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Biology inspires engineeringEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A report of the Cold Spring Harbor Laboratory/Wellcome Trust Meeting on Engineering Principles in Biology, Cambridge, UK, 14-16 October 2009. (Source: Genome Biology)
Source: Genome Biology - November 19, 2009 Category: Genetics & Stem Cells Source Type: journals

CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic featuresEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Our work reveals several key differences among CTCF occupancy-based classes and suggests a critical, yet distinct functional role played by low-occupancy sites. (Source: Genome Biology)
Source: Genome Biology - November 18, 2009 Category: Genetics & Stem Cells Authors: Kobby EssienSebastien VigneauSofia AprelevaLarry SinghMarisa BartolomeiSridhar Hannenhalli Source Type: journals

Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seqEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We find that ChIP-seq can be used not only to create gene regulatory maps but also to predict molecular interactions and to inform on the mechanisms for common quantitative variation. (Source: Genome Biology)
Source: Genome Biology - November 17, 2009 Category: Genetics & Stem Cells Authors: Mehdi MotallebipourAdam AmeurMadhu Sudhan Reddy BysaniKalicharan PatraOla WallermanJonathan MangionMelissa BarkerKevin McKernanJan KomorowskiClaes Wadelius Source Type: journals

BioGPS: an extensible and customizable portal for organizing and querying gene annotation resourcesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Online gene annotation resources are indispensable for analysis of genomics data. However, the landscape of these online resources is highly fragmented, and scientists often visit dozens of these sites for each gene in a candidate gene list. Here, we introduce BioGPS (http://biogps.gnf.org), a centralized gene portal for aggregating distributed gene annotation resources. Moreover, BioGPS embraces the principle of community intelligence, enabling any user to easily and directly contribute to the BioGPS platform. (Source: Genome Biology)
Source: Genome Biology - November 17, 2009 Category: Genetics & Stem Cells Authors: Chunlei WuCamilo OrozcoJason BoyerMarc LegliseJames GoodaleSerge BatalovChristopher HodgeJames HaaseJeff JanesJon HussAndrew Su Source Type: journals

Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arraysEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We describe a method for automatic detection of absolute segmental copy numbers and genotype status in complex cancer genome profiles measured by single nucleotide polymorphism (SNP) arrays. The method is based on pattern recognition of segmented and smoothed copy number and allelic imbalance profiles. Assignments were verified by DNA indexes of primary tumors and karyotypes of cell lines. The method performs well even for poor quality data, low tumor content, and highly rearranged tumor genomes. (Source: Genome Biology)
Source: Genome Biology - November 10, 2009 Category: Genetics & Stem Cells Authors: Tatiana PopovaElodie ManieDominique Stoppa-LyonnetGuillem RigaillEmmanuel BarillotMarc-Henri Stern Source Type: journals

Construction of a high-resolution genetic linkage map and comparative genome analysis for a reef-building coral Acropora milleporaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our study develops a framework that will be essential for future studies of adaptation in coral and it also provides an important resource for future genome sequence assembly and for comparative genomics studies on the evolution of metazoan genome structure. (Source: Genome Biology)
Source: Genome Biology - November 9, 2009 Category: Genetics & Stem Cells Authors: Shi WangLingling ZhangEli MeyerMikhail Matz Source Type: journals

High resolution discovery and confirmation of copy number variants in 90 Yoruba NigeriansEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Background: Copy number variants (CNVs) account for a large proportion of genetic variation in the genome. The initial discoveries of long (>100kb) CNVs in normal healthy individuals were made on BAC arrays and low resolution oligonucleotide arrays. Subsequent studies that used higher resolution microarrays and SNP genotyping arrays detected the presence of large numbers of CNVs that are (Source: Genome Biology)
Source: Genome Biology - November 9, 2009 Category: Genetics & Stem Cells Authors: Hajime MatsuzakiPei-Hua WangJing HuRich RavaGlenn Fu Source Type: journals

