Boolean implication networks derived from large scale, whole genome microarray datasets.

abstract：BACKGROUND:Is it possible to construct an accurate and detailed subgene-level map of a genome using bacterial artificial chromosome (BAC) end sequences, a sparse marker map, and the sequences of other genomes? RESULTS:A sheep BAC library, CHORI-243, was constructed and the BAC end sequences were determined and mapped ...

journal_title：Genome biology

authors： Dalrymple BP,Kirkness EF,Nefedov M,McWilliam S,Ratnakumar A,Barris W,Zhao S,Shetty J,Maddox JF,O'Grady M,Nicholas F,Crawford AM,Smith T,de Jong PJ,McEwan J,Oddy VH,Cockett NE,International Sheep Genomics Consortium.

更新日期：2007-01-01 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：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：:A report of the Keystone Symposium 'DNA Replication and Recombination' held in Keystone, USA, 27 February to 4 March 2011. ...

journal_title：Genome biology

authors： Johansson E,Speck C,Chabes A

更新日期：2011-01-01 00:00:00

abstract：:A report of the recent EMBO Conference 'From Functional Genomics to Systems Biology' held at the EMBL Advanced Training Centre, Heidelberg, Germany, 13-16 November 2010. ...

journal_title：Genome biology

authors： Fordyce P,Ingolia N

更新日期：2011-01-01 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：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：UNLABELLED:Ancient DNA is typically highly degraded with appreciable cytosine deamination, and contamination with present-day DNA often complicates the identification of endogenous molecules. Together, these factors impede accurate assembly of the endogenous ancient mitochondrial genome. We present schmutzi, an iterati...

journal_title：Genome biology

authors： Renaud G,Slon V,Duggan AT,Kelso J

更新日期：2015-10-12 00:00:00

abstract：BACKGROUND:In eukaryotic organisms, gene expression is regulated at multiple levels during the processes of transcription and translation. The absence of a tight regulatory network for transcription in the human malaria parasite suggests that gene expression may largely be controlled at post-transcriptional and transla...

journal_title：Genome biology

authors： Bunnik EM,Chung DW,Hamilton M,Ponts N,Saraf A,Prudhomme J,Florens L,Le Roch KG

更新日期：2013-11-22 00:00:00

abstract：BACKGROUND:Cell lineage-specific DNA methylation patterns distinguish normal human leukocyte subsets and can be used to detect and quantify these subsets in peripheral blood. We have developed an approach that uses DNA methylation to simultaneously quantify multiple leukocyte subsets, enabling investigation of immune m...

journal_title：Genome biology

authors： Accomando WP,Wiencke JK,Houseman EA,Nelson HH,Kelsey KT

更新日期：2014-03-05 00:00:00

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：: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：:Prokaryotic cyanobacteria express robust circadian (daily) rhythms under the control of a central clock. Recent studies shed light on the mechanisms governing circadian rhythms in cyanobacteria and highlight key differences between prokaryotic and eukaryotic clocks. ...

journal_title：Genome biology

authors： Johnson CH

更新日期：2004-01-01 00:00:00

abstract：:Compared to RNA-sequencing transcript differential analysis, gene-level differential expression analysis is more robust and experimentally actionable. However, the use of gene counts for statistical analysis can mask transcript-level dynamics. We demonstrate that 'analysis first, aggregation second,' where the p value...

journal_title：Genome biology

authors： Yi L,Pimentel H,Bray NL,Pachter L

更新日期：2018-04-12 00:00:00

abstract：BACKGROUND:Subcellular messenger RNA localization is important in most eukaryotic cells, even in unicellular organisms like yeast for which this process has been underestimated. Microarrays are rarely used to study subcellular mRNA localization at whole-genome level, but can be adapted to that purpose. This work focuse...

journal_title：Genome biology

authors： Sylvestre J,Vialette S,Corral Debrinski M,Jacq C

更新日期：2003-01-01 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:Sequencing the genomes of the first few eukaryotes created the impression that gene number shows no correlation with organism complexity, often referred to as the G-value paradox. Several attempts have previously been made to resolve this paradox, citing multifunctionality of proteins, alternative splicing, ...

journal_title：Genome biology

authors： Schad E,Tompa P,Hegyi H

更新日期：2011-12-19 00:00:00

abstract：:Understanding the functional impact of genomic variants is a major goal of modern genetics and personalized medicine. Although many synonymous and non-coding variants act through altering the efficiency of pre-mRNA splicing, it is difficult to predict how these variants impact pre-mRNA splicing. Here, we describe a ma...

