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Items: 40

1.

Salt and oxidative stresses uniquely regulate tomato cytokinin levels and transcriptomic response.

Keshishian EA, Hallmark HT, Ramaraj T, Plačková L, Sundararajan A, Schilkey F, Novák O, Rashotte AM.

Plant Direct. 2018 Jul 19;2(7):e00071. doi: 10.1002/pld3.71. eCollection 2018 Jul.

2.

Genome and evolution of the arbuscular mycorrhizal fungus Diversispora epigaea (formerly Glomus versiforme) and its bacterial endosymbionts.

Sun X, Chen W, Ivanov S, MacLean AM, Wight H, Ramaraj T, Mudge J, Harrison MJ, Fei Z.

New Phytol. 2019 Feb;221(3):1556-1573. doi: 10.1111/nph.15472. Epub 2018 Oct 13.

PMID:
30368822
3.

Exploring Frequented Regions in Pan-Genomic Graphs.

Cleary A, Ramaraj T, Kahanda I, Mudge J, Mumey B.

IEEE/ACM Trans Comput Biol Bioinform. 2018 Aug 9. doi: 10.1109/TCBB.2018.2864564. [Epub ahead of print]

PMID:
30106690
4.

Cranberry-derived proanthocyanidins induce a differential transcriptomic response within Candida albicans urinary biofilms.

Sundararajan A, Rane HS, Ramaraj T, Sena J, Howell AB, Bernardo SM, Schilkey FD, Lee SA.

PLoS One. 2018 Aug 8;13(8):e0201969. doi: 10.1371/journal.pone.0201969. eCollection 2018.

5.

Histone Citrullination Represses MicroRNA Expression, Resulting in Increased Oncogene mRNAs in Somatolactotrope Cells.

DeVore SB, Young CH, Li G, Sundararajan A, Ramaraj T, Mudge J, Schilkey F, Muth A, Thompson PR, Cherrington BD.

Mol Cell Biol. 2018 Sep 14;38(19). pii: e00084-18. doi: 10.1128/MCB.00084-18. Print 2018 Oct 1.

6.

Use of a draft genome of coffee (Coffea arabica) to identify SNPs associated with caffeine content.

Tran HTM, Ramaraj T, Furtado A, Lee LS, Henry RJ.

Plant Biotechnol J. 2018 Oct;16(10):1756-1766. doi: 10.1111/pbi.12912. Epub 2018 Apr 13.

7.

Correction to: The transcriptome landscape of early maize meiosis.

Dukowic-Schulze S, Sundararajan A, Mudge J, Ramaraj T, Farmer AD, Wang M, Sun Q, Pillardy J, Kianian S, Retzel EF, Pawlowski WP, Chen C.

BMC Plant Biol. 2018 Jan 15;18(1):12. doi: 10.1186/s12870-017-1224-y.

8.

Comparative Genomics of an Unusual Biogeographic Disjunction in the Cotton Tribe (Gossypieae) Yields Insights into Genome Downsizing.

Grover CE, Arick MA 2nd, 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, Wendel JF.

Genome Biol Evol. 2017 Dec 1;9(12):3328-3344. doi: 10.1093/gbe/evx248.

9.

Phytochemical constituents from dietary plant Citrus hystrix.

Sadasivam M, Kumarasamy C, Thangaraj A, Govindan M, Kasirajan G, Vijayan V, Devadasan V, Chia-Her L, Madhusudhanan GR, Ramaraj T, Palathurai Subramaniam M.

Nat Prod Res. 2018 Jul;32(14):1721-1726. doi: 10.1080/14786419.2017.1399386. Epub 2017 Nov 9.

PMID:
29117732
10.

Single-molecule sequencing and Hi-C-based proximity-guided assembly of amaranth (Amaranthus hypochondriacus) chromosomes provide insights into genome evolution.

Lightfoot DJ, Jarvis DE, Ramaraj T, Lee R, Jellen EN, Maughan PJ.

BMC Biol. 2017 Aug 31;15(1):74. doi: 10.1186/s12915-017-0412-4.

11.

Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula.

Moll KM, Zhou P, Ramaraj T, Fajardo D, Devitt NP, Sadowsky MJ, Stupar RM, Tiffin P, Miller JR, Young ND, Silverstein KAT, Mudge J.

BMC Genomics. 2017 Aug 4;18(1):578. doi: 10.1186/s12864-017-3971-4.

12.

Hybrid assembly with long and short reads improves discovery of gene family expansions.

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, Schatz MC, Tiffin P, Young ND, Silverstein KAT.

BMC Genomics. 2017 Jul 19;18(1):541. doi: 10.1186/s12864-017-3927-8.

13.

Crude oil impairs immune function and increases susceptibility to pathogenic bacteria in southern flounder.

Bayha KM, Ortell N, Ryan CN, Griffitt KJ, Krasnec M, Sena J, Ramaraj T, Takeshita R, Mayer GD, Schilkey F, Griffitt RJ.

