BMC GENOMICS - Texas A&M University (TAMU) Scholar

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Copy number variation and elevated genetic diversity at immune trait loci in Atlantic and Pacific herring.. 25:459. 2024
Comparative transcriptomic analysis of germinating rice seedlings to individual and combined anaerobic and cold stress.. 24:185. 2023
Potential key genes involved in metabolic resistance to malathion in the southern house mosquito, Culex quinquefasciatus, and functional validation of CYP325BC1 and CYP9M12 as candidate genes using RNA interference.. 24:160. 2023
Genome-wide association and genotype by environment interactions for growth traits in U.S. Red Angus cattle.. 23:517. 2022
Phenotypic variation and genome-wide association studies of main culm panicle node number, maximum node production rate, and degree-days to heading in rice.. 23:390. 2022
Borrelia burgdorferi infection modifies protein content in saliva of Ixodes scapularis nymphs.. 22:152. 2021
Mapping and characterization QTLs for phenological traits in seven pedigree-connected peach families.. 22:187. 2021
Whole genome comparisons reveal panmixia among fall armyworm (Spodoptera frugiperda) from diverse locations.. 22:179. 2021
Brown marmorated stink bug, Halyomorpha halys (Stl), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest.. 21:227. 2020
Identification and characterization of QTLs for fruit quality traits in peach through a multi-family approach.. 21:522. 2020
Transcriptomic analyses of Aedes aegypti cultured cells and ex vivo midguts in response to an excess or deficiency of heme: a quest for transcriptionally-regulated heme transporters.. 21:604. 2020
Genome-wide association and genotype by environment interactions for growth traits in U.S. Gelbvieh cattle.. 20:926. 2019
QTL-mapping and genomic prediction for bovine respiratory disease in U.S. Holsteins using sequence imputation and feature selection.. 20:555. 2019
Validation of 46 loci associated with female fertility traits in cattle.. 20:576. 2019
Identifying similar transcripts in a related organism from de Bruijn graphs of RNA-Seq data, with applications to the study of salt and waterlogging tolerance in Melilotus.. 20:425. 2019
Comparative genomics revealed the gene evolution and functional divergence of magnesium transporter families in Saccharum.. 20:83. 2019
Development of a highly efficient Axiom 70 K SNP array for Pyrus and evaluation for high-density mapping and germplasm characterization.. 20:331. 2019
Differential expression analysis of Trichoderma virens RNA reveals a dynamic transcriptome during colonization of Zea mays roots.. 20:280. 2019
Honey bee (Apis mellifera) larval pheromones may regulate gene expression related to foraging task specialization.. 20:592. 2019
Scalable optimal Bayesian classification of single-cell trajectories under regulatory model uncertainty.. 20:435. 2019
Transcriptomic analysis between Normal and high-intake feeding geese provides insight into adipose deposition and susceptibility to fatty liver in migratory birds. 20:372. 2019
Comparative omics and feeding manipulations in chicken indicate a shift of the endocrine role of visceral fat towards reproduction.. 19:295. 2018
Feature selection with interactions in logistic regression models using multivariate synergies for a GWAS application.. 19:170. 2018
Papain-like cysteine proteases in Carica papaya: lineage-specific gene duplication and expansion. 19:26-26. 2018
Molecular characterization of larval development from fertilization to metamorphosis in a reef-building coral.. 19:17. 2018
Robust mutant strain design by pessimistic optimization.. 18:677. 2017
Chemosensory gene expression in olfactory organs of the anthropophilic Anopheles coluzzii and zoophilic Anopheles quadriannulatus.. 18:751. 2017
HiMMe: using genetic patterns as a proxy for genome assembly reliability assessment.. 18:694. 2017
Draft de novo transcriptome assembly and proteome characterization of the electric lobe of Tetronarce californica: a molecular tool for the study of cholinergic neurotransmission in the electric organ.. 18:611. 2017
Genome-wide identification of soybean microRNA responsive to soybean cyst nematodes infection by deep sequencing.. 18:572. 2017
