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Journal Club

 Statistical Bioinformatics - JOURNAL CLUB [2019]

          We meet weekly on Tuesdays, 9:30 in the institute's seminar room

Journal Club archive: [2018] [2017] [2016] [2015] [2014] [2013] [2012]


Date  Lecturer         Topic

08.01.

Michael Huttner

Overview of internal Kubernetes Services // new Authentication System

15.01.

cancelled

                        ~ ~ ~ cancelled ~ ~ ~ 

22.01.

Rainer Spang

Discussion on Computer Science curriculum in the University of Regensburg

29.01.

cancelled

                         ~ ~ ~ cancelled ~ ~ ~ 

05.02.

Julian Lorenz

Principles of Software Engineering

12.02

Rudolf Schill 

Mutual Hazard Networks

19.02.

Marian Schön

Tissue deconvolution in action:

[Ng et al, 2019]

26.02.

Gunther Glehr

A Story about SWATH, datasets and lasso extensions in the context of lymphoma

05.03.

Christian Kohler

Open Source Software Licenses explained

12.03.

Stefan Hansch

dbGaP

19.03.

Thorsten Rehberg     

Tutorial: Writing R and Python Extensions with Compiled Code using HPC Features (AVX2/AVX512, C++11 Threads, BLAS and Cuda GPU acceleration)

26.03.

Claudio Lottaz

Interpretable Machine Learning

[talk] [book (on github)]

02.04.

workshop

Informatik der Zukunft (09:00 - 12:30)

(Vielberth - Gebäude)

09.04

Victoria-Marie Rothe

      Seminar Statistische Bioinformatik

Detecting effective multi-drug combinations

[talk] [computational challenge paper, Nature Biotechnology, 2014] [DIGREM paper (Zhang et al, Bioinformatics, 2018)]

16.04

Easter Holiday

                       ~ ~ ~ cancelled ~ ~ ~ 

23.04

Stefan Kirsch

(ITEM, Rgbg)

Oxford Nanopore Technologies

30.04.

Michael Huttner

Modern Language Design & Introduction into Rust

07.05.

cancelled

                        ~ ~ ~ cancelled ~ ~ ~ 

14.05.

Rudolf Schill

Introduction to Tensors

21.05.

Marian Schön

Low dimensional embedding: T-SNE and UMAP

28.05.

Kevin Rupp

         Seminar Statistische Bioinformatik

A complete statistical model for calibration of RNA-seq counts using external spike-ins and maximum likelihood theory [talk] [paper]

04.06.

Christoph Kopp

         Seminar Statistische Bioinformatik

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome [talk] [paper]

11.06.

Pentecost

                       ~ ~ ~ cancelled ~ ~ ~ 

18.06.

Martina Häckl

         Seminar Statistische Bioinformatik

DiPhiSeq: Robust comparison of expression levels on RNA-Seq data with large sample sizes [talk] [paper]

25.06.

Sibylle Wilfling

        Seminar Statistische Bioinformatik

Topconfects: a package for confident effect sizes in differential expression analysis provides a more biologically useful ranked gene list. [talk] [paper]

02.07.

cancelled

                      ~ ~ ~ cancelled ~ ~ ~

05.07. (Fr !)

Stefan Bentink 

Guest Speaker (former PhD student in Rainer Spangs' group)

09.07.

Victoria-Marie Rothe

Nucleosome Dynamics during the Erythrocytic Cycle of Plasmodium Falciparum

16.07.

cancelled

Symposium - Biomolecular Imaging Meets Immuno-Oncology

23.07.

Max Pichler

Machine Learning can infer trait matching and predict species interactions in ecological networks

30.07.

Daniel Grünbaum

Non-negative Matrix Factorization for the Analysis of Wafer Test Data

01.08. - 16.09.

Summer Break

                       ~ ~ ~ cancelled ~ ~ ~ 

17.09.

