20,643 results match your criteria Genomics [Journal]


Whole genome sequencing and genome annotation of the wild edible mushroom, Russula griseocarnosa.

Genomics 2019 Apr 17. Epub 2019 Apr 17.

Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.

Russula griseocarnosa is a species of edible ectomycorrhizal fungi with medicinal properties that grows in southern China. Total DNA was isolated from a fresh fruiting body of R. griseocarnosa and subjected to sequencing using Illumina Hiseq with the PacBio RS sequencing platform. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S08887543183067
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http://dx.doi.org/10.1016/j.ygeno.2019.04.012DOI Listing
April 2019
1 Read

HseSUMO: Sumoylation site prediction using half-sphere exposures of amino acids residues.

BMC Genomics 2019 Apr 18;19(Suppl 9):982. Epub 2019 Apr 18.

Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan.

Background: Post-translational modifications are viewed as an important mechanism for controlling protein function and are believed to be involved in multiple important diseases. However, their profiling using laboratory-based techniques remain challenging. Therefore, making the development of accurate computational methods to predict post-translational modifications is particularly important for making progress in this area of research. Read More

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http://dx.doi.org/10.1186/s12864-018-5206-8DOI Listing

HumCFS: a database of fragile sites in human chromosomes.

BMC Genomics 2019 Apr 18;19(Suppl 9):985. Epub 2019 Apr 18.

Center for Computational Biology, Indraprastha Institute of Information Technology, New Delhi, 110020, India.

Background: Fragile sites are the chromosomal regions that are susceptible to breakage, and their frequency varies among the human population. Based on the frequency of fragile site induction, they are categorized as common and rare fragile sites. Common fragile sites are sensitive to replication stress and often rearranged in cancer. Read More

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https://bmcgenomics.biomedcentral.com/articles/10.1186/s1286
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http://dx.doi.org/10.1186/s12864-018-5330-5DOI Listing
April 2019
1 Read

EvolStruct-Phogly: incorporating structural properties and evolutionary information from profile bigrams for the phosphoglycerylation prediction.

BMC Genomics 2019 Apr 18;19(Suppl 9):984. Epub 2019 Apr 18.

Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.

Background: Post-translational modification (PTM), which is a biological process, tends to modify proteome that leads to changes in normal cell biology and pathogenesis. In the recent times, there has been many reported PTMs. Out of the many modifications, phosphoglycerylation has become particularly the subject of interest. Read More

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http://dx.doi.org/10.1186/s12864-018-5383-5DOI Listing

APBioNet's annual International Conference on Bioinformatics (InCoB) returns to India in 2018.

BMC Genomics 2019 Apr 18;19(Suppl 9):266. Epub 2019 Apr 18.

Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.

InCoB, one of the largest annual bioinformatics conferences in the Asia-Pacific region since its launch in 2002, returned to New Delhi, India after 12 years, with a conference attendance of 314 delegates. The 2018 conference had sessions on Big Data and Algorithms, Next Generation Sequencing and Omics Science, Structure, Function and Interactions, Disease and Drug Discovery and Plant and Agricultural Bioinformatics. The conference also featured an industry track as well as panel discussions on Women in Bioinformatics and Democratization vs. Read More

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http://dx.doi.org/10.1186/s12864-019-5582-8DOI Listing
April 2019
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Sequence imputation from low density single nucleotide polymorphism panel in a black poplar breeding population.

BMC Genomics 2019 Apr 18;20(1):302. Epub 2019 Apr 18.

BioForA, INRA, ONF, 45075, Orléans, France, 2163 Avenue de la Pomme de Pin CS 40001 ARDON, Orléans Cedex 2, 45075, France.

Background: Genomic selection accuracy increases with the use of high SNP (single nucleotide polymorphism) coverage. However, such gains in coverage come at high costs, preventing their prompt operational implementation by breeders. Low density panels imputed to higher densities offer a cheaper alternative during the first stages of genomic resources development. Read More

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http://dx.doi.org/10.1186/s12864-019-5660-yDOI Listing

Comparative analysis of glyoxalase pathway genes in Erianthus arundinaceus and commercial sugarcane hybrid under salinity and drought conditions.

BMC Genomics 2019 Apr 18;19(Suppl 9):986. Epub 2019 Apr 18.

Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641007, India.

