A systems view of Drosophila segmentation.

abstract：BACKGROUND:Microarray technology is increasingly being applied in biological and medical research to address a wide range of problems, such as the classification of tumors. An important statistical problem associated with tumor classification is the identification of new tumor classes using gene-expression profiles. Tw...

journal_title：Genome biology

authors： Dudoit S,Fridlyand J

更新日期：2002-06-25 00:00:00

abstract：:Structural variants (SVs) remain challenging to represent and study relative to point mutations despite their demonstrated importance. We show that variation graphs, as implemented in the vg toolkit, provide an effective means for leveraging SV catalogs for short-read SV genotyping experiments. We benchmark vg against...

journal_title：Genome biology

authors： Hickey G,Heller D,Monlong J,Sibbesen JA,Sirén J,Eizenga J,Dawson ET,Garrison E,Novak AM,Paten B

更新日期：2020-02-12 00:00:00

abstract：:Mapping-by-sequencing has emerged as a powerful technique for genetic mapping in several plant and animal species. As this resequencing-based method requires a reference genome, its application to complex plant genomes with incomplete and fragmented sequence resources remains challenging. We perform exome sequencing o...

journal_title：Genome biology

authors： Mascher M,Jost M,Kuon JE,Himmelbach A,Aßfalg A,Beier S,Scholz U,Graner A,Stein N

更新日期：2014-06-10 00:00:00

abstract：:Many essential transcription factors have conserved roles in regulating biological programs, yet their genomic occupancy can diverge significantly. A new study demonstrates that such variations are primarily due to cis-regulatory sequences, rather than differences between the regulators or nuclear environments. ...

journal_title：Genome biology

authors： Zinzen RP,Furlong EE

更新日期：2008-01-01 00:00:00

abstract：:Injection of recombinant Cas9 protein and synthetic guide RNAs into mouse zygotes has been shown to facilitate gene disruption and knock-ins using the CRISPR system. These technologies may soon displace genetic modification using embryonic stem cells. ...

journal_title：Genome biology

authors： Skarnes WC

更新日期：2015-05-27 00:00:00

abstract：:Toxin/antitoxin (TA) systems, viewed as essential regulators of growth arrest and programmed cell death, are widespread among prokaryotes, but remain sparsely annotated. We present RASTA-Bacteria, an automated method allowing quick and reliable identification of TA loci in sequenced prokaryotic genomes, whether they a...

journal_title：Genome biology

authors： Sevin EW,Barloy-Hubler F

更新日期：2007-01-01 00:00:00

abstract：:A report of the Wellcome Trust Functional Genomics and Systems Biology Conference, Hinxton, UK, 29 November to 1 December 2011. ...

journal_title：Genome biology

authors： Bakal C

更新日期：2012-01-30 00:00:00

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:Candida glabrata is a pathogenic yeast of increasing medical concern. It has been regarded as asexual since it was first described in 1917, yet phylogenetic analyses have revealed that it is more closely related to sexual yeasts than other Candida species. We show here that the C. glabrata genome contains ma...

journal_title：Genome biology

authors： Wong S,Fares MA,Zimmermann W,Butler G,Wolfe KH

更新日期：2003-01-01 00:00:00

abstract：:A combined approach of whole genome shotgun sequencing and ultra-high density linkage mapping using skim sequencing of a segregating population is effective for assembling allopolyploid genomes. ...

journal_title：Genome biology

authors： Ming R,Man Wai C

更新日期：2015-01-31 00:00:00

abstract：BACKGROUND:ADAR proteins are among the most extensively studied RNA binding proteins. They bind to their target and deaminate specific adenosines to inosines. ADAR activity is essential, and the editing of a subset of their targets is critical for viability. Recently, a huge number of novel ADAR targets were detected b...

journal_title：Genome biology

authors： Pinto Y,Cohen HY,Levanon EY

更新日期：2014-01-07 00:00:00

abstract：:Gene expression analysis of microRNA molecules is becoming increasingly important. In this study we assess the use of the mean expression value of all expressed microRNAs in a given sample as a normalization factor for microRNA real-time quantitative PCR data and compare its performance to the currently adopted approa...

journal_title：Genome biology

authors： Mestdagh P,Van Vlierberghe P,De Weer A,Muth D,Westermann F,Speleman F,Vandesompele J

