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*100 Semi-supercentenarians and older as a proposed sample set for the Archon Genomics X PRIZE Validation Protocol* Nature Precedings
Thomas Perls; Nir Barzilai.
The "Archon Genomics X PRIZE Validation Protocol":http://precedings.nature.com/documents/5731/version/1 has been posted in part to solicit comments from the scientific community. Here, we suggest 100 subjects age >=105 years as the source of DNAs for the competition.

Tipo: Manuscript Palavras-chave: Biotechnology; Genetics & Genomics; Bioinformatics; Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/5756/version/1
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12x coverage 454/Sanger Hybrid Assembly of Cucumber (Cucumis sativus L. cv.Borszczagovski) genome - the most efficient way to begin post genomic era Nature Precedings
Rafał Wóycicki; Justyna Witkowicz; Magdalena Pawełkowicz; Ewa Siedlecka; Wojciech Gutman; Wojciech Pląder; Anna Seroczyńska; Mieczysław Śmiech; Katarzyna Niemirowicz-Szczytt; Stanisław Karpiński; Stefan Malepszy; Zbigniew Przybecki.
New sequencing technologies make it possible to achieve genome sequence fast and cheap. Since the assembly step of such next generation reads is still not well standardized it is the most cumbersome part of sequencing projects. 
We present here approaches undertaken on the way to the draft assembly the cucumber (Cucumis sativus L. cv. Borszczagowski) genome done with the use of 8x unpaired and 4x paired (3 Kbp) pyrosequenced 454 XLR Titanium reads, together BAC library ends fragments (12,7x physical coverage). Two different assembly approaches, namely Celera and Celera/Arachne were finally used. The Celera result was 15’196 contigs of 197 Mbp length and N50 27’086 bp and 4’157 scaffolds of 224 Mbp length...
Tipo: Poster Palavras-chave: Biotechnology; Genetics & Genomics; Bioinformatics; Plant Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/5466/version/1
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2011 German Escherichia coli O104:H4 outbreak: Alignment-free whole-genome phylogeny by feature frequency profiles Nature Precedings
Man Kit Cheung; Lei Li; Wenyan Nong; Hoi Shan Kwan.
Accuracy of SNP-based whole-genome phylogeny reconstruction relies heavily on quality of sequence alignment which is particularly hindered by poorly assembled genomes. Alignment-free methods might provide additional insights. Here, we constructed a whole-genome phylogeny of 10 isolates from the current German E. coli outbreak against 30 existing E. coli genomes as well as that of a historical EHEC isolate using the alignment-free feature frequency profile method. Our results revealed a high similarity among E. coli isolates from the current outbreak and the historical EHEC being the most closely related isolate sequenced thus far.
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6109/version/2
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2011 German Escherichia coli outbreak: Alignment-free whole-genome phylogeny by feature frequency profiles Nature Precedings
Man Kit Cheung; Lei LI; Wenyan Nong; Hoi Shan Kwan.
Accuracy of SNP-based whole-genome phylogeny reconstruction relies heavily on quality of sequence alignment which is particularly hindered by poorly assembled genomes. Alignment-free methods might provide additional insights. Here, we constructed a whole-genome phylogeny of 9 E.coli isolates from the 2011 German outbreak against existing E. coli genomes using the alignment-free feature frequency profile method. In addition, we looked for gene elements that distinguish the outbreak group from the other E. coli strains and possibly accounted for the emergence of the outbreak isolates using the distinguishing feature analysis.
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6109/version/1
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2011 German Escherichia coli outbreak: Prophage analysis of close-assembled TY2482 against 55989 using PHAST Nature Precedings
Man Kit Cheung; Lei LI; Wenyan Nong; Hoi Shan Kwan.
Using the Hiseq data of the German E. coli outbreak isolate TY2482, preliminary prophage analyses have been performed by some researchers previously. With the closed assembly of the same isolate being available, another round of analysis might help in resolving questions that remain unclear due to the incompleteness of the dataset.
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics.