PLoS One. 2017 May 2;12(5):e0176559. doi: 10.1371/journal.pone.0176559. eCollection 2017.

14.

Zinc-Dependent Transcriptional Regulation in Paracoccus denitrificans.

Neupane DP, Jacquez B, Sundararajan A, Ramaraj T, Schilkey FD, Yukl ET.

Front Microbiol. 2017 Apr 11;8:569. doi: 10.3389/fmicb.2017.00569. eCollection 2017.

15.

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

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.

BMC Genomics. 2017 Mar 27;18(1):261. doi: 10.1186/s12864-017-3654-1.

16.

The Amaranth Genome: Genome, Transcriptome, and Physical Map Assembly.

Clouse JW, Adhikary D, Page JT, Ramaraj T, Deyholos MK, Udall JA, Fairbanks DJ, Jellen EN, Maughan PJ.

Plant Genome. 2016 Mar;9(1). doi: 10.3835/plantgenome2015.07.0062. Erratum in: Plant Genome. 2016 Nov;9(3):.

17.

Gene Evolutionary Trajectories and GC Patterns Driven by Recombination in Zea mays.

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, Mudge J.

Front Plant Sci. 2016 Sep 22;7:1433. eCollection 2016.

18.

The complete chloroplast genome sequences for four Amaranthus species (Amaranthaceae).

Chaney L, Mangelson R, Ramaraj T, Jellen EN, Maughan PJ.

Appl Plant Sci. 2016 Sep 19;4(9). pii: apps.1600063. doi: 10.3732/apps.1600063. eCollection 2016 Sep.

19.

Augmenting Chinese hamster genome assembly by identifying regions of high confidence.

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.

Biotechnol J. 2016 Sep;11(9):1151-7. doi: 10.1002/biot.201500455. Epub 2016 Jul 19.

PMID:
27374913
20.

Characterization, correction and de novo assembly of an Oxford Nanopore genomic dataset from Agrobacterium tumefaciens.

Deschamps S, Mudge J, Cameron C, Ramaraj T, Anand A, Fengler K, Hayes K, Llaca V, Jones TJ, May G.

Sci Rep. 2016 Jun 28;6:28625. doi: 10.1038/srep28625.

21.

Novel Meiotic miRNAs and Indications for a Role of PhasiRNAs in Meiosis.

Dukowic-Schulze S, Sundararajan A, Ramaraj T, Kianian S, Pawlowski WP, Mudge J, Chen C.

Front Plant Sci. 2016 Jun 2;7:762. doi: 10.3389/fpls.2016.00762. eCollection 2016.

22.

De novo assembly of a tadpole shrimp (Triops newberryi) transcriptome and preliminary differential gene expression analysis.

Horn RL, Ramaraj T, Devitt NP, Schilkey FD, Cowley DE.

Mol Ecol Resour. 2017 Mar;17(2):161-171. doi: 10.1111/1755-0998.12555. Epub 2016 Jul 12.

23.

Complete Genome Sequence of Streptomyces venezuelae ATCC 15439, Producer of the Methymycin/Pikromycin Family of Macrolide Antibiotics, Using PacBio Technology.

He J, Sundararajan A, Devitt NP, Schilkey FD, Ramaraj T, Melançon CE 3rd.

Genome Announc. 2016 May 5;4(3). pii: e00337-16. doi: 10.1128/genomeA.00337-16.

24.

Genome Sequence of Janthinobacterium sp. CG23_2, a Violacein-Producing Isolate from an Antarctic Supraglacial Stream.

Smith HJ, Foreman CM, Akiyama T, Franklin MJ, Devitt NP, Ramaraj T.

Genome Announc. 2016 Jan 28;4(1). pii: e01468-15. doi: 10.1128/genomeA.01468-15.

25.

Composition, Diversity and Abundance of Gut Microbiome in Prediabetes and Type 2 Diabetes.

Lambeth SM, Carson T, Lowe J, Ramaraj T, Leff JW, Luo L, Bell CJ, Shah VO.

J Diabetes Obes. 2015 Dec 26;2(3):1-7.

26.

High-Quality Draft Genome Sequence of Actinobacterium Kibdelosporangium sp. MJ126-NF4, Producer of Type II Polyketide Azicemicins, Using Illumina and PacBio Technologies.

Ogasawara Y, Torrez-Martinez N, Aragon AD, Yackley BJ, Weber JA, Sundararajan A, Ramaraj T, Edwards JS, Melançon CE 3rd.

Genome Announc. 2015 Apr 2;3(2). pii: e00114-15. doi: 10.1128/genomeA.00114-15.

27.

Repertoire of virus-derived small RNAs produced by mosquito and mammalian cells in response to dengue virus infection.

Schirtzinger EE, Andrade CC, Devitt N, Ramaraj T, Jacobi JL, Schilkey F, Hanley KA.

Virology. 2015 Feb;476:54-60. doi: 10.1016/j.virol.2014.11.019. Epub 2014 Dec 17.

29.

