Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing.

abstract：BACKGROUND:The cotton (Gossypium spp.) fiber cell is an important unicellular model for studying cell differentiation. There is evidence suggesting that phosphorylation is a critical post-translational modification involved in regulation of a wide range of cell activities. Nevertheless, the sites of phosphorylation in ...

journal_title：BMC genomics

authors： Ma Q,Wu M,Pei W,Li H,Li X,Zhang J,Yu J,Yu S

更新日期：2014-06-12 00:00:00

abstract：BACKGROUND:Variation in gene expression between two Drosophila melanogaster strains, as revealed by transcriptional profiling, seldom corresponded to variation in proximal promoter sequence for 34 genes analyzed. Two sets of protein-coding genes were selected from pre-existing microarray data: (1) those whose expressio...

journal_title：BMC genomics

authors： Brown RP,Feder ME

更新日期：2005-08-17 00:00:00

abstract：BACKGROUND:The green crab Carcinus maenas is known for its high acclimation potential to varying environmental abiotic conditions. A high ability for ion and acid-base regulation is mainly based on an efficient regulation apparatus located in gill epithelia. However, at present it is neither known which ion transport p...

journal_title：BMC genomics

authors： Fehsenfeld S,Kiko R,Appelhans Y,Towle DW,Zimmer M,Melzner F

更新日期：2011-10-06 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

authors： Evans KJ

更新日期：2008-01-14 00:00:00

abstract：BACKGROUND:Macrosatellites are some of the largest variable number tandem repeats in the human genome, but what role these unusual sequences perform is unknown. Their importance to human health is clearly demonstrated by the 4q35 macrosatellite D4Z4 that is associated with the onset of the muscle degenerative disease f...

journal_title：BMC genomics

authors： Tremblay DC,Alexander G Jr,Moseley S,Chadwick BP

更新日期：2010-11-15 00:00:00

abstract：BACKGROUND:The main limitations in the analysis of viral metagenomes are perhaps the high genetic variability and the lack of information in extant databases. To address these issues, several bioinformatic tools have been specifically designed or adapted for metagenomics by improving read assembly and creating more sen...

journal_title：BMC genomics

authors： Vázquez-Castellanos JF,García-López R,Pérez-Brocal V,Pignatelli M,Moya A

更新日期：2014-01-18 00:00:00

abstract：BACKGROUND:Environmental heterogeneity continuously produces a selective pressure that results in genomic variation among organisms; understanding this relationship remains a challenge in evolutionary biology. Here, we evaluated the degree of genome-environmental association of seven stonefly species across a wide geog...

journal_title：BMC genomics

authors： Gamboa M,Watanabe K

更新日期：2019-01-24 00:00:00

abstract：BACKGROUND:Long non-coding RNAs (lncRNAs) regulate adipose tissue metabolism, however, their function on testosterone deficiency related obesity in humans is less understood. For this research, intact and castrated male pigs are the best model animal because of their similar proportional organ sizes, cardiovascular sys...

journal_title：BMC genomics

authors： Wang J,Hua L,Chen J,Zhang J,Bai X,Gao B,Li C,Shi Z,Sheng W,Gao Y,Xing B

更新日期：2017-07-19 00:00:00

abstract：BACKGROUND:Expression profiling has been proposed as a means for screening non-model organisms in their natural environments to identify genes potentially important in adaptive diversification. Tag profiling using high throughput sequencing is a relatively low cost means of expression profiling with deep coverage. Howe...

journal_title：BMC genomics

authors： Voelckel C,Gruenheit N,Biggs P,Deusch O,Lockhart P

更新日期：2012-07-19 00:00:00

abstract：BACKGROUND:The development of microarrays permits us to monitor transcriptomes on a genome-wide scale. To validate microarray measurements, quantitative-real time-reverse transcription PCR (Q-RT-PCR) is one of the most robust and commonly used approaches. The new challenge in gene quantification analysis is how to expl...

journal_title：BMC genomics

authors： Su LJ,Chang CW,Wu YC,Chen KC,Lin CJ,Liang SC,Lin CH,Whang-Peng J,Hsu SL,Chen CH,Huang CY

更新日期：2007-06-01 00:00:00

abstract：BACKGROUND:Cells transformed by human adenoviruses (Ad) exhibit differential capacities to induce tumours in immunocompetent rodents; for example, Ad12-transformed rodent cells are oncogenic whereas Ad5-transformed cells are not. The E1A gene determines oncogenic phenotype, is a transcriptional regulator and dysregulat...

