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Advanced Seminar / Oberseminar

Type Seminar
Lecturer Burkhard Rost
Time (Typically) Wednesday, 11:00 - 12:30
Room MI 01.09.034
Language English

 

Talks SoSe 2014- SoSe 2017


Oct 09  IDP Presentation Ghalia Rehawi
         

        ! Wednesday 11:00 am !

Sep 18  Theresa Wirth presents her Master thesis
         

        ! Wednesday 11:00 am !

Sep 11  Drillon Avdiu, 3 minutes talk
         

        ! Wednesday 11:00 am !

Sep 11  Tatjana Ammer final Master`s thesis presentation
         

        ! Wednesday 11:00 am !

Sep 11  Smith Agarwal final Master`s thesis presentation
         

        ! Wednesday 11:00 am !

Aug 20  Group Meeting: Franz Mader presents his Thesis "Predicting the Success of Insurance Submissions"
         

        ! Tuesday 2:00 pm !

Jul 10  Max MIller and Issar Arab
         

        ! Wednesday 11:00 am !

Jul 03  Tobias Piffrader
         

        ! Wednesday 11:00 am !

Jun 26  Smith Agarwal
         

        ! Wednesday 11:00 am !

Jun 26  Nathalie Gerstner
         

        ! Wednesday 11:00 am !

May 15  Theresa presents the current state of her thesis
         

        ! Wednesday 11:00 am !

Apr 24  Konstantin Weißenow presents Master`s Thesis
         

        ! Wednesday 11:00 am !

Apr 10  Michael Menden presents his work
         

        ! Wednesday 11:00 am !

Apr 03  Master thesis Guido Kubach
         

        ! Wednesday 11:00 am !

Apr 03  Bachelor thesis Anna Reithmeir
         

        ! Wednesday 11:00 am !

Apr 03  Franz Mader
         

        ! Wednesday 9:00 am !

Feb 20  Smith Agarwal
         

        ! Wednesday 11:00 am !

Nov 21  Karoline Lutz presents her Bachelor`s Thesis
         

        ! Wednesday 11:00 am !

Nov 07  Guido Kubach introduces his Master`s thesis Using Ancestral Sequence Reconstruction to improve prediction methods​
         

        ! Wednesday 11:00 am !

Oct 24  Alexandra Morscher presents her Master`s Thesis
         

        ! Wednesday 11:00 am !

Oct 24  Jiajun Qiu
         

        ! Wednesday 9:00 am !

Oct 17  Ziga Avsec presents Kipoi
         

        ! Wednesday 11:00 am !

Oct 17  Theresa's Master Thesis Introduction Talk
         

        ! Wednesday 11:00 am !

Sep 12  Leo Grupa presents his Bachelor`s thesis
         

        ! Wednesday 11:00 am !

Sep 12  Linus Scheibenreif
         

        ! Wednesday 9:00 am !

Jun 27  Anton Smirnov's Master Thesis Introduction
         

        ! Wednesday 11:00 am !

Jun 13  Anton Smirnov's Master Thesis Introduction
         

        ! Wednesday 11:00 am !

Jan 24  Roc Reguant presents his Master`s thesis
         

        ! Wednesday 11:00 am !

Jan 18  maybe today after the first lecture: Dmitrii Neachev presents his Master`s thesis
         

        ! Thursday 11:30 am !

Jan 10  Vasileios Magiogious presents his Master`s thesis
         

        ! Wednesday 11:00 am !

Nov 22  Alexander Galtsev thesis presentation
         

        ! Wednesday 9:00 am !

Nov 15  Michael Heinzinger presents Master`s thesis
         

        ! Wednesday 9:00 am !

Oct 25  Luisa Santus Bachelor`s Thesis Talk
         

        ! Wednesday 11:00 am !

Oct 25  Christian Dallago presents his Master`s thesis
         

        ! Wednesday 9:00 am !

Oct 04  Valérie Marot presents her Bachelor`s thesis
         

        ! Wednesday 11:00 am !

Sep 27  Madhukar Sollepura Prabhu Shankar presents his Master`s thesis
         

        ! Wednesday 9:00 am !

