abstract：:Nematodes are responsible for causing severe diseases in plants, humans and other animals. Infection is associated with the release of Excretory/Secretory (ES) proteins into host cytoplasm and interference with the host immune system which make them attractive targets for therapeutic use. The identification of ES prot...

journal_title：Genomics

authors： Gahoi S,Singh S,Gautam B

更新日期：2019-05-01 00:00:00

abstract：:In our previous studies, diploid and triploid hybrids have been detected from the hybridization of Epinephelus coioides♀ × E. lanceolatus♂. The triploid groupers have been found to be delayed in gonadal development, but the mechanism remains poorly understood. In this study, we examined the gonadal development, assaye...

journal_title：Genomics

authors： Xiao L,Wang D,Guo Y,Tang Z,Liu Q,Li S,Zhang Y,Lin H

更新日期：2019-05-01 00:00:00

abstract：:lncRNAs are a class of transcriptional RNA molecules of >200 nucleotides in length. However, the overall expression pattern and function of lncRNAs in sheep muscle is not clear. Here, we identified 1566 lncRNAs and 404 differentially expressed lncRNAs in sheep muscle from prenatal (110 days of fetus) and postnatal (2 ...

journal_title：Genomics

authors： Li CY,Li X,Liu Z,Ni W,Zhang X,Hazi W,Ma Q,Zhang Y,Cao Y,Qi J,Yao Y,Feng L,Wang D,Hou X,Yu S,Liu L,Zhang M,Hu S

更新日期：2019-03-01 00:00:00

abstract：:Non-coding RNA is no longer considered to be "junk" DNA, based on evidence uncovered in recent decades. In particular, the important role played by natural antisense transcripts (NATs) in regulating the expression of genes is receiving increasing attention. However, the regulatory mechanisms of NATs remain incompletel...

journal_title：Genomics

authors： Jung J,Lee S,Cho HS,Park K,Ryu JW,Jung M,Kim J,Kim H,Kim DS

更新日期：2019-03-01 00:00:00

abstract：:Long sequencing reads offer unprecedented opportunities in analysis and reconstruction of complex genomic regions. However, the gain in sequence length is often traded for quality. Therefore, recently several approaches have been proposed (e.g. higher sequencing coverage, hybrid assembly or sequence correction) to enh...

journal_title：Genomics

authors： Mahmoud M,Zywicki M,Twardowski T,Karlowski WM

更新日期：2019-01-01 00:00:00

abstract：:N6-methyladenine (6mA) is one kind of post-replication modification (PTM or PTRM) occurring in a wide range of DNA sequences. Accurate identification of its sites will be very helpful for revealing the biological functions of 6mA, but it is time-consuming and expensive to determine them by experiments alone. Unfortuna...

journal_title：Genomics

authors： Feng P,Yang H,Ding H,Lin H,Chen W,Chou KC

更新日期：2019-01-01 00:00:00

abstract：:Integrating gene expression into protein-protein interaction network (PPIN) leads to the construction of tissue-specific (TS) and housekeeping (HK) sub-networks, with distinctive TS- and HK-hubs. All such hub proteins are divided into multi-interface (MI) hubs and single-interface (SI) hubs, where MI hubs evolve slowe...

journal_title：Genomics

authors： Biswas K,Acharya D,Podder S,Ghosh TC

更新日期：2018-09-01 00:00:00

abstract：:For genetic linkage analysis of Japanese flounder, 160 doubled haploids (DH) were artificially produced using mitotic gynogenesis and were genotyped for 458 simple sequence repeat (SSR) markers, 101 of which show distortional segregation. The genetic linkage map was constructed by modifying recombination fractions bet...

journal_title：Genomics

authors： Zhao J,Han D,Shi K,Wang L,Gao J,Yang R

更新日期：2018-01-01 00:00:00

abstract：:It is usually assumed that co-expressed genes suggest co-regulation in the underlying regulatory network. Determining sets of co-expressed genes is an important task, based on some criteria of similarity. This task is usually performed by clustering algorithms, where the genes are clustered into meaningful groups base...

journal_title：Genomics

authors： Pagnuco IA,Pastore JI,Abras G,Brun M,Ballarin VL

更新日期：2017-10-01 00:00:00

abstract：:An alarming increase in the human population necessitates doubling the world food production in the next few decades. Although a number of possible biotechnological measures are under consideration, central to these efforts is the development of transgenic crops to produce more food, and the traits with which plants c...

journal_title：Genomics

authors： Ahmad N,Mukhtar Z

更新日期：2017-10-01 00:00:00

abstract：:The genome sequence of Mycobacterium tuberculosis strain H37Rv is an important and valuable reference point in the study of M. tuberculosis phylogeny, molecular epidemiology, and drug-resistance mutations. However, it is becoming apparent that use of H37Rv as a sole reference genome in analysing clinical isolates pres...

