Abstract:
BACKGROUND:Chemical bioavailability is an important dose metric in environmental risk assessment. Although many approaches have been used to evaluate bioavailability, not a single approach is free from limitations. Previously, we developed a new genomics-based approach that integrated microarray technology and regression modeling for predicting bioavailability (tissue residue) of explosives compounds in exposed earthworms. In the present study, we further compared 18 different regression models and performed variable selection simultaneously with parameter estimation. RESULTS:This refined approach was applied to both previously collected and newly acquired earthworm microarray gene expression datasets for three explosive compounds. Our results demonstrate that a prediction accuracy of R(2) = 0.71-0.82 was achievable at a relatively low model complexity with as few as 3-10 predictor genes per model. These results are much more encouraging than our previous ones. CONCLUSION:This study has demonstrated that our approach is promising for bioavailability measurement, which warrants further studies of mixed contamination scenarios in field settings.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Gong P,Nan X,Barker ND,Boyd RE,Chen Y,Wilkins DE,Johnson DR,Suedel BC,Perkins EJdoi
10.1186/s12864-016-2541-5subject
Has Abstractpub_date
2016-03-08 00:00:00pages
205issn
1471-2164pii
10.1186/s12864-016-2541-5journal_volume
17pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:The globe artichoke (Cynara cardunculus var. scolymus L.) is a significant crop in the Mediterranean basin. Despite its commercial importance and its both dietary and pharmaceutical value, knowledge of its genetics and genomics remains scant. Microsatellite markers have become a key tool in genetic and genom...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-454
更新日期:2009-09-28 00:00:00
abstract:BACKGROUND:Chinese bayberry (Myrica rubra Sieb. and Zucc.) is a subtropical evergreen tree originating in China. It has been cultivated in southern China for several thousand years, and annual production has reached 1.1 million tons. The taste and high level of health promoting characters identified in the fruit in rec...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-201
更新日期:2012-05-23 00:00:00
abstract:BACKGROUND:Copy number variation (CNV) is a major component of genomic variation, yet methods to accurately type genomic CNV lag behind methods that type single nucleotide variation. High-throughput sequencing can contribute to these methods by using sequence read depth, which takes the number of reads that map to a gi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2123-y
更新日期:2015-11-02 00:00:00
abstract:BACKGROUND:Proliferation and tumor differentiation captured by the genomic grade index (GGI) are important prognostic indicators in breast cancer (BC) especially for the estrogen receptor positive (ER+) disease. The aims of this study were to convert this microarray index to a qRT-PCR assay (PCR-GGI), which could be re...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-424
更新日期:2009-09-10 00:00:00
abstract:BACKGROUND:Distichiasis, an ocular disorder in which aberrant cilia (eyelashes) grow from the opening of the Meibomian glands of the eyelid, has been reported in Friesian horses. These misplaced cilia can cause discomfort, chronic keratitis, and corneal ulceration, potentially impacting vision due to corneal fibrosis, ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07265-8
更新日期:2020-11-30 00:00:00
abstract:BACKGROUND:Sub-optimal developmental diets often have adverse effects on long-term fitness and health. One hypothesis is that such effects are caused by mismatches between the developmental and adult environment, and may be mediated by persistent changes in gene expression. However, there are few experimental tests of ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3968-z
更新日期:2017-08-22 00:00:00
abstract:BACKGROUND:Foraminiferan protists, which are significant players in most marine ecosystems, are also genetic innovators, harboring unique modifications to proteins that make up the basic eukaryotic cell machinery. Despite their ecological and evolutionary importance, foraminiferan genomes are poorly understood due to t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-169
更新日期:2011-03-31 00:00:00
abstract:BACKGROUND:The importance of poultry as a global source of protein underpins the chicken genome and associated SNP data as key tools in selecting and breeding healthy robust birds with improved disease resistance. SNPs affecting host peptides involved in the innate defences tend to be rare, but three non-synonymous SNP...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4034-6