Serum-dependent transcriptional networks identify distinct functional roles for H-Ras and N-Ras during initial stages of the cell cycle.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Our observations confirm the notion of an absolute requirement for different peaks of Ras activity during the initial stages of the cell cycle and document the functional specificity of H-Ras and N-Ras during those processes. (Source: Genome Biology)
Source: Genome Biology - November 6, 2009 Category: Genetics & Stem Cells Authors: Esther CastellanoCarmen GuerreroAlejandro NunezJavier De Las RivasEugenio Santos Source Type: journals

The dog days of autumnEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Greg's two dogs are impressed that only a few genes control the different lengths, growth patterns and curl of their coats. (Source: Genome Biology)
Source: Genome Biology - November 4, 2009 Category: Genetics & Stem Cells Source Type: journals

Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L)Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Enrichment of siRNAs in ovules and fibers suggests active small RNA metabolism and chromatin modifications during fiber development, whereas general repression of miRNAs in fibers correlates with upregulation of a dozen validated miRNA targets encoding transcription and phytohormone response factors, including the genes found to be highly expressed in cotton fibers. Rapid and dynamic changes in siRNAs and miRNAs may contribute to ovule and fiber development in allotetraploid cotton. (Source: Genome Biology)
Source: Genome Biology - November 4, 2009 Category: Genetics & Stem Cells Authors: Mingxiong PangAndrew WoodwardVikram AgarwalXueying GuanMisook HaVanitharani RamachandranXuemei ChenBarbara TriplettDavid StellyZ Jeffrey Chen Source Type: journals

Comparing cellular proteomes by mass spectrometryEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Mass spectrometry and cryo-electron tomography together enable the determination of the absolute and relative abundances of proteins and their localization, laying the groundwork for comprehensive systems analyses of cells. (Source: Genome Biology)
Source: Genome Biology - October 28, 2009 Category: Genetics & Stem Cells Source Type: journals

Runaway repeats force expansion of the Phytophthora infestans genomeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Sequencing of the genome of the potato late blight pathogen Phytophthora infestans provides insight into genome structure and evolution within this genus of plant pathogenic oomycetes. (Source: Genome Biology)
Source: Genome Biology - October 27, 2009 Category: Genetics & Stem Cells Source Type: journals

The SR protein familyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
SummaryThe processing of pre-mRNAs is a fundamental step required for the expression of most metazoan genes. Members of the family of serine/arginine (SR)-rich proteins are critical components of the machineries carrying out these essential processing events, highlighting their importance in maintaining efficient gene expression. SR proteins are characterized by their ability to interact simultaneously with RNA and other protein components via an RNA recognition motif (RRM) and through a domain rich in arginine and serine residues, the RS domain. Their functional roles in gene expression are surprisingly diverse, ranging f...
Source: Genome Biology - October 27, 2009 Category: Genetics & Stem Cells Source Type: journals

Watching proteins in motionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A report of the 23rd Protein Symposium 'Proteins in Motion', Boston, USA, 23-27 July 2009. (Source: Genome Biology)
Source: Genome Biology - October 27, 2009 Category: Genetics & Stem Cells Source Type: journals

Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutationsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The 82 base-pair deletion found in the rph-pyrE operon of many endpoints may function to relieve a pyrimidine biosynthesis defect present in MG1655. In contrast, a variety of regulators acquire mutations in the different endpoints, suggesting flexibility in overcoming regulatory challenges in the adaptation. (Source: Genome Biology)
Source: Genome Biology - October 21, 2009 Category: Genetics & Stem Cells Authors: Tom ConradAndrew JoyceM Kenyon ApplebeeChristian BarrettBin XieYuan GaoBernhard Palsson Source Type: journals

