High throughput single-cell detection of multiplex CRISPR-edited gene modifications.

abstract：BACKGROUND:We propose a new method for supervised learning from gene expression data. We call it 'tree harvesting'. This technique starts with a hierarchical clustering of genes, then models the outcome variable as a sum of the average expression profiles of chosen clusters and their products. It can be applied to many...

journal_title：Genome biology

authors： Hastie T,Tibshirani R,Botstein D,Brown P

更新日期：2001-01-01 00:00:00

abstract：:The iCLIP and eCLIP techniques facilitate the detection of protein-RNA interaction sites at high resolution, based on diagnostic events at crosslink sites. However, previous methods do not explicitly model the specifics of iCLIP and eCLIP truncation patterns and possible biases. We developed PureCLIP ( https://github....

journal_title：Genome biology

authors： Krakau S,Richard H,Marsico A

更新日期：2017-12-28 00:00:00

abstract：BACKGROUND:Millions of humans and animals suffer from superficial infections caused by a group of highly specialized filamentous fungi, the dermatophytes, which exclusively infect keratinized host structures. To provide broad insights into the molecular basis of the pathogenicity-associated traits, we report the first ...

journal_title：Genome biology

authors： Burmester A,Shelest E,Glöckner G,Heddergott C,Schindler S,Staib P,Heidel A,Felder M,Petzold A,Szafranski K,Feuermann M,Pedruzzi I,Priebe S,Groth M,Winkler R,Li W,Kniemeyer O,Schroeckh V,Hertweck C,Hube B,White TC

更新日期：2011-01-01 00:00:00

abstract：:Two recent publications have demonstrated how delivering CRISPR nucleases provides a promising solution to the growing problem of bacterial antibiotic resistance. ...

journal_title：Genome biology

authors： Beisel CL,Gomaa AA,Barrangou R

更新日期：2014-11-08 00:00:00

abstract：BACKGROUND:Rare coding variants constitute an important class of human genetic variation, but are underrepresented in current databases that are based on small population samples. Recent studies show that variants altering amino acid sequence and protein function are enriched at low variant allele frequency, 2 to 5%, b...

journal_title：Genome biology

authors： Marth GT,Yu F,Indap AR,Garimella K,Gravel S,Leong WF,Tyler-Smith C,Bainbridge M,Blackwell T,Zheng-Bradley X,Chen Y,Challis D,Clarke L,Ball EV,Cibulskis K,Cooper DN,Fulton B,Hartl C,Koboldt D,Muzny D,Smith R,Soug

更新日期：2011-09-14 00:00:00

abstract：:Genetic mapping and determination of the organization of the wheat genome are changing the wheat-breeding process. New initiatives to analyze the expressed portion of the wheat genome and structural analysis of the genomes of Arabidopsis and rice are increasing our knowledge of the genes that are linked to key agronom...

journal_title：Genome biology

authors： Francki M,Appels R

更新日期：2002-01-01 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：:Transposable elements (TEs) are notable drivers of genetic innovation. Over evolutionary time, TE insertions can supply new promoter, enhancer, and insulator elements to protein-coding genes and establish novel, species-specific gene regulatory networks. Conversely, ongoing TE-driven insertional mutagenesis, nonhomolo...

journal_title：Genome biology

authors： Gerdes P,Richardson SR,Mager DL,Faulkner GJ

更新日期：2016-05-09 00:00:00

abstract：BACKGROUND:Many eukaryotic genomes encode cis-natural antisense transcripts (cis-NATs). Sense and antisense transcripts may form double-stranded RNAs that are processed by the RNA interference machinery into small interfering RNAs (siRNAs). A few so-called nat-siRNAs have been reported in plants, mammals, Drosophila, a...

journal_title：Genome biology

authors： Zhang X,Xia J,Lii YE,Barrera-Figueroa BE,Zhou X,Gao S,Lu L,Niu D,Chen Z,Leung C,Wong T,Zhang H,Guo J,Li Y,Liu R,Liang W,Zhu JK,Zhang W,Jin H

更新日期：2012-01-01 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：:MAP1-family proteins are classical microtubule-associated proteins (MAPs) that bind along the microtubule lattice. The founding members, MAP1A and MAP1B, are predominantly expressed in neurons, where they are thought to be important in the formation and development of axons and dendrites. Mammalian genomes usually con...

journal_title：Genome biology

authors： Halpain S,Dehmelt L

更新日期：2006-01-01 00:00:00

abstract：:The EpiGRAPH web service http://epigraph.mpi-inf.mpg.de/ enables biologists to uncover hidden associations in vertebrate genome and epigenome datasets. Users can upload sets of genomic regions and EpiGRAPH will test multiple attributes (including DNA sequence, chromatin structure, epigenetic modifications and evolutio...

journal_title：Genome biology

authors： Bock C,Halachev K,Büch J,Lengauer T

更新日期：2009-02-10 00:00:00

abstract：BACKGROUND:RNA splicing is a key post-transcriptional mechanism that generates protein diversity and contributes to the fine-tuning of gene expression, which may facilitate adaptation to environmental challenges. Here, we employ a systems approach to study alternative splicing changes upon enteric infection in females ...

journal_title：Genome biology

authors： Bou Sleiman M,Frochaux MV,Andreani T,Osman D,Guigo R,Deplancke B

更新日期：2020-01-17 00:00:00

abstract：:CRISPR guide RNA libraries have been iteratively improved to provide increasingly efficient reagents, although their large size is a barrier for many applications. We design an optimised minimal genome-wide human CRISPR-Cas9 library (MinLibCas9) by mining existing large-scale gene loss-of-function datasets, resulting ...