Background: Glyoxalase pathway is a reactive carbonyl species (RCS) scavenging mechanism involved in the detoxification of methylglyoxal (MG), which is a reactive α-ketoaldehyde. In plants under abiotic stress, the cellular toxicity is reduced through glyoxalase pathway genes, i.e. Read More

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http://dx.doi.org/10.1186/s12864-018-5349-7DOI Listing
April 2019
2 Reads

Analysis of microRNAs, phased small interfering RNAs and their potential targets in Rosarugosa Thunb.

BMC Genomics 2019 Apr 18;19(Suppl 9):983. Epub 2019 Apr 18.

Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, 650500, China.

Background: MicroRNAs (miRNAs) are small non-coding RNAs that play important roles by regulating other genes. Rosa rugosa Thunb. is an important ornamental and edible plant, yet there are only a few studies on the miRNAs and their functions in R. Read More

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http://dx.doi.org/10.1186/s12864-018-5325-2DOI Listing

SQUAT: a Sequencing Quality Assessment Tool for data quality assessments of genome assemblies.

BMC Genomics 2019 Apr 18;19(Suppl 9):238. Epub 2019 Apr 18.

Institute of Information Science, Academia Sinica, Taipei, Taiwan.

Background: With the rapid increase in genome sequencing projects for non-model organisms, numerous genome assemblies are currently in progress or available as drafts, but not made available as satisfactory, usable genomes. Data quality assessment of genome assemblies is gaining importance not only for people who perform the assembly/re-assembly processes, but also for those who attempt to use assemblies as maps in downstream analyses. Recent studies of the quality control, quality evaluation/ assessment of genome assemblies have focused on either quality control of reads before assemblies or evaluation of the assemblies with respect to their contiguity and correctness. Read More

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https://bmcgenomics.biomedcentral.com/articles/10.1186/s1286
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http://dx.doi.org/10.1186/s12864-019-5445-3DOI Listing
April 2019
2 Reads

Chloroplast genome of Hibiscus rosa-sinensis (Malvaceae): Comparative analyses and identification of mutational hotspots.

Genomics 2019 Apr 15. Epub 2019 Apr 15.

Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan. Electronic address:

Previous studies to resolve phylogenetic and taxonomic discrepancies of Hibiscus remained inconclusive. Here, we report chloroplast genome sequence of Hibiscus rosa-sinensis. Hibiscus rosa-sinensis chloroplast genome was 160,951 bp, comprising of large single copy (89,509 bp) and small single copy (20,246 bp) regions, separated by IRa and IRb (25,598 bp each). Read More

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http://dx.doi.org/10.1016/j.ygeno.2019.04.010DOI Listing

LncRNA UCA1 protects cardiomyocytes against hypoxia/reoxygenation induced apoptosis through inhibiting miR-143/MDM2/p53 axis.

Genomics 2019 Apr 15. Epub 2019 Apr 15.

Department of Vasculocardiology, The First Affiliated Hospital of Soochow University, Soochow 215006, PR China. Electronic address:

Background: lncUCA1 is abundantly expressed in the heart, indicating it may be important in maintaining normal myocardial function. However, the underlying mechanism of lncUCA1 in heart disease, particularly myocardial infarction (MI), is still in its infancy.

Methods: LncUCA1 and miR-143 expression were measured in hearts of MI models. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S08887543183052
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http://dx.doi.org/10.1016/j.ygeno.2019.04.009DOI Listing
April 2019
1 Read

Novel Stenotrophomonas maltophilia temperate phage DLP4 is capable of lysogenic conversion.

BMC Genomics 2019 Apr 16;20(1):300. Epub 2019 Apr 16.

Department of Biological Sciences, 6-065 Centennial Centre for Interdisciplinery Science, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada.

Background: Temperate bacteriophages are capable of lysogenic conversion of new bacterial hosts. This phenomenon is often ascribed to "moron" elements that are acquired horizontally and transcribed independently from the rest of the phage genes. Whereas some bacterial species exhibit relatively little prophage-dependent phenotypic changes, other bacterial species such as Stenotrophomonas maltophilia appear to commonly adopt prophage genetic contributions. Read More

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https://bmcgenomics.biomedcentral.com/articles/10.1186/s1286
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http://dx.doi.org/10.1186/s12864-019-5674-5DOI Listing
April 2019
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The first draft genomes of the ant Formica exsecta, and its Wolbachia endosymbiont reveal extensive gene transfer from endosymbiont to host.