An Optimization Framework for Unsupervised Identification of Rare Copy Number Variation from SNP Array DataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Copy number variants (CNVs) have roles in human disease, and DNA microarrays are important tools for identifying them. In this paper, we frame CNV identification as an objective function optimization problem. We apply our method to data from hundreds of samples, and demonstrate its ability to detect CNVs at a high level of sensitivity without sacrificing specificity. Its performance compares favorably with currently available methods and it reveals previously unreported gains and losses. (Source: Genome Biology)
Source: Genome Biology - October 21, 2009 Category: Genetics & Stem Cells Authors: Gokhan YavasMehmet KoyuturkMeral OzsoyogluMeetha GouldThomas LaFramboise Source Type: journals

Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcriptsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Targeted RNA-Seq combines next-generation sequencing with capture of sequences from a relevant subset of a transcriptome. When testing by capturing sequences from a tumor cDNA library by hybridization to oligonucleotide probes specific for 467 cancer-related genes, this method showed high selectivity, improved mutation detection enabling discovery of novel chimeric transcripts, and provided RNA expression data. Thus, targeted RNA-Seq produces an enhanced view of the molecular state of a set of 'high interest' genes. (Source: Genome Biology)
Source: Genome Biology - October 15, 2009 Category: Genetics & Stem Cells Authors: Joshua LevinMichael BergerXian AdiconisPeter RogovAlexandre MelnikovTimothy FennellChad NusbaumLevi GarrawayAndreas Gnirke Source Type: journals

Transcriptome analysis of functional differentiation between haploid and diploid cells of Emiliania huxleyi, a globally significant photosynthetic calcifying cellEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: This study permitted the identification of genes likely involved in diploid-specific biomineralization, haploid-specific motility, and transcriptional control. Greater transcriptome richness in diploid cells suggests they may be more versatile for exploiting a diversity of rich environments whereas haploid cells are intrinsically more streamlined. (Source: Genome Biology)
Source: Genome Biology - October 14, 2009 Category: Genetics & Stem Cells Authors: Peter von DassowHiroyuki OgataIan ProbertPatrick WinckerCorinne Da SilvaStephane AudicJean-Michel ClaverieColomban de Vargas Source Type: journals

Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levelsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We describe approaches for the accurate identification of nucleotide and structural variation in the genomes of vertebrate experimental organisms, and show how these techniques can be applied to help prioritize candidate genes within quantitative trait loci. (Source: Genome Biology)
Source: Genome Biology - October 12, 2009 Category: Genetics & Stem Cells Authors: Ian SudberyJim StalkerJared SimpsonThomas KeaneAlistair RustMatthew HurlesKlaudia WalterDee LynchLydia TeboulSteve BrownHeng LiZemin NingJoseph NadeauColleen CronigerRichard DurbinDavid Adams Source Type: journals

NeMeSys: a biological resource for narrowing the gap between sequence and function in the human pathogen Neisseria meningitidisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: By improving our capacity to understand gene function in an important human pathogen, NeMeSys is expected to contribute to the ongoing efforts aimed at understanding a prokaryotic cell comprehensively and eventually to the design of new therapies. (Source: Genome Biology)
Source: Genome Biology - October 8, 2009 Category: Genetics & Stem Cells Authors: Christophe RusniokDavid VallenetStephanie FloquetHelen EwlesCoralie Mouze-SoulamaDaniel BrownAurelie LajusCarmen BuchrieserClaudine MediguePhilippe GlaserVladimir Pelicic Source Type: journals

A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genomeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Nucleosomes have position-specific functions in controlling gene expression. A complete systematic genome-wide reference map of absolute and relative nucleosome positions is needed to minimize potential confusion when referring to the function of individual nucleosomes (or nucleosome-free regions) across datasets. We compiled six high-resolution genome-wide maps of Saccharomyces cerevisiae nucleosome positions from multiple labs and detection platforms, and report new insights. Data downloads, reference position assignment software, queries, and a visualization browser are available online http://atlas.bx.psu.edu/. (Source: Genome Biology)
Source: Genome Biology - October 7, 2009 Category: Genetics & Stem Cells Authors: Cizhong JiangB Franklin Pugh Source Type: journals