Genome-wide association study for feed efficiency and growth traits in U.S. beef cattle.. 18:386. 2017
Inferring microbial interaction networks from metagenomic data using SgLV-EKF algorithm.. 18:228. 2017
A scalable and memory-efficient algorithm for de novo transcriptome assembly of non-model organisms.. 18:387. 2017
Evolution and expression of the fructokinase gene family in Saccharum.. 18:197-197. 2017
Global gene expression in two potato cultivars in response to 'Candidatus Liberibacter solanacearum' infection.. 18:960. 2017
Genetic architecture of kernel composition in global sorghum germplasm.. 18:15. 2017
Genomic characterization of a core set of the USDA-NPGS Ethiopian sorghum germplasm collection: implications for germplasm conservation, evaluation, and utilization in crop improvement.. 18:108. 2017
TRPM2 SNP genotype previously associated with susceptibility to Rhodococcus equi pneumonia in Quarter Horse foals displays differential gene expression identified using RNA-Seq.. 17:993. 2016
CrossLink: a novel method for cross-condition classification of cancer subtypes.. 17 Suppl 7:549. 2016
A Colletotrichum graminicola mutant deficient in the establishment of biotrophy reveals early transcriptional events in the maize anthracnose disease interaction.. 17:202. 2016
Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum.. 17:446-446. 2016
Construction of high-resolution genetic maps of Zoysia matrella (L.) Merrill and applications to comparative genomic analysis and QTL mapping of resistance to fall armyworm.. 17:562-562. 2016
Erratum to: Exome genotyping, linkage disequilibrium and population structure in loblolly pine (Pinus taeda L.).. 17:869. 2016
Exome genotyping, linkage disequilibrium and population structure in loblolly pine (Pinus taeda L.).. 17:730. 2016
Genome-wide association study to identify potential genetic modifiers in a canine model for Duchenne muscular dystrophy.. 17:665. 2016
Structure, phylogeny, allelic haplotypes and expression of sucrose transporter gene families in Saccharum.. 17:88-88. 2016
Transcriptome analysis revealed the dynamic oil accumulation in Symplocos paniculata fruit.. 17:929. 2016
Rapid Increase in frequency of gene copy-number variants during experimental evolution in Caenorhabditis elegans.. 16:1044. 2015
Retraction Note: Species-specific chemosensory gene expression in the olfactory organs of the malaria vector Anopheles gambiae.. 16:572. 2015
Unique patterns of transcript and miRNA expression in the South American strong voltage electric eel (Electrophorus electricus).. 16:243. 2015
Host-specific transcriptomic pattern of Trichoderma virens during interaction with maize or tomato roots.. 16:8. 2015
Susceptibility loci revealed for bovine respiratory disease complex in pre-weaned holstein calves.. 15:1164-1164. 2014
QTLs associated with dry matter intake, metabolic mid-test weight, growth and feed efficiency have little overlap across 4 beef cattle studies.. 15:1004. 2014
De novo assembly and characterization of the transcriptome of the toxic dinoflagellate Karenia brevis.. 15:888. 2014
Development and bin mapping of gene-associated interspecific SNPs for cotton (Gossypium hirsutum L.) introgression breeding efforts.. 15:945. 2014
SNP array profiling of mouse cell lines identifies their strains of origin and reveals cross-contamination and widespread aneuploidy.. 15:847. 2014
A memory-efficient algorithm to obtain splicing graphs and de novo expression estimates from de Bruijn graphs of RNA-Seq data.. 15 Suppl 5:S6. 2014
An update of the goat genome assembly using dense radiation hybrid maps allows detailed analysis of evolutionary rearrangements in Bovidae.. 15:625. 2014
Genome-wide histone state profiling of fibroblasts from the opossum, Monodelphis domestica, identifies the first marsupial-specific imprinted gene.. 15:89. 2014
Supervised categorical principal component analysis for genome-wide association analyses.. 15 Suppl 1:S10-10. 2014
A 24-48 h fed Amblyomma americanum tick saliva immuno-proteome.. 15:518. 2014
Sequence alignment by passing messages. 15:s14-8. 2014
Sequence alignment by passing messages.. 15 Suppl 1:S14. 2014
Sex specific expression and distribution of small RNAs in papaya.. 15:20-20. 2014
