
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