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Tuesday, September 23, 2014
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Integrated In Silico Analysis of NGS Prostate Cancer Data via High-Resolution RNA-Seq Analysis
Sandeep Sanga , Antoaneta Vladimirova, Aubree Hoover

The goal: To get novel insights into the mechanisms of prostate adenocarcinoma by leveraging next generation sequencing (NGS) data, particularly human transcriptome data, through in silico data analysis and interpretation by Ingenuity’s IPA® software. CLC Genomics Workbench and CLC Genomics Server helped us assess short read RNA-Seq data.

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Gene Expression Profiling of Archived FFPE Samples
Silvia Rüberg, Sabine Classen, Jana Ciomperlik, Dirk Dietrich, Ines Dischinger, Alena Böttcher, Sabrina Schmitz and Bernhard Gerstmayer

According to the BBMRI (Biobanking and Biomolecular Resources Research Infrastructure) about 8,000,000 formalin-fixed paraffin-embedded (FFPE) samples derived from a multitude of different diseases have been collected in medical centers and biobanks all over Europe during the last decades.

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Differential Expression and Localization of Dicer1 and Ovarian Steroid Hormone Receptors in Human Fallopian Tubes
Ruijin Shao et al.

Dicer1 expression is upregulated in cell-specific fashion in human Fallopian tubes during ovulation. The stage-dependent expression of Dicer1 and its correlation with ERa, ERß2, and PRB mRNA suggests that tubal Dicer1 helps regulate tubal expression of steroid hormone receptors in a cycle-dependent manner and may contribute to tubal transport in humans.

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An improved data processing pipe-line for comprehensive H-NMR and X/MS -omics data
R. J. O. Torgrip, K. M. Åberg, E. Alm

In the post acqusition analysis of comprehensive -omics data the pre-processing pipe-line is crucial to extract the maximum possible amount of information from the data. Here we show a processing pipe-line for (1D)H-NMR and (2D)X/MS data comprising; feature detection, inter-sample feature alignment and internal-standard free normalization that outperforms today’s state-of-the-art processing schemes.

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Alignment of 1H-NMR data using a Generalized Fuzzy Hough Transform
Erik Alm, Leonard Csenki, Ralf J.O. Torgrip, K. Magnus Åberg, Lars I. Nord, Ina Schuppe-Koistinen and Johan Lindberg

In metabolic profiling, multivariate data analysis techniques are used to interpret 1D 1H–NMR data. Multivariate data analysis techniques require that peaks are located in the same variables in every spectrum – this requirement is not met in native NMR spectra. Current state-of-the-art alignment algorithms are unable to align peaks when the spatial order of the peaks changes. We present the Fuzzy Generalized Hough Transform alignment which solves the alignment problem.

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ROLE OF IRF-8 IN THE INTERFACE OF MELANOMA TUMOR CELL-IMMUNE SYSTEM INTERACTION.
Fabrizio Mattei, Giovanna Schiavoni, Massimo Spada, Francesca Spadaro and Lucia Gabriele

Interferon-regulatory factor-8 is essential for differentiation and function of dendritic cells and thus for the induction of competent immune responses. Here, we investigated the role of IRF-8 in affecting immune response against melanoma. Our results reveal a critical role of IRF-8 in controlling melanoma growth and suggest that IRF-8-mediated antitumor activity is the result of a coordinated action between DC-mediated immune response and the tumor suppressor function of IRF-8.

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Software for Genomic/Epigenomic Research
A.S.Tanas, V.V.Shkarupo, E.B.Kuznetsova, D.V.Zaletayev, V.V. Strelnikov

We present two computer programs: 1) AIMS in silico - a suggestion tool for Amplification of Intermethylated Sites experimental design and results analysis; and 2) PeakPick – a tool to view & analyse capillary electrophoregrams Our computer software is intended to standardize AIMS applications and to turn it into one of the principal approaches towards cancer methylomes studies as well as towards diagnostics in oncology, including early screening.

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Geneset-based cancer survival analysis: On the non-uniform distributiuon of p-values under the null hypothesis
Esteban Czwan, Benedikt Brors, David Kipling

Although null p-values are assumed to be uniformly distributed in gene expression experiments, the actual distribution often deviates from the assumed distribution. This can incorrectly associate the biology of a geneset with cancer prognosis in geneset-based survival studies. To assess the implications of this, a geneset-based method was developed. This method empirically approximates the distribution of null p-values and tests whether predefined sets of biologically-related genes are associate

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Clinical Outcomes and Emerging Challenges after 5 years of ART in Khayelitsha, South Africa
Gilles Van Cutsem1, Katherine Hilderbrand1,2, David Coetzee2,3, Carol Cragg3, Eric Goemaere1 & Andrew Boulle2,3

One of the first primary care antiretroviral treatment programs in Africa shows good patient outcomes at 5 years. Saturation of services has led to increased losses to follow-up.

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Showing Results 51 - 60 of 138
Scientific News
How Gene Expression Affects Facial Expressions
Researchers from USC have demonstrated how a mutation in TBX1 causes facial deformities associated with DiGeorge Syndrome.
Blood Test May Help Determine Psychosis Risk
A study led by University of North Carolina at Chapel Hill researchers represents an important step forward in the accurate diagnosis of people who are experiencing the earliest stages of psychosis.
How Epigenetic Memory is Passed Across Generations
Researchers traced markers of gene repression through cell division and showed that both sperm and eggs transmit a memory of gene repression to embryos.
Spontaneous Mutations in Key Brain Gene are a Cause of Autism
In addition, there is a direct link between TBR1 and FOXP2, a well-known language-related protein, researchers report.
Asuragen’s Xpansion Interpreter® Test Study of 1,040 Transmissions of Fragile X Alleles
Study reveals personalized risks for expansion from parent to child.
Genetics Reveals Patients Susceptible to Drug-induced Pancreatitis
Doctors have discovered that patients with a particular genetic variation are four times more likely to develop pancreatitis if they are prescribed a widely used group of drugs.
Blood Test To Diagnose Depression
Test identifies nine blood markers tied to depression; predicts who will benefit from therapy.
Genetic Testing for Prostate Cancer
Genetic testing can identify men at six-fold increased risk of prostate cancer.
Zebrafish Genes Linked To Human Respiratory Diseases
Genes have been discovered which may be synonymous with the genes for developing hair-like structures in the human airway.
Ancient Vertebrate Uses Familiar Tools
Sea lamprey studies show remarkably conserved gene expression patterns in jawless versus jawed vertebrates.
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