Accelerating research through reagent repositories: the genome editing example.


:Keith Joung, Dan Voytas and Joanne Kamens share insights into how the genome editing field was advanced by early access to biological resources and the role in this process that plasmid repositories play.


Genome Biol


Genome biology


Joung JK,Voytas DF,Kamens J




Has Abstract


2015-11-20 00:00:00












  • Exome-chip meta-analysis identifies novel loci associated with cardiac conduction, including ADAMTS6.

    abstract:BACKGROUND:Genome-wide association studies conducted on QRS duration, an electrocardiographic measurement associated with heart failure and sudden cardiac death, have led to novel biological insights into cardiac function. However, the variants identified fall predominantly in non-coding regions and their underlying me...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Prins BP,Mead TJ,Brody JA,Sveinbjornsson G,Ntalla I,Bihlmeyer NA,van den Berg M,Bork-Jensen J,Cappellani S,Van Duijvenboden S,Klena NT,Gabriel GC,Liu X,Gulec C,Grarup N,Haessler J,Hall LM,Iorio A,Isaacs A,Li-Gao R,

    更新日期:2018-07-17 00:00:00

  • Phytophthora capsici-tomato interaction features dramatic shifts in gene expression associated with a hemi-biotrophic lifestyle.

    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

    pub_type: 杂志文章


    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

  • A phospho-proteomic screen identifies substrates of the checkpoint kinase Chk1.

    abstract:BACKGROUND:The cell-cycle checkpoint kinase Chk1 is essential in mammalian cells due to its roles in controlling processes such as DNA replication, mitosis and DNA-damage responses. Despite its paramount importance, how Chk1 controls these functions remains unclear, mainly because very few Chk1 substrates have hitherto...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Blasius M,Forment JV,Thakkar N,Wagner SA,Choudhary C,Jackson SP

    更新日期:2011-08-18 00:00:00

  • THoR: a tool for domain discovery and curation of multiple alignments.

    abstract::We describe a tool, THoR, that automatically creates and curates multiple sequence alignments representing protein domains. This exploits both PSI-BLAST and HMMER algorithms and provides an accurate and comprehensive alignment for any domain family. The entire process is designed for use via a web-browser, with simple...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Dickens NJ,Ponting CP

    更新日期:2003-01-01 00:00:00

  • Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation.

    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

    pub_type: 杂志文章


    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

  • Discovery of estrogen receptor alpha target genes and response elements in breast tumor cells.

    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

    pub_type: 杂志文章,meta分析


    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

  • Pharmacogenomic analysis of patient-derived tumor cells in gynecologic cancers.

    abstract:BACKGROUND:Gynecologic malignancy is one of the leading causes of mortality in female adults worldwide. Comprehensive genomic analysis has revealed a list of molecular aberrations that are essential to tumorigenesis, progression, and metastasis of gynecologic tumors. However, targeting such alterations has frequently l...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Sa JK,Hwang JR,Cho YJ,Ryu JY,Choi JJ,Jeong SY,Kim J,Kim MS,Paik ES,Lee YY,Choi CH,Kim TJ,Kim BG,Bae DS,Lee Y,Her NG,Shin YJ,Cho HJ,Kim JY,Seo YJ,Koo H,Oh JW,Lee T,Kim HS,Song SY,Bae JS,Park WY,Han HD

    更新日期:2019-11-26 00:00:00

  • An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.