BMC Genomics 2019 Apr 16;20(1):301. Epub 2019 Apr 16.

Organismal and Evolutionary Biology Research Programme, Faculty of Biological and environmental sciences, University of Helsinki, P.O. Box 65, FI-00014, Helsinki, Finland.

Background: Adapting to changes in the environment is the foundation of species survival, and is usually thought to be a gradual process. However, transposable elements (TEs), epigenetic modifications, and/or genetic material acquired from other organisms by means of horizontal gene transfer (HGTs), can also lead to novel adaptive traits. Social insects form dense societies, which attract and maintain extra- and intracellular accessory inhabitants, which may facilitate gene transfer between species. Read More

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http://dx.doi.org/10.1186/s12864-019-5665-6DOI Listing

Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes.

BMC Genomics 2019 Apr 16;20(1):299. Epub 2019 Apr 16.

Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico.

Background: Crl, identified for curli production, is a small transcription factor that stimulates the association of the σ factor (RpoS) with the RNA polymerase core through direct and specific interactions, increasing the transcription rate of genes during the transition from exponential to stationary phase at low temperatures, using indole as an effector molecule. The lack of a comprehensive collection of information on the Crl regulon makes it difficult to identify a dominant function of Crl and to generate any hypotheses concerning its taxonomical distribution in archaeal and bacterial organisms.

Results: In this work, based on a systematic literature review, we identified the first comprehensive dataset of 86 genes under the control of Crl in the bacterium Escherichia coli K-12; those genes correspond to 40% of the σ regulon in this bacterium. Read More

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https://bmcgenomics.biomedcentral.com/articles/10.1186/s1286
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http://dx.doi.org/10.1186/s12864-019-5619-zDOI Listing
April 2019
1 Read

Selective translational usage of TSS and core promoters revealed by translatome sequencing.

BMC Genomics 2019 Apr 11;20(1):282. Epub 2019 Apr 11.

State Key laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.

Background: In mammals, fine-tuned regulation of gene expression leads to transcription initiation from diverse transcription start sites (TSSs) and multiple core promoters. Although polysome association is a critical step in translation, whether polysome selectively uses TSSs and core promoters and how this could impact translation remains elusive.

Results: In this study, we used CAGE followed by deep sequencing to globally profile the transcript 5' isoforms in the translatome and transcriptome of human HEK293 cells at single-nucleotide resolution. Read More

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https://bmcgenomics.biomedcentral.com/articles/10.1186/s1286
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http://dx.doi.org/10.1186/s12864-019-5650-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6463679PMC
April 2019
1 Read

Development of PCR markers specific to Dasypyrum villosum genome based on transcriptome data and their application in breeding Triticum aestivum-D. villosum#4 alien chromosome lines.

BMC Genomics 2019 Apr 15;20(1):289. Epub 2019 Apr 15.

Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.

Background: Dasypyrum villosum is an important wild species of wheat (Triticum aestivum L.) and harbors many desirable genes that can be used to improve various traits of wheat. Compared with other D. Read More

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http://dx.doi.org/10.1186/s12864-019-5630-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6466811PMC
April 2019
1 Read

A cmap-enabled gene expression signature-matching approach identifies small-molecule inducers of accelerated cell senescence.

BMC Genomics 2019 Apr 15;20(1):290. Epub 2019 Apr 15.

Department of Molecular Genetics and Cell Biology and Ludwig Center for Metastasis Research, The University of Chicago, 929 East 57th Street, GCIS W522A, Chicago, IL, 60637, USA.

Background: Diverse stresses including genotoxic therapy can induce proliferating cancer cells to undergo cellular senescence and take on the characteristic phenotypes of replicative cellular aging. This accelerated or therapy-induced senescence has been alternatively proposed to contribute to therapeutic efficacy or resistance. Toward better understanding this cell state, we sought to define the core transcriptome of accelerated senescence in cancer cells. Read More

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http://dx.doi.org/10.1186/s12864-019-5653-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6466706PMC

Overlap between eQTL and QTL associated with production traits and fertility in dairy cattle.

