Oberseminar 'Bioinformatics and Computational Biology' (WS 12/13)

Type: Seminar
Lecturer: Burkhard Rost
Time:   Thursday, 13:30 - 14:15
Room MI 01.09.034
Language English

Talks WS 2012/13

Mar 19  Marc Brehme
             A Conserved Core Chaperome Network Safeguards Proteostasis in Aging and Neurodegenerative diseases
             &
             Frank Wallrapp
             In-silico genome mining for novel enzymes: A sequence/structure-based strategy for prediction, discovery and profiling of enzymatic function
             !Tuesday 10am!

Feb 27  Zosia Gasik
            Chromosomal duplication in yeasts under heat stress
            ! Wednesday, 1 pm !

Feb 22  Christiane Gasperi
            Comparison of protein families for different organisms
            ! Friday, 11 am !

Jan 24   Christian Schäfer

Jan 17   Eva Reisinger 
            Understanding molecular mechanism: analysis of the SLAC1 protein family

Dec 6    Verena Link 
            An evaluation of SNP and functional site analysis methods based on structural and evolutionary inference approaches

Nov 22   Maria Kalemanov 
             Building PSSH2 - new comprehensive database of alignments between protein sequences and tertiary structures
             &
             
Veit Höhn                                                                           
             In-depth comparison of predicted high- and low-impact SNPs from the 1000 Genomes Project

Nov 8     Vivien Klose
             Predicting protein function through gene ontology

Oct 11    Peter Hönigschmid
             Improvement of DNA- and RNA-Protein Binding Prediction

Talks SS 2012

Sept 27  Peter Maximilian Hirschbeck
             Developing a serious game for bioinformatics: DNA sequencing

Aug 30   Tanya Goldberg 
             LocTree2 Predicts Localization for all Domains of Life

July 5     Andreas Nägele 
             Large-scale bayesian network structure learning

June 28  Tanya Goldberg 
             Sequence based annotation of bacterial Type III effector proteins
             &
             Maria Kalemanov
             HHblits and PSI-BLAST evaluation

June 21  Juan Miguel Cejuela
             Automatic protein name recognition

May 31   Shen Wei
             Extraction of Binding Residues from the Protein Data Bank

May 24   Benjamin Wellmann
             Evaluation of sequence-to-structure alignments

May 3     Thomas Hopf
             Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing

April 26  Bertram Müller-Myhsok
             
Genetic studies in unipolar depression: susceptibility, pharmacogenetics and epistasis


 

Talks WS 2011/2012

Mar 8     Paul Horton
             Excavating human NUMTs
             [Abstract]

Jan 26    Marco Punta
             Starting at Pfam: learning curve, challenges, development, research
             &           

             Marco de Vivo
             Dual-target rational drug design for treating inflammation

Jan 19    Maximilian Hecht
             Improve predictions of the functional effect of non-synonymous SNPs

Dec 20   Juan de Toro
             Prediction of carbohydrate-binding residues from amino acid sequence

Dec 8     Dominik Achten
             Prediction of carbohydrate-binding residues from amino acid sequence

Nov 10   Tanya Goldberg
             Predict Subcellular Localization in All Kingdoms 

Oct 27    Yannick Mahlich
             Sole usage of amino acid propensities results in robust performance for predicting
             structural change in protein fragments 

Oct 20    Jonas Reeb
             Evaluation of methods to predict transmembrane alpha-helices in proteins

Oct 13    Juan Miguel Cejuela
             Automatic Protein Name Recognition

Oct 6      Hedwig Kurka
              In silico Analysis of Clostridia difficile Strains Regarding Increased Virulence

Talks SS 2011

Sep 22   Juan de Toro Martin
             Adaptive response of pancreatic alpha cells and hepatic carbohydrate metabolism
              during chronic nutritional deprivation

Sep 15   Eibe Frank
             Multi-instance Learning in the WEKA software

July 7     Ariane Böhm
             Optimizing Graph Clusters for Local Classification and Regression Models

June 16  Tobias Hamp
             Quarterny Structure Prediction

June 9    Andrea Schafferhans
             (SNP) Sequence Annotation Pipeline(s) - Content and Visualisation

May 26   Christian Schäfer
             On the attempts of structural change prediction upon point mutation -
              Are we there yet?

May 19   Laszlo Kajan
             Rost Lab resources: will I reimplement the wheel? -
              how to find and share reusable components in the Rost Lab

May 12   Markus Schmidberger
             17 months at Rostlab and what the future brings

April 14  Arthur Dong
             Interaction of Neandertal SNPs

Large-scale protein flexibility analysis of single nucleotide polymorphisms using molecular dynamics simulations

Marco Offman, Rostlab, TUM and LRZ

Molecular Dynamics (MD) simulation can be used as a powerful prediction method in various fields of biologically-related sciences. We use MD to investigate differences between wiltype and mutant proteins in respect to their flexibility and eventually functionality. Nowadays, being able to run complex and time consuming simulations, such as MD, is becoming less of a problem as more and cheaper computational resource become available. Nevertheless, the automation of MD simulations and analysis of the produced results is still very complex and time consuming. Therefore, we have decided to create an automatic pipeline that uses the MD simulation package GROMACS and other software to fully automate the whole process. This pipeline consists of three separate main scripts: 1. AGroS: Automatic Gromacs Simulations; 2. GroSA: Gromacs Simulation Analysis; 3. AGroSA: Automatic Gromacs Statistical Analysis.
 

Excavating human NUMTs

Paul Horton, AIST, CBRC, Japan

It is well known that remnants of partial or whole copies of mitochondrial DNA (NUMT)s are found in nuclear genomes.  Since whole genome sequences have become available, many bioinformatics studies have identified putative NUMTs and from those attempted to infer the factors involved in NUMT creation.

These studies conclude that NUMTs represent randomly chosen regions of the mitochondrial genome.  There is less consensus regarding the nuclear insertion sites of NUMTs - previous studies have discussed the possible role of retrotransposons, but some recent ones have reported no correlation or even anti-correlation between NUMT sites and retrotransposons. These studies have generally defined NUMT sites using BLAST with default parameters.

We analyze a redefined set of human NUMTs, computed with a carefully considered protocol.  We discover that the inferred insertion points of NUMTs have a strong tendency to have high predicted DNA curvature, occur in experimentally defined nucleosome depleted regions, and often occur immediately adjacent to A+T oligomers.  We also show clear evidence that their flanking regions are indeed rich in retrotransposons.  Finally we show that parts of the mitochondrial genome D-loop are under-represented as a source of NUMTs in primate evolution.

References:
J. Tsuji, et alMammalian NUMT insertion is non-randomNAR, under revision.