A reappraisal of the phylogenetic placement of the Aquilegia whole-genome duplication.

abstract：:A report on the 23rd Fungal Genetics Conference, Pacific Grove, USA, 15-20 March 2005. ...

journal_title：Genome biology

authors： Dean R,Mitchell T,Donofrio N,Jeong JS,Powell A

更新日期：2005-01-01 00:00:00

abstract：:Fine-tuning quantitative traits for continuous subtle phenotypes is highly advantageous. We engineer the highly conserved upstream open reading frame (uORF) of FvebZIPs1.1 in strawberry (Fragaria vesca), using base editor A3A-PBE. Seven novel alleles are generated. Sugar content of the homozygous T1 mutant lines is 33...

journal_title：Genome biology

authors： Xing S,Chen K,Zhu H,Zhang R,Zhang H,Li B,Gao C

更新日期：2020-09-03 00:00:00

abstract：BACKGROUND:Protein domains are commonly used to assess the functional roles and evolutionary relationships of proteins and protein families. Here, we use the Pfam protein family database to examine a set of candidate partial domains. Pfam protein domains are often thought of as evolutionarily indivisible, structurally ...

journal_title：Genome biology

authors： Triant DA,Pearson WR

更新日期：2015-05-15 00:00:00

abstract：BACKGROUND:Transcription regulatory networks are composed of interactions between transcription factors and their target genes. Whereas unicellular networks have been studied extensively, metazoan transcription regulatory networks remain largely unexplored. Caenorhabditis elegans provides a powerful model to study such...

journal_title：Genome biology

authors： Reece-Hoyes JS,Deplancke B,Shingles J,Grove CA,Hope IA,Walhout AJ

更新日期：2005-01-01 00:00:00

abstract：BACKGROUND:High-density oligonucleotide microarrays provide a powerful tool for assessing differential mRNA expression levels. Characterizing the noise resulting from the enzymatic and hybridization steps, called type I noise, is essential for attributing significance measures to the differential expression scores. We ...

journal_title：Genome biology

authors： Naef F,Hacker CR,Patil N,Magnasco M

更新日期：2002-01-01 00:00:00

abstract：BACKGROUND:To understand the heterogeneous behaviors of individual cancer cells, it is essential to investigate gene expression levels as well as their divergence between different individual cells. Recent advances in next-generation sequencing-related technologies have enabled us to conduct a single-cell RNA-Seq analy...

journal_title：Genome biology

authors： Suzuki A,Matsushima K,Makinoshima H,Sugano S,Kohno T,Tsuchihara K,Suzuki Y

更新日期：2015-04-03 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：BACKGROUND:There are significant limitations in existing methods for the genome-wide identification of genes whose expression patterns affect traits. RESULTS:The transcriptomes of five tissues from 27 genetically diverse maize inbred lines were deeply sequenced to identify genes exhibiting high and low levels of expre...

journal_title：Genome biology

authors： Lin HY,Liu Q,Li X,Yang J,Liu S,Huang Y,Scanlon MJ,Nettleton D,Schnable PS

更新日期：2017-10-17 00:00:00

abstract：BACKGROUND:Whole-exome sequencing (WES) has been successful in identifying genes that cause familial Parkinson's disease (PD). However, until now this approach has not been deployed to study large cohorts of unrelated participants. To discover rare PD susceptibility variants, we performed WES in 1148 unrelated cases an...

journal_title：Genome biology

authors： Jansen IE,Ye H,Heetveld S,Lechler MC,Michels H,Seinstra RI,Lubbe SJ,Drouet V,Lesage S,Majounie E,Gibbs JR,Nalls MA,Ryten M,Botia JA,Vandrovcova J,Simon-Sanchez J,Castillo-Lizardo M,Rizzu P,Blauwendraat C,Chouhan AK

更新日期：2017-01-30 00:00:00

abstract：:The WOX genes form a plant-specific subclade of the eukaryotic homeobox transcription factor superfamily, which is characterized by the presence of a conserved DNA-binding homeodomain. The analysis of WOX gene expression and function shows that WOX family members fulfill specialized functions in key developmental proc...

journal_title：Genome biology

authors： van der Graaff E,Laux T,Rensing SA

更新日期：2009-01-01 00:00:00

abstract：BACKGROUND:One challenge facing biologists is to tease out useful information from massive data sets for further analysis. A pathway-based analysis may shed light by projecting candidate genes onto protein functional relationship networks. We are building such a pathway-based analysis system. RESULTS:We have construct...

journal_title：Genome biology

authors： Wu G,Feng X,Stein L

更新日期：2010-01-01 00:00:00

abstract：:A report on the Keystone symposium 'Non-coding RNAs' held at Snowbird, Utah, USA, 31 March to 5 April 2012. ...

journal_title：Genome biology

authors： Hacisuleyman E,Cabili MN,Rinn JL

更新日期：2012-05-25 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：BACKGROUND:Methylation of nucleotides, notably in the forms of 5-methylcytosine (5mC) in DNA and N6-methyladenosine (m6A) in mRNA, carries important information for gene regulation. 5mC has been elucidated to participate in the regulation of fruit ripening, whereas the function of m6A in this process and the interplay ...