journal_title：Genome biology

authors： Gonçalves E,Thomas M,Behan FM,Picco G,Pacini C,Allen F,Vinceti A,Sharma M,Jackson DA,Price S,Beaver CM,Dovey O,Parry-Smith D,Iorio F,Parts L,Yusa K,Garnett MJ

更新日期：2021-01-21 00:00:00

abstract：BACKGROUND:The Asian tiger mosquito Aedes albopictus is globally expanding and has become the main vector for human arboviruses in Europe. With limited antiviral drugs and vaccines available, vector control is the primary approach to prevent mosquito-borne diseases. A reliable and accurate DNA sequence of the Ae. albop...

journal_title：Genome biology

authors： Palatini U,Masri RA,Cosme LV,Koren S,Thibaud-Nissen F,Biedler JK,Krsticevic F,Johnston JS,Halbach R,Crawford JE,Antoshechkin I,Failloux AB,Pischedda E,Marconcini M,Ghurye J,Rhie A,Sharma A,Karagodin DA,Jenrette J,Ga

更新日期：2020-08-26 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：BACKGROUND:Most studies of molecular evolution are focused on individual genes and proteins. However, understanding the design principles and evolutionary properties of molecular networks requires a system-wide perspective. In the present work we connect molecular evolution on the gene level with system properties of a...

journal_title：Genome biology

authors： Vitkup D,Kharchenko P,Wagner A

更新日期：2006-01-01 00:00:00

abstract：BACKGROUND:Phylogenetic analysis of the Archaea has been mainly established by 16S rRNA sequence comparison. With the accumulation of completely sequenced genomes, it is now possible to test alternative approaches by using large sequence datasets. We analyzed archaeal phylogeny using two concatenated datasets consistin...

journal_title：Genome biology

authors： Brochier C,Forterre P,Gribaldo S

更新日期：2004-01-01 00:00:00

abstract：:Toxin/antitoxin (TA) systems, viewed as essential regulators of growth arrest and programmed cell death, are widespread among prokaryotes, but remain sparsely annotated. We present RASTA-Bacteria, an automated method allowing quick and reliable identification of TA loci in sequenced prokaryotic genomes, whether they a...

journal_title：Genome biology

authors： Sevin EW,Barloy-Hubler F

更新日期：2007-01-01 00:00:00

abstract：:According to a recent article published in Genome Biology, Duggan and coworkers sequenced and partially assembled five genomes of smallpox vaccines from the nineteenth century. No information regarding the ends of genomes was presented, and they are important to understand the evolutionary relationship of the differen...

journal_title：Genome biology

authors： Brinkmann A,Souza ARV,Esparza J,Nitsche A,Damaso CR

更新日期：2020-12-04 00:00:00

abstract：BACKGROUND:Parasitism is a highly successful mode of life and one that requires suites of gene adaptations to permit survival within a potentially hostile host. Among such adaptations is the secretion of proteins capable of modifying or manipulating the host environment. Nippostrongylus brasiliensis is a well-studied m...

journal_title：Genome biology

authors： Harcus YM,Parkinson J,Fernández C,Daub J,Selkirk ME,Blaxter ML,Maizels RM

更新日期：2004-01-01 00:00:00

abstract：:The genome-wide investigation of DNA methylation levels has been limited to reference transposable element positions. The methylation analysis of non-reference and mobile transposable elements has only recently been performed, but required both genome resequencing and MethylC-seq datasets. We have created epiTEome, a ...

journal_title：Genome biology

authors： Daron J,Slotkin RK

更新日期：2017-05-12 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：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:As the rough draft of the human genome sequence nears a finished product and other genome-sequencing projects accumulate sequence data exponentially, bioinformatics is emerging as an important tool for studies of transposon biology. In particular, L1 elements exhibit a variety of sequence structures after in...

journal_title：Genome biology

authors： Szak ST,Pickeral OK,Makalowski W,Boguski MS,Landsman D,Boeke JD

更新日期：2002-09-19 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:Recent advancements in next-generation sequencing have rapidly improved our ability to study genomic material at an unprecedented scale. Despite substantial improvements in sequencing technologies, errors present in the data still risk confounding downstream analysis and limiting the applicability of sequenc...

journal_title：Genome biology

authors： Mitchell K,Brito JJ,Mandric I,Wu Q,Knyazev S,Chang S,Martin LS,Karlsberg A,Gerasimov E,Littman R,Hill BL,Wu NC,Yang HT,Hsieh K,Chen L,Littman E,Shabani T,Enik G,Yao D,Sun R,Schroeder J,Eskin E,Zelikovsky A,S

更新日期：2020-03-17 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：:A combined approach of whole genome shotgun sequencing and ultra-high density linkage mapping using skim sequencing of a segregating population is effective for assembling allopolyploid genomes. ...

journal_title：Genome biology

authors： Ming R,Man Wai C

更新日期：2015-01-31 00:00:00

abstract：:Giving access to sequence and annotation data for genome assemblies is important because, while facilitating research, it places both assembly and annotation quality under scrutiny, resulting in improvements to both. Therefore we announce Avianbase, a resource for bird genomics, which provides access to data released ...

journal_title：Genome biology

authors： Eöry L,Gilbert MT,Li C,Li B,Archibald A,Aken BL,Zhang G,Jarvis E,Flicek P,Burt DW

更新日期：2015-01-29 00:00:00