Network security and data integrity in academia: an assessment and a proposal for large-scale archiving.

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：: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：:DNA arrays are valuable tools in molecular biology laboratories. Their rapid acceptance was aided by the release of plans for a pin-spotting microarrayer by researchers at Stanford. Inkjet microarraying is a flexible, complementary technique that allows the synthesis of arrays of any oligonucleotide sequences de novo....

journal_title：Genome biology

authors： Lausted C,Dahl T,Warren C,King K,Smith K,Johnson M,Saleem R,Aitchison J,Hood L,Lasky SR

更新日期：2004-01-01 00:00:00

abstract：BACKGROUND:The development of mass spectrometric (MS) techniques now allows the investigation of very complex protein mixtures ranging from subcellular structures to tissues. Body fluids are also popular targets of proteomic analysis because of their potential for biomarker discovery. Seminal plasma has not yet receive...

journal_title：Genome biology

authors： Pilch B,Mann M

更新日期：2006-01-01 00:00:00

abstract：BACKGROUND:The direct examination of large, unbiased samples of young gene duplicates in their early stages of evolution is crucial to understanding the origin, divergence and preservation of new genes. Furthermore, comparative analysis of multiple genomes is necessary to determine whether patterns of gene duplication ...

journal_title：Genome biology

authors： Katju V,Farslow JC,Bergthorsson U

更新日期：2009-01-01 00:00:00

abstract：BACKGROUND:Gene expression signatures indicative of tumor proliferative capacity and tumor-immune cell interactions have emerged as principal biology-driven predictors of breast cancer outcomes. How these signatures relate to one another in biological and prognostic contexts remains to be clarified. RESULTS:To investi...

journal_title：Genome biology

authors： Nagalla S,Chou JW,Willingham MC,Ruiz J,Vaughn JP,Dubey P,Lash TL,Hamilton-Dutoit SJ,Bergh J,Sotiriou C,Black MA,Miller LD

更新日期：2013-04-29 00:00:00

abstract：BACKGROUND:A key step in domestication of the grapevine was the transition from separate sexes (dioecy) in wild Vitis vinifera ssp. sylvestris (V. sylvestris) to hermaphroditism in cultivated Vitis vinifera ssp. sativa (V. vinifera). It is known that V. sylvestris has an XY system and V. vinifera a modified Y haplotype...

journal_title：Genome biology

authors： Badouin H,Velt A,Gindraud F,Flutre T,Dumas V,Vautrin S,Marande W,Corbi J,Sallet E,Ganofsky J,Santoni S,Guyot D,Ricciardelli E,Jepsen K,Käfer J,Berges H,Duchêne E,Picard F,Hugueney P,Tavares R,Bacilieri R,Rustenh

更新日期：2020-09-07 00:00:00

abstract：:Tissues are complex milieus consisting of numerous cell types. Several recent methods have attempted to enumerate cell subsets from transcriptomes. However, the available methods have used limited sources for training and give only a partial portrayal of the full cellular landscape. Here we present xCell, a novel gene...

journal_title：Genome biology

authors： Aran D,Hu Z,Butte AJ

更新日期：2017-11-15 00:00:00

abstract：:The first highly specific knockouts of a microRNA, miR155, in mice result in multiple defects in adaptive immunity, and also show the feasibility of investigating at least some microRNAs by gene knockout. ...

journal_title：Genome biology

authors： Moffett HF,Novina CD

更新日期：2007-01-01 00:00:00

abstract：:A subset of X-linked genes escapes silencing by X inactivation and is expressed from both X chromosomes in mammalian females. Species-specific differences in the identity of these genes have recently been discovered, suggesting a role in the evolution of sex differences. Chromatin analyses have aimed to discover how g...

journal_title：Genome biology

authors： Berletch JB,Yang F,Disteche CM

更新日期：2010-01-01 00:00:00

abstract：BACKGROUND:Protein synthesis is tightly regulated and alterations to translation are characteristic of many cancers.Translation regulation is largely exerted at initiation through the eukaryotic translation initiation factor 4 F (eIF4F). eIF4F is pivotal for oncogenic signaling as it integrates mitogenic signals to amp...

journal_title：Genome biology

authors： Rubio CA,Weisburd B,Holderfield M,Arias C,Fang E,DeRisi JL,Fanidi A

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:The identification of genetic changes that confer drug resistance or other phenotypic changes in pathogens can help optimize treatment strategies, support the development of new therapeutic agents, and provide information about the likely function of genes. Elucidating mechanisms of phenotypic drug resistanc...

journal_title：Genome biology

authors： Dharia NV,Sidhu AB,Cassera MB,Westenberger SJ,Bopp SE,Eastman RT,Plouffe D,Batalov S,Park DJ,Volkman SK,Wirth DF,Zhou Y,Fidock DA,Winzeler EA

更新日期：2009-02-13 00:00:00

abstract：:We used scaled factorial moments to search for intermittency in the log expression ratios (LERs) for thousands of genes spotted on cDNA microarrays (gene chips). Results indicate varying levels of intermittency in gene expression. The observation of intermittency in the data analyzed provides a complimentary handle on...

