SeAMotE: a method for high-throughput motif discovery in nucleic acid sequences.

abstract：BACKGROUND:The origin and importance of exon-intron architecture comprises one of the remaining mysteries of gene evolution. Several studies have investigated the variations of intron length, GC content, ordinal position in a gene and divergence. However, there is little study about the structural variation of exons an...

journal_title：BMC genomics

authors： Zhu L,Zhang Y,Zhang W,Yang S,Chen JQ,Tian D

更新日期：2009-01-24 00:00:00

abstract：:An amendment to this paper has been published and can be accessed via the original article. ...

journal_title：BMC genomics

authors： Levin M,Scheibe M,Butter F

更新日期：2020-11-12 00:00:00

abstract：BACKGROUND:DNA methylation at promoters is largely correlated with inhibition of gene expression. However, the role of DNA methylation at enhancers is not fully understood, although a crosstalk with chromatin marks is expected. Actually, there exist contradictory reports about positive and negative correlations between...

journal_title：BMC genomics

authors： Sharifi-Zarchi A,Gerovska D,Adachi K,Totonchi M,Pezeshk H,Taft RJ,Schöler HR,Chitsaz H,Sadeghi M,Baharvand H,Araúzo-Bravo MJ

更新日期：2017-12-12 00:00:00

abstract：BACKGROUND:Habitats colonized by acidophiles as an ideal physical barrier may induce genetic exchange of microbial members within the common communities, but little is known about how species in extremely acidic environments diverge and evolve. RESULTS:Using the acidophilic sulfur-oxidizer Acidithiobacillus as a case ...

journal_title：BMC genomics

authors： Zhang X,Liu X,Li L,Wei G,Zhang D,Liang Y,Miao B

更新日期：2019-05-30 00:00:00

abstract：BACKGROUND:Intramuscular fat (IMF) is one of the most important factors positively associated with meat quality. Triglycerides (TGs), as the main component of IMF, play an essential role in muscle lipid metabolism. This transcriptome analysis of pectoralis muscle tissue aimed to identify functional genes and biological...

journal_title：BMC genomics

authors： Liu L,Liu X,Cui H,Liu R,Zhao G,Wen J

更新日期：2019-11-15 00:00:00

abstract：BACKGROUND:Cryptic unstable transcripts (CUTs) are a largely unexplored class of nuclear exosome degraded, non-coding RNAs in budding yeast. It is highly debated whether CUT transcription has a functional role in the cell or whether CUTs represent noise in the yeast transcriptome. We sought to ascertain the extent of c...

journal_title：BMC genomics

authors： Vera JM,Dowell RD

更新日期：2016-04-26 00:00:00

abstract：BACKGROUND:The effective use of mutant populations for reverse genetic screens relies on the population-wide characterization of the induced mutations. Genome- and population-wide characterization of the mutations found in fast neutron populations has been hindered, however, by the wide range of mutations generated and...

journal_title：BMC genomics

authors： Lemay MA,Torkamaneh D,Rigaill G,Boyle B,Stec AO,Stupar RM,Belzile F

更新日期：2019-08-06 00:00:00

abstract：BACKGROUND:Genetic association studies that seek to explain the inheritance of complex traits typically fail to explain a majority of the heritability of the trait under study. Thus, we are left with a gap in the map from genotype to phenotype. Several approaches have been used to fill this gap, including those that at...

journal_title：BMC genomics

authors： Harrison BR,Wang L,Gajda E,Hoffman EV,Chung BY,Pletcher SD,Raftery D,Promislow DEL

更新日期：2020-05-04 00:00:00

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

authors： Scaglione D,Acquadro A,Portis E,Taylor CA,Lanteri S,Knapp SJ

更新日期：2009-09-28 00:00:00

abstract：BACKGROUND:The endothelial PAS domain protein 1 (EPAS1) activates genes that are involved in erythropoiesis and angiogenesis, thus favoring a better delivery of oxygen to the tissues and is a plausible candidate to influence athletic performance. Using innovative statistical methods we compared genotype distributions a...

journal_title：BMC genomics

authors： Voisin S,Cieszczyk P,Pushkarev VP,Dyatlov DA,Vashlyayev BF,Shumaylov VA,Maciejewska-Karlowska A,Sawczuk M,Skuza L,Jastrzebski Z,Bishop DJ,Eynon N

更新日期：2014-05-18 00:00:00

abstract：BACKGROUND:DNA methylation is a key modulator of gene expression in mammalian development and cellular differentiation, including neurons. To date, the role of DNA modifications in long-term potentiation (LTP) has not been explored. RESULTS:To investigate the occurrence of DNA methylation changes in LTP, we undertook ...

