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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
Feb 12 Claudio Benedetti Master thesis talk
! Wednesday 11:00 am !
Feb 12 Stefan van Rest from Remissio presents his company`s work
! Wednesday 11:00 am !
Jan 15 Frank Wallrapp talks about his work
! Wednesday 11:00 am !
Oct 09 IDP Presentation Ghalia Rehawi
! Wednesday 11:00 am !
Sep 18 Theresa Wirth presents her Master thesis
! Wednesday 11:00 am !
Sep 11 Smith Agarwal final Master`s thesis presentation
! Wednesday 11:00 am !
Sep 11 Tatjana Ammer final Master`s thesis presentation
! Wednesday 11:00 am !
Sep 11 Drillon Avdiu, 3 minutes talk
! 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 Bachelor thesis Anna Reithmeir
! Wednesday 11:00 am !
Apr 03 Master thesis Guido Kubach
! 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 Theresa's Master Thesis Introduction Talk
! Wednesday 11:00 am !
Oct 17 Ziga Avsec presents Kipoi
! 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 Tanzeem`s presents her Master`s thesis
! Wednesday 9:00 am !
Sep 27 Madhukar Sollepura Prabhu Shankar presents his 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 Master thesis talk Jade Martins
! Wednesday 11:00 am !
Apr 26 Tanzeem Haque`s mid-Master`s thesis talk
! Wednesday 11:00 am !
Feb 22 Tanya`s talk about Machine Learning
! Wednesday 9:00 am !
Feb 15 Praktische Arbeit Valerie Marot
! Wednesday 11:00 am !
Feb 15 Prof. Jürgen Cox, MPI of Biochemistry
! Wednesday 11:00 am !
Feb 08 Dr. Luisa Jiménez-Soto, Max von Pettenkofer Institut LMU
! 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 !
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 !
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 IDP talk Madhukar Shankar
! Wednesday 9:00 am !
Mar 02 guest Jessica Jordan
! 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 Sonja Ansorge
Master`s Thesis Talk: A Framework for the Identification and Visuallization of Timed Patterns
! 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 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
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
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 al. Mammalian NUMT insertion is non-random, NAR, under revision.
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