Molecular networks involved in mouse cerebral corticogenesis and spatio-temporal regulation of Sox4 and Sox11 novel antisense transcripts revealed by transcriptome profilingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We report validated gene expression profiles that have implications for understanding the association between differentially expressed transcripts, novel targets and related disorders pertaining to cerebral corticogenesis. The study reports, for the first time, spatio-temporally regulated Sox4 and Sox11 antisense transcripts in brain, neural stem/progenitor cells and P19 cells suggesting they have an important role in cerebral corticogenesis and neuronal/glial cell differentiation. (Source: Genome Biology)
Source: Genome Biology - October 1, 2009 Category: Genetics & Stem Cells Authors: King-Hwa LingChelsee HewittTim BeissbarthLavinia HydeKakoli BanerjeePike-See CheahPing CannonChristopher HahnPaul ThomasGordon SmythSeong-Seng TanTim ThomasHamish Scott Source Type: journals

An issue to rememberEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Thumbing through a recent copy of a journal reveals unexpected riches. (Source: Genome Biology)
Source: Genome Biology - September 28, 2009 Category: Genetics & Stem Cells Source Type: journals

Common variants in polygenic schizophreniaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Common variant single-nucleotide polymorphisms at the MHC locus have recently been associated with schizophrenia. Together with known associations with rare copy-number variants affecting many genes, this reveals the highly polygenic etiology of the disease. (Source: Genome Biology)
Source: Genome Biology - September 28, 2009 Category: Genetics & Stem Cells Source Type: journals

The netrin protein familyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
SummaryThe name netrin is derived from the Sanskrit Netr, meaning 'guide'. Netrins are a family of extracellular proteins that direct cell and axon migration during embryogenesis. Three secreted netrins (netrins 1, 3 and 4), and two glycosylphosphatidylinositol (GPI)-anchored membrane proteins, netrins G1 and G2, have been identified in mammals. The secreted netrins are bifunctional, acting as attractants for some cell types and repellents for others. Receptors for the secreted netrins include the Deleted in Colorectal Cancer (DCC) family, the Down's syndrome cell adhesion molecule (DSCAM), and the UNC-5 homolog family: Un...
Source: Genome Biology - September 28, 2009 Category: Genetics & Stem Cells Source Type: journals

Joining forces in the quest for orthologsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Better orthology-prediction resources would be beneficial for the whole biological community. A recent meeting discussed how to coordinate and leverage current efforts. (Source: Genome Biology)
Source: Genome Biology - September 28, 2009 Category: Genetics & Stem Cells Source Type: journals

Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacteriumEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: A comparison of a series of 027 isolates showed that some of these genes appeared to have been gained by 027 strains over the past two decades. This study provides genetic markers for the identification of 027 strains and offers a unique opportunity to explain the recent emergence of a hypervirulent bacterium. (Source: Genome Biology)
Source: Genome Biology - September 24, 2009 Category: Genetics & Stem Cells Authors: Richard StablerMiao HeLisa DawsonMelissa MartinEsmeralda ValienteCraig CortonTrevor LawleyMohammed SebaihiaMichael QuailGraham RoseDale GerdingMaryse GibertMichel PopoffJulian ParkhillGordon DouganBrendan Wren Source Type: journals

High resolution transcriptome maps for wild-type and NMD mutant C. elegans through developmentEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We generated a high-resolution transcriptome map for C. elegans and used it to identify endogenous targets of NMD. We find that these transcripts arise principally through splicing errors, strengthening the prevailing view that splicing and NMD are highly interlinked processes. (Source: Genome Biology)
Source: Genome Biology - September 23, 2009 Category: Genetics & Stem Cells Authors: Arun RamaniAndrew NelsonPhilipp KapranovIan BellThomas GingerasAndrew Fraser Source Type: journals