Draft Genome Sequences of Vancomycin-Susceptible Staphylococcus aureus Related to Heterogeneous Vancomycin-Intermediate S. aureus.

Ramaraj T, Matyi SA, Sundararajan A, Lindquist IE, Devitt NP, Schilkey FD, Lamichhane-Khadka R, Hoyt PR, Mudge J, Gustafson JE.

Genome Announc. 2014 Oct 9;2(5). pii: e01033-14. doi: 10.1128/genomeA.01033-14.

30.

A candidate plasma protein classifier to identify Alzheimer's disease.

Zhao X, Lejnine S, Spond J, Zhang C, Ramaraj TC, Holder DJ, Dai H, Weiner R, Laterza OF.

J Alzheimers Dis. 2015;43(2):549-63. doi: 10.3233/JAD-141149.

PMID:
25114072
31.

Draft Genomes of Heterogeneous Vancomycin-Intermediate Staphylococcus aureus Strain MM66 and MM66 Derivatives with Altered Vancomycin Resistance Levels.

Matyi SA, Ramaraj T, Sundararajan A, Lindquist IE, Devitt NP, Schilkey FD, Lamichhane-Khadka R, Hoyt PR, Mudge J, Gustafson JE.

Genome Announc. 2014 Jul 10;2(4). pii: e00688-14. doi: 10.1128/genomeA.00688-14.

32.

The transcriptome landscape of early maize meiosis.

Dukowic-Schulze S, Sundararajan A, Mudge J, Ramaraj T, Farmer AD, Wang M, Sun Q, Pillardy J, Kianian S, Retzel EF, Pawlowski WP, Chen C.

BMC Plant Biol. 2014 May 3;14:118. doi: 10.1186/1471-2229-14-118. Erratum in: BMC Plant Biol. 2018 Jan 15;18(1):12.

33.

Improved Hybrid Genome Assemblies of Two Strains of Bacteroides xylanisolvens, SD_CC_1b and SD_CC_2a, Obtained Using Illumina and 454 Sequencing Technologies.

Ramaraj T, Sundararajan A, Schilkey FD, Delvecchio VG, Donlon M, Ziemer C, Mudge J.

Genome Announc. 2014 Apr 3;2(2). pii: e00237-14. doi: 10.1128/genomeA.00237-14.

34.

Sequencing-based large-scale genomics approaches with small numbers of isolated maize meiocytes.

Dukowic-Schulze S, Sundararajan A, Ramaraj T, Mudge J, Chen C.

Front Plant Sci. 2014 Feb 25;5:57. doi: 10.3389/fpls.2014.00057. eCollection 2014.

35.

Genome and secretome analysis of the hemibiotrophic fungal pathogen, Moniliophthora roreri, which causes frosty pod rot disease of cacao: mechanisms of the biotrophic and necrotrophic phases.

Meinhardt LW, Costa GG, Thomazella DP, Teixeira PJ, Carazzolle MF, Schuster SC, Carlson JE, Guiltinan MJ, Mieczkowski P, Farmer A, Ramaraj T, Crozier J, Davis RE, Shao J, Melnick RL, Pereira GA, Bailey BA.

BMC Genomics. 2014 Feb 27;15:164. doi: 10.1186/1471-2164-15-164.

36.

Molecular and biological characterization of a new isolate of guinea pig cytomegalovirus.

Schleiss MR, McAllister S, Armién AG, Hernandez-Alvarado N, Fernández-Alarcón C, Zabeli JC, Ramaraj T, Crow JA, McVoy MA.

Viruses. 2014 Jan 27;6(2):448-75. doi: 10.3390/v6020448.

37.

Genome Sequence of a Novel, Newly Identified Isolate of Guinea Pig Cytomegalovirus, the CIDMTR Strain.

Schleiss MR, Hernandez-Alvarado N, Ramaraj T, Crow JA.

Genome Announc. 2013 Dec 26;1(6). pii: e01052-13. doi: 10.1128/genomeA.01052-13.

38.

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.

Francis F, Kim J, Ramaraj T, Farmer A, Rush MC, Ham JH.

Mol Genet Genomics. 2013 Apr;288(3-4):195-203. doi: 10.1007/s00438-013-0744-x. Epub 2013 Apr 6.

PMID:
23563926
39.

Antigen-antibody interface properties: composition, residue interactions, and features of 53 non-redundant structures.

Ramaraj T, Angel T, Dratz EA, Jesaitis AJ, Mumey B.

Biochim Biophys Acta. 2012 Mar;1824(3):520-32. doi: 10.1016/j.bbapap.2011.12.007. Epub 2012 Jan 10.

40.

Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis.

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, Pando MJ, Clendenen LE, Ganusova EE, Schilkey FD, Ramaraj T, Khan OA, Huntley JJ, Luo S, Kwok PY, Wu TD, Schroth GP, Oksenberg JR, Hauser SL, Kingsmore SF.

Nature. 2010 Apr 29;464(7293):1351-6. doi: 10.1038/nature08990.

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