journal_title：Genomics

authors： O'Toole RF,Gautam SS

更新日期：2017-10-01 00:00:00

abstract：:Farletuzumab (FAR) is a humanized monoclonal antibody (mAb) that binds to folate receptor alpha. A Ph3 trial in ovarian cancer patients treated with carboplatin/taxane plus FAR or placebo did not meet the primary statistical endpoint. Subgroup analysis demonstrated that subjects with high FAR exposure levels (Cmin>57....

journal_title：Genomics

authors： O'Shannessy DJ,Bendas K,Schweizer C,Wang W,Albone E,Somers EB,Weil S,Meredith RK,Wustner J,Grasso L,Landers M,Nicolaides NC

更新日期：2017-07-01 00:00:00

abstract：:Mammalian genomes include DNA segments that are imprinted (CpG-methylated) only on one of the two parental chromosomes, leading to parent-of-origin-specific gene expression. The process is regulated by Imprinting Control Regions (ICRs) and germline Differentially Methylated Regions (gDMRs). Previously, ZFP57 was shown...

journal_title：Genomics

authors： Bina M

更新日期：2017-07-01 00:00:00

abstract：:One of the most critical periods of embryonic loss in pig is day 12 of pregnancy, when implantation begins. Here, we analyzed the gene expression on day 12 of pregnancy and non-pregnancy in the porcine endometrium using RNA sequencing (RNA-seq). 237 mRNAs, 34 lncRNAs and 1 miRNA were significantly differentially expre...

journal_title：Genomics

authors： Wang Y,Hu T,Wu L,Liu X,Xue S,Lei M

更新日期：2017-01-01 00:00:00

abstract：:Glaucoma is a very common disorder of the eye wherein the disturbance of the structural or functional integrity of the optic nerve causes characteristic atrophic changes in the optic nerve, which may lead to specific visual field defects over time. Primary open angle glaucoma (POAG) is most frequent among the three pr...

journal_title：Genomics

authors： Kumar S,Malik MA,K S,Sihota R,Kaur J

更新日期：2017-01-01 00:00:00

abstract：:Premature ovarian failure (POF) is characterized by heterogeneous genetic causes such as chromosomal abnormalities and variants in causal genes. Recently, development of techniques made next generation sequencing (NGS) possible to detect genome wide variants including chromosomal abnormalities. Among 37 Korean POF pat...

journal_title：Genomics

authors： Lee Y,Kim C,Park Y,Pyun JA,Kwack K

更新日期：2016-12-01 00:00:00

abstract：:Co-expression networks may provide insights into the patterns of molecular interactions that underlie cellular processes. To obtain a better understanding of miRNA expression patterns in gastric adenocarcinoma and to provide markers that can be associated with histopathological findings, we performed weighted gene cor...

journal_title：Genomics

authors： Yepes S,López R,Andrade RE,Rodriguez-Urrego PA,López-Kleine L,Torres MM

更新日期：2016-08-01 00:00:00

abstract：:The field of molecular evolution started with the alignment of a few protein sequences in the early 1960s. Among the first results found, the genetic equidistance result has turned out to be the most unexpected. It directly inspired the ad hoc universal molecular clock hypothesis that in turn inspired the neutral theo...

journal_title：Genomics

authors： Luo D,Huang S

更新日期：2016-07-01 00:00:00

abstract：:Traditionally, somatic mutations are detected by examining DNA sequence. The maturity of sequencing technology has allowed researchers to screen for somatic mutations in the whole genome. Increasingly, researchers have become interested in identifying somatic mutations through RNAseq data. With this motivation, we eva...

journal_title：Genomics

authors： Sheng Q,Zhao S,Li CI,Shyr Y,Guo Y

更新日期：2016-05-01 00:00:00

abstract：:Proteins of the DUF1313 family contain a highly conserved domain and are only found in plants; they play important roles in most plant functions. In this study, 269 DUF1313 genes from 81 photoautotrophic species were identified; they were classified into three major types based on the amino acid substitutions in the c...

journal_title：Genomics

authors： Li J,Hu E,Chen X,Xu J,Lan H,Li C,Hu Y,Lu Y

更新日期：2016-05-01 00:00:00

abstract：OBJECTIVE:Cytokines strongly induce expression of the inducible nitric oxide synthase (iNOS) in rodent but not in human endothelial cells. We recently identified NOS2 as a potential target of the histone methyltransferase enhancer of zeste homolog 2 which mediates trimethylation of histone 3 at lysine 27 (H3K27me3). M...

