Computational Strategies for Scalable Genomics Analysis.

abstract：:N6-methyladenosine (m6A) is the most abundant RNA modification. It has been involved in the regulation of RNA metabolism, including degradation and translation, in both physiological and disease conditions. A recent study showed that m6A-mediated degradation of key transcripts also plays a role in the control of T cel...

journal_title：Genes

authors： Furlan M,Galeota E,de Pretis S,Caselle M,Pelizzola M

更新日期：2019-01-08 00:00:00

abstract：:High-throughput technologies have allowed researchers to obtain genome-wide data from a wide array of experimental model systems. Unfortunately, however, new data generation tends to significantly outpace data re-utilization, and most high throughput datasets are only rarely used in subsequent studies or to generate n...

journal_title：Genes

authors： Halajyan A,Weingart N,Yeahia M,Loza-Coll M

更新日期：2019-06-01 00:00:00

abstract：:Epigenetics contributes to molecular mechanisms leading to tumor cell transformation and systemic progression of cancer. However, the dynamics of epigenetic remodeling during metastasis remains unexplored. In this context, circulating tumor cells (CTCs) might enable a direct insight into epigenetic mechanisms relevant...

journal_title：Genes

authors： Pixberg CF,Schulz WA,Stoecklein NH,Neves RP

更新日期：2015-10-21 00:00:00

abstract：:Both type 1 and type 2 diabetes are conditions that are associated with the loss of insulin-producing β-cells within the pancreas. An active research therefore aims at regenerating these β-cells with the hope that they could restore euglycemia. The approaches classically used consist in mimicking embryonic development...

journal_title：Genes

authors： Balaji S,Napolitano T,Silvano S,Friano ME,Garrido-Utrilla A,Atlija J,Collombat P

更新日期：2018-09-07 00:00:00

abstract：:DNA methylation plays several roles in regulating neuronal proliferation, differentiation, and physiological functions. The major de novo methyltransferase, DNMT3, controls the DNA methylation pattern in neurons according to environmental stimulations and behavioral regulations. Previous studies demonstrated that knoc...

journal_title：Genes

authors： Lai YH,Audira G,Liang ST,Siregar P,Suryanto ME,Lin HC,Villalobos O,Villaflores OB,Hao E,Lim KH,Hsiao CD

更新日期：2020-11-07 00:00:00

abstract：:Perennial agriculture has been proposed as an option to improve the sustainability of cropping systems, by increasing the efficiency of resource use, while also providing ecosystem services. Neo-domestication, the contemporary domestication of plants that have not previously been used in agriculture, can be used to ge...

journal_title：Genes

authors： Kantar MB,Hüber S,Herman A,Bock DG,Baute G,Betts K,Ott M,Brandvain Y,Wyse D,Stupar RM,Rieseberg LH

更新日期：2018-08-21 00:00:00

abstract：:Protein sequence, structure, and function are inherently linked through evolution and population genetics. Our knowledge of protein structure comes from solved structures in the Protein Data Bank (PDB), our knowledge of sequence through sequences found in the NCBI sequence databases (http://www.ncbi.nlm.nih.gov/), and...

journal_title：Genes

authors： Siltberg-Liberles J,Grahnen JA,Liberles DA

更新日期：2011-10-28 00:00:00

abstract：:Fat deposition in pigs, which significantly contributes to meat quality, fattening efficiency, reproductive performance, and immunity, is critically affected by preadipocyte adipogenic differentiation. We elucidated adipogenesis in pigs using transcriptome analysis. Preadipocytes from subcutaneous adipose tissue (SAT)...

journal_title：Genes

authors： Zhao X,Chen S,Tan Z,Wang Y,Zhang F,Yang T,Liu Y,Ao H,Xing K,Wang C

更新日期：2019-07-19 00:00:00

abstract：:Divergent selection between ecologically dissimilar habitats promotes local adaptation, which can lead to reproductive isolation (RI). Populations in the Poecilia mexicana species complex have independently adapted to toxic hydrogen sulfide and show varying degrees of RI. Here, we examined the variation in the mate ch...

journal_title：Genes

authors： Zimmer C,Riesch R,Jourdan J,Bierbach D,Arias-Rodriguez L,Plath M

更新日期：2018-05-02 00:00:00

abstract：:Gene duplication is an important evolutionary mechanism allowing to provide new genetic material and thus opportunities to acquire new gene functions for an organism, with major implications such as speciation events. Various processes are known to allow a gene to be duplicated and different models explain how duplica...