Sep 27  Tanzeem`s presents her Master`s thesis
         

        ! Wednesday 9:00 am !

Jul 12  Joel Daon presents his Bachelor`s thesis
         

        ! Wednesday 11:00 am !

Jun 28  Caroline Gergen presents her Bachelor`s thesis
         

        ! Wednesday 11:00 am !

Jun 21  Shpend Mahmuti presents his Master`s thesis
         

        ! Wednesday 11:00 am !

Jun 14  Maria Schelling Master`s thesis talk
         

        ! Wednesday 11:00 am !

May 17  Michael Heinzinger presents Master`s thesis progress
         

        ! Wednesday 11:00 am !

Apr 26  Tanzeem Haque`s mid-Master`s thesis talk
         

        ! Wednesday 11:00 am !

Apr 26  Master thesis talk Jade Martins
         

        ! Wednesday 11:00 am !

Feb 22  Tanya`s talk about Machine Learning
         

        ! Wednesday 9:00 am !

Feb 15  Prof. Jürgen Cox, MPI of Biochemistry
         

        ! Wednesday 11:00 am !

Feb 15  Praktische Arbeit Valerie Marot
         

        ! Wednesday 11:00 am !

Feb 08  Dr. Luisa Jiménez-Soto, Max von Pettenkofer Institut LMU
         

        ! Wednesday 11:00 am !

Jan 25  Andreas Simon Master`s thesis talk: Examining effects of active agents on drug targets for different patient groups to classify drug efficiacy based on routine data analysis
         

        ! Wednesday 11:00 am !

Jan 25  Caroline Gergen presents her future Bachelor`s thesis
         

        ! Wednesday 11:00 am !

Jan 25  5-minutes talk Max Miller
         

        ! Wednesday 11:00 am !

Dec 14  Sohel Mahmoud: Data Processing, Data Mining and Machine Learning in the field of Cancer Genomics
         

        ! Wednesday 11:30 am !

Dec 14  Michael Heinziger presents ideas for his future Master's thesis
         

        ! Wednesday 11:00 am !

Dec 07  Isabel Reinhardt presents her Master`s thesis
         

        ! Wednesday 11:15 am !

Dec 07  5-minutes-talk Jiajun Qiu
         

        ! Wednesday 11:00 am !

Nov 09  Yannick`s 5-minutes-talk (+ maybe Edda)
         

        ! Wednesday 9:00 am !

Nov 02  Master Thesis Alexandru Buftea
         

        ! Wednesday 11:00 am !

Oct 26  Beibei Jiang gives a progress report of he PhD thesis
         

        ! Wednesday 11:00 am !

Oct 12  Gastvortrag Mark Teese “Novel patterns of amino acid conservation in transmembrane domains”
         

        ! Wednesday 11:00 am !

Oct 05  thesis talk Theresa Wirth
         

        ! Wednesday 9:00 am !

Oct 05  Hannah Carter, University of California, San Diego, will give a talk
         

        ! Wednesday 9:00 am !

Sep 28  Max Miller talks about his latest publication
         

        ! Wednesday 11:00 am !

Sep 21  Madox Sesen Bachelor Thesis talk
         

        ! Wednesday 9:00 am !

Sep 21  Matthias Heining (TUM junior fellow) presents his work
         

        ! Wednesday 9:00 am !

Aug 24  Master Thesis talk Sven Punga
         

        ! Wednesday 9:00 am !

May 04  Joel Daon presents his future Bachelor thesis
         

        ! Wednesday 11:00 am !

Apr 27  Thomas Schwarzmayr, PhD student at Helmholtz, talks about his PhD thesis
         

        ! Wednesday 9:00 am !

Mar 10  Nikolaus Fortelny on Predicting protein quantity from mRNA – evaluation and performance
         

        ! Thursday 10:00 am !

Mar 09  Bachelor thesis talk Jakob Sturm
         

        ! Wednesday 11:00 am !

Mar 03  Guest talk Agnieszka Szczesniak from Google
         

        ! Thursday 11:00 am !

Mar 02  guest Jessica Jordan
         

        ! Wednesday 9:00 am !

Mar 02  IDP talk Madhukar Shankar
         

        ! Wednesday 9:00 am !

