Crucial timing in schizophrenia: role of DNA methylation in early neurodevelopment.

abstract：BACKGROUND:Tumors comprise a complex microenvironment of interacting malignant and stromal cell types. Much of our understanding of the tumor microenvironment comes from in vitro studies isolating the interactions between malignant cells and a single stromal cell type, often along a single pathway. RESULT:To develop a...

journal_title：Genome biology

authors： Gentles AJ,Hui AB,Feng W,Azizi A,Nair RV,Bouchard G,Knowles DA,Yu A,Jeong Y,Bejnood A,Forgó E,Varma S,Xu Y,Kuong A,Nair VS,West R,van de Rijn M,Hoang CD,Diehn M,Plevritis SK

更新日期：2020-05-07 00:00:00

abstract：BACKGROUND:Progressive neurological dysfunction is a key aspect of human aging. Because of underlying differences in the aging of mice and humans, useful mouse models have been difficult to obtain and study. We have used gene-expression analysis and polymorphism screening to study molecular senescence of the retina and...

journal_title：Genome biology

authors： Carter TA,Greenhall JA,Yoshida S,Fuchs S,Helton R,Swaroop A,Lockhart DJ,Barlow C

更新日期：2005-01-01 00:00:00

abstract：:Genetic studies have identified more than 150 autoimmune loci, and next-generation sequencing will identify more. Is it time to make human the model organism for autoimmune research? ...

journal_title：Genome biology

authors： Plenge R

更新日期：2010-01-01 00:00:00

abstract：:Two recent publications have demonstrated how delivering CRISPR nucleases provides a promising solution to the growing problem of bacterial antibiotic resistance. ...

journal_title：Genome biology

authors： Beisel CL,Gomaa AA,Barrangou R

更新日期：2014-11-08 00:00:00

abstract：BACKGROUND:Population genetic theory predicts that rapid adaptation is largely driven by complex traits encoded by many loci of small effect. Because large-effect loci are quickly fixed in natural populations, they should not contribute much to rapid adaptation. RESULTS:To investigate the genetic architecture of therm...

journal_title：Genome biology

authors： Mallard F,Nolte V,Tobler R,Kapun M,Schlötterer C

更新日期：2018-08-20 00:00:00

abstract：BACKGROUND:Metastatic progress is the primary cause of death in most cancers, yet the regulatory dynamics driving the cellular changes necessary for metastasis remain poorly understood. Multi-omics approaches hold great promise for addressing this challenge; however, current analysis tools have limited capabilities to ...

journal_title：Genome biology

authors： Ghaffari S,Hanson C,Schmidt RE,Bouchonville KJ,Offer SM,Sinha S

更新日期：2021-01-07 00:00:00

abstract：:Although chromosomal deletions and inversions are important in cancer, conventional methods for detecting DNA rearrangements require laborious indirect assays. Here we develop fluorescent reporters to rapidly quantify CRISPR/Cas9-mediated deletions and inversions. We find that inversion depends on the non-homologous e...

journal_title：Genome biology

authors： Li Y,Park AI,Mou H,Colpan C,Bizhanova A,Akama-Garren E,Joshi N,Hendrickson EA,Feldser D,Yin H,Anderson DG,Jacks T,Weng Z,Xue W

更新日期：2015-05-28 00:00:00

abstract：BACKGROUND:Transposable elements (TEs) are major components of large plant genomes and main drivers of genome evolution. The most recent assembly of hexaploid bread wheat recovered the highly repetitive TE space in an almost complete chromosomal context and enabled a detailed view into the dynamics of TEs in the A, B, ...

journal_title：Genome biology

authors： Wicker T,Gundlach H,Spannagl M,Uauy C,Borrill P,Ramírez-González RH,De Oliveira R,International Wheat Genome Sequencing Consortium.,Mayer KFX,Paux E,Choulet F

更新日期：2018-08-17 00:00:00

abstract：:Not so fast. The Iqbal et. al. study and the associated Whitelaw commentary highlight the appropriately high standards of study design and interpretation needed to obtain good evidence for or against epigenetic inheritance. Please see related article: www.dx.doi.org/10.1186/s13059-015-0714-1. ...

journal_title：Genome biology

authors： Nadeau JH

更新日期：2015-07-11 00:00:00

abstract：BACKGROUND:Altering the biochemical makeup of chromatin by the incorporation of histone variants during development represents a key mechanism in regulating gene expression. The histone variant H2A.B, H2A.B.3 in mice, appeared late in evolution and is most highly expressed in the testis. In the mouse, it is encoded by ...