BMC Genomics 2019 Apr 15;20(1):291. Epub 2019 Apr 15.

Faculty of Veterinary & Agricultural Science, University of Melbourne, Parkville, Victoria, Australia.

Background: Identifying causative mutations or genes through which quantitative trait loci (QTL) act has proven very difficult. Using information such as gene expression may help to identify genes and mutations underlying QTL. Our objective was to identify regions associated both with production traits or fertility and with gene expression, in dairy cattle. Read More

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http://dx.doi.org/10.1186/s12864-019-5656-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6466667PMC

Mutational hotspots of HSP47 and its potential role in cancer and bone-disorders.

Genomics 2019 Apr 12. Epub 2019 Apr 12.

Department of Genetics & Molecular Biology in Botany, Institute of Botany, Christian-Albrechts-University at Kiel, Germany. Electronic address:

Heat shock protein 47 kDa (HSP47) serves as a client-specific chaperone, essential for collagen biosynthesis and its folding and structural assembly. To date, there is no comprehensive study on mutational hotspots. Using five different human mutational databases, we deduced a comprehensive list of human HSP47 mutations with 24, 67, 50, 43 and 2 deleterious mutations from the 1000 genomes data, gnomAD, COSMICv86, cBioPortal, and CanVar, respectively. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S08887543183067
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http://dx.doi.org/10.1016/j.ygeno.2019.04.007DOI Listing
April 2019
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Paternal inheritance of diet induced metabolic traits correlates with germline regulation of diet induced coding gene expression.

Genomics 2019 Apr 12. Epub 2019 Apr 12.

CSIR-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research, New Delhi, India. Electronic address:

Inheritance of induced traits through the germline is poorly understood and controversial. The ideal evidence correlating induced and inherited traits with germline gene expression remains largely obscure. Using a Drosophila coding transcriptome level model of paternal high sugar diet induced alterations in triglyceride levels across generations, in conjunction with pre-existing data, we show here highly significant overlap of differentially expressed genes between the ancestral generation, the resulting sperm and embryos, and the future generation individuals. Read More

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http://dx.doi.org/10.1016/j.ygeno.2019.04.008DOI Listing

Transcriptome analysis of Burkholderia pseudomallei SCV reveals an association with virulence, stress resistance and intracellular persistence.

Genomics 2019 Apr 10. Epub 2019 Apr 10.

Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia. Electronic address:

Differences in expression of potential virulence and survival genes were associated with B. pseudomallei colony morphology variants. Microarray was used to investigate B. Read More

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http://dx.doi.org/10.1016/j.ygeno.2019.04.002DOI Listing

Highly accurate-single chromosomal complete genomes using IonTorrent and MinION sequencing of clinical pathogens.

Genomics 2019 Apr 10. Epub 2019 Apr 10.

Department of Clinical Microbiology, Christian Medical College, Vellore 632004, Tamil Nadu, India. Electronic address:

Oxford Nanopore MinION sequencing technology has been gaining immense importance in identification of pathogen and antimicrobial resistance, though with 10-15% error rate. Short read technologies generates high accurate genome but with multiple fragments of genome. This study proposes a novel workflow to reduce the indels resulted from MinION long read sequencing by overlaying short read sequences from IonTorrent in the clinical isolates. Read More

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http://dx.doi.org/10.1016/j.ygeno.2019.04.006DOI Listing

An improved protein extraction method applied to cotton leaves is compatible with 2-DE and LC-MS.

BMC Genomics 2019 Apr 11;20(1):285. Epub 2019 Apr 11.

Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, China.

Background: Two-dimensional electrophoresis (2-DE) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) are widely used in plant proteomics research. However, these two techniques cannot be simultaneously satisfied by traditional protein extraction methods when investigate cotton leaf proteome.

Results: Here, we evaluated the efficiency of three different protein extraction methods for 2-DE and LC-MS/MS analyses of total proteins obtained from cotton leaves. Read More

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http://dx.doi.org/10.1186/s12864-019-5658-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6458646PMC

A splice donor variant in CCDC189 is associated with asthenospermia in Nordic Red dairy cattle.

BMC Genomics 2019 Apr 11;20(1):286. Epub 2019 Apr 11.

Animal Genomics, ETH Zurich, 8001, Zurich, Switzerland.