Dec 16  Juan Miguel Cejuela on BLAH2
         

        ! Wednesday 11:00 am !

Dec 16  Maximilian Miller presents his future research and PhD thesis
         

        ! Wednesday 11:00 am !

Dec 09  Carsten Uhlig, Bachelor Thesis
          NLP for Mutation Mentions Extraction

        ! Wednesday 11:00 am !

Dec 02  Ashish Baghudana, Master Thesis
          BioNLP for Transcription Factor to Gene relationship Extraction

        ! Wednesday 11:00 am !

Dec 02  Thomas Hopf`s Tutorial
         

        ! Wednesday 11:00 am !

Nov 25  Michael Folgmann from TUM Medienzentrum explains which services they offer in order to faciliate teaching
         

        ! Wednesday 9:00 am !

Nov 18  Thomas Hopf
          Thomas will talk about his work in the field of variants and variant effects

        ! Wednesday 10:30 am !

Nov 11  Jakob Sturm presents his Bachelor thesis (halftime talk)
         

        ! Wednesday 9:00 am !

Nov 11  Hossain Mahmud
         

        ! Wednesday 9:00 am !

Oct 28  Tim explains PPCache
         

        ! Wednesday 10:30 am !

Oct 21  Benedikt Rauscher
          VAPoR: A Visual web pipeline for Annotation of host/pathogen interactions in Plant Resistance

        ! Wednesday 10:30 am !

Oct 14  Linh Tran
          IDP final presentation: large-scale application for new protein-protein prediction method

        ! Wednesday 10:30 am !

Oct 14  Sonja Ansorge
          Master`s Thesis Talk: A Framework for the Identification and Visuallization of Timed Patterns

        ! Wednesday 10:30 am !

Oct 07  David Dao
          IDP talk: Visualization of the phylogeny of organisms using Java Script

        ! Wednesday 10:30 am !

Sep 30  Pandu Bachelors Thesis
         

        ! Wednesday 10:30 am !

Sep 23  Meshal Ansari
          Bachelor's Thesis talk: Extension of a Pipeline for the Analysis of Cancer Mutation Data

        ! Wednesday 10:30 am !

Sep 21  Schneider & Djabali groups visit the Rostlab (Mon & Tue) & Oktoberfest!
          All groups will present their various research topics, http://wwwen.uni.lu/lcsb - http://www.imetum.tum.de/forschung/epigenetik/allgemein/

        ! Monday 9:00 am !

Sep 02  Maximilian Weinberger
          Bachelor Thesis talk: Enabling Rapid and Easy Data Access to ProteomicsDB via a Stand-Alone Java Application

        ! Wednesday 10:30 am !

Aug 26  Aleksander Cislak "Full-text and keywords indexes for string research"
         

        ! Wednesday 9:00 am !

Jul 22  André Ofner, Bachelor Thesis
         

        ! Wednesday 10:30 am !

Jul 01  Jonas Raedle
         

        ! Wednesday 9:00 am !

May 20  Betz Alexander
         

        ! Wednesday 9:00 am !

Apr 29  Shrikant Vinchurkar, Masters Thesis
          Text mining of Protein Subcellular Localizations

        ! Wednesday 10:30 am !

Apr 29  Silvana Wolf
          Analysis of nuclear transport signals

        ! Wednesday 9:00 am !

Mar 25  Katharina Hembach, Masters Thesis
         

        ! Wednesday 10:30 am !

Dec 11  IDP (4 Students) -- Text annotations of Protein Mutations
         

        ! Thursday 3:15 pm !

Dec 01  Karsten Borgwardt
         

        ! Monday 1:00 pm !

Nov 27  Aquaria demo by Sean O Donoghue
          How to use Aquaria to produce insight from protein structures.

        ! Thursday 3:15 pm !

Nov 27  Kujtim's Thesis Presentation
         

        ! Thursday 10:30 am !

Nov 27  Ankit's Thesis Presentation
         

        ! Thursday 10:00 am !

Nov 06  Julian Heinrich
          Julian (fron Sean O’Donoghue’s group) will talk about “Visualising Biological Data for Research and for Outreach”

        ! Thursday 3:15 pm !