journal_title：BMC genomics

authors： Maag JL,Kaczorowski DC,Panja D,Peters TJ,Bramham CR,Wibrand K,Dinger ME

更新日期：2017-03-23 00:00:00

abstract：BACKGROUND:MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate gene expression by targeting specific mRNA species for degradation or interfering with translation. Specific miRNAs are key regulators of adipogenesis, and are expressed at different levels in adipose tissue from lean and obese mice. The deg...

journal_title：BMC genomics

authors： Link JC,Hasin-Brumshtein Y,Cantor RM,Chen X,Arnold AP,Lusis AJ,Reue K

更新日期：2017-01-17 00:00:00

abstract：BACKGROUND:Rhizobial symbionts belong to the classes Alphaproteobacteria and Betaproteobacteria (called "alpha" and "beta"-rhizobia). Most knowledge on the genetic basis of symbiosis is based on model strains belonging to alpha-rhizobia. Mimosa pudica is a legume that offers an excellent opportunity to study the adapta...

journal_title：BMC genomics

authors： Klonowska A,Melkonian R,Miché L,Tisseyre P,Moulin L

更新日期：2018-01-30 00:00:00

abstract：BACKGROUND:A disease-causing mutation refers to a heritable genetic change that is associated with a specific phenotype (disease). The detection of a mutation from a patient's sample is critical for the diagnosis, treatment, and prognosis of the disease. There are numerous databases and applications with which to archi...

journal_title：BMC genomics

authors： Jho S,Kim BC,Ghang H,Kim JH,Park D,Kim HM,Jung SY,Yoo KY,Kim HJ,Lee S,Bhak J

更新日期：2009-12-03 00:00:00

abstract：BACKGROUND:Evolutionary theory indicates that the dynamics of aging in the soma and reproductive tissues may be distinct. This difference arises from the fact that only the germline lineage establishes future generations. In the soma, changes in the landscape of heterochromatin have been proposed to have an important r...

journal_title：BMC genomics

authors： Erwin AA,Blumenstiel JP

更新日期：2019-04-23 00:00:00

abstract：BACKGROUND:High throughput molecular sequencing and increased biospecimen variety have introduced significant informatics challenges for research biorepository infrastructures. We applied a modular system integration approach to develop an operational biorepository management system. This method enables aggregation of ...

journal_title：BMC genomics

authors： Felmeister AS,Masino AJ,Rivera TJ,Resnick AC,Pennington JW

更新日期：2016-08-18 00:00:00

abstract：BACKGROUND:Candida albicans is a diploid pathogenic fungus not yet amenable to routine genetic investigations. Understanding aspects of the regulation of its biological functions and the assembly of its protein complexes would lead to further insight into the biology of this common disease-causing microbial agent. RES...

journal_title：BMC genomics

authors： Lavoie H,Sellam A,Askew C,Nantel A,Whiteway M

更新日期：2008-12-02 00:00:00

abstract：BACKGROUND:Aneuploidies are copy number variants that affect entire chromosomes. They are seen commonly in cancer, embryonic stem cells, human embryos, and in various trisomic diseases. Aneuploidies frequently affect only a subset of cells in a sample; this is known as "mosaic" aneuploidy. A cell that harbours an aneup...

journal_title：BMC genomics

authors： Griffiths JA,Scialdone A,Marioni JC

更新日期：2017-11-25 00:00:00

abstract：BACKGROUND:Cultivated peanut (Arachis hypogaea L.) is an important oil and protein crop, but it has low disease resistance; therefore, it is important to reveal the number, sequence features, function, and evolution of genes that confer resistance. Nucleotide-binding site-leucine-rich repeats (NBS-LRRs) are resistance ...

journal_title：BMC genomics

authors： Song H,Guo Z,Hu X,Qian L,Miao F,Zhang X,Chen J

更新日期：2019-11-13 00:00:00

abstract：BACKGROUND:The tuberous root of sweet potato is an important agricultural and biological organ. There are not sufficient transcriptomic and genomic data in public databases for understanding of the molecular mechanism underlying the tuberous root formation and development. Thus, high throughput transcriptome sequencing...

journal_title：BMC genomics

authors： Wang Z,Fang B,Chen J,Zhang X,Luo Z,Huang L,Chen X,Li Y

更新日期：2010-12-24 00:00:00

abstract：BACKGROUND:Bacterial invasive infection and host immune response is fundamental to the understanding of pathogen pathogenesis and the discovery of effective therapeutic drugs. However, there are very few experimental studies on the signaling cross-talks between bacteria and human host to date. METHODS:In this work, ta...