Many LINE1 elements contribute to the transcriptome of human somatic cellsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: A large number of different L1 element sites are expressed in human somatic tissues, and this expression varies among different individuals. Paradoxically, few elements were tagged at high frequency, indicating that the majority of expressed L1s are transcribed at low levels. Based on our preliminary expression studies of a limited number of elements in a single family, we predict a significant degree of inter-individual transcript-level polymorphism in this class of sequence. (Source: Genome Biology)
Source: Genome Biology - September 21, 2009 Category: Genetics & Stem Cells Authors: Sanjida RangwalaLili ZhangHaig Kazazian Source Type: journals

Simultaneous alignment of short reads against multiple genomesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Genome resequencing with short reads generally relies on alignments against a single reference. GenomeMapper supports simultaneous mapping of short reads against multiple genomes by integrating related genomes (e.g., individuals of the same species) into a single graph structure. It constitutes the first approach for handling multiple references, and introduces representations for alignments against complex structures. Demonstrated benefits include access to polymorphisms that cannot be identified by alignments against the reference alone. Download GenomeMapper at http://1001genomes.org. (Source: Genome Biology)
Source: Genome Biology - September 16, 2009 Category: Genetics & Stem Cells Authors: Korbinian SchneebergerJorg HagmannStephan OssowskiNorman WarthmannSandra GesingOliver KohlbacherDetlef Weigel Source Type: journals

Gene networks in Drosophila melanogaster: integrating experimental data to predict gene functionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Here we present the the first genome-wide functional gene network in Drosophila melanogaster. The network enables the exploration, mining, and reanalysis of experimental data, as well as the interpretation of new data. The inferred annotations provide testable hypotheses of previously uncharacterized genes. (Source: Genome Biology)
Source: Genome Biology - September 15, 2009 Category: Genetics & Stem Cells Authors: James CostelloMehmet DalkilicScott BeasonJeff GehlhausenRupali PatwardhanSumit MiddhaBrian EadsJusten Andrews Source Type: journals

Reverse-engineering Arabidopsis thaliana transcriptional network under changing environmental conditionsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: These data suggest that A. thaliana has evolved a high connectivity in terms of transcriptional regulations among cellular functions involved in response and adaptation to changing environments; while gene networks constitutively expressed or less related to stress response are characterized by a lower connectivity. Taken together, these findings suggest conserved regulatory strategies that have been selected during the evolutionary history of this Eukaryote. (Source: Genome Biology)
Source: Genome Biology - September 14, 2009 Category: Genetics & Stem Cells Authors: Javier CarreraGuillermo RodrigoAlfonso JaramilloSantiago Elena Source Type: journals

De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We report a method for assembling draft genome sequences of eukaryotic organisms that integrates sequence information from different sources, and demonstrate its effectiveness by assembling a ~32.5 Mb draft genome sequence for the forest pathogen Grosmannia clavigera, an ascomycete fungus. We also developed a method for assessing draft assemblies using Illumina paired end read data and demonstrate how we are using it to guide future sequence finishing. Our results demonstrate that eukaryotic genome sequences can be accurately assembled by combining Illumina, 454 and Sanger sequence data. (Source: Genome Biology)
Source: Genome Biology - September 10, 2009 Category: Genetics & Stem Cells Authors: Scott DiGuistiniNancy LiaoDarren PlattGordon RobertsonMichael SeidelSimon ChanT Roderick DockingInanc BirolRobert HoltMartin HirstElaine MardisMarco MarraRichard HamelinJorg BohlmannColette BreuilSteven Jones Source Type: journals

Identification of secondary targets of N-containing bisphosphonates in mammalian cells via parallel competition analysis of the barcoded yeast deletion collectionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The dataset obtained from the yeast screen was validated in a mammalian system, allowing the discovery of new biological processes involved in the cellular response to nitrogen-containing bisphosphonates and opening up opportunities for development of new anticancer drugs. (Source: Genome Biology)
Source: Genome Biology - September 9, 2009 Category: Genetics & Stem Cells Authors: Nicoletta BiviMilena RomanelloRichard HarrisonIan ClarkeDavid HoyleLuigi MoroFulvia OrtolaniAntonella BonettiFranco QuadrifoglioGianluca TellDaniela Delneri Source Type: journals

