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Monday - 12 May 2014

09:00 a.m. Welcome
09:15 a.m. Roza Parol-Kryger: Low coverage re-sequencing in sugar beet for anchoring assembly sequences to genome position\\Tatjana Iljasenko: Overview of methods used for the analysis of rare variant associations in genome wide association studies\\Anna Kuosmanen: LORAS: Using approximate seeds in the alignment of long DNA reads
10:45 a.m. Coffee Break
11:15 a.m. Nadia Kamal: Identification of flowering time control genes in grapevine\\Wolfgang Kopp: Computation of the position specific score distribution for first order background models\\Anna Ramisch: Compressed sensing in disease classification
12:45 a.m. Lunch Break
01:45 p.m. Benedikt Löwes: Computational determination of new functional RNAs from viral genomes\\Nina Luhmann: Ancestral reconstruction and scaffolding of ancient contigs in a phylogenetic framework\\Benedikt Brink: Polyomics visualization
03:15 p.m. Coffee Break
03:45 p.m. Invited Talk: apl. Prof. Dr. Jörn Kalinowski: Why we sequence – a biologist’s perspective
04:30 p.m. End of Talks
05:30 p.m. City Tour, Start at the Sparrenburg
07:30 p.m. Dinner: Nichtschwimmer Bielefeld

Tuesday - 13 May 2014

10:00 a.m. Nicole Althermeler: Deep groundwater metagenomics - computational analysis of microbial communities and metabolic pathways\\Tina Zekic: Direct comparison of metatranscriptomic and metagenomic sequential data\\Madis Rumming: MeGeMeBase - Data warehouse for metadata-based analysis of bacterial and archaeal genomes in metagenome studies
11:30 a.m. Coffee Break
12:00 a.m. Invited Talk: Prof. Dr. Alice McHardy (Düsseldorf, Germany): Inference of genotype-phenotype relationships
12:45 a.m. Lunch Break
01:45 p.m. Anna Cichonska: Predicting quantitative binding affinities between drug compounds and protein kinaeses\\Huibin Shen: Molecular fingerprint prediction with multiple kernel learning\\Bjørn Bredesen: Motif-SVM: Modelling local motif occurrence combinatorics using support vector machines
03:15 p.m. Coffee Break
03:45 p.m. Daniel Valenzuela: Pan-genome indexing for variation calling\\Guillaume Holley: Efficient implementation of an annotated de-Bruijn graph for pan-genome storage\\Andrey Akinshin: Symmetry in gene network models
05:30 p.m. End of Talks, official end of the workshop
09:00 p.m. tba

Why we sequence – a biologist’s perspective

by apl. Prof. Dr. Jörn Kalinowski

Since the 1970ies, DNA sequencing is used to decipher the genetic inventories of organisms, starting with single genes and pen-and-paper “bioinformatics”. Massive technical advances in sequencing today allow to take deep looks into natural diversity and gene regulation, making bioinformatics an essential part of genomics and transcriptomics research. The presentation aims to give a biologist’s perspective on some scientific challenges that can be addressed by sequencing and presents examples ranging from useful (biotechnological) or harmfull (pathogenic) microorganisms up to microbial communities and to microbial transcriptomes, including its still inherent challenges for bioinformatics.

Inference of genotype-phenotype relationships

by Prof. Dr. Alice McHardy

Next generation sequencing allows to extensively survey the genome-wide genetic diversity of microbial communities, as well as populations from all domains of life. A major challenge is the development of computational methods for hypothesis generation and basic computational analysis of these large-scale data sets. I will present our recent work on computational methods for metagenome analysis. We are working on methods for predicting and characterizing microbial phenotypes as well as identifying the relevant protein repertoire for a given phenotype, focusing hereby on microbial plant biomass degradation.

brew/program.txt · Last modified: 2016/05/11 18:32 (external edit)