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N2N - CS seminar - Mark van de Wiel - Empirical Bayes in Genomics - 11/12@15h

You are cordially invited to the following seminar organized jointly by N2N (From Nucleotides to Networks) and CS (Center for Statistics - Adolphe Quetelet Seminar Series).

"How to learn from a lot: Empirical Bayes in Genomics" by Dr. Mark van de Wiel.

The seminar is scheduled on Thursday December 11 at 15h00 at Monasterium PoortAckere, room Sint-Lucas, Oude Houtlei 56, 9000 Gent (prior to the PhD defence of Bie Verbist on "Low-Frequency Variant Detection in Viral Populations using Massively Parallel Sequencing Data").

N2N was involved in the genome sequence of the orchid Phalaenopsis equestris

Orchidaceae is one of the most diverse plant families and renowned for its spectacular flowers and other reproductive and ecological adaptations. Here, we present the first whole genome sequence of a tropical epiphytic orchid, Phalaenopsis equestris, a frequently used parent species for orchid breeding. Over 1.0 Gb of sequence could be assembled, which corresponds to approximately 93% of the estimated total genome size, and 29,431 protein-coding genes were predicted.

An update on LNCipedia: a database for annotated human lncRNA sequences

The human genome is pervasively transcribed, producing thousands of non-coding RNA transcripts. The majority of these transcripts are long non-coding RNAs (lncRNAs) and novel lncRNA genes are being identified at rapid pace. To streamline these efforts, we created LNCipedia, an online repository of lncRNA transcripts and annotation. Here, we present LNCipedia 3.0 (http://www.lncipedia.org), the latest version of the publicly available human long non-coding RNA (lncRNA) database.

Accepted paper: PLAZA 3.0: an access point for plant comparative genomics

Comparative sequence analysis has significantly altered our view on the complexity of genome organization and gene functions in different kingdoms. PLAZA 3.0 is designed to make comparative genomics data for plants available through a user-friendly web interface. Structural and functional annotation, gene families, protein domains, phylogenetic trees, and detailed information about genome organization can easily be queried and visualized.

accepted paper: SNP-guided identification of monoallelic DNA-methylation events from enrichment-based sequencing data

Monoallelic gene expression is typically initiated early in the development of an organism. Dysregulation of monoallelic gene expression has already been linked to several non-Mendelian inherited genetic disorders. In humans, DNA-methylation is deemed to be an important regulator of monoallelic gene expression, but only few examples are known. One important reason is that current, cost-affordable truly genome-wide methods to assess DNA-methylation are based on sequencing post enrichment.

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary

In 2009, the Van de Peer lab proposed a correlation between whole genome duplications in plants and the Cretaceous-Paleogene extinction event, the most recent mass extinction, which wiped out 70% of all life on earth, including the dinosaurs. Since this finding was met with some skepticism, the researchers have revisited this hypothesis, using 40 whole genome sequences and the most sophisticated evolutionary models and dating techniques available, and ... the story still stands.

N2N in Nature Comm.: Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations

The HEK293 human cell lineage is widely used in cell biology and biotechnology. Here we use whole-genome resequencing of six 293 cell lines to study the dynamics of this aneuploid genome in response to the manipulations used to generate common 293 cell derivatives, such as transformation and stable clone generation (293T); suspension growth adaptation (293S); and cytotoxic lectin selection (293SG). Remarkably, we observe that copy number alteration detection could identify the genomic region that enabled cell survival under selective conditions (i.c. ricin selection).

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