更新日期：2009-01-01 00:00:00

abstract：BACKGROUND:Protein synthesis is tightly regulated and alterations to translation are characteristic of many cancers.Translation regulation is largely exerted at initiation through the eukaryotic translation initiation factor 4 F (eIF4F). eIF4F is pivotal for oncogenic signaling as it integrates mitogenic signals to amp...

journal_title：Genome biology

authors： Rubio CA,Weisburd B,Holderfield M,Arias C,Fang E,DeRisi JL,Fanidi A

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:MicroRNAs (miRNAs) are oligoribonucleotides with an important role in regulation of gene expression at the level of translation. Despite imperfect target complementarity, they can also significantly reduce mRNA levels. The validity of miRNA target gene predictions is difficult to assess at the protein level....

journal_title：Genome biology

authors： Arora A,Simpson DA

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:Plant-microbe interactions feature complex signal interplay between pathogens and their hosts. Phytophthora species comprise a destructive group of fungus-like plant pathogens, collectively affecting a wide range of plants important to agriculture and natural ecosystems. Despite the availability of genome se...

journal_title：Genome biology

authors： Jupe J,Stam R,Howden AJ,Morris JA,Zhang R,Hedley PE,Huitema E

更新日期：2013-06-25 00:00:00

abstract：BACKGROUND:Acute myeloid leukemia (AML) comprises a group of diseases characterized by the abnormal development of malignant myeloid cells. Recent studies have demonstrated an important role for aberrant transcriptional regulation in AML pathophysiology. Although several transcription factors (TFs) involved in myeloid ...

journal_title：Genome biology

authors： Chang LW,Payton JE,Yuan W,Ley TJ,Nagarajan R,Stormo GD

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:Single-cell micro-metastases of solid tumors often occur in the bone marrow. These disseminated tumor cells (DTCs) may resist therapy and lay dormant or progress to cause overt bone and visceral metastases. The molecular nature of DTCs remains elusive, as well as when and from where in the tumor they origina...

journal_title：Genome biology

authors： Demeulemeester J,Kumar P,Møller EK,Nord S,Wedge DC,Peterson A,Mathiesen RR,Fjelldal R,Zamani Esteki M,Theunis K,Fernandez Gallardo E,Grundstad AJ,Borgen E,Baumbusch LO,Børresen-Dale AL,White KP,Kristensen VN,Van Loo P,

更新日期：2016-12-09 00:00:00

abstract：BACKGROUND:Protein domains display a range of structural diversity, with numerous additions and deletions of secondary structural elements between related domains. We have observed a small number of cases of surprising large-scale deletions of core elements of structural domains. We propose a new concept called domain ...

journal_title：Genome biology

authors： Prakash A,Bateman A

更新日期：2015-04-30 00:00:00

abstract：BACKGROUND:The forkhead transcription factor FOXM1 is a key regulator of the cell cycle. It is frequently over-expressed in cancer and is emerging as an important therapeutic target. In breast cancer FOXM1 expression is linked with estrogen receptor (ERα) activity and resistance to endocrine therapies, with high levels...

journal_title：Genome biology

authors： Sanders DA,Ross-Innes CS,Beraldi D,Carroll JS,Balasubramanian S

更新日期：2013-01-24 00:00:00

abstract：:Trans-splicing is an unusual process in which two separate RNA strands are spliced together to yield a mature mRNA. We present a novel computational approach which has an overall accuracy of 82% and can predict 92% of known trans-splicing sites. We have applied our method to chromosomes 1 and 3 of Leishmania major, wi...

journal_title：Genome biology

authors： Gopal S,Awadalla S,Gaasterland T,Cross GA

更新日期：2005-01-01 00:00:00

abstract：BACKGROUND:Osteogenesis is a highly regulated developmental process and continues during the turnover and repair of mature bone. Runx2, the master regulator of osteoblastogenesis, directs a transcriptional program essential for bone formation through genetic and epigenetic mechanisms. While individual Runx2 gene target...

journal_title：Genome biology

authors： Wu H,Whitfield TW,Gordon JA,Dobson JR,Tai PW,van Wijnen AJ,Stein JL,Stein GS,Lian JB

