EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data.

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:There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challe...

journal_title：Genome biology

authors： Brownstein CA,Beggs AH,Homer N,Merriman B,Yu TW,Flannery KC,DeChene ET,Towne MC,Savage SK,Price EN,Holm IA,Luquette LJ,Lyon E,Majzoub J,Neupert P,McCallie D Jr,Szolovits P,Willard HF,Mendelsohn NJ,Temme R,Finkel R

更新日期：2014-03-25 00:00:00

abstract：BACKGROUND:Pseudogenes reveal ancestral gene functions. Some obligate intracellular bacteria, such as Mycobacterium leprae and Rickettsia spp., carry substantial fractions of pseudogenes. Until recently, horizontal gene transfers were considered to be rare events in obligate host-associated bacteria. RESULTS:We presen...

journal_title：Genome biology

authors： Fuxelius HH,Darby AC,Cho NH,Andersson SG

更新日期：2008-01-01 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：BACKGROUND:Complete genomic sequences of closely related organisms, such as the chlamydiae, afford the opportunity to assess significant strain differences against a background of many shared characteristics. The chlamydiae are ubiquitous intracellular parasites that are important pathogens of humans and other organism...

journal_title：Genome biology

authors： Xie G,Bonner CA,Jensen RA

更新日期：2002-08-29 00:00:00

abstract：BACKGROUND:While the song of all songbirds is controlled by the same neural circuit, the hormone dependence of singing behavior varies greatly between species. For this reason, songbirds are ideal organisms to study ultimate and proximate mechanisms of hormone-dependent behavior and neuronal plasticity. RESULTS:We pre...

journal_title：Genome biology

authors： Frankl-Vilches C,Kuhl H,Werber M,Klages S,Kerick M,Bakker A,de Oliveira EH,Reusch C,Capuano F,Vowinckel J,Leitner S,Ralser M,Timmermann B,Gahr M

更新日期：2015-01-29 00:00:00

abstract：:Identifying the biochemical basis of microbial phenotypes is a main objective of comparative genomics. Here we present a novel method using multivariate machine learning techniques for comparing automatically derived metabolic reconstructions of sequenced genomes on a large scale. Applying our method to 266 genomes di...

journal_title：Genome biology

authors： Kastenmüller G,Schenk ME,Gasteiger J,Mewes HW

更新日期：2009-01-01 00:00:00

abstract：:Our knowledge on tissue- and disease-specific functions of human genes is rather limited and highly context-specific. Here, we have developed a method for the comparison of mRNA expression levels of most human genes across 9,783 Affymetrix gene expression array experiments representing 43 normal human tissue types, 68...

journal_title：Genome biology

authors： Kilpinen S,Autio R,Ojala K,Iljin K,Bucher E,Sara H,Pisto T,Saarela M,Skotheim RI,Björkman M,Mpindi JP,Haapa-Paananen S,Vainio P,Edgren H,Wolf M,Astola J,Nees M,Hautaniemi S,Kallioniemi O

更新日期：2008-01-01 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:Genome editing of malaria parasites is key to the generation of live attenuated parasites used in experimental vaccination approaches. DNA repair in Plasmodium generally occurs only through homologous recombination. This has been used to generate transgenic parasites that lack one to three genes, leading to ...

journal_title：Genome biology

authors： Singer M,Marshall J,Heiss K,Mair GR,Grimm D,Mueller AK,Frischknecht F

更新日期：2015-11-17 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：:Extracting biological information from microarray data requires appropriate statistical methods. The simplest statistical method for detecting differential expression is the t test, which can be used to compare two conditions when there is replication of samples. With more than two conditions, analysis of variance (AN...

journal_title：Genome biology

authors： Cui X,Churchill GA

更新日期：2003-01-01 00:00:00

abstract：BACKGROUND:Understanding the embryonic stem cell (ESC) fate decision between self-renewal and proper differentiation is important for developmental biology and regenerative medicine. Attention has focused on mechanisms involving histone modifications, alternative pre-messenger RNA splicing, and cell-cycle progression. ...

journal_title：Genome biology

authors： Xu Y,Zhao W,Olson SD,Prabhakara KS,Zhou X

更新日期：2018-09-14 00:00:00

abstract：:Ancient DNA research is revealing a human history far more complex than that inferred from parsimonious models based on modern DNA. Here, we review some of the key events in the peopling of the world in the light of the findings of work on ancient DNA. ...