Ano: 2011 URL: http://precedings.nature.com/documents/6110/version/1
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9aaTAD Prediction result (2006) Nature Precedings
Martin Piskacek.
Recently reported, 9aaTAD transcription factors p53, VP16, MLL/ALL, E2A, HSF1, NF-IL6, NFAT1 and NF-kB interact directly with the general coactivator CBP/p300 aside from already referred TAF9. All four domains of CBP/p300 - KIX, TAZ1, TAZ2 and IBiD provide multiple interactions with 9aaTADs, e.g. p53. Annotation of predicted 9aa TAD using Pattern search ScanProsite on ExPASy and relevant experimental data are listed.
Tipo: Manuscript Palavras-chave: Genetics & Genomics.
Ano: 2009 URL: http://precedings.nature.com/documents/3984/version/1
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9aaTADs mimic DNA to interact with a pseudo-DNA Binding Domain KIX of Med15 (Molecular Chameleons) Nature Precedings
martin piskacek.
The KIX-domain of Gal11/MED15 was shown to interact with short transactivation domain of Pdr1 and Oaf1 (12 and 9 amino acids respectively) annotated to 9aaTAD family. Reported NMR data revealed a surprising sequence similarity of KIX domain and basic-leucine zipper (bZIP).
Tipo: Manuscript Palavras-chave: Genetics & Genomics.
Ano: 2009 URL: http://precedings.nature.com/documents/3939/version/1
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A Critical Evaluation of Clinical Trials in Cancer and Pharmacogenomics Nature Precedings
I. C. Baianu.
A critical overview of recent clinical trials in cancer is presented focused on signaling pathways blockers or inhibitors with a view to developing successful clinical trials employing personalized cancer therapies. Rational, pharmacogenomic strategies in cancer trials should be adopted that include specific molecular targeting based on adequate data for, and detailed modeling of, cancer cell genomes, modifications of cancer signaling pathways and epigenetic mechanisms. Novel translational oncogenomics research is rapidly expanding through the application of highly sensitive and specific advanced technology, research findings and computational tools and complex models to both pharmaceutical and clinical problems. Multiple sample analyses from several...
Tipo: Manuscript Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics & Genomics; Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2012 URL: http://precedings.nature.com/documents/7052/version/1
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A Database for TSSs of Human MicroRNAs Nature Precedings
Malay Bhattacharyya; Sanghamitra Bandyopadhyay.
MicroRNAs (miRNAs) are small endogeneous non-coding RNAs of about 22nt length. These short RNAs regulate the expression of mRNAs by hybridizing with their 3'-UTRs or by translational repression. They have been shown to take crucial roles in many biological processes. Many of the current studies are focused over how mature miRNAs regulate mRNAs, even though there is very limited knowledge about their transcriptional loci. Primary miRNAs (pri-miRs) are first transcribed from the DNA, followed by the formation of precursor miRNA (pre-miR) by endonucleases activity, which finally produces mature miRNAs. Unfortunately, the identification of the loci of pri-miRs, and the associated information about transcription start sites (TSSs) and promoters is...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2012 URL: http://precedings.nature.com/documents/6832/version/1
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A database of orthologous exons in primates for comparative analysis of RNA-seq data Nature Precedings
Ran Blekhman.
RNA-seq technology facilitates the study of gene expression at the level of individual exons and transcripts. Moreover, RNA-seq enables unbiased comparative analysis of expression levels across species. Such analyses typically start by mapping sequenced reads to the appropriate reference genome before comparing expression levels across species. However, this comparison requires prior knowledge of orthology at the exon level. With this in mind, I constructed a database of orthologous exons across three primate species (human, chimpanzee, and rhesus macaque). The database facilitates cross-species comparative analysis of exon- and transcript-level regulation. A web application allowing for an easy database query: http://giladlab.uchicago.edu/orthoExon/
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2012 URL: http://precedings.nature.com/documents/7054/version/1
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A Draft Sequence of the Puerto Rican Parrot Genome (Amazona vittata) – a Genome Project funded by a Local Community Effort Nature Precedings
Taras K. Oleksyk.