A global survey identifies novel upstream components of the Ath5 neurogenic networkEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our analysis establishes functional groups of genes controlling different regulatory phases, including the onset of Ath5 expression at cell-cycle exit and its down-regulation prior to terminal RGC differentiation. These results extent the current model of the GRN controlling retinal neurogenesis in vertebrates. (Source: Genome Biology)
Source: Genome Biology - September 6, 2009 Category: Genetics & Stem Cells Authors: Marcel SourenJuan Ramon Martinez-MoralesPanagiota MakriBeate WittbrodtJoachim Wittbrodt Source Type: journals

Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage networkEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We integrate 16 genomic features to construct an evidence-weighted functional-linkage network (FLN) comprising 21,657 human genes. The FLN is used to prioritize candidate genes for 110 diseases, and to reliably disclose hidden associations between disease pairs having dissimilar phenotypes, such as hypercholesterolemia and Alzheimer's disease. Many of these disease-disease associations are supported by epidemiology, but with no previous genetic basis. Such associations can drive novel hypotheses on molecular mechanisms of diseases and therapies. (Source: Genome Biology)
Source: Genome Biology - September 2, 2009 Category: Genetics & Stem Cells Authors: Bolan LinghuEvan SnitkinZhenjun HuYu XiaCharles DeLisi Source Type: journals

The promise and reality of personal genomicsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The publication of the highest-quality and best-annotated personal genome yet tells us much about sequencing technology, something about genetic ancestry, but still little of medical relevance. (Source: Genome Biology)
Source: Genome Biology - September 1, 2009 Category: Genetics & Stem Cells Source Type: journals

Predicting drug side-effects by chemical systems biologyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
New approaches to predicting ligand similarity and protein interactions can explain unexpected observations of drug inefficacy or side-effects. (Source: Genome Biology)
Source: Genome Biology - September 1, 2009 Category: Genetics & Stem Cells Source Type: journals

mRNA expression profiles show differential regulatory effects of microRNAs between ER+ and ER- breast cancerEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Regulatory effect score is a promising indicator to measure microRNAs' inhibitory effect. Most microRNAs exhibit higher RE-scores in ER- than in ER+ samples, suggesting that they have stronger inhibitory effect in ER- breast cancers. (Source: Genome Biology)
Source: Genome Biology - August 31, 2009 Category: Genetics & Stem Cells Authors: Chao ChengXuping FuPedro AlvesMark Gerstein Source Type: journals

New tricks for an old-favorite modelEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A report of the 24th International Conference on Yeast Genetics and Molecular Biology, Manchester, UK, 19-24 July 2009. (Source: Genome Biology)
Source: Genome Biology - August 31, 2009 Category: Genetics & Stem Cells Source Type: journals

Nation of twitsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Gregory Petsko bemoans the rise of the Twittering classes. (Source: Genome Biology)
Source: Genome Biology - August 27, 2009 Category: Genetics & Stem Cells Source Type: journals

Assisted assembly: how to improve a de novo genome assembly by using related speciesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We describe a new assembly concept, where a genome assembly with low sequence coverage, either throughout the genome or locally, due to cloning bias, is considerably improved through assisted assembly. In the assisted assembly process a related reference genome is used to validate and leverage the information captured in the low coverage reads. We show that the information provided by aligning the WGS reads of the target against a reference genome can be effectively used to substantially improve the assembly of the target, both by covering more of the genome (5 to 15%) and long range connectivity (in some cases more than 5...
Source: Genome Biology - August 26, 2009 Category: Genetics & Stem Cells Authors: Sante GnerreEric LanderKerstin Lindblad-TohDavid Jaffe Source Type: journals

