Decoding dosage compensation.

abstract：:Our knowledge on tissue- and disease-specific functions of human genes is rather limited and highly context-specific. Here, we have developed a method for the comparison of mRNA expression levels of most human genes across 9,783 Affymetrix gene expression array experiments representing 43 normal human tissue types, 68...

journal_title：Genome biology

authors： Kilpinen S,Autio R,Ojala K,Iljin K,Bucher E,Sara H,Pisto T,Saarela M,Skotheim RI,Björkman M,Mpindi JP,Haapa-Paananen S,Vainio P,Edgren H,Wolf M,Astola J,Nees M,Hautaniemi S,Kallioniemi O

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:Acute myeloid leukemia (AML) comprises a group of diseases characterized by the abnormal development of malignant myeloid cells. Recent studies have demonstrated an important role for aberrant transcriptional regulation in AML pathophysiology. Although several transcription factors (TFs) involved in myeloid ...

journal_title：Genome biology

authors： Chang LW,Payton JE,Yuan W,Ley TJ,Nagarajan R,Stormo GD

更新日期：2008-01-01 00:00:00

abstract：:Key components of the programmed cell death pathway are conserved between Caenorhabditis elegans, Drosophila melanogaster and humans. The search for additional homologs has been facilitated by the availability of the entire genomic sequence for each of these organisms. ...

journal_title：Genome biology

authors： Tittel JN,Steller H

更新日期：2000-01-01 00:00:00

abstract：BACKGROUND:Single-cell transcriptomics is rapidly advancing our understanding of the cellular composition of complex tissues and organisms. A major limitation in most analysis pipelines is the reliance on manual annotations to determine cell identities, which are time-consuming and irreproducible. The exponential growt...

journal_title：Genome biology

authors： Abdelaal T,Michielsen L,Cats D,Hoogduin D,Mei H,Reinders MJT,Mahfouz A

更新日期：2019-09-09 00:00:00

abstract：BACKGROUND:Chronic psychological stress is associated with accelerated aging and increased risk for aging-related diseases, but the underlying molecular mechanisms are unclear. RESULTS:We examined the effect of lifetime stressors on a DNA methylation-based age predictor, epigenetic clock. After controlling for blood c...

journal_title：Genome biology

authors： Zannas AS,Arloth J,Carrillo-Roa T,Iurato S,Röh S,Ressler KJ,Nemeroff CB,Smith AK,Bradley B,Heim C,Menke A,Lange JF,Brückl T,Ising M,Wray NR,Erhardt A,Binder EB,Mehta D

更新日期：2015-12-17 00:00:00

abstract：BACKGROUND:MicroRNAs (miRNAs) are a class of small, non-coding regulatory RNAs that regulate gene expression by guiding target mRNA cleavage or translational inhibition. So far, identification of miRNAs has been limited to a few model plant species, such as Arabidopsis, rice and Populus, whose genomes have been sequenc...

journal_title：Genome biology

authors： Yao Y,Guo G,Ni Z,Sunkar R,Du J,Zhu JK,Sun Q

更新日期：2007-01-01 00:00:00

abstract：BACKGROUND:Genome editing of malaria parasites is key to the generation of live attenuated parasites used in experimental vaccination approaches. DNA repair in Plasmodium generally occurs only through homologous recombination. This has been used to generate transgenic parasites that lack one to three genes, leading to ...

journal_title：Genome biology

authors： Singer M,Marshall J,Heiss K,Mair GR,Grimm D,Mueller AK,Frischknecht F

更新日期：2015-11-17 00:00:00

abstract：BACKGROUND:Bacillus subtilis is an organism of interest because of its extensive industrial applications, its similarity to pathogenic organisms, and its role as the model organism for Gram-positive, sporulating bacteria. In this work, we introduce a new genome-scale metabolic model of B. subtilis 168 called iBsu1103. ...

journal_title：Genome biology

authors： Henry CS,Zinner JF,Cohoon MP,Stevens RL

更新日期：2009-01-01 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：: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:In multicellular organisms, alternative splicing is central to tissue differentiation and identity. Unicellular protists lack multicellular tissue but differentiate into variable cell types during their life cycles. The role of alternative splicing in transitions between cell types and establishing cellular ...

journal_title：Genome biology

authors： Yeoh LM,Goodman CD,Mollard V,McHugh E,Lee VV,Sturm A,Cozijnsen A,McFadden GI,Ralph SA

更新日期：2019-08-01 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 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: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：:Nuclear pore complexes, the conduits for information exchange between the nucleus and cytoplasm, appear broadly similar in eukaryotes from yeast to human. Precisely how nuclear pore complexes regulate macromolecular and ionic traffic remains unknown, but recent advances in the identification and characterization of co...

