Epigenetic engineering and the art of epigenetic manipulation.

abstract：BACKGROUND:Reconstruction of ancestral karyotypes is critical for our understanding of genome evolution, allowing for the identification of the gross changes that shaped extant genomes. The identification of such changes and their time of occurrence can shed light on the biology of each species, clade and their evoluti...

journal_title：Genome biology

authors： Damas J,Kim J,Farré M,Griffin DK,Larkin DM

更新日期：2018-10-05 00:00:00

abstract：:A new study shows that genomic introgression between two Heliconius butterfly species is not solely confined to color pattern loci. ...

journal_title：Genome biology

authors： Ffrench-Constant RH

更新日期：2016-02-27 00:00:00

abstract：:The protein folding game Foldit shows that games are an effective way to recruit, engage and organize ordinary citizens to help solve difficult scientific problems. ...

journal_title：Genome biology

authors： Good BM,Su AI

更新日期：2011-12-28 00:00:00

abstract：:CRISPR-Cas9 gene editing has transformed our ability to rapidly interrogate the functional impact of somatic mutations in human cancers. Droplet-based technology enables the analysis of Cas9-introduced gene edits in thousands of single cells. Using this technology, we analyze Ba/F3 cells engineered to express single o...

journal_title：Genome biology

authors： Ten Hacken E,Clement K,Li S,Hernández-Sánchez M,Redd R,Wang S,Ruff D,Gruber M,Baranowski K,Jacob J,Flynn J,Jones KW,Neuberg D,Livak KJ,Pinello L,Wu CJ

更新日期：2020-10-20 00:00:00

abstract：:Epithelial tissues house gammadelta T cells, which are important for the mucosal immune system and may be involved in controlling malignancies, infections and inflammation. Whole-genome gene-expression analysis provides a new way to study the signals required for the activation of gammadelta T cells, their mode of act...

journal_title：Genome biology

authors： Boismenu R,Havran WL

更新日期：2001-01-01 00:00:00

abstract：BACKGROUND:The development of mass spectrometric (MS) techniques now allows the investigation of very complex protein mixtures ranging from subcellular structures to tissues. Body fluids are also popular targets of proteomic analysis because of their potential for biomarker discovery. Seminal plasma has not yet receive...

journal_title：Genome biology

authors： Pilch B,Mann M

更新日期：2006-01-01 00:00:00

abstract：:We introduce ABLE (Approximate Blockwise Likelihood Estimation), a novel simulation-based composite likelihood method that uses the blockwise site frequency spectrum to jointly infer past demography and recombination. ABLE is explicitly designed for a wide variety of data from unphased diploid genomes to genome-wide m...

journal_title：Genome biology

authors： Beeravolu CR,Hickerson MJ,Frantz LAF,Lohse K

更新日期：2018-09-25 00:00:00

abstract：BACKGROUND:The draft genome sequence of the ascidian Ciona intestinalis, along with associated gene models, has been a valuable research resource. However, recently accumulated expressed sequence tag (EST)/cDNA data have revealed numerous inconsistencies with the gene models due in part to intrinsic limitations in gene...

journal_title：Genome biology

authors： Satou Y,Mineta K,Ogasawara M,Sasakura Y,Shoguchi E,Ueno K,Yamada L,Matsumoto J,Wasserscheid J,Dewar K,Wiley GB,Macmil SL,Roe BA,Zeller RW,Hastings KE,Lemaire P,Lindquist E,Endo T,Hotta K,Inaba K

更新日期：2008-10-14 00:00:00

abstract：BACKGROUND:Host-associated microbiomes, the microorganisms occurring inside and on host surfaces, influence evolutionary, immunological, and ecological processes. Interactions between host and microbiome affect metabolism and contribute to host adaptation to changing environments. Meta-analyses of host-associated bacte...

journal_title：Genome biology

authors： Woodhams DC,Bletz MC,Becker CG,Bender HA,Buitrago-Rosas D,Diebboll H,Huynh R,Kearns PJ,Kueneman J,Kurosawa E,LaBumbard BC,Lyons C,McNally K,Schliep K,Shankar N,Tokash-Peters AG,Vences M,Whetstone R

更新日期：2020-02-03 00:00:00

abstract：BACKGROUND:Diet is a major contributor to metabolic disease risk, but there is controversy as to whether increased incidences of diseases such as non-alcoholic fatty liver disease arise from consumption of saturated fats or free sugars. Here, we investigate whether a sub-set of triacylglycerols (TAGs) were associated w...

journal_title：Genome biology

authors： Sanders FWB,Acharjee A,Walker C,Marney L,Roberts LD,Imamura F,Jenkins B,Case J,Ray S,Virtue S,Vidal-Puig A,Kuh D,Hardy R,Allison M,Forouhi N,Murray AJ,Wareham N,Vacca M,Koulman A,Griffin JL