journal_title：Genome biology

authors： Anuar ND,Kurscheid S,Field M,Zhang L,Rebar E,Gregory P,Buchou T,Bowles J,Koopman P,Tremethick DJ,Soboleva TA

更新日期：2019-01-31 00:00:00

abstract：:A report of the 6th Georgia Tech-Oak Ridge National Lab International Conference on Bioinformatics 'In silico Biology: Gene Discovery and Systems Genomics', Atlanta, USA, 15-17 November, 2007. ...

journal_title：Genome biology

authors： Weng Z,Guigó R

更新日期：2008-01-01 00:00:00

abstract：:Single-cell transcriptomics requires a method that is sensitive, accurate, and reproducible. Here, we present CEL-Seq2, a modified version of our CEL-Seq method, with threefold higher sensitivity, lower costs, and less hands-on time. We implemented CEL-Seq2 on Fluidigm's C1 system, providing its first single-cell, on-...

journal_title：Genome biology

authors： Hashimshony T,Senderovich N,Avital G,Klochendler A,de Leeuw Y,Anavy L,Gennert D,Li S,Livak KJ,Rozenblatt-Rosen O,Dor Y,Regev A,Yanai I

更新日期：2016-04-28 00:00:00

abstract：:The iCLIP and eCLIP techniques facilitate the detection of protein-RNA interaction sites at high resolution, based on diagnostic events at crosslink sites. However, previous methods do not explicitly model the specifics of iCLIP and eCLIP truncation patterns and possible biases. We developed PureCLIP ( https://github....

journal_title：Genome biology

authors： Krakau S,Richard H,Marsico A

更新日期：2017-12-28 00:00:00

abstract：BACKGROUND:Hypoxia-inducible factor 1 (HIF-1) plays a key role in cellular adaptation to hypoxia. To better understand the determinants of HIF-1 binding and transactivation, we used ChIP-chip and gene expression profiling to define the relationship between the epigenetic landscape, sites of HIF-1 binding, and genes tra...

journal_title：Genome biology

authors： Xia X,Kung AL

更新日期：2009-01-01 00:00:00

abstract：BACKGROUND:Two distinct classes of regulators have been implicated in regulating neuronal gene expression and mediating neuronal identity: transcription factors such as REST/NRSF (RE1 silencing transcription factor) and CREB (cAMP response element-binding protein), and microRNAs (miRNAs). How these two classes of regul...

journal_title：Genome biology

authors： Wu J,Xie X

更新日期：2006-01-01 00:00:00

abstract：BACKGROUND:Mitogen-activated protein kinases (MAPKs) are key regulators of immune responses in animals and plants. In Arabidopsis, perception of microbe-associated molecular patterns (MAMPs) activates the MAPKs MPK3, MPK4 and MPK6. Increasing information depicts the molecular events activated by MAMPs in plants, but th...

journal_title：Genome biology

authors： Frei dit Frey N,Garcia AV,Bigeard J,Zaag R,Bueso E,Garmier M,Pateyron S,de Tauzia-Moreau ML,Brunaud V,Balzergue S,Colcombet J,Aubourg S,Martin-Magniette ML,Hirt H

更新日期：2014-06-30 00:00:00

abstract：BACKGROUND:Polyploidy is ubiquitous in eukaryotic plant and fungal lineages, and it leads to the co-existence of several copies of similar or related genomes in one nucleus. In plants, polyploidy is considered a major factor in successful domestication. However, polyploidy challenges chromosome folding architecture in ...

journal_title：Genome biology

authors： Concia L,Veluchamy A,Ramirez-Prado JS,Martin-Ramirez A,Huang Y,Perez M,Domenichini S,Rodriguez Granados NY,Kim S,Blein T,Duncan S,Pichot C,Manza-Mianza D,Juery C,Paux E,Moore G,Hirt H,Bergounioux C,Crespi M,Mahfouz

更新日期：2020-04-29 00:00:00

abstract：BACKGROUND:Xanthomonas campestris pathovar campestris (Xcc) is the causal agent of black rot disease of crucifers worldwide. The molecular genetic diversity and host specificity of Xcc are poorly understood. RESULTS:We constructed a microarray based on the complete genome sequence of Xcc strain 8004 and investigated t...

journal_title：Genome biology

authors： He YQ,Zhang L,Jiang BL,Zhang ZC,Xu RQ,Tang DJ,Qin J,Jiang W,Zhang X,Liao J,Cao JR,Zhang SS,Wei ML,Liang XX,Lu GT,Feng JX,Chen B,Cheng J,Tang JL