Background: Cattle populations are highly amenable to the genetic mapping of male reproductive traits because longitudinal data on ejaculate quality and dense microarray-derived genotypes are available for thousands of artificial insemination bulls. Two young Nordic Red bulls delivered sperm with low progressive motility (i.e. Read More

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http://dx.doi.org/10.1186/s12864-019-5628-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6460654PMC
April 2019
1 Read

Effects of a previously selected antibiotic resistance on mutations acquired during development of a second resistance in Escherichia coli.

BMC Genomics 2019 Apr 11;20(1):284. Epub 2019 Apr 11.

Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.

Background: The effect of mutations conferring antibiotic resistance can depend on the genetic background. To determine if a previously de novo acquired antibiotic resistance influences the adaptation to a second antibiotic, antibiotic resistance was selected for by exposure to stepwise increasing sublethal levels of amoxicillin, enrofloxacin, kanamycin, or tetracycline. E. Read More

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http://dx.doi.org/10.1186/s12864-019-5648-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6458618PMC

Comparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis.

BMC Genomics 2019 Apr 11;20(1):283. Epub 2019 Apr 11.

College of Life Sciences / National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources / Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, People's Republic of China.

Background: Members of the genus Bacillus are important plant growth-promoting rhizobacteria that serve as biocontrol agents. Bacillus paralicheniformis MDJK30 is a PGPR isolated from the peony rhizosphere and can suppress plant-pathogenic bacteria and fungi. To further uncover the genetic mechanism of the plant growth-promoting traits of MDJK30 and its closely related strains, we used comparative genomics to provide insights into the genetic diversity and evolutionary relationship between B. Read More

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http://dx.doi.org/10.1186/s12864-019-5646-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6458615PMC

Genome-wide identification and expression profiling of trihelix gene family under abiotic stresses in wheat.

BMC Genomics 2019 Apr 11;20(1):287. Epub 2019 Apr 11.

The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, 430074, China.

Background: The trihelix gene family is a plant-specific transcription factor family that plays important roles in plant growth, development, and responses to abiotic stresses. However, to date, no systemic characterization of the trihelix genes has yet been conducted in wheat and its close relatives.

Results: We identified a total of 94 trihelix genes in wheat, as well as 22 trihelix genes in Triticum urartu, 29 in Aegilops tauschii, and 31 in Brachypodium distachyon. Read More

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http://dx.doi.org/10.1186/s12864-019-5632-2DOI Listing
April 2019
2 Reads

Systematic identification and validation of the reference genes from 60 RNA-Seq libraries in the scallop Mizuhopecten yessoensis.

BMC Genomics 2019 Apr 11;20(1):288. Epub 2019 Apr 11.

MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao, China.

Background: Reverse transcription quantitative PCR (RT-qPCR) is widely used for gene expression analysis in various organisms. Its accuracy largely relies on the stability of reference genes, making reference gene selection a vital step in RT-qPCR experiments. However, previous studies in mollusks only focused on the reference genes widely used in vertebrates. Read More

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https://bmcgenomics.biomedcentral.com/articles/10.1186/s1286
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http://dx.doi.org/10.1186/s12864-019-5661-xDOI Listing
April 2019
1 Read

Genome sequence analysis of 91 Salmonella Enteritidis isolates from mice caught on poultry farms in the mid 1990s.

Genomics 2019 Apr 8. Epub 2019 Apr 8.

Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, MD 20740.

A total of 91 draft genome sequences were used to analyze isolates of Salmonella enterica serovar Enteritidis obtained from feral mice caught on poultry farms in Pennsylvania. One objective was to find mutations disrupting open reading frames (ORFs) and another was to determine if ORF-disruptive mutations were present in isolates obtained from other sources. A total of 83 mice were obtained between 1995-1998. Read More

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http://dx.doi.org/10.1016/j.ygeno.2019.04.005DOI Listing

Transcriptional changes in response to ketamine ester-analogs SN 35210 and SN 35563 in the rat brain.

BMC Genomics 2019 Apr 11;20(1):281. Epub 2019 Apr 11.

Waikato District Health Board, Pembroke Street, Hamilton, 3204, New Zealand.