更新日期：2014-03-21 00:00:00

abstract：:A report of the second annual Beyond the Genome conference held on the 19-22 September 2011 at The Universities at Shady Grove, Rockville, Maryland, USA, where increases in computing that may help make personal genomics a reality were a major focus. ...

journal_title：Genome biology

authors： Kristensen DM

更新日期：2011-10-24 00:00:00

abstract：:The use of DNA sequences to estimate the timing of evolutionary events is increasingly popular, although it is fraught with practical difficulties. But the exponential growth of relevant information and improved methods of analysis are providing increasingly reliable sequence-derived dates, and it may become possible ...

journal_title：Genome biology

authors： Wray GA

更新日期：2002-01-01 00:00:00

abstract：:Most microbes cannot be easily cultured, and metagenomics provides a means to study them. Current techniques aim to resolve individual genomes from metagenomes, so-called metagenome-assembled genomes (MAGs). Leading approaches depend upon time series or transect studies, the efficacy of which is a function of communit...

journal_title：Genome biology

authors： DeMaere MZ,Darling AE

更新日期：2019-02-26 00:00:00

abstract：BACKGROUND:While large-scale cancer genomic projects are comprehensively characterizing the mutational spectrum of various cancers, so far little attention has been devoted to either define the antigenicity of these mutations or to characterize the immune responses they elicit. Here we present a strategy to characteriz...

journal_title：Genome biology

authors： Angelova M,Charoentong P,Hackl H,Fischer ML,Snajder R,Krogsdam AM,Waldner MJ,Bindea G,Mlecnik B,Galon J,Trajanoski Z

更新日期：2015-03-31 00:00:00

abstract：BACKGROUND:The assessment and characterization of the gut microbiome has become a focus of research in the area of human autoimmune diseases. Ankylosing spondylitis is an inflammatory autoimmune disease and evidence showed that ankylosing spondylitis may be a microbiome-driven disease. RESULTS:To investigate the relat...

journal_title：Genome biology

authors： Wen C,Zheng Z,Shao T,Liu L,Xie Z,Le Chatelier E,He Z,Zhong W,Fan Y,Zhang L,Li H,Wu C,Hu C,Xu Q,Zhou J,Cai S,Wang D,Huang Y,Breban M,Qin N,Ehrlich SD

更新日期：2017-07-27 00:00:00

abstract：:We polled the Editorial Board of Genome Biology to ask where they see genomics going in the next few years. Here are some of their responses. ...

journal_title：Genome biology

authors： Cheifet B

更新日期：2019-01-22 00:00:00

abstract：BACKGROUND:The influence of genetic variation on complex diseases is potentially mediated through a range of highly dynamic epigenetic processes exhibiting temporal variation during development and later life. Here we present a catalogue of the genetic influences on DNA methylation (methylation quantitative trait loci ...

journal_title：Genome biology

authors： Gaunt TR,Shihab HA,Hemani G,Min JL,Woodward G,Lyttleton O,Zheng J,Duggirala A,McArdle WL,Ho K,Ring SM,Evans DM,Davey Smith G,Relton CL

更新日期：2016-03-31 00:00:00

abstract：BACKGROUND:Functional characterization of non-coding elements in the human genome is a major genomic challenge and the maturation of genome-editing technologies is revolutionizing our ability to achieve this task. Oncogene-induced senescence, a cellular state of irreversible proliferation arrest that is enforced follow...

journal_title：Genome biology

authors： Han R,Li L,Ugalde AP,Tal A,Manber Z,Barbera EP,Chiara VD,Elkon R,Agami R

更新日期：2018-08-17 00:00:00

abstract：BACKGROUND:The human genome contains "dark" gene regions that cannot be adequately assembled or aligned using standard short-read sequencing technologies, preventing researchers from identifying mutations within these gene regions that may be relevant to human disease. Here, we identify regions with few mappable reads ...

journal_title：Genome biology

authors： Ebbert MTW,Jensen TD,Jansen-West K,Sens JP,Reddy JS,Ridge PG,Kauwe JSK,Belzil V,Pregent L,Carrasquillo MM,Keene D,Larson E,Crane P,Asmann YW,Ertekin-Taner N,Younkin SG,Ross OA,Rademakers R,Petrucelli L,Fryer JD

更新日期：2019-05-20 00:00:00