journal_title：Genome biology

authors： Adam SA

更新日期：2001-01-01 00:00:00

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

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

abstract：BACKGROUND:X chromosome inactivation is a spectacular example of epigenetic silencing. In order to deduce how this complex system evolved, we examined X inactivation in a model marsupial, the tammar wallaby (Macropus eugenii). In marsupials, X inactivation is known to be paternal, incomplete and tissue-specific, and oc...

journal_title：Genome biology

authors： Al Nadaf S,Waters PD,Koina E,Deakin JE,Jordan KS,Graves JA

更新日期：2010-01-01 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：:An exciting recent study examining the methylation profile of human brain tissue implicates early-life epigenetic disruption in the neurodevelopmental origin of schizophrenia. ...

journal_title：Genome biology

authors： Ryan J,Saffery R

更新日期：2014-10-29 00:00:00

abstract：:A report on the 11th Cold Spring Harbor Laboratory/Wellcome Trust conference on Genome Informatics, Cold Spring Harbor Laboratories, New York, USA, November 2-5, 2011. ...

journal_title：Genome biology

authors： Chambers EV,Kindt AS,Semple CA

更新日期：2011-12-28 00:00:00

abstract：:Genomic and proteomic studies have identified hundreds of proteins from mitochondria. A recent study has added a functional twist to these systematic approaches and identified novel mitochondrial modifiers and regulators. ...

journal_title：Genome biology

authors： Dimmer KS,Rapaport D

更新日期：2008-01-01 00:00:00

abstract：:Trans-splicing is an unusual process in which two separate RNA strands are spliced together to yield a mature mRNA. We present a novel computational approach which has an overall accuracy of 82% and can predict 92% of known trans-splicing sites. We have applied our method to chromosomes 1 and 3 of Leishmania major, wi...

journal_title：Genome biology

authors： Gopal S,Awadalla S,Gaasterland T,Cross GA

更新日期：2005-01-01 00:00:00

abstract：:A report on the Epigenetic Engineering Meeting hosted by the Barts Institute of Cancer, held in London, UK, May 7, 2014. ...

journal_title：Genome biology

authors： Magnani L

更新日期：2014-01-01 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：: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：BACKGROUND:Rates of recombination can vary among genomic regions in eukaryotes, and this is believed to have major effects on their genome organization in terms of base composition, DNA repeat density, intron size, evolutionary rates and gene order. In highly self-fertilizing species such as Arabidopsis thaliana, howev...

journal_title：Genome biology

authors： Marais G,Charlesworth B,Wright SI

更新日期：2004-01-01 00:00:00

abstract：:Map based cloning in Arabidopsis thaliana can be a difficult and time-consuming process, specifically if the phenotype is subtle and scoring labour intensive. Here, we have re-sequenced the 120-Mb genome of a novel Arabidopsis clock mutant early bird (ebi-1) in Wassilewskija (Ws-2). We demonstrate the utility of seque...

journal_title：Genome biology

authors： Ashelford K,Eriksson ME,Allen CM,D'Amore R,Johansson M,Gould P,Kay S,Millar AJ,Hall N,Hall A

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:A large fraction of the human genome is attributable to L1 retrotransposon sequences. Not only do L1s themselves make up a significant portion of the genome, but L1-encoded proteins are thought to be responsible for the transposition of other repetitive elements and processed pseudogenes. In addition, L1s ca...

journal_title：Genome biology

authors： Szak ST,Pickeral OK,Landsman D,Boeke JD

更新日期：2003-01-01 00:00:00

abstract：:Levels of transcripts sharing microRNA response elements are co-regulated. These RNA-RNA interactions imply that combinations of microRNAs modulate cell-specific transcript networks. ...

journal_title：Genome biology

authors： Marques AC,Tan J,Ponting CP

更新日期：2011-11-21 00:00:00

abstract：:Single-cell transcriptomics requires a method that is sensitive, accurate, and reproducible. Here, we present CEL-Seq2, a modified version of our CEL-Seq method, with threefold higher sensitivity, lower costs, and less hands-on time. We implemented CEL-Seq2 on Fluidigm's C1 system, providing its first single-cell, on-...

journal_title：Genome biology

authors： Hashimshony T,Senderovich N,Avital G,Klochendler A,de Leeuw Y,Anavy L,Gennert D,Li S,Livak KJ,Rozenblatt-Rosen O,Dor Y,Regev A,Yanai I

更新日期：2016-04-28 00:00:00