Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA.

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:Adult T cell acute lymphoblastic leukemia (T-ALL) is a rare disease that affects less than 10 individuals in one million. It has been less studied than its cognate pediatric malignancy, which is more prevalent. A higher percentage of the adult patients relapse, compared to children. It is thus essential to s...

journal_title：Genome biology

authors： Sentís I,Gonzalez S,Genescà E,García-Hernández V,Muiños F,Gonzalez C,López-Arribillaga E,Gonzalez J,Fernandez-Ibarrondo L,Mularoni L,Espinosa L,Bellosillo B,Ribera JM,Bigas A,Gonzalez-Perez A,Lopez-Bigas N

更新日期：2020-11-23 00:00:00

abstract：BACKGROUND:Chromosome instability leads to aneuploidy, a state in which cells have abnormal numbers of chromosomes, and is found in two out of three cancers. In a chromosomal instable p53 deficient mouse model with accelerated lymphomagenesis, we previously observed whole chromosome copy number changes affecting all ly...

journal_title：Genome biology

authors： Bakker B,Taudt A,Belderbos ME,Porubsky D,Spierings DC,de Jong TV,Halsema N,Kazemier HG,Hoekstra-Wakker K,Bradley A,de Bont ES,van den Berg A,Guryev V,Lansdorp PM,Colomé-Tatché M,Foijer F

更新日期：2016-05-31 00:00:00

abstract：BACKGROUND:The human lung tissue microbiota remains largely uncharacterized, although a number of studies based on airway samples suggest the existence of a viable human lung microbiota. Here we characterized the taxonomic and derived functional profiles of lung microbiota in 165 non-malignant lung tissue samples from ...

journal_title：Genome biology

authors： Yu G,Gail MH,Consonni D,Carugno M,Humphrys M,Pesatori AC,Caporaso NE,Goedert JJ,Ravel J,Landi MT

更新日期：2016-07-28 00:00:00

abstract：BACKGROUND:The identification of causal genes from genome-wide association studies (GWAS) is the next important step for the translation of genetic findings into biologically meaningful mechanisms of disease and potential therapeutic targets. Using novel chromatin interaction detection techniques and allele specific as...

journal_title：Genome biology

authors： McGovern A,Schoenfelder S,Martin P,Massey J,Duffus K,Plant D,Yarwood A,Pratt AG,Anderson AE,Isaacs JD,Diboll J,Thalayasingam N,Ospelt C,Barton A,Worthington J,Fraser P,Eyre S,Orozco G

更新日期：2016-11-01 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:Retroviral elements are pervasively transcribed and dynamically regulated during development. While multiple histone- and DNA-modifying enzymes have broadly been associated with their global silencing, little is known about how the many diverse retroviral families are each selectively recognized. RESULTS:He...

journal_title：Genome biology

authors： Mak KS,Burdach J,Norton LJ,Pearson RC,Crossley M,Funnell AP

更新日期：2014-04-30 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：BACKGROUND:Abundant pseudogenes are a feature of mammalian genomes. Processed pseudogenes (PPs) are reverse transcribed from mRNAs. Recent molecular biological studies show that mammalian long interspersed element 1 (L1)-encoded proteins may have been involved in PP reverse transcription. Here, we present the first com...

journal_title：Genome biology

authors： Ohshima K,Hattori M,Yada T,Gojobori T,Sakaki Y,Okada N

更新日期：2003-01-01 00:00:00

abstract：:The first genome sequence of the extinct European wild aurochs reveals the genetic foundation of native British and Irish landraces of cattle.See related Research article: www.dx.doi.org/10.1186/s13059-015-0790-2. ...

journal_title：Genome biology

authors： Orlando L

更新日期：2015-10-26 00:00:00

abstract：BACKGROUND:Despite decades of research, the molecular mechanisms responsible for the evolution of morphological diversity remain poorly understood. While current models assume that species-specific morphologies are governed by differential use of conserved genetic regulatory circuits, it is debated whether non-conserve...

journal_title：Genome biology

authors： Milde S,Hemmrich G,Anton-Erxleben F,Khalturin K,Wittlieb J,Bosch TC

更新日期：2009-01-01 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：:To discover driver fusions beyond canonical exon-to-exon chimeric transcripts, we develop CICERO, a local assembly-based algorithm that integrates RNA-seq read support with extensive annotation for candidate ranking. CICERO outperforms commonly used methods, achieving a 95% detection rate for 184 independently validat...

journal_title：Genome biology

authors： Tian L,Li Y,Edmonson MN,Zhou X,Newman S,McLeod C,Thrasher A,Liu Y,Tang B,Rusch MC,Easton J,Ma J,Davis E,Trull A,Michael JR,Szlachta K,Mullighan C,Baker SJ,Downing JR,Ellison DW,Zhang J

更新日期：2020-05-28 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：:Single-cell RNA-seq in samples from the human neocortex demonstrate that long noncoding RNAs (lncRNAs) are abundantly expressed in specific individual brain cells, despite being hard to detect in bulk samples. This result suggests that the lncRNAs might have important functions in specific cell types in the brain. ...