journal_title：BMC genomics

authors： Strath J,Georgopoulos LJ,Kellam P,Blair GE

更新日期：2009-02-06 00:00:00

abstract：BACKGROUND:The σ(54) subunit controls a unique class of promoters in bacteria. Such promoters, without exception, require enhancer binding proteins (EBPs) for transcription initiation. Desulfovibrio vulgaris Hildenborough, a model bacterium for sulfate reduction studies, has a high number of EBPs, more than most sequen...

journal_title：BMC genomics

authors： Kazakov AE,Rajeev L,Chen A,Luning EG,Dubchak I,Mukhopadhyay A,Novichkov PS

更新日期：2015-11-10 00:00:00

abstract：BACKGROUND:Cornu aspersum is a quite intriguing species from the point of view of ecology and evolution and its potential use in medical and environmental applications. It is a species of economic importance since it is farmed and used for culinary purposes. However, the genomic tools that would allow a thorough insigh...

journal_title：BMC genomics

authors： Parmakelis A,Kotsakiozi P,Kontos CK,Adamopoulos PG,Scorilas A

更新日期：2017-06-28 00:00:00

abstract：BACKGROUND:The occurrence of liver cancer is higher in males than in females, and the incidence increases during aging. Signaling pathways regulated by retinoid x receptor alpha (RXRalpha) are involved in hepatocellular carcinogenesis. The phenotype of hepatocyte RXRalpha deficient mice is different between genders. To...

journal_title：BMC genomics

authors： Guo M,Gong L,He L,Lehman-McKeeman L,Wan YJ

更新日期：2008-08-28 00:00:00

abstract：BACKGROUND:In the model legume Medicago truncatula, the near saturation genome-wide Tnt1 insertion mutant population in ecotype R108 is a valuable tool in functional genomics studies. Forward genetic screens have identified many Tnt1 mutants defective in nodule development and symbiotic nitrogen fixation (SNF). However...

journal_title：BMC genomics

authors： Veerappan V,Jani M,Kadel K,Troiani T,Gale R,Mayes T,Shulaev E,Wen J,Mysore KS,Azad RK,Dickstein R

更新日期：2016-02-27 00:00:00

abstract：BACKGROUND:Many biological systems respond to the presence or absence of gravity. Since experiments performed in space are expensive and can only be undertaken infrequently, Earth-based simulation techniques are used to investigate the biological response to weightlessness. A high gradient magnetic field can be used to...

journal_title：BMC genomics

authors： Herranz R,Larkin OJ,Dijkstra CE,Hill RJ,Anthony P,Davey MR,Eaves L,van Loon JJ,Medina FJ,Marco R

更新日期：2012-02-01 00:00:00

abstract：BACKGROUND:Toxigenic Vibrio cholerae serogroup O1 is the causative pathogen in the sixth and seventh cholera pandemics. Cholera toxin is the major virulent factor but other virulence and virulence-related factors play certain roles in the pathogenesis and survival in the host. Along with the evolution of the epidemic s...

journal_title：BMC genomics

authors： Li Z,Pang B,Wang D,Li J,Xu J,Fang Y,Lu X,Kan B

更新日期：2019-05-09 00:00:00

abstract：BACKGROUND:In contrast to unidirectional promoters wherein antisense transcription results in short transcripts which are rapidly degraded, bidirectional promoters produce mature transcripts in both sense and antisense orientation. To understand the molecular mechanism of how productive bidirectional transcription is r...

journal_title：BMC genomics

authors： Jangid RK,Kelkar A,Muley VY,Galande S

更新日期：2018-05-02 00:00:00

abstract：BACKGROUND:Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici, is a costly global disease that burdens farmers with yield loss and high fungicide expenses. This sophisticated biotrophic parasite infiltrates wheat leaves and develops infection structures inside host cells, appropriating nutrients while sup...

journal_title：BMC genomics

authors： Mueth NA,Ramachandran SR,Hulbert SH

更新日期：2015-09-21 00:00:00

abstract：BACKGROUND:Interactions between fish and pathogens, that may be harmless under natural conditions, often result in serious diseases in aquaculture systems. This is especially important due to the fact that the strains used in aquaculture are derived from wild strains that may not have had enough time to adapt to new di...

journal_title：BMC genomics

authors： Rodríguez-Ramilo ST,Toro MA,Bouza C,Hermida M,Pardo BG,Cabaleiro S,Martínez P,Fernández J

更新日期：2011-11-02 00:00:00

abstract：BACKGROUND:Understanding the diversity of repair outcomes after introducing a genomic cut is essential for realizing the therapeutic potential of genomic editing technologies. Targeted PCR amplification combined with Next Generation Sequencing (NGS) or enzymatic digestion, while broadly used in the genome editing field...