journal_title：Genome biology

authors： Zhou L,Tian S,Qin G

更新日期：2019-08-06 00:00:00

abstract：BACKGROUND:Deciphering physical protein-protein interactions is fundamental to elucidating both the functions of proteins and biological processes. The development of high-throughput experimental technologies such as the yeast two-hybrid screening has produced an explosion in data relating to interactions. Since manual...

journal_title：Genome biology

authors： Huang M,Ding S,Wang H,Zhu X

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:Analysis of somatic mutations provides insight into the mutational processes that have shaped the cancer genome, but such analysis currently requires large cohorts. We develop deconstructSigs, which allows the identification of mutational signatures within a single tumor sample. RESULTS:Application of decon...

journal_title：Genome biology

authors： Rosenthal R,McGranahan N,Herrero J,Taylor BS,Swanton C

更新日期：2016-02-22 00:00:00

abstract：:An ancestral supersoldier phenotype of Pheidole ants can be recovered when selection for supersoldiers re-emerges, indicating that the developmental potential for caste pathways is retained. ...

journal_title：Genome biology

authors： Boomsma JJ,Nygaard S

更新日期：2012-02-22 00:00:00

abstract：BACKGROUND:While CRISPR-Cas systems hold tremendous potential for engineering the human genome, it is unclear how well each system performs against one another in both non-homologous end joining (NHEJ)-mediated and homology-directed repair (HDR)-mediated genome editing. RESULTS:We systematically compare five different...

journal_title：Genome biology

authors： Wang Y,Liu KI,Sutrisnoh NB,Srinivasan H,Zhang J,Li J,Zhang F,Lalith CRJ,Xing H,Shanmugam R,Foo JN,Yeo HT,Ooi KH,Bleckwehl T,Par YYR,Lee SM,Ismail NNB,Sanwari NAB,Lee STV,Lew J,Tan MH

更新日期：2018-05-29 00:00:00

abstract：:Keith Joung, Dan Voytas and Joanne Kamens share insights into how the genome editing field was advanced by early access to biological resources and the role in this process that plasmid repositories play. ...

journal_title：Genome biology

authors： Joung JK,Voytas DF,Kamens J

更新日期：2015-11-20 00:00:00

abstract：:Vascular endothelia comprise a diverse population of cells that specialize in response to genetic programs and environmental cues to take on distinct roles in different vessels, tissues, and organs, and in response to pathophysiological stresses. Characterization of endothelial-cell diversity will facilitate the devel...

journal_title：Genome biology

authors： Conway EM,Carmeliet P

更新日期：2004-01-01 00:00:00

abstract：:A report on the Epigenetic Engineering Meeting hosted by the Barts Institute of Cancer, held in London, UK, May 7, 2014. ...

journal_title：Genome biology

authors： Magnani L

更新日期：2014-01-01 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：BACKGROUND:Piwi-interacting RNAs (piRNAs) are a class of short (~26-31-nucleotide) non-protein-coding RNAs expressed in the metazoan germline. The piRNA pathway in arthropods is best understood in the ovary of Drosophila melanogaster, where it acts to silence active transposable elements (TEs). Maternal loading of piRN...

journal_title：Genome biology

authors： Ninova M,Griffiths-Jones S,Ronshaugen M

更新日期：2017-09-26 00:00:00

abstract：BACKGROUND:We propose that a computerized, internet-based graphical description language for systems biology will be essential for describing, archiving and analyzing complex problems of biological function in health and disease. RESULTS:We outline here a conceptual basis for designing such a language and describe Bio...

journal_title：Genome biology

authors： Cook DL,Farley JF,Tapscott SJ

更新日期：2001-01-01 00:00:00

abstract：:We demonstrate that loss-of-function yeast phenotypes are predictable by guilt-by-association in functional gene networks. Testing 1,102 loss-of-function phenotypes from genome-wide assays of yeast reveals predictability of diverse phenotypes, spanning cellular morphology, growth, metabolism, and quantitative cell sha...

journal_title：Genome biology

authors： McGary KL,Lee I,Marcotte EM

更新日期：2007-01-01 00:00:00

abstract：:Many differential gene expression analyses are conducted with an inadequate number of biological replicates. We describe an easy and effective RNA-seq approach using molecular barcoding to enable profiling of a large number of replicates simultaneously. This approach significantly improves the performance of different...

journal_title：Genome biology

authors： Li Y,Yang H,Zhang H,Liu Y,Shang H,Zhao H,Zhang T,Tu Q

更新日期：2020-03-23 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：BACKGROUND:In multicellular organisms, alternative splicing is central to tissue differentiation and identity. Unicellular protists lack multicellular tissue but differentiate into variable cell types during their life cycles. The role of alternative splicing in transitions between cell types and establishing cellular ...

journal_title：Genome biology

authors： Yeoh LM,Goodman CD,Mollard V,McHugh E,Lee VV,Sturm A,Cozijnsen A,McFadden GI,Ralph SA

更新日期：2019-08-01 00:00:00

abstract：:Transcription factor binding sites compete for a limited pool of bioavailable transcription factor molecules to fine tune gene expression. ...

journal_title：Genome biology

authors： Karreth FA,Tay Y,Pandolfi PP

更新日期：2014-04-28 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