Decontamination of ambient RNA in single-cell RNA-seq with DecontX.

abstract：:The mouse is an important model of human genetic disease. Describing phenotypes of mutant mice in a standard, structured manner that will facilitate data mining is a major challenge for bioinformatics. Here we describe a novel, compositional approach to this problem which combines core ontologies from a variety of sou...

journal_title：Genome biology

authors： Gkoutos GV,Green EC,Mallon AM,Hancock JM,Davidson D

更新日期：2005-01-01 00:00:00

abstract：:As DNA sequencing outpaces improvements in computer speed, there is a critical need to accelerate tasks like alignment and SNP calling. Crossbow is a cloud-computing software tool that combines the aligner Bowtie and the SNP caller SOAPsnp. Executing in parallel using Hadoop, Crossbow analyzes data comprising 38-fold ...

journal_title：Genome biology

authors： Langmead B,Schatz MC,Lin J,Pop M,Salzberg SL

更新日期：2009-01-01 00:00:00

abstract：BACKGROUND:The current bovine genomic reference sequence was assembled from a Hereford cow. The resulting linear assembly lacks diversity because it does not contain allelic variation, a drawback of linear references that causes reference allele bias. High nucleotide diversity and the separation of individuals by hundr...

journal_title：Genome biology

authors： Crysnanto D,Pausch H

更新日期：2020-07-27 00:00:00

abstract：BACKGROUND:Synthetic genetic interactions have recently been mapped on a genome scale in the budding yeast Saccharomyces cerevisiae, providing a functional view of the central processes of eukaryotic life. Currently, comprehensive genetic interaction networks have not been determined for other species, and we therefore...

journal_title：Genome biology

authors： Koch EN,Costanzo M,Bellay J,Deshpande R,Chatfield-Reed K,Chua G,D'Urso G,Andrews BJ,Boone C,Myers CL

更新日期：2012-07-02 00:00:00

abstract：BACKGROUND:The role played by microRNAs (miRs) as common regulators in physiologic processes such as development and various disease states was recently highlighted. Retinitis pigmentosa (RP) linked to RHO (which encodes rhodopsin) is the most frequent form of inherited retinal degeneration that leads to blindness, for...

journal_title：Genome biology

authors： Loscher CJ,Hokamp K,Kenna PF,Ivens AC,Humphries P,Palfi A,Farrar GJ

更新日期：2007-01-01 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:Aging and sun exposure are the leading causes of skin cancer. It has been shown that epigenetic changes, such as DNA methylation, are well established mechanisms for cancer, and also have emerging roles in aging and common disease. Here, we directly ask whether DNA methylation is altered following skin aging...

journal_title：Genome biology

authors： Vandiver AR,Irizarry RA,Hansen KD,Garza LA,Runarsson A,Li X,Chien AL,Wang TS,Leung SG,Kang S,Feinberg AP

更新日期：2015-04-16 00:00:00

abstract：BACKGROUND:Mutations in genes encoding ribosomal proteins (RPs) have been shown to cause an array of cellular and developmental defects in a variety of organisms. In Drosophila melanogaster, disruption of RP genes can result in the 'Minute' syndrome of dominant, haploinsufficient phenotypes, which include prolonged dev...

journal_title：Genome biology

authors： Marygold SJ,Roote J,Reuter G,Lambertsson A,Ashburner M,Millburn GH,Harrison PM,Yu Z,Kenmochi N,Kaufman TC,Leevers SJ,Cook KR

更新日期：2007-01-01 00:00:00

abstract：:Abhay Sharma brings two arguments in favor of transgenerational epigenetic inheritance (TGEI) in mammals when criticizing our work. He uses probability calculations and finds that the probability of obtaining the number of common changes in the in utero-exposed prospermatogonia and the same cells in the next generatio...

journal_title：Genome biology

authors： Szabó PE

更新日期：2016-05-16 00:00:00

abstract：BACKGROUND:Estrogens and their receptors are important in human development, physiology and disease. In this study, we utilized an integrated genome-wide molecular and computational approach to characterize the interaction between the activated estrogen receptor (ER) and the regulatory elements of candidate target gene...

journal_title：Genome biology

authors： Lin CY,Ström A,Vega VB,Kong SL,Yeo AL,Thomsen JS,Chan WC,Doray B,Bangarusamy DK,Ramasamy A,Vergara LA,Tang S,Chong A,Bajic VB,Miller LD,Gustafsson JA,Liu ET

更新日期：2004-01-01 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 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：:PIWI proteins, a subfamily of PAZ/PIWI Domain family RNA-binding proteins, are best known for their function in silencing transposons and germline development by partnering with small noncoding RNAs called PIWI-interacting RNAs (piRNAs). However, recent studies have revealed multifaceted roles of the PIWI-piRNA pathwa...

journal_title：Genome biology

authors： Wang C,Lin H

更新日期：2021-01-08 00:00:00

abstract：BACKGROUND:Drug resistance remains a major public health challenge for malaria treatment and eradication. Individual loci associated with drug resistance to many antimalarials have been identified, but their epistasis with other resistance mechanisms has not yet been elucidated. RESULTS:We previously described two mut...

journal_title：Genome biology

authors： Herman JD,Rice DP,Ribacke U,Silterra J,Deik AA,Moss EL,Broadbent KM,Neafsey DE,Desai MM,Clish CB,Mazitschek R,Wirth DF

更新日期：2014-01-01 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：BACKGROUND:Pluripotency of embryonic stem (ES) cells is controlled in part by chromatin-modifying factors that regulate histone H3 lysine 4 (H3K4) methylation. However, it remains unclear how H3K4 demethylation contributes to ES cell function. RESULTS:Here, we show that KDM5B, which demethylates lysine 4 of histone H3...