Background: Ketamine ester analogs, SN 35210 and SN 35563, demonstrate different pharmacological profiles to ketamine in animal models. Both confer hypnosis with predictably rapid offset yet, paradoxically, SN35563 induces a prolonged anti-nociceptive state. To explore underlying mechanisms, broad transcriptome changes were measured and compared across four relevant target regions of the rat brain. Read More

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http://dx.doi.org/10.1186/s12864-019-5649-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6458767PMC

Differential expression analysis of Trichoderma virens RNA reveals a dynamic transcriptome during colonization of Zea mays roots.

BMC Genomics 2019 Apr 11;20(1):280. Epub 2019 Apr 11.

Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA.

Background: Trichoderma spp. are majorly composed of plant-beneficial symbionts widely used in agriculture as bio-control agents. Studying the mechanisms behind Trichoderma-derived plant benefits has yielded tangible bio-industrial products. Read More

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http://dx.doi.org/10.1186/s12864-019-5651-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6458689PMC

DeepHistone: a deep learning approach to predicting histone modifications.

BMC Genomics 2019 Apr 4;20(Suppl 2):193. Epub 2019 Apr 4.

MOE Key Laboratory of Bioinformatics; Bioinformatics Division, Beijing National Laboratory for Information Science and Technology, Tsinghua University, Beijing, 100084, China.

Motivation: Quantitative detection of histone modifications has emerged in the recent years as a major means for understanding such biological processes as chromosome packaging, transcriptional activation, and DNA damage. However, high-throughput experimental techniques such as ChIP-seq are usually expensive and time-consuming, prohibiting the establishment of a histone modification landscape for hundreds of cell types across dozens of histone markers. These disadvantages have been appealing for computational methods to complement experimental approaches towards large-scale analysis of histone modifications. Read More

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http://dx.doi.org/10.1186/s12864-019-5489-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456942PMC

Improving the sensitivity of long read overlap detection using grouped short k-mer matches.

BMC Genomics 2019 Apr 4;20(Suppl 2):190. Epub 2019 Apr 4.

Electronic Engineering Department, City University of Hong Kong, Hong Kong SAR, China.

Background: Single-molecule, real-time sequencing (SMRT) developed by Pacific BioSciences produces longer reads than second-generation sequencing technologies such as Illumina. The increased read length enables PacBio sequencing to close gaps in genome assembly, reveal structural variations, and characterize the intra-species variations. It also holds the promise to decipher the community structure in complex microbial communities because long reads help metagenomic assembly. Read More

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https://bmcgenomics.biomedcentral.com/articles/10.1186/s1286
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http://dx.doi.org/10.1186/s12864-019-5475-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456931PMC
April 2019
1 Read

Explore mediated co-varying dynamics in microbial community using integrated local similarity and liquid association analysis.

BMC Genomics 2019 Apr 4;20(Suppl 2):185. Epub 2019 Apr 4.

Department of Medicine, Stanford University School of Medicine, 269 Campus Dr., Stanford, CA, 94305, USA.

Background: Discovering the key microbial species and environmental factors of microbial community and characterizing their relationships with other members are critical to ecosystem studies. The microbial co-occurrence patterns across a variety of environmental settings have been extensively characterized. However, previous studies were limited by their restriction toward pairwise relationships, while there was ample evidence of third-party mediated co-occurrence in microbial communities. Read More

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https://bmcgenomics.biomedcentral.com/articles/10.1186/s1286
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http://dx.doi.org/10.1186/s12864-019-5469-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456937PMC
April 2019
2 Reads

MRCNN: a deep learning model for regression of genome-wide DNA methylation.

BMC Genomics 2019 Apr 4;20(Suppl 2):192. Epub 2019 Apr 4.

School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China.

Background: Determination of genome-wide DNA methylation is significant for both basic research and drug development. As a key epigenetic modification, this biochemical process can modulate gene expression to influence the cell differentiation which can possibly lead to cancer. Due to the involuted biochemical mechanism of DNA methylation, obtaining a precise prediction is a considerably tough challenge. Read More

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http://dx.doi.org/10.1186/s12864-019-5488-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6457069PMC

Large-scale 3D chromatin reconstruction from chromosomal contacts.

BMC Genomics 2019 Apr 4;20(Suppl 2):186. Epub 2019 Apr 4.

Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR.