Marian Schön

Coding Guidelines for Spang-Lab-Projects

24.09

Hike Weltenburg

                        ~ ~ ~ cancelled ~ ~ ~

01.10

Gunther Glehr

(10:00 s.t)

Flow Cytometry - Principles, Challenges, Algorithms

08.10.

cancelled

due to lecture " Computational Statistics für Physiker und Bioinformatiker" by Michael Altenbuchinger, PhD

15.10

Claudio Lottaz

Excerpts from the Code of Ethics and Professional Conduct by the ACM [paper] [talk]

22.10.

Christian Kohler

Let's Encrypt Certificates For Docker Container - The Smart Way

29.10.

Jakob Simeth

Cell Prototype Selection for DTD

05.11.

Michael Huttner

L-Patho: Preprocessing huge images for deep learning

12.11.

Johannes Falk

            Maria Attenberger

Bachelorthesis: Explorative Analysis of Lymphoma DNA Methylation Data using Digital Tissue Deconvolution

Bachelorthesis:Validating DTD Immune Cell Estimations via Survival Analyses in Lymphoma

19.11.

Rudi Schill

Tensor Trains

References:

Tensors and Latent Variable Models

Hand-waving and Interpretive Dance: An Introductory Course on Tensor Networks

A literature survey of low-rank tensor approximation techniques

Tensor Networks in a Nutshell

26.11.

Marian Schön

Intratumor heterogeneity of nodal B cell lymphomas

03.12.

(09:30)

            Felix Gottschlich 

           Seminar Algorithmische Bioinformatik

A framework and an algorithm to detect low-abundance DNA by a handy sequencer and a palm-sized computer [paper] [talk]

03.12.

(10:15)

          Julian Lorenz

           Seminar Algorithmische Bioinformatik

A Sequence-Based Novel Approach for Quality Evaluation of Third-Generation Sequencing Reads [paper] [talk]

10.12.

(09:30)

Marcel  Mück

           Seminar Algorithmische Bioinformatik

Long-read amplicon denoising [paper]

10.12.

(10:15)

Johannes Falk

           Seminar Algorithmische Bioinformatik

Hercules: a profile HMM-based hybrid error correction algorithm for long reads [paper]

17.12.

(09:30)

Martina Häckl

          Seminar Algorithmische Bioinformatik

Novel algorithms for efficient subsequence searching and mapping in nanopore raw signals towards targeted sequencing [paper]

17.12.

(10:15)

Sibylle Wilfling

          Seminar Algorithmische Bioinformatik

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation [paper]

14.01.2020

(09:30)

Andreas Lösch

          Seminar Algorithmische Bioinformatik

Race in a genome: long read sequencing, ethnicity-specific reference genomes and the shifting horizon of race [paper]

14.01.2020

(10:15)

Robert Bosek        

          Seminar Algorithmische Bioinformatik

High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution [paper]

21.01.2020

Rainer Spang

28.01.2020

Gunther Glehr

04.02.2020

Kevin Rupp

11.02.2020

cancelled

  ~ ~ ~ Microarray Analysis Coures ~ ~ ~

18.02.2020

Christoph Kopp

25.02.2020

Victoria-Marie Rothe

Master Thesis talk

03.03.2020

Claudio Lottaz

10.03.2020

Christian Kohler

17.03.2020

Michael Huttner

24.03.2020

Rudi Schill

31.03.2020

Marian Schön

07.04.2020

Easter

14.04.2020

Easter




Genomische Datenanalyse

Information and material for the microarray workshop

Genomische Datenanalyse

 

  Lecture Practical
Room check information in VVZ #57046 check information in VVZ #57046
Tutor Rainer Spang

 

Description

The workshop provides an introduction to the analysis of genomic data. The analysis of microarray data sets is practiced using the statistical software R and Bioconductor.

 

Schedule

Lecture  Mo-Fr  10:00h - 12:00h (st)
Practical  Mo-Fr  13:00h - 18:00h (st)

 

Lecture Slides

Day Lecture Practical
1 Introduction A gentle Introduction into R
2 Normalization Quality Control and Normalization
3 Screening Differential Geneexpressionanalysis
4

Clustering

Clustering
5 Classification Classification

Slides last updated on 2019-07-31 .

  1. Department of Medicine
  2. Institute of Functional Genomics

Teaching Statistical Bioinformatics

 

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