journal_title：Genome biology

authors： Kidder BL,Hu G,Zhao K

更新日期：2014-02-04 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：:We describe an algorithm, multi-species cMonkey, for the simultaneous biclustering of heterogeneous multiple-species data collections and apply the algorithm to a group of bacteria containing Bacillus subtilis, Bacillus anthracis, and Listeria monocytogenes. The algorithm reveals evolutionary insights into the surpris...

journal_title：Genome biology

authors： Waltman P,Kacmarczyk T,Bate AR,Kearns DB,Reiss DJ,Eichenberger P,Bonneau R

更新日期：2010-01-01 00:00:00

abstract：:A report on the 23rd annual meeting on 'The Biology of Genomes', 11-15 May 2010, Cold Spring Harbor, USA. ...

journal_title：Genome biology

authors： Capra JA,Carbone L,Riesenfeld SJ,Wall JD

更新日期：2010-01-01 00:00:00

abstract：BACKGROUND:CTCF binding contributes to the establishment of a higher-order genome structure by demarcating the boundaries of large-scale topologically associating domains (TADs). However, despite the importance and conservation of TADs, the role of CTCF binding in their evolution and stability remains elusive. RESULTS...

journal_title：Genome biology

authors： Kentepozidou E,Aitken SJ,Feig C,Stefflova K,Ibarra-Soria X,Odom DT,Roller M,Flicek P

更新日期：2020-01-07 00:00:00

abstract：BACKGROUND:Differentiation of metazoan cells requires execution of different gene expression programs but recent single-cell transcriptome profiling has revealed considerable variation within cells of seeming identical phenotype. This brings into question the relationship between transcriptome states and cell phenotype...

journal_title：Genome biology

authors： Dueck H,Khaladkar M,Kim TK,Spaethling JM,Francis C,Suresh S,Fisher SA,Seale P,Beck SG,Bartfai T,Kuhn B,Eberwine J,Kim J

更新日期：2015-06-09 00:00:00

abstract：BACKGROUND:Mycoparasitism, a lifestyle where one fungus is parasitic on another fungus, has special relevance when the prey is a plant pathogen, providing a strategy for biological control of pests for plant protection. Probably, the most studied biocontrol agents are species of the genus Hypocrea/Trichoderma. RESULTS...

journal_title：Genome biology

authors： Kubicek CP,Herrera-Estrella A,Seidl-Seiboth V,Martinez DA,Druzhinina IS,Thon M,Zeilinger S,Casas-Flores S,Horwitz BA,Mukherjee PK,Mukherjee M,Kredics L,Alcaraz LD,Aerts A,Antal Z,Atanasova L,Cervantes-Badillo MG,Challac

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:The vast number of precise intercellular connections within vertebrate nervous systems is only partly explained by the comparatively few known extracellular guidance cues. Large families of neural orphan receptor proteins have been identified and are likely to contribute to these recognition processes but du...

journal_title：Genome biology

authors： Söllner C,Wright GJ

更新日期：2009-01-01 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：:DNA sequence data are being produced at an ever-increasing rate. The Bowtie sequence-alignment algorithm uses advanced data structures to help data analysis keep pace with data generation. ...

journal_title：Genome biology

authors： Flicek P

更新日期：2009-01-01 00:00:00

abstract：:In most eukaryotes, histones, which are the major structural components of chromatin, are expressed as a family of sequence variants encoded by multiple genes. Because different histone variants can contribute to a distinct or unique nucleosomal architecture, this heterogeneity can be exploited to regulate a wide rang...

journal_title：Genome biology

authors： Brown DT

更新日期：2001-01-01 00:00:00

abstract：BACKGROUND:Circular RNAs are a class of endogenous RNAs with various functions in eukaryotic cells. Worthy of note, circular RNAs play a critical role in cancer. Currently, nothing is known about their role in head and neck squamous cell carcinoma (HNSCC). The identification of circular RNAs in HNSCC might become usefu...

journal_title：Genome biology

authors： Verduci L,Ferraiuolo M,Sacconi A,Ganci F,Vitale J,Colombo T,Paci P,Strano S,Macino G,Rajewsky N,Blandino G

更新日期：2017-12-20 00:00:00

abstract：:A variety of base editors have been developed to achieve C-to-T editing in different genomic contexts. Here, we compare a panel of five base editors on their C-to-T editing efficiencies and product purity at commonly editable sites, including some human pathogenic C-to-T mutations. We further profile the accessibiliti...

journal_title：Genome biology

authors： Wang Y,Gao R,Wu J,Xiong YC,Wei J,Zhang S,Yang B,Chen J,Yang L

更新日期：2019-10-23 00:00:00

abstract：BACKGROUND:Progressive neurological dysfunction is a key aspect of human aging. Because of underlying differences in the aging of mice and humans, useful mouse models have been difficult to obtain and study. We have used gene-expression analysis and polymorphism screening to study molecular senescence of the retina and...

journal_title：Genome biology

authors： Carter TA,Greenhall JA,Yoshida S,Fuchs S,Helton R,Swaroop A,Lockhart DJ,Barlow C

更新日期：2005-01-01 00:00:00

abstract：:Identification of causal mutations in barley and wheat is hampered by their large genomes and suppressed recombination. To overcome these obstacles, we have developed MutChromSeq, a complexity reduction approach based on flow sorting and sequencing of mutant chromosomes, to identify induced mutations by comparison to ...

journal_title：Genome biology

authors： Sánchez-Martín J,Steuernagel B,Ghosh S,Herren G,Hurni S,Adamski N,Vrána J,Kubaláková M,Krattinger SG,Wicker T,Doležel J,Keller B,Wulff BB

更新日期：2016-10-31 00:00:00