journal_title：Genome biology

authors： Haber M,Mezzavilla M,Xue Y,Tyler-Smith C

更新日期：2016-01-11 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：:Interpretation of the clinical significance of genomic alterations remains the most severe bottleneck preventing the realization of personalized medicine in cancer. We propose a knowledge commons to facilitate collaborative contributions and open discussion of clinical decision-making based on genomic events in cancer...

journal_title：Genome biology

authors： Good BM,Ainscough BJ,McMichael JF,Su AI,Griffith OL

更新日期：2014-08-27 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: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：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：:The ability to accurately quantify all the microRNAs (miRNAs) in a sample is important for understanding miRNA biology and for development of new biomarkers and therapeutic targets. We develop a new method for preparing miRNA sequencing libraries, RealSeq®-AC, that involves ligating the miRNAs with a single adapter an...

journal_title：Genome biology

authors： Barberán-Soler S,Vo JM,Hogans RE,Dallas A,Johnston BH,Kazakov SA

更新日期：2018-09-03 00:00:00

abstract：:Exome sequencing is poised to yield substantial insights into human genetic variation and evolutionary history, but there are significant challenges to overcome before this becomes a reality. ...

journal_title：Genome biology

authors： Tennessen JA,O'Connor TD,Bamshad MJ,Akey JM

更新日期：2011-09-14 00:00:00

abstract：:We have developed an ontology to provide standardized nomenclature for anatomical terms in the postnatal mouse. The Adult Mouse Anatomical Dictionary is structured as a directed acyclic graph, and is organized hierarchically both spatially and functionally. The ontology will be used to annotate and integrate different...

journal_title：Genome biology

authors： Hayamizu TF,Mangan M,Corradi JP,Kadin JA,Ringwald M

更新日期：2005-01-01 00:00:00

abstract：:Recent genomic studies showing abnormalities in the fibroblast growth factor system in the postmortem brains of people with major depressive disorder support previous indications of a role for growth factors in mood disorders. Similar molecular pathways, volumetric changes, and the effects of exercise on mood suggest ...

journal_title：Genome biology

authors： Niculescu AB

更新日期：2005-01-01 00:00:00

abstract：:The definition of cell identity is a central problem in biology. While single-cell RNA-seq provides a wealth of information regarding cell states, better methods are needed to map their identity, especially during developmental transitions. Here, we use repositories of cell type-specific transcriptomes to quantify ide...

journal_title：Genome biology

authors： Efroni I,Ip PL,Nawy T,Mello A,Birnbaum KD

更新日期：2015-01-22 00:00:00

abstract：:By using chromosome conformation capture technology, a recent study has revealed two alternative three-dimensional folding states of the human genome during the cell cycle. ...

journal_title：Genome biology

authors： Giorgetti L,Servant N,Heard E

更新日期：2013-12-24 00:00:00

abstract：:The accurate placement of an ancient whole-genome duplication (WGD) in relation to the lineage divergence is important. Here, we re-investigated the Aquilegia coerulea WGD and found it is more likely lineage-specific rather than shared by all eudicots. ...

journal_title：Genome biology

authors： Shi T,Chen J

更新日期：2020-12-08 00:00:00

abstract：:The accuracy of base calls produced by Illumina sequencers is adversely affected by several processes, with laser cross-talk and cluster phasing being prominent. We introduce an explicit statistical model of the sequencing process that generalizes current models of phasing and cross-talk and forms the basis of a base ...

journal_title：Genome biology

authors： Massingham T,Goldman N

更新日期：2012-02-29 00:00:00

abstract：:We assess five years of usage of the major genome-wide collections of mutants from Saccharomyces cerevisiae: single deletion mutants, double mutants conferring 'synthetic' lethality and the 'TRIPLES' collection of mutants obtained by random transposon insertion. Over 100 experimental conditions have been tested and mo...

journal_title：Genome biology

authors： Scherens B,Goffeau A

更新日期：2004-01-01 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：BACKGROUND:Pseudomonas aeruginosa is a ubiquitous environmental bacterium and an important opportunistic human pathogen. Generally, the acquisition of genes in the form of pathogenicity islands distinguishes pathogenic isolates from nonpathogens. We therefore sequenced a highly virulent strain of P. aeruginosa, PA14, a...

journal_title：Genome biology

authors： Lee DG,Urbach JM,Wu G,Liberati NT,Feinbaum RL,Miyata S,Diggins LT,He J,Saucier M,Déziel E,Friedman L,Li L,Grills G,Montgomery K,Kucherlapati R,Rahme LG,Ausubel FM

更新日期：2006-01-01 00:00:00