Background: Recent advances in genome analysis have established that chromatin has preferred 3D conformations, which bring distant loci into contact. Identifying these contacts is important for us to understand possible interactions between these loci. This has motivated the creation of the Hi-C technology, which detects long-range chromosomal interactions. Read More

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http://dx.doi.org/10.1186/s12864-019-5470-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456969PMC

Meta-network: optimized species-species network analysis for microbial communities.

BMC Genomics 2019 Apr 4;20(Suppl 2):187. Epub 2019 Apr 4.

Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.

Background: The explosive growth of microbiome data provides ample opportunities to gain a better understanding of the microbes and their interactions in microbial communities. Given these massive data, optimized data mining methods become important and necessary to perform deep and comprehensive analysis. Among the various priorities for microbiome data mining, the examination of species-species co-occurrence patterns becomes one of the key themes in urgent need. Read More

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http://dx.doi.org/10.1186/s12864-019-5471-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6457071PMC

A distance-type measure approach to the analysis of copy number variation in DNA sequencing data.

BMC Genomics 2019 Apr 4;20(Suppl 2):195. Epub 2019 Apr 4.

Department of Statistics and Biostatistics Center, The George Washington University, Rome Hall, 7th Floor, 801, 22nd Street NW, Washington D.C, 20052, USA.

Background: The next generation sequencing technology allows us to obtain a large amount of short DNA sequence (DNA-seq) reads at a genome-wide level. DNA-seq data have been increasingly collected during the recent years. Count-type data analysis is a widely used approach for DNA-seq data. Read More

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https://bmcgenomics.biomedcentral.com/articles/10.1186/s1286
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http://dx.doi.org/10.1186/s12864-019-5491-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456939PMC
April 2019
3 Reads

A secure SNP panel scheme using homomorphically encrypted K-mers without SNP calling on the user side.

BMC Genomics 2019 Apr 4;20(Suppl 2):188. Epub 2019 Apr 4.

Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea.

Background: Single Nucleotide Polymorphism (SNP) in the genome has become crucial information for clinical use. For example, the targeted cancer therapy is primarily based on the information which clinically important SNPs are detectable from the tumor. Many hospitals have developed their own panels that include clinically important SNPs. Read More

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http://dx.doi.org/10.1186/s12864-019-5473-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456943PMC

Signal enrichment with strain-level resolution in metagenomes using topological data analysis.

BMC Genomics 2019 Apr 4;20(Suppl 2):194. Epub 2019 Apr 4.

Computational Biology Center, IBM T. J. Watson Research Center, Yorktown Heights, NY, USA.

Background: A metagenome is a collection of genomes, usually in a micro-environment, and sequencing a metagenomic sample en masse is a powerful means for investigating the community of the constituent microorganisms. One of the challenges is in distinguishing between similar organisms due to rampant multiple possible assignments of sequencing reads, resulting in false positive identifications. We map the problem to a topological data analysis (TDA) framework that extracts information from the geometric structure of data. Read More

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https://bmcgenomics.biomedcentral.com/articles/10.1186/s1286
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http://dx.doi.org/10.1186/s12864-019-5490-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456948PMC
April 2019
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Microbiota in the apical root canal system of tooth with apical periodontitis.

BMC Genomics 2019 Apr 4;20(Suppl 2):189. Epub 2019 Apr 4.

Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China.

Background: Apical periodontitis (AP) is essentially an inflammatory disease of microbial etiology primarily caused by infection of the pulp and root canal system. Variation of the bacterial communities caused by AP, as well as their changes responding to dental therapy, are of utmost importance to understand the pathogensis of the apical periodontitis and establishing effective antimicrobial therapeutic strategies. This study aims to uncover the composition and diversity of microbiota associated to the root apex to identify the relevant bacteria highly involved in AP, with the consideration of root apex samples from the infected teeth (with/without root canal treatment), healthy teeth as well as the healthy oral. Read More

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http://dx.doi.org/10.1186/s12864-019-5474-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456935PMC

GPU accelerated sequence alignment with traceback for GATK HaplotypeCaller.

BMC Genomics 2019 Apr 4;20(Suppl 2):184. Epub 2019 Apr 4.

Delft University of Technology, Mekelweg 4, Delft, 2628 CD, The Netherlands.