更新日期:2017-08-18 00:00:00
abstract:BACKGROUND:Juncus effusus L. (family: Juncaceae; order: Poales) is a helophytic rush growing in temperate damp or wet terrestrial habitats and is of almost cosmopolitan distribution. The species has been studied intensively with respect to its interaction with co-occurring plants as well as microbes being involved in m...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5886-8
更新日期:2019-06-13 00:00:00
abstract:BACKGROUND:Increasing evidence suggests that overlapping genes are much more common in eukaryotic genomes than previously thought. In this study we identified and characterized the overlapping genes in a set of 13,484 pairs of human-mouse orthologous genes. RESULTS:About 10% of the genes under study are overlapping ge...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-169
更新日期:2008-04-14 00:00:00
abstract:BACKGROUND:Adjuvant Radiotherapy (RT) after surgical removal of tumors proved beneficial in long-term tumor control and treatment planning. For many years, it has been well concluded that radio-sensitivities of tumors upon radiotherapy decrease according to the sizes of tumors and RT models based on Poisson statistics ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-S2-S9
更新日期:2008-09-16 00:00:00
abstract:BACKGROUND:Fungal pathogens of plants produce diverse repertoires of secondary metabolites, which have functions ranging from iron acquisition, defense against immune perturbation, to toxic assaults on the host. The wheat pathogen Zymoseptoria tritici causes Septoria tritici blotch, a foliar disease which is a signific...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3969-y
更新日期:2017-08-17 00:00:00
abstract:BACKGROUND:Lysophosphatidic acid acyltransferase (LPAAT) encoded by a multigene family is a rate-limiting enzyme in the Kennedy pathway in higher plants. Cotton is the most important natural fiber crop and one of the most important oilseed crops. However, little is known on genes coding for LPAATs involved in oil biosy...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3594-9
更新日期:2017-03-01 00:00:00
abstract:BACKGROUND:Helitrons are class-II eukaryotic transposons that transpose via a rolling circle mechanism. Due to their ability to capture and mobilize gene fragments, they play an important role in the evolution of their host genomes. We have used a bioinformatics approach for the identification of helitrons in two Pleur...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1071
更新日期:2014-12-05 00:00:00
abstract:BACKGROUND:Many gram-negative bacteria use type III secretion systems (T3SSs) to translocate effector proteins into host cells. T3SS effectors can give some bacteria a competitive edge over others within the same environment and can help bacteria to invade the host cells and allow them to multiply rapidly within the ho...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3363-1
更新日期:2016-12-19 00:00:00
abstract:BACKGROUND:Equine influenza is a major health problem of equines worldwide. The polymerase genes of influenza virus have key roles in virus replication, transcription, transmission between hosts and pathogenesis. Hence, the comprehensive genetic and codon usage bias of polymerase genes of equine influenza virus (EIV) w...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4063-1
更新日期:2017-08-23 00:00:00
abstract:BACKGROUND:About 6 million Americans suffer from heart failure and 70% of heart failure cases are caused by myocardial infarction (MI). Following myocardial infarction, increased cytokines induce two major types of macrophages: classically activated macrophages which contribute to extracellular matrix destruction and a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-S6-S21
更新日期:2012-01-01 00:00:00
abstract:BACKGROUND:In biomedical research, gene expression profiling studies have been extensively conducted. The analysis of gene expression data has led to a deeper understanding of human genetics as well as practically useful models. Clustering analysis has been a critical component of gene expression data analysis and can ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3990-1
更新日期:2017-08-16 00:00:00
abstract:BACKGROUND:Lipopolysaccharide (LPS) endotoxin stimulates pro-inflammatory pathways and is a key player in the pathological mechanisms involved in the development of endometritis. This study aimed to investigate LPS-induced DNA methylation changes in bovine endometrial epithelial cells (bEECs), which may affect endometr...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06777-7
