Thiruvarangan Ramaraj

Thiruvarangan Ramaraj
DePaul University · School of Computing

PhD

About

130
Publications
14,384
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
1,761
Citations
Additional affiliations
July 2019 - present
DePaul University
Position
  • Professor (Assistant)
May 2013 - April 2016
Murdoch University
Position
  • Fellow
November 2012 - August 2019
National Center for Genome Resources
Position
  • Analyst
Education
August 2005 - May 2010
Montana State University
Field of study
  • Computer Science (Computational Biology/Bioinformatics)
January 2002 - May 2005
Ball State University
Field of study
  • Computer Science
June 1997 - May 2001
Annamalai University
Field of study
  • Computer Science & Engineering

Publications

Publications (130)
Preprint
Full-text available
Domestication in the cotton genus is remarkable in that it has occurred independently four different times at two different ploidy levels. Relatively little is known about genome evolution and domestication in the cultivated diploid species Gossypium herbaceum and G. arboreum , because of the absence of wild representatives for the latter species,...
Chapter
Amaranth is an emerging pseudocereal native to the New World that has gained increased attention in recent years because of its nutritional quality, particularly its seed protein, with high levels of essential amino acid lysine. This chapter will concentrate on the research advancements made on organelle genomes, particularly the chloroplast genome...
Article
Full-text available
Tobacco etch virus (TEV; genus Potyvirus) is flexuous rod shaped with a single molecule of single-stranded RNA and causes serious yield losses in species in the Solanaceae. Three TEV strains (HAT, Mex21, and N) are genetically distinct and cause different disease symptoms in plants. Here, a transcriptomic RNA sequencing approach was taken for each...
Article
Full-text available
Physical inactivity leads to losses of bone mass and strength in most mammalian species. In contrast, hibernating bears show no bone loss over the prolonged periods (4-6 months) of immobility during winter, which suggests that they have adaptive mechanisms to preserve bone mass. To identify transcriptional changes that underlie molecular mechanisms...
Article
Full-text available
Pseudomonas aeruginosa is an opportunistic pathogen that forms surface-associated microbial communities (biofilms) on artificial implant devices and on human tissue. Biofilm infections are difficult to treat with antibiotics, in part, because the bacteria in biofilms are physiologically heterogeneous. One measure of biological heterogeneity in a po...
Article
Full-text available
One of the extraordinary aspects of plant genome evolution is variation in chromosome number, particularly that among closely related species. This is exemplified by the cotton genus (Gossypium) and its relatives, where most species and genera have a base chromosome number of 13. The two exceptions are sister genera that have n = 12 (the Hawaiian K...
Article
Full-text available
As many bacteria detected in Antarctic environments are neither true psychrophiles nor endemic species, their proliferation in spite of environmental extremes gives rise to genome adaptations. Janthinobacterium sp. CG23_2 is a bacterial isolate from the Cotton Glacier stream, Antarctica. To understand how Janthinobacterium sp. CG23_2 has adapted to...
Conference Paper
Full-text available
Connecting genetic variation (genotype) to trait variation (phenotype) is a critical but often difficult step in genetic research. A genome-wide association study (GWAS) is a common approach to connect underlying genetic variation to complex phenotypic traits, allowing for phenotypic prediction. GWAS is important in many disciplines, including iden...
Poster
Connecting genetic variation (genotype) to trait variation (phenotype) is a critical but often difficult step in genetic research. A genome-wide association study (GWAS) is a common approach to connect underlying genetic variation to complex phenotypic traits, allowing for phenotypic prediction. GWAS is important in many disciplines, including iden...
Article
Full-text available
Cotton is an agriculturally important crop. Because of its importance, a genome sequence of a diploid cotton species (Gossypium raimondii, D-genome) was first assembled using Sanger sequencing data in 2012. Improvements to DNA sequencing technology have improved accuracy and correctness of assembled genome sequences. Here we report a new de novo ge...
Data
Table S6a 10 most common pathways. Table S6b 80 enzymes recorded from 1444 TAVs. Table S6c 79 pathways recorded from 1444 TAVs. Table S7 Detailed information of 66 SNPs associated with caffeine detected by KEGG pathway analysis.
Data
Table S1 Parameters of Illumina data and PacBio data. Table S2 Assembly statistics among different assemblers with Illumina sequencing reads. Table S3 Assembly improvement using GAPCloser and Scaffolders with Illumina sequencing reads. Table S4 Assembly improvement using GapClosers and Scaffolders with PacBio longreads. Table S5 Statistics of g...
Article
Arbuscular mycorrhizal (AM) fungi form endosymbioses with most plants, and they themselves are hosts for Mollicutes/Mycoplasma‐related endobacteria (MRE). Despite their significance, genomic information for AM fungi and their MRE are relatively sparse, which hinders our understanding of their biology and evolution. We assembled the genomes of the A...
Article
We consider the problem of identifying regions within a pan-genome De Bruijn graph that are traversed by many sequence paths. We define such regions and the subpaths that traverse them as frequented regions (FRs). In this work, we formalize the FR problem and describe an efficient algorithm for finding FRs. Subsequently, we propose some application...
Article
Full-text available
Candida albicans is one of the most common causes of hospital-acquired urinary tract infections (UTIs). However, azoles are poorly active against biofilms, echinocandins do not achieve clinically useful urinary concentrations, and amphotericin B exhibits severe toxicities. Thus, novel strategies are needed to prevent Candida UTIs, which are often a...