journal_title：Genome biology

authors： Adamson SI,Zhan L,Graveley BR

更新日期：2018-06-01 00:00:00

abstract：BACKGROUND:Variants of microRNAs (miRNAs), called isomiRs, are commonly reported in deep-sequencing studies; however, the functional significance of these variants remains controversial. Observational studies show that isomiR patterns are non-random, hinting that these molecules could be regulated and therefore functio...

journal_title：Genome biology

authors： Cloonan N,Wani S,Xu Q,Gu J,Lea K,Heater S,Barbacioru C,Steptoe AL,Martin HC,Nourbakhsh E,Krishnan K,Gardiner B,Wang X,Nones K,Steen JA,Matigian NA,Wood DL,Kassahn KS,Waddell N,Shepherd J,Lee C,Ichikawa J,McKer

更新日期：2011-12-30 00:00:00

abstract：BACKGROUND:The lifelong accumulation of somatic mutations underlies age-related phenotypes and cancer. Mutagenic forces are thought to shape the genome of aging cells in a tissue-specific way. Whole genome analyses of somatic mutation patterns, based on both types and genomic distribution of variants, can shed light on...

journal_title：Genome biology

authors： Franco I,Helgadottir HT,Moggio A,Larsson M,Vrtačnik P,Johansson A,Norgren N,Lundin P,Mas-Ponte D,Nordström J,Lundgren T,Stenvinkel P,Wennberg L,Supek F,Eriksson M

更新日期：2019-12-18 00:00:00

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：:Cryptochromes are photoreceptors that regulate entrainment by light of the circadian clock in plants and animals. They also act as integral parts of the central circadian oscillator in animal brains and as receptors controlling photomorphogenesis in response to blue or ultraviolet (UV-A) light in plants. Cryptochromes...

journal_title：Genome biology

authors： Lin C,Todo T

更新日期：2005-01-01 00:00:00

abstract：BACKGROUND:Previous methods employed for the identification of synergistic transcription factors (TFs) are based on either TF enrichment from co-regulated genes or phylogenetic footprinting. Despite the success of these methods, both have limitations. RESULTS:We propose a new strategy to identify synergistic TFs by fu...

journal_title：Genome biology

authors： Hu Z,Hu B,Collins JF

更新日期：2007-01-01 00:00:00

abstract：:Many existing pipelines for scRNA-seq data apply pre-processing steps such as normalization or imputation to account for excessive zeros or "drop-outs." Here, we extensively analyze diverse UMI data sets to show that clustering should be the foremost step of the workflow. We observe that most drop-outs disappear once ...

journal_title：Genome biology

authors： Kim TH,Zhou X,Chen M

更新日期：2020-08-06 00:00:00

abstract：BACKGROUND:Massively parallel pyrosequencing systems have increased the efficiency of DNA sequencing, although the published per-base accuracy of a Roche GS20 is only 96%. In genome projects, highly redundant consensus assemblies can compensate for sequencing errors. In contrast, studies of microbial diversity that cat...

journal_title：Genome biology

authors： Huse SM,Huber JA,Morrison HG,Sogin ML,Welch DM

更新日期：2007-01-01 00:00:00

abstract：BACKGROUND:The nature of the protein molecular clock, the protein-specific rate of amino acid substitutions, is among the central questions of molecular evolution. Protein expression level is the dominant determinant of the clock rate in a number of organisms. It has been suggested that highly expressed proteins evolve...

journal_title：Genome biology

authors： Plata G,Gottesman ME,Vitkup D

更新日期：2010-01-01 00:00:00

abstract：BACKGROUND:The functional impact of genetic variation has been extensively surveyed, revealing that genetic changes correlated to phenotypes lie mostly in non-coding genomic regions. Studies have linked allele-specific genetic changes to gene expression, DNA methylation, and histone marks but these investigations have ...

journal_title：Genome biology

authors： Cheung WA,Shao X,Morin A,Siroux V,Kwan T,Ge B,Aïssi D,Chen L,Vasquez L,Allum F,Guénard F,Bouzigon E,Simon MM,Boulier E,Redensek A,Watt S,Datta A,Clarke L,Flicek P,Mead D,Paul DS,Beck S,Bourque G,Lathrop M,

更新日期：2017-03-10 00:00:00

abstract：BACKGROUND:Phenotypic plasticity refers to the range of phenotypes a single genotype can express as a function of its environment. These phenotypic variations are attributable to the effect of the environment on the expression and function of genes influencing plastic traits. We investigated phenotypic plasticity in gr...

journal_title：Genome biology

authors： Dal Santo S,Tornielli GB,Zenoni S,Fasoli M,Farina L,Anesi A,Guzzo F,Delledonne M,Pezzotti M

更新日期：2013-06-07 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: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