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Teaching II

Tentative Program of the Winter 2017 Research Seminar on Next-Generation Sequencing / Screening support by bioinformatics

Thu/Fri Feb 16 and 17, 2017, Research Seminar, planned schedule:

Thu Feb 16
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9-10:30 Intro talks: Georg Fuellen (on synergy), Steffen Moeller (on data workflows)
11-12:30 Result presentations: Stephan Struckmann on fibrosis data, Mathias Ernst on embryology and/or leukemia data, Mohamed Hamed on leukemia (or neuro) data
14-15:30 PhD project presentations: Yvonne Gladbach on leukemia (or neuro) data, Sarah Fischer on Lincs data
16-17 Student talks: Christopher Pohl and Vivian Retzlaff on the latest L1000 paper

Fri Feb 17
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9-17h Lectures by Leila Taher on R and NGS.

Tentative Program of the Summer 2016 Research Seminar on Next-Generation Sequencing

Tue Aug 18

10:00-12:00 Georg Fuellen: Introductory Presentation

14:00-16:00 Presentations by others from the VIP project team

Wed Aug 19
** Date/time may still change **

10:00-11:00 Georg Fuellen: Addenda
11:00-12:00 Steffi Falk:

13:00-13:30 Eike Strathmann / Thomas Werner (by skype)
13:30-14:30 Leukemia and MitoAge
15:30-16:30 Fibrosis (venue: Augenklinik)

Fri Aug 21

10:00-12:00 Wrap up, Research strategy discussion

Mon 29.2. 16-18h, Die 1.3. 9-15h, Besprechungsraum IBIMA, Guest Event: Prof. Dr. Leila Taher, Erlangen: "Genome Analysis: Genome Rearrangement, Clustering and Motiv Analysis".

Das IBIMA bietet Promotionsthemen für Medizinstudierende an, die Interesse an Datenauswertungen haben.

Wenn Sie beispielsweise Interesse an der Auswertung von Hochdurchsatzdaten wie Genomdaten (SNP-Daten und copy number variations), Genexpressionsdaten (Next-Generation Sequencing und Microarrays) oder Proteomdaten haben, bitte kontaktieren Sie Prof. Georg Fuellen (fuellen uni-rostock.de). Für Kollaborationen mit einer Reihe von Instituten und Kliniken suchen wir DoktorandInnen (für Dr. med.), die bei Computeranalysen (ähnlich den in der Vorlesung im QB vorgestellten) von realen Datensätzen mithelfen möchten. Auch Arbeiten mit theoretischen und praktischen Anteilen (Laborarbeit) sind möglich. Das Schreiben mindestens einer Originalarbeit (in englischer Sprache), welche die Resultate der Analysen beschreibt, sollte dabei Teil Ihrer Promotionsbemühungen sein.

Spezifische Promotionsprojekte in der Bioinformatik

Project I:

Use (and ultimately develop) computational biology approaches to describe the logic of regulatory sequences underlying cellular differentiation. For this purpose, we will integrate multiple layers of regulatory information, including spatiotemporal gene expression patterns (microarrays, RNA-seq), genome-wide maps for transcription factor binding (ChIP-seq), and open chromatin profiling data (DNa-seq, FAIRE-seq).

Project II:

Use of Hi-C data to identify gene targets of regulatory sequences. We will develop probabilistic models integrating sequence features, such conservation level, putative transcription factor binding sites, and distance to the gene promoter, as well as high-throughput data from RNA-seq, ChIP-seq, and DNa-seq from public databases.

Project III:

Network-based approaches to identify putative functional mutations in the non-coding genome. We will combine data from GWAS with functional genomics and systems biology approaches to study how mutations in regulatory sequences can contribute to disease.

Program of the Winter 2015 Research Seminar on Small Molecule Effects and Gene Expression

Tue March 3:

10:00 h Organizing... (Lunch ordering...?)

10:00 h-13:00 h Georg Fuellen: Introductory Presentation (incl. one break)

 

13:00-14:30 Lunch

 

14:30 -15:00    Johann Mähr: Protein Networks as Logic Functions in Development and Cancer

15:00-15:30     Markus Pieth: Kinase inhibitors in CML

15:30-16:00     Stephan Struckmann: Identify Transcriptional Disease Effects by Dysrecgulation, or by Conservation Across Tissues: Two Interesting Approaches

 

16:30-17:00     Mathias Ernst: Comparative drug pair screening across multiple gliosblastoma cell lines & Analysis of epistatic interaction data: Using means and variances in different ways

17:00-17:30     Yang Du: 1, Network-based Ranking - Explore Google’s PageRank™ in biological networks; 2. Mechanistic network models in Systems Biology and Toxicology - More on Selventa’s RCR

17:30-18:00     Gregor Warsow: NetPathMiner; "Network target for screening synergistic drug combinations"

 

Wed March 4:

10:00               Organizing... (Lunch ordering...?)

10:00-10:30     Georg Fuellen: Addenda

10:30-11:00     Further co-worker presentations

 

11:00-12:00     Lunch

 

12:00-12:30     Soft-skills lab

12:30-13:00     Wrap-up

 

14:00               (Internal project meetings)

 

Thu March 5:

(Internal project meetings) ++++ Lunch ++++ Research strategy discussion

Fri March 6:

Cell biology of podocytes, lymphocytes and fibroblasts ++++ Lunch ++++ Wrap-Up