journal_title：Genome biology

authors： Ma Q,Chang HY

更新日期：2016-04-14 00:00:00

abstract：BACKGROUND:Dictyostelium discoideum is a eukaryote with a simple lifestyle and a relatively small genome whose sequence has been fully determined. It is widely used for studies on cell signaling, movement and multicellular development. Ras guanine-nucleotide exchange factors (RasGEFs) are the proteins that activate Ras...

journal_title：Genome biology

authors： Wilkins A,Szafranski K,Fraser DJ,Bakthavatsalam D,Müller R,Fisher PR,Glöckner G,Eichinger L,Noegel AA,Insall RH

更新日期：2005-01-01 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：BACKGROUND:Reliable information extraction applications have been a long sought goal of the biomedical text mining community, a goal that if reached would provide valuable tools to benchside biologists in their increasingly difficult task of assimilating the knowledge contained in the biomedical literature. We present ...

journal_title：Genome biology

authors： Baumgartner WA Jr,Lu Z,Johnson HL,Caporaso JG,Paquette J,Lindemann A,White EK,Medvedeva O,Cohen KB,Hunter L

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:The initiation and subsequent evolution of cancer are largely driven by a relatively small number of somatic mutations with critical functional impacts, so-called driver mutations. Identifying driver mutations in a patient's tumor cells is a central task in the era of precision cancer medicine. Over the deca...

journal_title：Genome biology

authors： Chen H,Li J,Wang Y,Ng PK,Tsang YH,Shaw KR,Mills GB,Liang H

更新日期：2020-02-20 00:00:00

abstract：:Many drugs have unknown, controversial or multiple mechanisms of action. Four recent 'chemical genomic' studies, using genome-scale collections of yeast gene deletions that were either arrayed or barcoded, have presented complementary approaches to identifying gene-drug and pathway-drug interactions. ...

journal_title：Genome biology

authors： Brenner C

更新日期：2004-01-01 00:00:00

abstract：BACKGROUND:Chromatin organizes DNA and regulates its transcriptional activity through epigenetic modifications. Heterochromatic regions of the genome are generally transcriptionally silent, while euchromatin is more prone to transcription. During DNA replication, both genetic information and chromatin modifications mus...

journal_title：Genome biology

authors： Bourguet P,López-González L,Gómez-Zambrano Á,Pélissier T,Hesketh A,Potok ME,Pouch-Pélissier MN,Perez M,Da Ines O,Latrasse D,White CI,Jacobsen SE,Benhamed M,Mathieu O

更新日期：2020-11-25 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：:We describe a method for extracting Boolean implications (if-then relationships) in very large amounts of gene expression microarray data. A meta-analysis of data from thousands of microarrays for humans, mice, and fruit flies finds millions of implication relationships between genes that would be missed by other meth...

journal_title：Genome biology

authors： Sahoo D,Dill DL,Gentles AJ,Tibshirani R,Plevritis SK

更新日期：2008-10-30 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：BACKGROUND:DNase-seq and ATAC-seq are broadly used methods to assay open chromatin regions genome-wide. The single nucleotide resolution of DNase-seq has been further exploited to infer transcription factor binding sites (TFBSs) in regulatory regions through footprinting. Recent studies have demonstrated the sequence b...

journal_title：Genome biology

authors： Karabacak Calviello A,Hirsekorn A,Wurmus R,Yusuf D,Ohler U

更新日期：2019-02-21 00:00:00

abstract：BACKGROUND:The relationships between proteins are often asymmetric: one protein (A) depends for its function on another protein (B), but the second protein does not depend on the first. In metabolic networks there are multiple pathways that converge into one central pathway. The enzymes in the converging pathways depen...

journal_title：Genome biology

authors： Notebaart RA,Kensche PR,Huynen MA,Dutilh BE

更新日期：2009-02-12 00:00:00

abstract：:Recent experiments show that properly controlled recombination between homologous DNA molecules is essential for the maintenance of genome stability and for the prevention of tumorigenesis. ...

journal_title：Genome biology

authors： Modesti M,Kanaar R

更新日期：2001-01-01 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:Nuclear factor I-A (NFI-A), a phylogenetically conserved transcription/replication protein, plays a crucial role in mouse brain development. Previous studies have shown that disruption of the Nfia gene in mice leads to perinatal lethality, corpus callosum agenesis, and hydrocephalus. RESULTS:To identify pot...

journal_title：Genome biology

authors： Wong YW,Schulze C,Streichert T,Gronostajski RM,Schachner M,Tilling T

更新日期：2007-01-01 00:00:00

abstract：:The functional annotation of proteins identified in genome sequencing projects is based on similarities to homologs in the databases. As a result of the possible strategies for divergent evolution, homologous enzymes frequently do not catalyze the same reaction, and we conclude that assignment of function from sequenc...

journal_title：Genome biology

authors： Gerlt JA,Babbitt PC

更新日期：2000-01-01 00:00:00