journal_title：Genomics

authors： Dreger H,Ludwig A,Weller A,Baumann G,Stangl V,Stangl K

更新日期：2016-04-01 00:00:00

abstract：:Blood-based epigenome-wide association studies that aim at comparing CpG methylation between colorectal cancer (CRC) patients and controls can lead to the discovery of diagnostic or prognostic biomarkers. Numerous confounders can lead to spurious associations. We aimed to see if 5-fluorouracil (5-FU)/leucovorin chemot...

journal_title：Genomics

authors： Lemire M,Zaidi SH,Zanke BW,Gallinger S,Hudson TJ,Cleary SP

更新日期：2015-12-01 00:00:00

abstract：:The molecular mechanism involved in BmNPV resistance was investigated using a genome wide microarray in midgut tissue of Indian silkworm Bombyx mori. In resistant race (Sarupat), 735 genes up-regulated and 589 genes down-regulated at 12 h post BmNPV infection. Similarly, in case of susceptible race (CSR-2), 2183 genes...

journal_title：Genomics

authors： Lekha G,Gupta T,Awasthi AK,Murthy GN,Trivedy K,Ponnuvel KM

更新日期：2015-12-01 00:00:00

abstract：:The expression of plasma proteins changes dramatically as a result of cytokine induction, particularly interleukin-6, and their levels are used as clinical markers of inflammation. miRNAs are important regulators of gene expression and play significant roles in many inflammatory diseases and processes. The interaction...

journal_title：Genomics

authors： Lukowski SW,Fish RJ,Martin-Levilain J,Gonelle-Gispert C,Bühler LH,Maechler P,Dermitzakis ET,Neerman-Arbez M

更新日期：2015-08-01 00:00:00

abstract：UNLABELLED:Pancreatic cancer is one of the most aggressive malignant tumors, mainly due to an aggressive metastasis spreading. In recent years, circulating tumor cells became associated to tumor metastasis. Little is known about their expression profiles. The aim of this study was to develop a complete workflow making ...

journal_title：Genomics

authors： Görner K,Bachmann J,Holzhauer C,Kirchner R,Raba K,Fischer JC,Martignoni ME,Schiemann M,Alunni-Fabbroni M

更新日期：2015-07-01 00:00:00

abstract：:The retina and its adjacent supporting tissues - retinal pigmented epithelium (RPE) and choroid - are critical structures in human eyes required for normal visual perception. Abnormal changes in these layers have been implicated in diseases such as age-related macular degeneration and glaucoma. With the advent of high...

journal_title：Genomics

authors： Tian L,Kazmierkiewicz KL,Bowman AS,Li M,Curcio CA,Stambolian DE

更新日期：2015-05-01 00:00:00

abstract：:Runs of homozygosity are common in European populations and are indicative of consanguinity, restricted population size and recessively inherited traits. Here, we map runs of homozygosity (ROHs) in an Irish case-control cohort for amyotrophic lateral sclerosis (ALS), a devastating neurological condition with high heri...

journal_title：Genomics

authors： McLaughlin RL,Kenna KP,Vajda A,Heverin M,Byrne S,Donaghy CG,Cronin S,Bradley DG,Hardiman O

更新日期：2015-04-01 00:00:00

abstract：:RNA-seq is the method of choice for getting a primary list of genes for non-model organisms. Once this is achieved, one would proceed to annotate the newly discovered genes and consequently strive to position the organism in an evolutionary context. These kinds of studies involving high-throughput sequencing generate ...

journal_title：Genomics

authors： Zahavi T,Stelzer G,Strauss L,Salmon AY,Salmon-Divon M

更新日期：2015-03-01 00:00:00

abstract：:Use of mixed models is in the spotlight as an emerging method for genome-wide association studies (GWASs). This study investigated the statistical power for identifying nucleotide variants associated with quantitative traits using the mixed model methodology. Quantitative traits were simulated through design of herita...

journal_title：Genomics

authors： Shin J,Lee C

更新日期：2015-01-01 00:00:00

abstract：:Changing bovine milk fatty acid (FA) composition through selection can decrease saturated FA (SFA) consumption, improve human health and provide a means for manipulating processing properties of milk. Our study determined associations between milk FA composition and genes from triacylglycerol (TAG) biosynthesis pathwa...

journal_title：Genomics

authors： Nafikov RA,Schoonmaker JP,Korn KT,Noack K,Garrick DJ,Koehler KJ,Minick-Bormann J,Reecy JM,Spurlock DE,Beitz DC