The genome of the Puerto Rican parrot (Amazona vittata) has been sequenced and assembled in an international collaboration supported by many individual donations from the people of Puerto Rico. This is a critically endangered endemic bird, the only surviving native parrot species in the territory of the United States, and the first parrot belonging to the large genus Amazona to have its genome sequenced and assembled. A genome of one A. vittata female was sequenced resulting in a total of almost 42.5 billion nucleotide bases equivalent to 26.89X average coverage depth. After filtering out the short fragments (<500bp), the assembly resulted in 259,423 short fragment library contigs, half of them (N50) of at least 6,983 bp in length, with a...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6552/version/1
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A Drosophila systems model of withdrawal from chronic pentylenetetrazole relevant in post-epileptogenesis Nature Precedings
Priyanka Singh; Farhan Mohammad; Abhay Sharma.
Rodent kindling induced by pentylenetetrazole (PTZ) is an established model of epileptogenesis and antiepileptic drug (AED) testing. Recently, a Drosophila systems model has been described in which chronic PTZ causes a decreased climbing speed in adult males on 7th day. Some AEDs ameliorate development of this locomotor deficit. Time-series of microarray expression profiles of heads of flies treated with PTZ has been found to resemble transcriptomic alterations associated with epileptogenesis. In the fly model, withdrawal from seven day long PTZ treatment causes an increased climbing speed on 7th consequent day. Here, we present a systems model of the post-PTZ withdrawal regime. Unlike AED-untreated individuals, flies treated with any of the five AEDs...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3447/version/1
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A Formal Ontology of Sequences Nature Precedings
Robert Hoehndorf; Janet Kelso; Heinrich Herre.
The Sequence Ontology is an OBO Foundry ontology that provides categories of sequences and sequence features that are applied to the annotation of genomes. To facilitate interoperability with other domain ontologies and to provide a foundation for automated inference, we provide here an axiom system for the Sequence and Junction categories in first- and second-order predicate logics.
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3537/version/1
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A Genome-Wide Analysis Reveals Significant Overlap of Transcription and DNA Repair in Stationary Phase Yeast Nature Precedings
Aviv de Morgan; Leonid Brodsky; Yefim Ronin; Eviatar Nevo; Abraham Korol; Yechezkel Kashi.
The association between transcription and DNA repair is acknowledged as a player in the generation of mutations in a non-random fashion in prokaryotes and eukaryotes. Previous studies demonstrated that the transcription complex is capable of directing DNA repair to sites of transcription. This process is especially important to growth-arrested cells, in which many DNA repair capacities are diminished; it may also lead to mutations preferentially in transcribed genes. Using microarray analysis of growth-arrested yeast cultures, we demonstrated on a genomic scale, the co-localization of a DNA-turnover marker, indicative of DNA-repair-associated DNA synthesis, with genes persistently transcribed during stationary phase. This may serve as a clue regarding the...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Evolutionary Biology.
Ano: 2008 URL: http://precedings.nature.com/documents/1543/version/1
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A Latent Variable Approach to Multivariate Quantitative Trait Loci Nature Precedings
Bob O'Hara; Päivi Komulainen; Outi Savolainen; Mikko J. Sillanpää.
A novel approach based on latent variable modelling is presented for the analysis of multivariate quantitative and qualitative trait loci. The approach is general in the sense that it enables the joint analysis of many kinds of quantitative and qualitative traits (including count data and censored traits) in a single modelling framework. In the framework, the observations are modelled as functions of latent variables, which are then affected by quantitative trait loci. Separating the analysis in this way means that measurement errors in the phenotypic observations can be included easily in the model, providing robust inferences. The performance of the method is illustrated using two real multivariate datasets, from barley and Scots pine.
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2010 URL: http://precedings.nature.com/documents/4137/version/1
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A Linked Data Approach to Help Identify Therapeutic Targets for Cancer Nature Precedings
Helena Deus.