更新日期：2018-06-20 00:00:00

abstract：BACKGROUND:RNA sequencing has opened new avenues for the study of transcriptome composition. Significant evidence has accumulated showing that the human transcriptome contains in excess of a hundred thousand different transcripts. However, it is still not clear to what extent this diversity prevails when considering th...

journal_title：Genome biology

authors： Gonzàlez-Porta M,Frankish A,Rung J,Harrow J,Brazma A

更新日期：2013-07-01 00:00:00

abstract：BACKGROUND:Comparisons between C3 and C4 grasses often utilize C3 species from the subfamilies Ehrhartoideae or Pooideae and C4 species from the subfamily Panicoideae, two clades that diverged over 50 million years ago. The divergence of the C3 panicoid grass Dichanthelium oligosanthes from the independent C4 lineages ...

journal_title：Genome biology

authors： Studer AJ,Schnable JC,Weissmann S,Kolbe AR,McKain MR,Shao Y,Cousins AB,Kellogg EA,Brutnell TP

更新日期：2016-10-28 00:00:00

abstract：BACKGROUND:Gene dosage change is a mild perturbation that is a valuable tool for pathway reconstruction in Drosophila. While it is often assumed that reducing gene dose by half leads to two-fold less expression, there is partial autosomal dosage compensation in Drosophila, which may be mediated by feedback or buffering...

journal_title：Genome biology

authors： Malone JH,Cho DY,Mattiuzzo NR,Artieri CG,Jiang L,Dale RK,Smith HE,McDaniel J,Munro S,Salit M,Andrews J,Przytycka TM,Oliver B

更新日期：2012-04-24 00:00:00

abstract：BACKGROUND:Aging and sun exposure are the leading causes of skin cancer. It has been shown that epigenetic changes, such as DNA methylation, are well established mechanisms for cancer, and also have emerging roles in aging and common disease. Here, we directly ask whether DNA methylation is altered following skin aging...

journal_title：Genome biology

authors： Vandiver AR,Irizarry RA,Hansen KD,Garza LA,Runarsson A,Li X,Chien AL,Wang TS,Leung SG,Kang S,Feinberg AP

更新日期：2015-04-16 00:00:00

abstract：:The honey bee Apis mellifera displays the most complex behavior of any insect. This, and its utility to humans, makes it a fascinating object of study for biologists. Such studies are now further enabled by the release of the honey-bee genome sequence. ...

journal_title：Genome biology

authors： Ashburner M,Kyriacou CP

更新日期：2006-01-01 00:00:00

abstract：:Identification of causal mutations in barley and wheat is hampered by their large genomes and suppressed recombination. To overcome these obstacles, we have developed MutChromSeq, a complexity reduction approach based on flow sorting and sequencing of mutant chromosomes, to identify induced mutations by comparison to ...

journal_title：Genome biology

authors： Sánchez-Martín J,Steuernagel B,Ghosh S,Herren G,Hurni S,Adamski N,Vrána J,Kubaláková M,Krattinger SG,Wicker T,Doležel J,Keller B,Wulff BB

更新日期：2016-10-31 00:00:00

abstract：BACKGROUND:The mobilization of transposable elements (TEs) is suppressed by host genome defense mechanisms. Recent studies showed that the cis-regulatory region of Arabidopsis thaliana COPIA78/ONSEN retrotransposons contains heat-responsive elements (HREs), which cause their activation during heat stress. However, it r...

journal_title：Genome biology

authors： Pietzenuk B,Markus C,Gaubert H,Bagwan N,Merotto A,Bucher E,Pecinka A

更新日期：2016-10-11 00:00:00

abstract：:Single-cell RNA-sequencing (scRNA-seq) has emerged as a revolutionary tool that allows us to address scientific questions that eluded examination just a few years ago. With the advantages of scRNA-seq come computational challenges that are just beginning to be addressed. In this article, we highlight the computational...

journal_title：Genome biology

authors： Bacher R,Kendziorski C

更新日期：2016-04-07 00:00:00

abstract：BACKGROUND:Despite their regional economic importance and being increasingly reared globally, the origins and evolution of the llama and alpaca remain poorly understood. Here we report reference genomes for the llama, and for the guanaco and vicuña (their putative wild progenitors), compare these with the published alp...

journal_title：Genome biology

authors： Fan R,Gu Z,Guang X,Marín JC,Varas V,González BA,Wheeler JC,Hu Y,Li E,Sun X,Yang X,Zhang C,Gao W,He J,Munch K,Corbett-Detig R,Barbato M,Pan S,Zhan X,Bruford MW,Dong C