Background: Pairwise sequence alignment is widely used in many biological tools and applications. Existing GPU accelerated implementations mainly focus on calculating optimal alignment score and omit identifying the optimal alignment itself. In GATK HaplotypeCaller (HC), the semi-global pairwise sequence alignment with traceback has so far been difficult to accelerate effectively on GPUs. Read More

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http://dx.doi.org/10.1186/s12864-019-5468-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456962PMC

Estimating the total genome length of a metagenomic sample using k-mers.

BMC Genomics 2019 Apr 4;20(Suppl 2):183. Epub 2019 Apr 4.

MOE Key Laboratory of Bioinformatics Division and Center for Synthetic & System Biology, BNRIST, Beijing, 100084, China.

Background: Metagenomic sequencing is a powerful technology for studying the mixture of microbes or the microbiomes on human and in the environment. One basic task of analyzing metagenomic data is to identify the component genomes in the community. This task is challenging due to the complexity of microbiome composition, limited availability of known reference genomes, and usually insufficient sequencing coverage. Read More

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http://dx.doi.org/10.1186/s12864-019-5467-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456951PMC

ENIGMA: an enterotype-like unigram mixture model for microbial association analysis.

BMC Genomics 2019 Apr 4;20(Suppl 2):191. Epub 2019 Apr 4.

Division of Systems Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan.

Background: One of the major challenges in microbial studies is detecting associations between microbial communities and a specific disease. A specialized feature of microbiome count data is that intestinal bacterial communities form clusters called as "enterotype", which are characterized by differences in specific bacterial taxa, making it difficult to analyze these data under health and disease conditions. Traditional probabilistic modeling cannot distinguish between the bacterial differences derived from enterotype and those related to a specific disease. Read More

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http://dx.doi.org/10.1186/s12864-019-5476-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456936PMC
April 2019
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Genome-wide analysis of epigenetic dynamics across human developmental stages and tissues.

BMC Genomics 2019 Apr 4;20(Suppl 2):221. Epub 2019 Apr 4.

Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, Shanghai, China.

Background: Epigenome is highly dynamic during the early stages of embryonic development. Epigenetic modifications provide the necessary regulation for lineage specification and enable the maintenance of cellular identity. Given the rapid accumulation of genome-wide epigenomic modification maps across cellular differentiation process, there is an urgent need to characterize epigenetic dynamics and reveal their impacts on differential gene regulation. Read More

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http://dx.doi.org/10.1186/s12864-019-5472-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6457072PMC
April 2019
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TSEE: an elastic embedding method to visualize the dynamic gene expression patterns of time series single-cell RNA sequencing data.

BMC Genomics 2019 Apr 4;20(Suppl 2):224. Epub 2019 Apr 4.

Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China.

Background: Time series single-cell RNA sequencing (scRNA-seq) data are emerging. However, the analysis of time series scRNA-seq data could be compromised by 1) distortion created by assorted sources of data collection and generation across time samples and 2) inheritance of cell-to-cell variations by stochastic dynamic patterns of gene expression. This calls for the development of an algorithm able to visualize time series scRNA-seq data in order to reveal latent structures and uncover dynamic transition processes. Read More

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http://dx.doi.org/10.1186/s12864-019-5477-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456934PMC

Insight into the combinatorial transcriptional regulation on α-amylase gene in animal groups with different dietary nutrient content.

Genomics 2019 Apr 6. Epub 2019 Apr 6.

Center for Computational Research, New York State Center of Excellence in Bioinformatics & Life Sciences, State University of New York at Buffalo, Buffalo, NY 14260, USA; Department of Ophthalmology, State University of New York at Buffalo, Buffalo, NY 14260, USA; Department of Biostatistics, State University of New York at Buffalo, Buffalo, NY 14260, USA; Department of Medicine, State University of New York at Buffalo, Buffalo, NY 14260, USA; SUNY Eye Institute, Buffalo, NY 14260, USA. Electronic address:

Gene expression is generally regulated by multiple transcription factors (TFs). Despite previous findings of individual TFs regulating pancreatic α-amylase gene expression, the combinatorial transcriptional regulation is not fully understood. To gain insight into multiple TF regulation for pancreatic α-amylase gene, we employed a function conservation approach to predict interacting TFs regulating pancreatic α-amylase gene for 3 dietary animal groups. Read More

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http://dx.doi.org/10.1016/j.ygeno.2019.04.004DOI Listing