journal_title：Genome biology

authors： Peterson LE,Lau K

更新日期：2002-05-29 00:00:00

abstract：:In a recent study, Petrovski and Goldstein reported that (non-Finnish) Europeans have significantly fewer nonsynonymous singletons in Online Mendelian Inheritance in Man (OMIM) disease genes compared with Africans, Latinos, South Asians, East Asians, and other unassigned non-Europeans. We use simulations of Exome Aggr...

journal_title：Genome biology

authors： Kessler MD,O'Connor TD

更新日期：2017-02-27 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:Candida glabrata is a pathogenic yeast of increasing medical concern. It has been regarded as asexual since it was first described in 1917, yet phylogenetic analyses have revealed that it is more closely related to sexual yeasts than other Candida species. We show here that the C. glabrata genome contains ma...

journal_title：Genome biology

authors： Wong S,Fares MA,Zimmermann W,Butler G,Wolfe KH

更新日期：2003-01-01 00:00:00

abstract：:A report on the 2004 meeting on Molecular Genetics of Bacteria and Bacteriophages, Cold Spring Harbor, USA, 25-29 August 2004. ...

journal_title：Genome biology

authors： Lawrence JG

更新日期：2004-01-01 00:00:00

abstract：:A genomic analysis of heterogeneous colorectal tumor samples has uncovered interactions between immunophenotype and various aspects of tumor biology, with implications for informing the choice of immunotherapies for specific patients and guiding the design of personalized neoantigen-based vaccines. ...

journal_title：Genome biology

authors： Havel JJ,Chan TA

更新日期：2015-03-31 00:00:00

abstract：BACKGROUND:Is it possible to construct an accurate and detailed subgene-level map of a genome using bacterial artificial chromosome (BAC) end sequences, a sparse marker map, and the sequences of other genomes? RESULTS:A sheep BAC library, CHORI-243, was constructed and the BAC end sequences were determined and mapped ...

journal_title：Genome biology

authors： Dalrymple BP,Kirkness EF,Nefedov M,McWilliam S,Ratnakumar A,Barris W,Zhao S,Shetty J,Maddox JF,O'Grady M,Nicholas F,Crawford AM,Smith T,de Jong PJ,McEwan J,Oddy VH,Cockett NE,International Sheep Genomics Consortium.

更新日期：2007-01-01 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：: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

authors： Adamson SI,Zhan L,Graveley BR

更新日期：2018-06-01 00:00:00

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：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：BACKGROUND:RNA sequencing has opened new avenues for the study of transcriptome composition. Significant evidence has accumulated showing that the human transcriptome contains in excess of a hundred thousand different transcripts. However, it is still not clear to what extent this diversity prevails when considering th...

journal_title：Genome biology

authors： Gonzàlez-Porta M,Frankish A,Rung J,Harrow J,Brazma A

更新日期：2013-07-01 00:00:00

abstract：BACKGROUND:Single-cell micro-metastases of solid tumors often occur in the bone marrow. These disseminated tumor cells (DTCs) may resist therapy and lay dormant or progress to cause overt bone and visceral metastases. The molecular nature of DTCs remains elusive, as well as when and from where in the tumor they origina...

journal_title：Genome biology

authors： Demeulemeester J,Kumar P,Møller EK,Nord S,Wedge DC,Peterson A,Mathiesen RR,Fjelldal R,Zamani Esteki M,Theunis K,Fernandez Gallardo E,Grundstad AJ,Borgen E,Baumbusch LO,Børresen-Dale AL,White KP,Kristensen VN,Van Loo P,

更新日期：2016-12-09 00:00:00

abstract：BACKGROUND:The chromodomain helicase DNA-binding family of ATP-dependent chromatin remodeling factors play essential roles during eukaryote growth and development. They are recruited by specific transcription factors and regulate the expression of developmentally important genes. Here, we describe an unexpected role in...

journal_title：Genome biology

authors： Yang R,Zheng Z,Chen Q,Yang L,Huang H,Miki D,Wu W,Zeng L,Liu J,Zhou JX,Ogas J,Zhu JK,He XJ,Zhang H

更新日期：2017-05-31 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：BACKGROUND:The genomic binding of CTCF is highly conserved across mammals, but the mechanisms that underlie its stability are poorly understood. One transcription factor known to functionally interact with CTCF in the context of X-chromosome inactivation is the ubiquitously expressed YY1. Because combinatorial transcri...

journal_title：Genome biology

authors： Schwalie PC,Ward MC,Cain CE,Faure AJ,Gilad Y,Odom DT,Flicek P

更新日期：2013-12-31 00:00:00

abstract：BACKGROUND:Targeted deep sequencing is increasingly used to detect low-allelic fraction variants; it is therefore essential that errors that constitute baseline noise and impose a practical limit on detection are characterized. In the present study, we systematically evaluate the extent to which errors are incurred dur...

journal_title：Genome biology

authors： Park G,Park JK,Shin SH,Jeon HJ,Kim NKD,Kim YJ,Shin HT,Lee E,Lee KH,Son DS,Park WY,Park D

更新日期：2017-07-21 00:00:00

abstract：:Protein kinases are critical to cellular signalling and post-translational gene regulation, but their biological substrates are difficult to identify. We show that cyclin-dependent kinase (CDK) consensus motifs are frequently clustered in CDK substrate proteins. Based on this, we introduce a new computational strategy...

journal_title：Genome biology

authors： Moses AM,Hériché JK,Durbin R

更新日期：2007-01-01 00:00:00