journal_title：Genes

authors： Lallemand T,Leduc M,Landès C,Rizzon C,Lerat E

更新日期：2020-09-04 00:00:00

abstract：:Hypersialylation caused by the overexpression of sialyltransferases (STs) is a common feature in cancer that is associated with several characteristics of tumorigenesis. Thus, identifying cancer-associated STs is critical for cancer therapy. However, ST screening has been frequently conducted in cell line models. In t...

journal_title：Genes

authors： Kan JY,Moi SH,Hung WC,Hou MF,Chen FM,Shih SL,Shiau JP,Li CL,Chiang CP

更新日期：2020-11-28 00:00:00

abstract：:Satellite DNAs are tandemly repeated sequences preferentially assembled into large arrays within constitutive heterochromatin and their transcription is often activated by stress conditions, particularly by heat stress. Bioinformatic analyses of sequenced genomes however reveal single repeats or short arrays of satell...

journal_title：Genes

authors： Feliciello I,Sermek A,Pezer Ž,Matulić M,Ugarković Đ

更新日期：2020-06-18 00:00:00

abstract：:The Muraenidae is one of the largest and most complex anguilliform families. Despite their abundance and important ecological roles, morays are little studied, especially cytogenetically, and both their phylogenetic relationships and the taxonomy of their genera are controversial. With the aim of extending the karyolo...

journal_title：Genes

authors： Coluccia E,Deidda F,Lobina C,Melis R,Porcu C,Agus B,Salvadori S

更新日期：2020-11-06 00:00:00

abstract：:Although bacterial genomes have been traditionally viewed as being very compact, with relatively low amounts of repetitive and non-coding DNA, this view has dramatically changed in recent years. The increase of available complete bacterial genomes has revealed that many species present abundant repetitive DNA (i.e., i...

journal_title：Genes

authors： Gil R,Latorre A

更新日期：2012-10-12 00:00:00

abstract：:While methods for detecting SNVs and indels in circulating tumor DNA (ctDNA) with hybridization capture-based next-generation sequencing (NGS) have been available, copy number variations (CNVs) detection is more challenging. Here, we present a method enabling CNV detection from a 150-gene panel using a very low amount...

journal_title：Genes

authors： Peng H,Lu L,Zhou Z,Liu J,Zhang D,Nan K,Zhao X,Li F,Tian L,Dong H,Yao Y

更新日期：2019-11-14 00:00:00

abstract：:Autoimmune blistering dermatoses (ABDs) are characterized by autoantibodies to keratinocyte surface antigens and molecules within the dermal-epidermal junction causing disruption of skin integrity. The affinity of Fc receptors (FcRs) causing an autoimmune response in ABDs may vary based on single-nucleotide polymorphi...

journal_title：Genes

authors： Gornowicz-Porowska J,Kowalczyk MJ,Seraszek-Jaros A,Bowszyc-Dmochowska M,Kaczmarek E,Żaba R,Dmochowski M

更新日期：2020-03-30 00:00:00

abstract：:Cancer stem cells (CSCs), having both self-renewal and tumorigenic capacity, utilize an energy metabolism system different from that of non-CSCs. Lipid droplets (LDs) are organelles that store neutral lipids, including triacylglycerol. Previous studies demonstrated that LDs are formed and store lipids as an energy sou...

journal_title：Genes

authors： Kuramoto K,Yamamoto M,Suzuki S,Togashi K,Sanomachi T,Kitanaka C,Okada M

更新日期：2021-01-14 00:00:00

abstract：:The nitrogen use efficiency (NUE) of crop plants is limited and enhancing it in rice, a major cereal crop, would be beneficial for farmers and the environment alike. Here we report the genome-wide transcriptome analysis of two rice genotypes, IR 64 (IR64) and Nagina 22 (N22) under optimal (+N) and chronic starvation (...

journal_title：Genes

authors： Sinha SK,Sevanthi V AM,Chaudhary S,Tyagi P,Venkadesan S,Rani M,Mandal PK

更新日期：2018-04-11 00:00:00

abstract：:Cerebral ischaemia is the most common cause of impaired brain function. Biologically active peptides represent potential drugs for reducing the damage that occurs after ischaemia. The synthetic melanocortin derivative, ACTH(4-7)PGP (Semax), has been used successfully in the treatment of patients with severe impairment...

journal_title：Genes

authors： Filippenkov IB,Stavchansky VV,Denisova AE,Yuzhakov VV,Sevan'kaeva LE,Sudarkina OY,Dmitrieva VG,Gubsky LV,Myasoedov NF,Limborska SA,Dergunova LV

更新日期：2020-06-22 00:00:00

abstract：:Meiosis yields haploid gametes following two successive divisions of a germ cell in the absence of intervening DNA replication. Balanced segregation of homologous chromosomes in Meiosis I is aided by a proteinaceous structure, the synaptonemal complex (SC). The objective of this study was to determine total average au...