Species-specific chemosensory gene expression in the olfactory organs of the malaria vector Anopheles gambiae. 15:1089-1089. 2014
Supervised categorical principal component analysis for genome-wide association analyses.. 15 Suppl 1. 2014
Alterations in expression of endometrial genes coding for proteins secreted into the uterine lumen during conceptus elongation in cattle.. 14:321-321. 2013
Pearl millet [Pennisetum glaucum (L.) R. Br.] consensus linkage map constructed using four RIL mapping populations and newly developed EST-SSRs.. 14:159. 2013
Construction of a plant-transformation-competent BIBAC library and genome sequence analysis of polyploid Upland cotton (Gossypium hirsutum L.).. 14:208. 2013
Digital genotyping of sorghum - a diverse plant species with a large repeat-rich genome.. 14:448. 2013
Draft genome sequence of the rubber tree Hevea brasiliensis.. 14:75-75. 2013
Global Rsh-dependent transcription profile of Brucella suis during stringent response unravels adaptation to nutrient starvation and cross-talk with other stress responses.. 14:459. 2013
Intronic non-CG DNA hydroxymethylation and alternative mRNA splicing in honey bees.. 14:666. 2013
Transcriptome profiling reveals links between ParS/ParR, MexEF-OprN, and quorum sensing in the regulation of adaptation and virulence in Pseudomonas aeruginosa.. 14:618. 2013
Reducing confounding and suppression effects in TCGA data: an integrated analysis of chemotherapy response in ovarian cancer.. 13 Suppl 6:S13. 2012
Copy number expansion of the STX17 duplication in melanoma tissue from Grey horses.. 13:365. 2012
High-throughput comparison of gene fitness among related bacteria.. 13:212. 2012
Heritable genome-wide variation of gene expression and promoter methylation between wild and domesticated chickens.. 13:59. 2012
Whole-genome sequencing and genetic variant analysis of a Quarter Horse mare.. 13:78. 2012
Asymmetric purine-pyrimidine distribution in cellular small RNA population of papaya.. 13:682-682. 2012
Bio-crude transcriptomics: gene discovery and metabolic network reconstruction for the biosynthesis of the terpenome of the hydrocarbon oil-producing green alga, Botryococcus braunii race B (Showa).. 13:576-576. 2012
Construction of physical maps for the sex-specific regions of papaya sex chromosomes.. 13:176. 2012
Integrated analysis of microRNA expression and mRNA transcriptome in lungs of avian influenza virus infected broilers.. 13:278. 2012
Rapid gene-based SNP and haplotype marker development in non-model eukaryotes using 3'UTR sequencing.. 13:18. 2012
The Caulobacter crescentus phage phiCbK: genomics of a canonical phage.. 13:542. 2012
Transcriptome analysis reveals unique metabolic features in the Cryptosporidium parvum Oocysts associated with environmental survival and stresses.. 13:647. 2012
A hidden Markov model-based algorithm for identifying tumour subtype using array CGH data.. 12 Suppl 5:S10-S10. 2011
Genomic signatures and gene networking: challenges and promises.. 12 Suppl 5:I1-I1. 2011
A comparative physical map reveals the pattern of chromosomal evolution between the turkey (Meleagris gallopavo) and chicken (Gallus gallus) genomes.. 12:447. 2011
An Expressed Sequence Tag collection from the male antennae of the Noctuid moth Spodoptera littoralis: a resource for olfactory and pheromone detection research.. 12:86. 2011
Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid.. 12:514. 2011
Whole genome sequencing of peach (Prunus persica L.) for SNP identification and selection.. 12:569. 2011
Identification of differentially expressed miRNAs in chicken lung and trachea with avian influenza virus infection by a deep sequencing approach (vol 11, pg 373, 2010). 11:373. 2010
The non-clonality of drug resistance in Beijing-genotype isolates of Mycobacterium tuberculosis from the Western Cape of South Africa.. 11:670. 2010
Genomic survey of the ectoparasitic mite Varroa destructor, a major pest of the honey bee Apis mellifera.. 11:602. 2010
Heading down the wrong pathway: on the influence of correlation within gene sets.. 11:574. 2010
The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences.. 11:420. 2010
A BAC/BIBAC-based physical map of chickpea, Cicer arietinum L.. 11:501. 2010
Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes. 11:261-261. 2010