Cancer is still one of the leading causes of death in the developed world. To address this problem, the US National Institutes of Health (NIH) has launched The Cancer Genome Atlas (TCGA), a large scale systematic approach to characterize tumor samples from 20 cancer types and approximately 10,000 donor patients by using multiple high-throughput approaches. 

Multidisciplinary projects such as TCGA and related projects across Europe aim at identifying cancer “driver” mutations to be used as therapeutic targets or diagnostic tests. Extracting and aggregating the knowledge necessary to identify such mutations remains a challenge primarily due to the need to reliably integrate the experimental datasets...
Tipo: Poster Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2011 URL: http://precedings.nature.com/documents/6169/version/1
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A Micropropagation, Molecular and Physiochemical Analysis of Canola Brassica napus L. From Seeds Nature Precedings
Israr Khan; Muhammad Shuaib; Sikandar Khan; Muhammad Amir Zia; Haji Akbar.
Canola is important for its oil, anticarcinogenic phytochemicals and low saturated fat content and has wide scope for further improvement through genetic transformations. Micropropagation is the practice of rapidly multiplying stock plant material to produce a large number of disease free progeny plants, using modern asceptic plant tissue culture methods and also to conserve germ plasm. A combination of auxin and cytikinin and a shock on growth regulator free medium is used for micropropagation. Molecular and physiochemical analysis done to know variation in seeds protein content and electric conductivity.
Tipo: Manuscript Palavras-chave: Biotechnology; Genetics & Genomics; Molecular Cell Biology; Plant Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4781/version/2
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A multiple-instance scoring method to predict tissue-specific cis-regulatory motifs and regions Nature Precedings
Jin Gu.
Transcription is the central process of gene regulation. In higher eukaryotes, the transcription of a gene is usually regulated by multiple cis-regulatory regions (CRRs). In different tissues, different transcription factors bind to their cis-regulatory motifs in these CRRs to drive tissue-specific expression patterns of their target genes. By combining the genome-wide gene expression data with the genomic sequence data, we proposed multiple-instance scoring (MIS) method to predict the tissue-specific motifs and the corresponding CRRs. The method is mainly based on the assumption that only a subset of CRRs of the expressed gene should function in the studied tissue. By testing on the simulated datasets and the fly muscle dataset, MIS can identify true...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/4038/version/1
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A network-based signaling mechanism of cancer development and progression Nature Precedings
Edwin Wang.
We conducted a comprehensive analysis of a manually curated human signaling network containing 1634 nodes and 5089 signaling regulatory relations by integrating cancer-associated genetically and epigenetically altered genes. We find that cancer mutating genes are enriched in positive signaling regulatory loops, whereas the cancer-associated methylating genes are enriched in negative signaling regulatory loops. We further characterized an overall picture of the cancer-signaling architectural and functional organization. From the network, we extracted an oncogene-signaling map, which contains 326 nodes, 892 links and the interconnections of mutated and methylated genes. The map can be decomposed into 12 topological regions or oncogene-signaling blocks,...
Tipo: Presentation Palavras-chave: Cancer; Genetics & Genomics; Bioinformatics.
Ano: 2008 URL: http://precedings.nature.com/documents/2238/version/1
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A normalization technique for next generation sequencing experiments Nature Precedings
Günter Klambauer; Karin Schwarzbauer; Andreas Mayr; Sepp Hochreiter.
Next generation sequencing (NGS) are these days one of the key technologies in biology. NGS' cost effectiveness and capability of finding the smallest variations in the genome makes them increasingly popular. For studies aiming at genome assembly, differences in read count statistics do not affect the outcome. However, these differences bias the outcome if the goal is to identify structural DNA characteristics like copy number variations (CNVs). Thus a normalization step must removed such random read count variations subsequently read counts from different experiments are comparable. Especially after normalization the commonly used assumption of Poisson read count distribution in windows on the chromosomes is more justified. Strong deviations of...
Tipo: Poster Palavras-chave: Genetics & Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2010 URL: http://precedings.nature.com/documents/4710/version/2
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