    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

    pub_type: 杂志文章


    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

  • Using orthologous and paralogous proteins to identify specificity determining residues.

    abstract:BACKGROUND:Concepts of orthology and paralogy are become increasingly important as whole-genome comparison allows their identification in complete genomes. Functional specificity of proteins is assumed to be conserved among orthologs and is different among paralogs. We used this assumption to identify residues which de...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Mirny LA,Gelfand MS

    更新日期:2002-01-01 00:00:00

  • Sequence-based genomics.

    abstract::A report on the Genome-Based Pathogen Biology meeting, Hinxton, UK, 7-10 July 2002. ...

    journal_title:Genome biology



    authors: Simpson AJ

    更新日期:2002-08-27 00:00:00

  • Selection in the evolution of gene duplications.

    abstract:BACKGROUND:Gene duplications have a major role in the evolution of new biological functions. Theoretical studies often assume that a duplication per se is selectively neutral and that, following a duplication, one of the gene copies is freed from purifying (stabilizing) selection, which creates the potential for evolut...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Kondrashov FA,Rogozin IB,Wolf YI,Koonin EV

    更新日期:2002-01-01 00:00:00

  • Using the canary genome to decipher the evolution of hormone-sensitive gene regulation in seasonal singing birds.

    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

    pub_type: 杂志文章


    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

  • Modular organization in the reductive evolution of protein-protein interaction networks.

    abstract:BACKGROUND:The variation in the sizes of the genomes of distinct life forms remains somewhat puzzling. The organization of proteins into domains and the different mechanisms that regulate gene expression are two factors that potentially increase the capacity of genomes to create more complex systems. High-throughput pr...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Tamames J,Moya A,Valencia A

    更新日期:2007-01-01 00:00:00

  • Decreasing miRNA sequencing bias using a single adapter and circularization approach.

    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

    pub_type: 杂志文章


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

    更新日期:2018-09-03 00:00:00

  • High tandem repeat content in the genome of the short-lived annual fish Nothobranchius furzeri: a new vertebrate model for aging research.

    abstract:BACKGROUND:The annual fish Nothobranchius furzeri is the vertebrate with the shortest known life span in captivity. Fish of the GRZ strain live only three to four months under optimal laboratory conditions, show explosive growth, early sexual maturation and age-dependent physiological and behavioral decline, and expres...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Reichwald K,Lauber C,Nanda I,Kirschner J,Hartmann N,Schories S,Gausmann U,Taudien S,Schilhabel MB,Szafranski K,Glöckner G,Schmid M,Cellerino A,Schartl M,Englert C,Platzer M

    更新日期:2009-02-11 00:00:00

  • Protein-protein interactions of the hyperthermophilic archaeon Pyrococcus horikoshii OT3.

    abstract:BACKGROUND:Although 2,061 proteins of Pyrococcus horikoshii OT3, a hyperthermophilic archaeon, have been predicted from the recently completed genome sequence, the majority of proteins show no similarity to those from other organisms and are thus hypothetical proteins of unknown function. Because most proteins operate ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Usui K,Katayama S,Kanamori-Katayama M,Ogawa C,Kai C,Okada M,Kawai J,Arakawa T,Carninci P,Itoh M,Takio K,Miyano M,Kidoaki S,Matsuda T,Hayashizaki Y,Suzuki H

    更新日期:2005-01-01 00:00:00

  • A computational framework for boosting confidence in high-throughput protein-protein interaction datasets.

    abstract::Improving the quality and coverage of the protein interactome is of tantamount importance for biomedical research, particularly given the various sources of uncertainty in high-throughput techniques. We introduce a structure-based framework, Coev2Net, for computing a single confidence score that addresses both false-p...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Hosur R,Peng J,Vinayagam A,Stelzl U,Xu J,Perrimon N,Bienkowska J,Berger B

    更新日期:2012-08-31 00:00:00

  • A versatile reporter system for CRISPR-mediated chromosomal rearrangements.

    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

    pub_type: 杂志文章


    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

  • Accelerated exon evolution within primate segmental duplications.

    abstract:BACKGROUND:The identification of signatures of natural selection has long been used as an approach to understanding the unique features of any given species. Genes within segmental duplications are overlooked in most studies of selection due to the limitations of draft nonhuman genome assemblies and to the methodologic...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Lorente-Galdos B,Bleyhl J,Santpere G,Vives L,Ramírez O,Hernandez J,Anglada R,Cooper GM,Navarro A,Eichler EE,Marques-Bonet T

    更新日期:2013-01-29 00:00:00

  • Gene expression analysis of nuclear factor I-A deficient mice indicates delayed brain maturation.