Natural selection retains overrepresented out-of-frame stop codons against frameshift peptides in prokaryotes.. 11:491. 2010
Population- and genome-specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat (Triticum aestivum L.).. 11:727. 2010
Reproducibility of quantitative RT-PCR array in miRNA expression profiling and comparison with microarray analysis.. 10:407-407. 2009
Gene expression profiling in peanut using high density oligonucleotide microarrays.. 10:265-265. 2009
Genetic analysis of an F(2) intercross between two chicken lines divergently selected for body-weight.. 10:248. 2009
A high resolution RH map of the bovine major histocompatibility complex.. 10:182. 2009
Construction and sequence sampling of deep-coverage, large-insert BAC libraries for three model lepidopteran species.. 10:283. 2009
Identification of differentially expressed miRNAs in chicken lung and trachea with avian influenza virus infection by a deep sequencing approach.. 10:512. 2009
Ixodes scapularis tick serine proteinase inhibitor (serpin) gene family; annotation and transcriptional analysis.. 10:217-217. 2009
Evolutionary origin of regulatory regions of retrogenes in Drosophila.. 9:241. 2008
Genomic resources for Myzus persicae: EST sequencing, SNP identification, and microarray design.. 8:423. 2007
High resolution radiation hybrid maps of bovine chromosomes 19 and 29: comparison with the bovine genome sequence assembly.. 8:310. 2007
A high resolution radiation hybrid map of bovine chromosome 14 identifies scaffold rearrangement in the latest bovine assembly.. 8:254. 2007
Differential gene expression in femoral bone from red junglefowl and domestic chicken, differing for bone phenotypic traits.. 8:208. 2007
A BAC pooling strategy combined with PCR-based screenings in a large, highly repetitive genome enables integration of the maize genetic and physical maps.. 8:47. 2007
CMD: a Cotton Microsatellite Database resource for Gossypium genomics.. 7:132. 2006
Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum.. 7:199. 2006
Genomic organization, annotation, and ligand-receptor inferences of chicken chemokines and chemokine receptor genes based on comparative genomics.. 6. 2005
ASAP: amplification, sequencing & annotation of plastomes.. 6:176. 2005
Genomic organization, annotation, and ligand-receptor inferences of chicken chemokines and chemokine receptor genes based on comparative genomics.. 6:45. 2005
A first generation whole genome RH map of the river buffalo with comparison to domestic cattle.. 9:631-631.
Application of dissociation curve analysis to radiation hybrid panel marker scoring: generation of a map of river buffalo (B. bubalis) chromosome 20.. 9:544.
Chromosome-level genome assemblies and genetic maps reveal heterochiasmy and macrosynteny in endangered Atlantic Acropora.. 25:1119.
Genome-wide characterization of long intergenic non-coding RNAs (lincRNAs) provides new insight into viral diseases in honey bees Apis cerana and Apis mellifera.. 16:680.
Transcriptome analysis reveals in vitro cultured Withania somnifera leaf and root tissues as a promising source for targeted withanolide biosynthesis.. 16:14.
Transcriptome sequencing of two parental lines of cabbage (Brassica oleracea L. var. capitata L.) and construction of an EST-based genetic map.. 15:149.
Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing.. 16:1.
ClusterM: a scalable algorithm for computational prediction of conserved protein complexes across multiple protein interaction networks. 2020
Identifying similar transcripts in a related organism from de Bruijn graphs of RNA-Seq data, with applications to the study of salt and waterlogging tolerance in Melilotus 2019
A divide-and-conquer algorithm for large-scale de novo transcriptome assembly through combining small assemblies from existing algorithms. 2017
Assessing the efficacy of molecularly targeted agents on cell line-based platforms by using system identification. 2012
Boolean modeling and fault diagnosis in oxidative stress response. 2012
Adaptive reference update (ARU) algorithm. A stochastic search algorithm for efficient optimization of multi-drug cocktails. 2012
Application of Max-SAT-based ATPG to optimal cancer therapy design. 2012

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