更新日期：2007-01-01 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

abstract：:Derived from the maize Mu1 transposon, RescueMu provides strategies for maize gene discovery and mutant phenotypic analysis. 9.92 Mb of gene-enriched sequences next to RescueMu insertion sites were co-assembled with expressed sequence tags and analyzed. Multiple plasmid recoveries identified probable germinal insertio...

journal_title：Genome biology

authors： Fernandes J,Dong Q,Schneider B,Morrow DJ,Nan GL,Brendel V,Walbot V

更新日期：2004-01-01 00:00:00

abstract：BACKGROUND:The cellular mechanisms that underlie metal toxicity and detoxification are rather variegated and incompletely understood. Genomic phenotyping was used to assess the roles played by all nonessential Saccharomyces cerevisiae proteins in modulating cell viability after exposure to cadmium, nickel, and other me...

journal_title：Genome biology

authors： Ruotolo R,Marchini G,Ottonello S

更新日期：2008-04-07 00:00:00

abstract：:The first highly specific knockouts of a microRNA, miR155, in mice result in multiple defects in adaptive immunity, and also show the feasibility of investigating at least some microRNAs by gene knockout. ...

journal_title：Genome biology

authors： Moffett HF,Novina CD

更新日期：2007-01-01 00:00:00

abstract：BACKGROUND:X chromosome inactivation is a spectacular example of epigenetic silencing. In order to deduce how this complex system evolved, we examined X inactivation in a model marsupial, the tammar wallaby (Macropus eugenii). In marsupials, X inactivation is known to be paternal, incomplete and tissue-specific, and oc...

journal_title：Genome biology

authors： Al Nadaf S,Waters PD,Koina E,Deakin JE,Jordan KS,Graves JA

更新日期：2010-01-01 00:00:00

abstract：BACKGROUND:DNA methylation plays an essential role in regulating gene expression under a variety of conditions and it has therefore been hypothesized to underlie the transitions between life cycle stages in parasitic nematodes. So far, however, 5'-cytosine methylation has not been detected during any developmental stag...

journal_title：Genome biology

authors： Gao F,Liu X,Wu XP,Wang XL,Gong D,Lu H,Xia Y,Song Y,Wang J,Du J,Liu S,Han X,Tang Y,Yang H,Jin Q,Zhang X,Liu M

更新日期：2012-10-17 00:00:00

abstract：BACKGROUND:The genomic binding of CTCF is highly conserved across mammals, but the mechanisms that underlie its stability are poorly understood. One transcription factor known to functionally interact with CTCF in the context of X-chromosome inactivation is the ubiquitously expressed YY1. Because combinatorial transcri...

journal_title：Genome biology

authors： Schwalie PC,Ward MC,Cain CE,Faure AJ,Gilad Y,Odom DT,Flicek P

更新日期：2013-12-31 00:00:00

abstract：:Existing circular RNA (circRNA) databases have become essential for transcriptomics. However, most are unsuitable for mining in-depth information for candidate circRNA prioritization. To address this, we integrate circular transcript collections to develop the circAtlas database based on 1070 RNA-seq samples collected...

journal_title：Genome biology

authors： Wu W,Ji P,Zhao F

更新日期：2020-04-28 00:00:00

abstract：BACKGROUND:The development of complex organisms is believed to involve progressive restrictions in cellular fate. Understanding the scope and features of chromatin dynamics during embryogenesis, and identifying regulatory elements important for directing developmental processes remain key goals of developmental biology...

journal_title：Genome biology

authors： Thomas S,Li XY,Sabo PJ,Sandstrom R,Thurman RE,Canfield TK,Giste E,Fisher W,Hammonds A,Celniker SE,Biggin MD,Stamatoyannopoulos JA

更新日期：2011-01-01 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：:The ability to quantitatively measure the expression of all genes in a given tissue or cell with a single assay is an exciting promise of gene-expression profiling technology. An in situ-synthesized 60-mer oligonucleotide microarray designed to detect transcripts from all mouse genes was validated, as well as a set of...

journal_title：Genome biology

authors： Carter MG,Sharov AA,VanBuren V,Dudekula DB,Carmack CE,Nelson C,Ko MS

更新日期：2005-01-01 00:00:00

abstract：:A direct impediment to the optimal use of online databases is the increasing prevalence, severity, and toll of computer and network security incidents. Funding agencies should set up working groups that can provide essential services such as universal backup, archival storage, and mirroring of community resources, con...

journal_title：Genome biology

authors： Smith A,Greenbaum D,Douglas SM,Long M,Gerstein M

更新日期：2005-01-01 00:00:00