Depletion of T-cell intracellular antigen (TIA)-proteins promotes cell proliferationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Collectively, our findings suggest a role for TIA-proteins as cellular sensors, which modulate gene expression control at transcriptional and post-transcriptional levels coupling cell proliferation responses and metabolic homeostasis to cell survival and growth. (Source: Genome Biology)
Source: Genome Biology - August 25, 2009 Category: Genetics & Stem Cells Authors: Raquel ReyesJose AlcaldeJose Izquierdo Source Type: journals

The claudinsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
SummaryThe claudin multigene family encodes tetraspan membrane proteins that are crucial structural and functional components of tight junctions, which have important roles in regulating paracellular permeability and maintaining cell polarity in epithelial and endothelial cell sheets. In mammals, the claudin family consists of 24 members, which exhibit complex tissue-specific patterns of expression. The extracellular loops of claudins from adjacent cells interact with each other to seal the cellular sheet and regulate paracellular transport between the luminal and basolateral spaces. The claudins interact with multiple pro...
Source: Genome Biology - August 25, 2009 Category: Genetics & Stem Cells Source Type: journals

Reprogramming the epigenome during germline and seed developmentEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Gene silencing by DNA methylation and small RNAs is globally reconfigured during gametogenesis in Arabidopsis, affecting transposon activity, gene regulation and development. (Source: Genome Biology)
Source: Genome Biology - August 23, 2009 Category: Genetics & Stem Cells Source Type: journals

Community-wide analysis of microbial genome sequence signaturesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: An important conclusion is that shared environmental pressures and interactions among coevolving organisms do not obscure genome signatures in acid mine drainage communities. Thus, genome signatures can be used to assign sequence fragments to populations, an essential prerequisite if metagenomics is to provide ecological and biochemical insights into the functioning of microbial communities. (Source: Genome Biology)
Source: Genome Biology - August 20, 2009 Category: Genetics & Stem Cells Authors: Gregory DickAnders AnderssonBrett BakerSheri SimmonsBrian ThomasA Pepper YeltonJillian Banfield Source Type: journals

Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Genomic regulatory blocks are chromosomal regions spanned by long clusters of highly conserved noncoding elements devoted to long-range regulation of developmental genes, often immobilizing other, unrelated genes into long-lasting syntenic arrangements. Synorth, (http://synorth.genereg.net/), is a web resource for exploring and categorizing the syntenic relationships in genomic regulatory blocks across multiple genomes, tracing their evolutionary fate after teleost whole genome duplication at the level of genomic regulatory block loci, individual genes, and their phylogenetic context. (Source: Genome Biology)
Source: Genome Biology - August 20, 2009 Category: Genetics & Stem Cells Authors: Xianjun DongDavid FredmanBoris Lenhard Source Type: journals

Improved base calling for the Illumina Genome Analyzer using machine learning strategiesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present Ibis (Improved base identification system), an accurate, fast and easy-to-use base caller that significantly reduces the error rate and increases the output of usable reads. Ibis is faster and more robust with respect to chemistry and technology than other publicly available packages. Ibis is freely available under the GPL from http://bioinf.eva.mpg.de/Ibis/. (Source: Genome Biology)
Source: Genome Biology - August 13, 2009 Category: Genetics & Stem Cells Authors: Martin KircherUdo StenzelJanet Kelso Source Type: journals

Virus-mediated mRNA decay by hyperadenylationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Degradation of cellular mRNAs during Kaposi's sarcoma-associated herpesvirus infection is associated with hyperadenylation of transcripts and a relocalization of cytoplasmic poly(A)-binding proteins to the nucleus. (Source: Genome Biology)
Source: Genome Biology - August 10, 2009 Category: Genetics & Stem Cells Source Type: journals

Malaria genomics meets drug-resistance phenotyping in the fieldEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A report of the 2nd Wellcome Trust Conference on Genomic Epidemiology of Malaria, Hinxton, UK, 14-17 June 2009. (Source: Genome Biology)
Source: Genome Biology - August 10, 2009 Category: Genetics & Stem Cells Source Type: journals