    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

    pub_type: 杂志文章


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

    更新日期:2007-01-01 00:00:00

  • Preferential binding of HIF-1 to transcriptionally active loci determines cell-type specific response to hypoxia.

    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

    pub_type: 杂志文章


    authors: Xia X,Kung AL

    更新日期:2009-01-01 00:00:00

  • Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment.

    abstract:BACKGROUND:Understanding the design logic of living systems requires the understanding and comparison of proteomes. Proteomes define the commonalities between organisms more precisely than genomic sequences. Because uncertainties remain regarding the accuracy of proteomic data, several issues need to be resolved before...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Shevchenko A,Roguev A,Schaft D,Buchanan L,Habermann B,Sakalar C,Thomas H,Krogan NJ,Shevchenko A,Stewart AF

    更新日期:2008-01-01 00:00:00

  • Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control.

    abstract:BACKGROUND:Ichthyophthirius multifiliis, commonly known as Ich, is a highly pathogenic ciliate responsible for 'white spot', a disease causing significant economic losses to the global aquaculture industry. Options for disease control are extremely limited, and Ich's obligate parasitic lifestyle makes experimental stud...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Coyne RS,Hannick L,Shanmugam D,Hostetler JB,Brami D,Joardar VS,Johnson J,Radune D,Singh I,Badger JH,Kumar U,Saier M,Wang Y,Cai H,Gu J,Mather MW,Vaidya AB,Wilkes DE,Rajagopalan V,Asai DJ,Pearson CG,Findly RC,Di

    更新日期:2011-10-17 00:00:00

  • Reduced intrinsic DNA curvature leads to increased mutation rate.

    abstract:BACKGROUND:Mutation rates vary across the genome. Many trans factors that influence mutation rates have been identified, as have specific sequence motifs at the 1-7-bp scale, but cis elements remain poorly characterized. The lack of understanding regarding why different sequences have different mutation rates hampers o...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Duan C,Huan Q,Chen X,Wu S,Carey LB,He X,Qian W

    更新日期:2018-09-14 00:00:00

  • The amazing world of bacterial structured RNAs.

    abstract::The discovery of several new structured non-coding RNAs in bacterial and archaeal genomes and metagenomes raises burning questions about their biological and biochemical functions. ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Westhof E

    更新日期:2010-01-01 00:00:00

  • Statistical tools for synthesizing lists of differentially expressed features in related experiments.

    abstract::We propose a novel approach for finding a list of features that are commonly perturbed in two or more experiments, quantifying the evidence of dependence between the experiments by a ratio. We present a Bayesian analysis of this ratio, which leads us to suggest two rules for choosing a cut-off on the ranked list of p ...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Blangiardo M,Richardson S

    更新日期:2007-01-01 00:00:00

  • Influence of metabolic network structure and function on enzyme evolution.

    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

    pub_type: 杂志文章


    authors: Vitkup D,Kharchenko P,Wagner A

    更新日期:2006-01-01 00:00:00

  • SAGE profiling of the forelimb and hindlimb.

    abstract::A recent study has used serial analysis of gene expression to compare mouse forelimb and hindlimb gene-expression profiles. The method successfully identified known regulators of limb identity and has generated a candidate set of differentially expressed genes that may regulate limb identity. ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Logan M

    更新日期:2002-01-01 00:00:00

  • Alternative splicing links histone modifications to stem cell fate decision.

    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

    pub_type: 杂志文章


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

    更新日期:2018-09-14 00:00:00

  • Vex-seq: high-throughput identification of the impact of genetic variation on pre-mRNA splicing efficiency.

    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

    pub_type: 杂志文章


    authors: Adamson SI,Zhan L,Graveley BR

    更新日期:2018-06-01 00:00:00