Oct 17  Juanmi is awesome
         

        ! Friday 2:30 pm !

Sep 25  Sebastian Seitz
          Sorting the nuclear proteome by machine learning.

        ! Thursday 1:30 pm !

Sep 04  Bernd Ahlborn
          Bernd will talk about his Diploma thesis

        ! Thursday 1:30 pm !

 

 

 

 

Talks WS 2013/14

Mar 27  Johannes Söding
          Leveraging evolutionary information for protein structure and function production More than 10 years after the human genome project, we still know only a fraction of the structures and functions of human proteins. My lab develops methods for very sensitive sequence search and alignment methods that are based on the pairwise comparison of sequence profiles. Such methods have led to remarkable improvements in protein structure and function prediction over the last 10 years. I will explain how the evolutionary information contained in sequence profiles can enable us to detect homologous relationships across billions of years. I will then give an overview of the state-of-the-art as well as our contributions to this field and also sketch ideas that offer great potential to further enhance the scope of sequence-based protein structure and function prediction methods.

        ! Thursday 1:15 pm !

 

Mar 06  Frank Wallrapp
          Last Presentation at Rostlab & Farewell + cookies

        ! Thursday 1:30 pm !

 

Feb 13  Esmeralda Vicedo
          Disorder in yeast

Feb 06  Michael Bernhofer
          MSc thesis presentation: Transmembrane Helix Prediction in Proteins

Feb 06  Aleksandr Sorokoumov
          IDP Presentation

Jan 16  The Bioinformatics Game is here!
         

Dec 12  Mikael Boden
          Introduction TBA

        ! Thursday 3:30 pm !

 

Dec 12  Kujtim Rrahmani
          IDP Presentation

Dec 05  Jonathan Boidol
          TCGA Analysis

Nov 28  Tatyana Goldberg
          LocTree 3: web server for new localization tool

Nov 28  Guy Yachdav
          Update on server

Nov 14  Louise Funke and the iGEM Team
          They will talk about what happened since their last visit, their success at the iGEM contest and their future plans.

Nov 12  Chiara Zecchin
          Department of Bioengineering, University of Padova. Online prediction of glucose concentration in type 1 diabetes by neural networks.

        ! Tuesday 10:00 am !

 

Oct 24  Timothy Angelotti
          Protein trafficking within cells

 

Talks SS 2013

Sep 19  Anupama Jhawil and Vikram Ravindrav
             ISIS 2 - protein binding-site prediction
             &
             Nikos Papadopoulos
             Intrinsic protein disorder in the human herpesviruses

Aug 29  Visiting Students

             AutoAnnotator - annotating proteins from gene fragments. Developed in the course of the International Genetically Engineered Machine competition (iGEM)

Aug 20  Frank Wallrapp
             A sequence/structure based strategy for prediction and characterization of enzymatic function

July 10  Michael Kiening

             Improvement of sequence based protein function prediction organisms
            ! Wednesday, 12.30 pm !

July 04  Laszlo Kajan
             FreeContact: fast and free direct protein residue-residue contact prediction

June 20  Rebecca Kaßner
             Genotype to Phenotype prediction in Yeast

June 12  Toni Kazic
             From Complex Phenotypes to Network Inference
 

 

Talks SS 2013

Sep 19  Anupama Jhawil and Vikram Ravindrav
             ISIS 2 - protein binding-site prediction
             &
             Nikos Papadopoulos
             Intrinsic protein disorder in the human herpesviruses

Aug 29  Visiting Students

             AutoAnnotator - annotating proteins from gene fragments. Developed in the course of the International Genetically Engineered Machine competition (iGEM)

Aug 20  Frank Wallrapp
             A sequence/structure based strategy for prediction and characterization of enzymatic function

July 10  Michael Kiening

             Improvement of sequence based protein function prediction organisms
            ! Wednesday, 12.30 pm !

July 04  Laszlo Kajan
             FreeContact: fast and free direct protein residue-residue contact prediction

June 20  Rebecca Kaßner
             Genotype to Phenotype prediction in Yeast

June 12  Toni Kazic
             From Complex Phenotypes to Network Inference
 

 

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

 

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.