更新日期：2014-12-01 00:00:00

abstract：:The key regulatory elements for PKD2 transcription remain unclear. To identify these core elements, we characterized porcine PKD2 promoter with bioinformatics and molecular tools and found porcine PKD2 promoter bearing typical features of enriched CpG and less TATA. Further studies demonstrated that the core region wa...

journal_title：Genomics

authors： Wang Q,Han G,Ye J,Gao X,Niu H,Zhao J,Chai Y,Li N,Yin H

更新日期：2014-12-01 00:00:00

abstract：:Paulownia tomentosa is an important foundation forest tree species in semiarid areas. The lack of genetic information hinders research into the mechanisms involved in its response to abiotic stresses. Here, short-read sequencing technology (Illumina) was used to de novo assemble the transcriptome on P. tomentosa. A to...

journal_title：Genomics

authors： Dong Y,Fan G,Deng M,Xu E,Zhao Z

更新日期：2014-10-01 00:00:00

abstract：BACKGROUND:mRNA polyadenylation, the addition of a poly(A) tail to the 3'-end of pre-mRNA, is a process critical to gene expression and regulation in eukaryotes. To understand the molecular mechanisms governing polyadenylation and other relevant biological processes, it is important to identify these poly(A) tails accu...

journal_title：Genomics

authors： Morton JT,Abrudan P,Figueroa N,Liang C,Karro JE

更新日期：2014-09-01 00:00:00

abstract：:WRKY proteins constitute a large family of transcription factors. In this study, we identified 81 WRKY genes (named HbWRKY1 to HbWRKY81) in the latest rubber tree genome. Tissue-specific expression profiles showed that 74 HbWRKYs were expressed in at least one of the tissues and the other 7 genes showed very low expre...

journal_title：Genomics

authors： Li HL,Guo D,Yang ZP,Tang X,Peng SQ

更新日期：2014-07-01 00:00:00

abstract：UNLABELLED:Next-generation sequencing data can be mapped to a reference genome to identify single-nucleotide polymorphisms/variations (SNPs/SNVs; called SNPs hereafter). In theory, SNPs can be compared across several samples and the differences can be used to create phylogenetic trees depicting relatedness among the sa...

journal_title：Genomics

authors： Faison WJ,Rostovtsev A,Castro-Nallar E,Crandall KA,Chumakov K,Simonyan V,Mazumder R

更新日期：2014-07-01 00:00:00

abstract：:A computational and in silico system level framework was developed to identify and prioritize the antibacterial drug targets in Clostridium botulinum (Clb), the causative agent of flaccid paralysis in humans that can be fatal in 5 to 10% of cases. This disease is difficult to control due to the emergence of drug-resis...

journal_title：Genomics

authors： Muhammad SA,Ahmed S,Ali A,Huang H,Wu X,Yang XF,Naz A,Chen J

更新日期：2014-07-01 00:00:00

abstract：:Double-stranded RNA (dsRNA) is produced in host cells during viral replication. The effects of DNA demethylation on gene expression in dsRNA transfected swine cells are unclear. The study aims to profile the transcriptome changes which are induced by DNA methyltransferase inhibitor (Aza-CdR) in porcine PK15 cells tran...

journal_title：Genomics

authors： Wang X,Ao H,Zhai L,Bai L,He W,Yu Y,Wang C

更新日期：2014-05-01 00:00:00

abstract：:A key challenge in analyzing metagenomics data pertains to assembly of sequenced DNA fragments (i.e. reads) originating from various microbes in a given environmental sample. Several existing methodologies can assemble reads originating from a single genome. However, these methodologies cannot be applied for efficient...

journal_title：Genomics

authors： Reddy RM,Mohammed MH,Mande SS

更新日期：2014-02-01 00:00:00

abstract：:Elucidating the molecular basis of hepatocellular carcinoma (HCC) is crucial to developing targeted diagnostics and therapies for this deadly disease. The landscape of somatic genomic rearrangements (GRs), which can lead to oncogenic gene fusions, remains poorly characterized in HCC. We have predicted 4314 GRs includi...

journal_title：Genomics

authors： Fernandez-Banet J,Lee NP,Chan KT,Gao H,Liu X,Sung WK,Tan W,Fan ST,Poon RT,Li S,Ching K,Rejto PA,Mao M,Kan Z

更新日期：2014-02-01 00:00:00

abstract：:The rice genome annotation has been greatly improved in recent years, largely due to the availability of full length cDNA sequences derived from many tissues. Among those yet to be studied is the aleurone layer, which produces hydrolases for mobilization of seed storage reserves during seed germination and post germin...

journal_title：Genomics

authors： Watanabe KA,Ringler P,Gu L,Shen QJ

更新日期：2014-01-01 00:00:00