更新日期:2020-06-03 00:00:00
abstract:BACKGROUND:Studying functional divergences between paralogs that originated from genome duplication is a significant topic in investigating molecular evolution. Genes that exhibit basal level cyclic expression patterns including circadian and light responsive genes are important physiological regulators. Temporal shift...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07202-9
更新日期:2020-11-11 00:00:00
abstract:BACKGROUND:Ubiquitination is an important post-translational modification involved in diverse biological processes. Therefore, genomewide representation of the ubiquitination system for a species is important. DESCRIPTION:SCUD is a web-based database for the ubiquitination system in Saccharomyces cerevisiae (Baker's y...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-440
更新日期:2008-09-24 00:00:00
abstract:INTRODUCTION:In the classification of Mass Spectrometry (MS) proteomics data, peak detection, feature selection, and learning classifiers are critical to classification accuracy. To better understand which methods are more accurate when classifying data, some publicly available peak detection algorithms for Matrix assi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-S1-S3
更新日期:2009-07-07 00:00:00
abstract:BACKGROUND:The Andean cultivar Paloma is resistant to Mesoamerican and Andean races of Colletotrichum lindemuthianum, the fungal pathogen that causes the destructive anthracnose disease in common bean. Remarkably, Paloma is resistant to Mesoamerican races 2047 and 3481, which are among the most virulent races of the an...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3685-7
更新日期:2017-04-18 00:00:00
abstract:BACKGROUND:Many reptiles exhibit temperature-dependent sex determination (TSD). The initial cue in TSD is incubation temperature, unlike genotypic sex determination (GSD) where it is determined by the presence of specific alleles (or genetic loci). We used patterns of gene expression to identify candidates for genes wi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-308
更新日期:2012-07-15 00:00:00
abstract:BACKGROUND:Magnaporthe oryzae (anamorph Pyricularia oryzae) is the causal agent of blast disease of Poaceae crops and their wild relatives. To understand the genetic mechanisms that drive host specialization of M. oryzae, we carried out whole genome resequencing of four M. oryzae isolates from rice (Oryza sativa), one ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2690-6
更新日期:2016-05-18 00:00:00
abstract:BACKGROUND:Aging is affected by genetic and environmental factors, and cigarette smoking is strongly associated with accumulation of senescent cells. In this study, we wanted to identify genes that may potentially be beneficial for cell survival in response to cigarette smoke and thereby may contribute to development o...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5409-z
更新日期:2019-01-09 00:00:00
abstract:BACKGROUND:Insertion sequences (ISs) are approximately 1 kbp long "jumping" genes found in prokaryotes. ISs encode the protein Transposase, which facilitates the excision and reinsertion of ISs in genomes, making these sequences a type of class I ("cut-and-paste") Mobile Genetic Elements. ISs are proposed to be involve...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1386-7
更新日期:2015-03-17 00:00:00
abstract:BACKGROUND:Analysis of single nucleotide polymorphisms (SNPs) derived from whole-genome studies allows for rapid evaluation of genome-wide diversity, and genomic epidemiology studies of Plasmodium falciparum provide insights into parasite population structure, gene flow, drug resistance and vaccine development. In area...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-719
更新日期:2014-08-26 00:00:00
abstract:BACKGROUND:On a single strand of genomic DNA the number of As is usually about equal to the number of Ts (and similarly for Gs and Cs), but deviations have been noted for transcribed regions and origins of replication. RESULTS:The mouse genome is shown to have a segmented structure defined by strand bias. Transcriptio...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-16
更新日期:2008-01-14 00:00:00
abstract:BACKGROUND:Bacteriophages are the most abundant and diverse entities in the biosphere, and this diversity is driven by constant predator-prey evolutionary dynamics and horizontal gene transfer. Phage genome sequences are under-sampled and therefore present an untapped and uncharacterized source of genetic diversity, ty...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5647-8
更新日期:2019-05-09 00:00:00