journal_title：BMC genomics

authors： Giannoukos G,Ciulla DM,Marco E,Abdulkerim HS,Barrera LA,Bothmer A,Dhanapal V,Gloskowski SW,Jayaram H,Maeder ML,Skor MN,Wang T,Myer VE,Wilson CJ

更新日期：2018-03-21 00:00:00

abstract：BACKGROUND:Lysophosphatidic acid (LPA) is a lipid mediator that acts through specific G protein-coupled receptors to stimulate the proliferation, migration and survival of many cell types. LPA signaling has been implicated in development, wound healing and cancer. While LPA signaling pathways have been studied extensiv...

journal_title：BMC genomics

authors： Stortelers C,Kerkhoven R,Moolenaar WH

更新日期：2008-08-14 00:00:00

abstract：BACKGROUND:Gene ontology analysis using the microarray database generated in a previous study by this laboratory was used to further evaluate how maternal dietary supplementation with pyridoxine combined with different sources of selenium (Se) affected global gene expression of expanded porcine blastocysts. Data were g...

journal_title：BMC genomics

authors： Dalto DB,Tsoi S,Dyck MK,Matte JJ

更新日期：2018-11-21 00:00:00

abstract：BACKGROUND:The large amount of data produced by high-throughput sequencing poses new computational challenges. In the last decade, several tools have been developed for the identification of transcription and splicing factor binding sites. RESULTS:Here, we introduce the SeAMotE (Sequence Analysis of Motifs Enrichment)...

journal_title：BMC genomics

authors： Agostini F,Cirillo D,Ponti RD,Tartaglia GG

更新日期：2014-10-23 00:00:00

abstract：BACKGROUND:Next generation sequencing (NGS) has become a universal practice in modern molecular biology. As the throughput of sequencing experiments increases, the preparation of conventional multiplexed libraries becomes more labor intensive. Conventional library preparation typically requires quality control (QC) tes...

journal_title：BMC genomics

authors： Chiniquy J,Garber ME,Mukhopadhyay A,Hillson NJ

更新日期：2020-01-28 00:00:00

abstract：BACKGROUND:Protein Disulfide Isomerases are thiol oxidoreductase chaperones from thioredoxin superfamily with crucial roles in endoplasmic reticulum proteostasis, implicated in many diseases. The family prototype PDIA1 is also involved in vascular redox cell signaling. PDIA1 is coded by the P4HB gene. While forced chan...

journal_title：BMC genomics

authors： Kajihara D,Hon CC,Abdullah AN,Wosniak J Jr,Moretti AIS,Poloni JF,Bonatto D,Hashimoto K,Carninci P,Laurindo FRM

更新日期：2020-11-04 00:00:00

abstract：BACKGROUND:The Cleavage Stimulation Factor (CstF) is a required protein complex for eukaryotic mRNA 3'-processing. CstF interacts with 3'-processing downstream elements (DSEs) through its 64-kDa subunit, CstF-64; however, the exact nature of this interaction has remained unclear. We used EST-to-genome alignments to ide...

journal_title：BMC genomics

authors： Salisbury J,Hutchison KW,Graber JH

更新日期：2006-03-16 00:00:00

abstract：BACKGROUND:Reading disability (RD) is a common syndrome with a large genetic component. Chromosome 6 has been identified in several linkage studies as playing a significant role. A more recent study identified a peak of transmission disequilibrium to marker JA04 (G72384) on chromosome 6p22.3, suggesting that a gene is ...

journal_title：BMC genomics

authors： Londin ER,Meng H,Gruen JR

更新日期：2003-06-30 00:00:00

abstract：BACKGROUND:Long terminal repeat retrotransposons are the most abundant transposons in plants. They play important roles in alternative splicing, recombination, gene regulation, and defense mechanisms. Large-scale sequencing projects for plant genomes are currently underway. Software tools are important for annotating l...

journal_title：BMC genomics

authors： Valencia JD,Girgis HZ

更新日期：2019-06-03 00:00:00

abstract：BACKGROUND:The ciliate Paramecium bursaria harbors several hundred cells of the green-alga Chlorella sp. in their cytoplasm. Irrespective of the mutual relation between P. bursaria and the symbiotic algae, both cells retain the ability to grow without the partner. They can easily reestablish endosymbiosis when put in c...

journal_title：BMC genomics

authors： Kodama Y,Suzuki H,Dohra H,Sugii M,Kitazume T,Yamaguchi K,Shigenobu S,Fujishima M

更新日期：2014-03-10 00:00:00