更新日期：2020-07-02 00:00:00

abstract：BACKGROUND:Early single-cell RNA-seq (scRNA-seq) studies suggested that it was unusual to see more than one isoform being produced from a gene in a single cell, even when multiple isoforms were detected in matched bulk RNA-seq samples. However, these studies generally did not consider the impact of dropouts or isoform ...

journal_title：Genome biology

authors： Westoby J,Artemov P,Hemberg M,Ferguson-Smith A

更新日期：2020-03-23 00:00:00

abstract：BACKGROUND:Gene expression signatures indicative of tumor proliferative capacity and tumor-immune cell interactions have emerged as principal biology-driven predictors of breast cancer outcomes. How these signatures relate to one another in biological and prognostic contexts remains to be clarified. RESULTS:To investi...

journal_title：Genome biology

authors： Nagalla S,Chou JW,Willingham MC,Ruiz J,Vaughn JP,Dubey P,Lash TL,Hamilton-Dutoit SJ,Bergh J,Sotiriou C,Black MA,Miller LD

更新日期：2013-04-29 00:00:00

abstract：:The majority of disease resistance genes in plants encode nucleotide-binding site leucine-rich repeat (NBS-LRR) proteins. This large family is encoded by hundreds of diverse genes per genome and can be subdivided into the functionally distinct TIR-domain-containing (TNL) and CC-domain-containing (CNL) subfamilies. The...

journal_title：Genome biology

authors： McHale L,Tan X,Koehl P,Michelmore RW

更新日期：2006-01-01 00:00:00

abstract：:The recent completion of the DNA sequence of human chromosome 21 has provided the first look at the 225 genes that are candidates for involvement in Down syndrome (trisomy 21). A broad functional classification of these genes, their expression data and evolutionary conservation, and comparison with the gene content of...

journal_title：Genome biology

authors： Gardiner K,Davisson M

更新日期：2000-01-01 00:00:00

abstract：:High-throughput technologies have enabled the systematic identification and characterization of most, or possibly all, of the components governing segmentation in the fruit fly Drosophila. What have we learned? ...

journal_title：Genome biology

authors： Levine M

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:Differentiation of metazoan cells requires execution of different gene expression programs but recent single-cell transcriptome profiling has revealed considerable variation within cells of seeming identical phenotype. This brings into question the relationship between transcriptome states and cell phenotype...

journal_title：Genome biology

authors： Dueck H,Khaladkar M,Kim TK,Spaethling JM,Francis C,Suresh S,Fisher SA,Seale P,Beck SG,Bartfai T,Kuhn B,Eberwine J,Kim J

更新日期：2015-06-09 00:00:00

abstract：:A novel in vivo screening approach has identified KLF17 as a key metastasis suppressor gene that acts through regulation of Id1 transcription factor-dependent induction of the epithelial-to-mesenchymal transition. ...

journal_title：Genome biology

authors： Iwanicki MP,Brugge JS

更新日期：2009-01-01 00:00:00

abstract：BACKGROUND:Despite decades of research, the agent responsible for transmitting spongiform encephalopathies (TSEs) has not been identified. The Prion hypothesis, which dominates the field, supposes that modified host PrP protein, termed PrPSc, acts as the transmissible agent. This model fits the observation that TSE dis...

journal_title：Genome biology

authors： Gibson TJ

更新日期：2001-01-01 00:00:00

abstract：:Bisulfite sequencing (BS-seq) is the gold standard for studying genome-wide DNA methylation. We developed MOABS to increase the speed, accuracy, statistical power and biological relevance of BS-seq data analysis. MOABS detects differential methylation with 10-fold coverage at single-CpG resolution based on a Beta-Bino...

journal_title：Genome biology

authors： Sun D,Xi Y,Rodriguez B,Park HJ,Tong P,Meong M,Goodell MA,Li W

更新日期：2014-02-24 00:00:00

abstract：:Reliable orthology prediction is central to comparative genomics. Although orthology is defined by phylogenetic criteria, most automated prediction methods are based on pairwise sequence comparisons. Recently, automated phylogeny-based orthology prediction has emerged as a feasible alternative for genome-wide studies....

journal_title：Genome biology

authors： Gabaldón T

更新日期：2008-10-30 00:00:00

abstract：:ELXR (Exon Locator and Extractor for Resequencing) streamlines the process of determining exon/intron boundaries and designing PCR and sequencing primers for high-throughput resequencing of exons. We have pre-computed ELXR primer sets for all exons identified from the human, mouse, and rat mRNA reference sequence (Ref...

journal_title：Genome biology

authors： Schageman JJ,Horton CJ,Niu S,Garner HR,Pertsemlidis A

更新日期：2004-01-01 00:00:00