journal_title：BMC genomics

authors： Mei S,Flemington EK,Zhang K

更新日期：2018-06-28 00:00:00

abstract：BACKGROUND:Respiratory syncytial virus (RSV) is an important cause of lower respiratory tract infection in young children. The degree of disease severity is determined by the host response to infection. Lung macrophages play an important early role in the host response to infection and we have used a systems-based appr...

journal_title：BMC genomics

authors： Ravi LI,Li L,Sutejo R,Chen H,Wong PS,Tan BH,Sugrue RJ

更新日期：2013-03-18 00:00:00

abstract：BACKGROUND:Crustacean moulting is a complex process involving many regulatory pathways. A holistic approach to examine differential gene expression profiles of transcripts relevant to the moulting process, across all moult cycle stages, was used in this study. Custom cDNA microarrays were constructed for Portunus pelag...

journal_title：BMC genomics

authors： Kuballa AV,Holton TA,Paterson B,Elizur A

更新日期：2011-03-12 00:00:00

abstract：BACKGROUND:The genome of pathogenic Leptospira interrogans contains two chromosomes. Plasmids and prophages are known to play specific roles in gene transfer in bacteria and can potentially serve as efficient genetic tools in these organisms. Although plasmids and prophage remnants have recently been reported in Leptos...

journal_title：BMC genomics

authors： Zhu W,Wang J,Zhu Y,Tang B,Zhang Y,He P,Zhang Y,Liu B,Guo X,Zhao G,Qin J

更新日期：2015-02-15 00:00:00

abstract：BACKGROUND:Bordetella petrii is the only environmental species hitherto found among the otherwise host-restricted and pathogenic members of the genus Bordetella. Phylogenetically, it connects the pathogenic Bordetellae and environmental bacteria of the genera Achromobacter and Alcaligenes, which are opportunistic patho...

journal_title：BMC genomics

authors： Gross R,Guzman CA,Sebaihia M,dos Santos VA,Pieper DH,Koebnik R,Lechner M,Bartels D,Buhrmester J,Choudhuri JV,Ebensen T,Gaigalat L,Herrmann S,Khachane AN,Larisch C,Link S,Linke B,Meyer F,Mormann S,Nakunst D,Rückert

更新日期：2008-09-30 00:00:00

abstract：BACKGROUND:Two-component systems (TCS) play critical roles in sensing and responding to environmental cues. Azospirillum is a plant growth-promoting rhizobacterium living in the rhizosphere of many important crops. Despite numerous studies about its plant beneficial properties, little is known about how the bacterium s...

journal_title：BMC genomics

authors： Borland S,Oudart A,Prigent-Combaret C,Brochier-Armanet C,Wisniewski-Dyé F

更新日期：2015-10-22 00:00:00

abstract：BACKGROUND:Due to the predominant usage of short-read sequencing to date, most bacterial genome sequences reported in the last years remain at the draft level. This precludes certain types of analyses, such as the in-depth analysis of genome plasticity. RESULTS:Here we report the finalized genome sequence of the envir...

journal_title：BMC genomics

authors： Pfeiffer F,Zamora-Lagos MA,Blettinger M,Yeroslaviz A,Dahl A,Gruber S,Habermann BH

更新日期：2018-01-05 00:00:00

abstract：BACKGROUND:Hop (Humulus lupulus L.) is an economically important plant forming organogenic nodules which can be used for genetic transformation and micropropagation. We are interested in the mechanisms underlying reprogramming of cells through stress and hormone treatments. RESULTS:An integrated molecular and metabolo...

journal_title：BMC genomics

authors： Fortes AM,Santos F,Choi YH,Silva MS,Figueiredo A,Sousa L,Pessoa F,Santos BA,Sebastiana M,Palme K,Malhó R,Verpoorte R,Pais MS

更新日期：2008-09-29 00:00:00

abstract：BACKGROUND:Metal tolerance is often an integrative result of metal uptake and distribution, which are fine-tuned by a network of signaling cascades and metal transporters. Thus, with the goal of advancing the molecular understanding of such metal homeostatic mechanisms, comparative RNAseq-based transcriptome analysis w...

journal_title：BMC genomics

authors： Cheng D,Tan M,Yu H,Li L,Zhu D,Chen Y,Jiang M

更新日期：2018-09-26 00:00:00

abstract：BACKGROUND:Advances in human genomics have allowed unprecedented productivity in terms of algorithms, software, and literature available for translating raw next-generation sequence data into high-quality information. The challenges of variant identification in organisms with lower quality reference genomes are less we...

journal_title：BMC genomics

authors： Baes CF,Dolezal MA,Koltes JE,Bapst B,Fritz-Waters E,Jansen S,Flury C,Signer-Hasler H,Stricker C,Fernando R,Fries R,Moll J,Garrick DJ,Reecy JM,Gredler B

更新日期：2014-11-01 00:00:00