Data
Genes up-expressed in WT biofilm cells relative to WT planktonic cells. Sheet 1 contains gene expression information. Sheet 2 contains GO term enrichment analysis. (XLSX)
Data
Comparison of differentially-expressed genes with published studies. (XLSM)
Data
Genes up-expressed in PAC-treated planktonic cells relative to WT planktonic cells. Sheet 1 contains gene expression information. Sheet 2 contains GO term enrichment analysis. (XLSX)
Data
Genes up-expressed in PAC-treated biofilm cells relative to WT planktonic cells. Sheet 1 contains gene expression information. Sheet 2 contains upregulated genes shared between PAC-treated planktonic cells and PAC-treated biofilm cells relative to WT planktonic cells, and GO term enrichment analysis of this data. (XLSX)
Data
Genes down expressed in PAC-treated biofilm cells relative to biofilm control cells. Sheet 1 contains gene expression information. Sheet 2 contains GO term enrichment analysis. (XLSX)
Data
Genes down-expressed in PAC-treated planktonic cells relative to WT planktonic cells. Sheet 1 contains gene expression information. Sheet 2 contains GO term enrichment analysis. (XLSX)
Data
Genes-down expressed in WT biofilm cells relative to WT planktonic cells. Sheet 1 contains gene expression information. Sheet 2 contains GO term enrichment analysis. (XLSX)
Data
Genes up expressed in PAC-treated biofilm cells relative to biofilm control cells. Sheet 1 contains gene expression information. Sheet 2 contains GO term enrichment analysis. (XLSX)
Data
Genes down-expressed in PAC-treated biofilm cells relative to WT planktonic cells. Sheet 1 contains gene expression information. Sheet 2 contains downregulated genes shared between PAC-treated planktonic cells and PAC-treated biofilm cells relative to WT planktonic cells, and GO term enrichment analysis of this data. (XLSX)
Article
Full-text available
Peptidylarginine deiminase (PAD) enzymes convert histone arginine residues into citrulline to modulate chromatin organization and gene expression. Although PADs are expressed in anterior pituitary gland cells, their functional role and expression in pituitary adenomas is unknown. To begin to address these questions, we first examined normal human p...
Article
Full-text available
Cytokinins are well‐known to be involved in processes responsible for plant growth and development. More recently, these hormones have begun to be associated with stress responses as well. However, it is unclear how changes in cytokinin biosynthesis, signaling, or transport relate to stress effects. This study examines in parallel how two different...
Article
Full-text available
Arabica coffee (Coffea arabica) has a small gene pool limiting genetic improvement. Selection for caffeine content within this gene pool would be assisted by identification of the genes controlling this important trait. Sequencing of DNA bulks from 18 genotypes with extreme high or low caffeine content from a population of 232 genotypes was used to...
Article
Full-text available
Correction: Following publication of the original article [1], the authors reported that the number of genes overlaying the bar graph in Fig. 3A were incorrectly counted and inserted (i.e. including a title tile, and in inverse order). The corrected numbers are below and match with the listed genes supplied in Additional File: Table S2.
Article
Full-text available
Long-distance insular dispersal is associated with divergence and speciation because of founder effects and strong genetic drift. The cotton tribe (Gossypieae) has experienced multiple trans-oceanic dispersals, generating an aggregate geographic range that encompasses much of the tropics and subtropics worldwide. Two genera in the Gossypieae, Kokia...
Article
Full-text available
Background: Amaranth (Amaranthus hypochondriacus) was a food staple among the ancient civilizations of Central and South America that has recently received increased attention due to the high nutritional value of the seeds, with the potential to help alleviate malnutrition and food security concerns, particularly in arid and semiarid regions of th...
Conference Paper
Full-text available
We consider the problem of identifying regions within a pan-genome de Bruijn graph that are traversed by many sequence paths. We define such regions and the subpaths that traverse them as frequented regions (FRs). In this work we formalize the FR problem and describe an efficient algorithm for finding FRs. Subsequently, we propose some applications...
Article
Full-text available
Background Third generation sequencing technologies, with sequencing reads in the tens- of kilo-bases, facilitate genome assembly by spanning ambiguous regions and improving continuity. This has been critical for plant genomes, which are difficult to assemble due to high repeat content, gene family expansions, segmental and tandem duplications, and...
Article
Full-text available
Background Long-read and short-read sequencing technologies offer competing advantages for eukaryotic genome sequencing projects. Combinations of both may be appropriate for surveys of within-species genomic variation. Methods We developed a hybrid assembly pipeline called “Alpaca” that can operate on 20X long-read coverage plus about 50X short-in...
Article
Full-text available
Exposure to crude oil or its individual constituents can have detrimental impacts on fish species, including impairment of the immune response. Increased observations of skin lesions in northern Gulf of Mexico fish during the 2010 Deepwater Horizon oil spill indicated the possibility of oil-induced immunocompromisation resulting in bacterial or vir...
Data
Amount of sediment, loading rate of Slick B oil, initial and final tPAH50 concentrations, and percent total organic carbon (TOC) of treatments. ǂ Initial measurements taken one day prior to experiment initiation; final measurements taken at experiment termination after 15-d with clean water flow-through. * Samples for TOC measurements taken during...