journal_title：Genes

authors： Vranis NM,Van der Heijden GW,Malki S,Bortvin A

更新日期：2010-12-15 00:00:00

abstract：:Post-translational modification (PTM) is a critical biological reaction which adds to the diversification of the proteome. With numerous known modifications being studied, pupylation has gained focus in the scientific community due to its significant role in regulating biological processes. The traditional experimenta...

journal_title：Genes

authors： Singh V,Sharma A,Dehzangi A,Tsunoda T

更新日期：2020-11-28 00:00:00

abstract：:The homeodomain-leucine zipper (HD-Zip) transcription factor family is a key transcription factor family and unique to the plant kingdom. It consists of a homeodomain and a leucine zipper that serve in combination as a dimerization motif. The family can be classified into four subfamilies, and these subfamilies partic...

journal_title：Genes

authors： Song A,Li P,Xin J,Chen S,Zhao K,Wu D,Fan Q,Gao T,Chen F,Guan Z

更新日期：2016-05-17 00:00:00

abstract：:In angiosperms, meiotic failure coupled with the formation of genetically unreduced gametophytes in ovules (apomeiosis) constitute major components of gametophytic apomixis. These aberrant developmental events are generally thought to be caused by mutation. However, efforts to locate the responsible mutations have fai...

journal_title：Genes

authors： Mateo de Arias M,Gao L,Sherwood DA,Dwivedi KK,Price BJ,Jamison M,Kowallis BM,Carman JG

更新日期：2020-12-02 00:00:00

abstract：:The rapid accumulation of ancient human genomes from various areas and time periods potentially enables the expansion of studies of biodiversity, biogeography, forensics, population history, and epidemiology into past populations. However, most ancient DNA (aDNA) data were generated through microarrays designed for mo...

journal_title：Genes

authors： Esposito U,Das R,Syed S,Pirooznia M,Elhaik E

更新日期：2018-12-12 00:00:00

abstract：:DNA methylation patterns have been shown to change throughout the normal aging process. Several studies have found epigenetic aging markers using age predictors, but these studies only focused on blood-specific or tissue-common methylation patterns. Here, we constructed nine tissue-specific age prediction models using...

journal_title：Genes

authors： Choi H,Joe S,Nam H

更新日期：2019-11-04 00:00:00

abstract：:Deinococcus species display a high degree of resistance to radiation and desiccation due to their ability to protect critical proteome from oxidatively generated damage; however, the underlying mechanisms are not understood. Comparative analysis of DNA repair proteins reported here has identified 22 conserved signatur...

journal_title：Genes

authors： Hassan FMN,Gupta RS

更新日期：2018-03-08 00:00:00

abstract：:Mutations affecting the Retinitis Pigmentosa GTPase Regulator (RPGR) gene are the commonest cause of X-linked and recessive retinitis pigmentosa (RP), accounting for 10%-20% of all cases of RP. The phenotype is one of the most severe amongst all causes of RP, characteristic for its early onset and rapid progression to...

journal_title：Genes

authors： Cehajic Kapetanovic J,McClements ME,Martinez-Fernandez de la Camara C,MacLaren RE

更新日期：2019-09-04 00:00:00

abstract：:White mold (WM) is a devastating fungal disease affecting common bean (Phaseolus vulgaris L.). In this research, a genome-wide association study (GWAS) for WM resistance was conducted using 294 lines of the Spanish diversity panel. One single-locus method and six multi-locus methods were used in the GWAS. Response to ...

journal_title：Genes

authors： Campa A,García-Fernández C,Ferreira JJ

更新日期：2020-12-12 00:00:00

abstract：:Mgaloblishvili, a Vitis vinifera cultivar, exhibits unique resistance traits against Plasmopara viticola, the downy mildew agent. This offers the unique opportunity of exploring the molecular responses in compatible and incompatible plant-pathogen interaction. In this study, whole transcriptomes of Mgaloblishvili, Pin...

journal_title：Genes

authors： Toffolatti SL,De Lorenzis G,Brilli M,Moser M,Shariati V,Tavakol E,Maddalena G,Passera A,Casati P,Pindo M,Cestaro A,Maghradze D,Failla O,Bianco PA,Quaglino F

更新日期：2020-02-28 00:00:00

abstract：:The SLC6A4 gene has been implicated in psychiatric disorder susceptibility and antidepressant response variability. The SLC6A4 promoter is defined by a variable number of homologous 20-24 bp repeats (5-HTTLPR), and long (L) and short (S) alleles are associated with higher and lower expression, respectively. However, t...

journal_title：Genes

authors： Botton MR,Yang Y,Scott ER,Desnick RJ,Scott SA

更新日期：2020-11-12 00:00:00