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2019

 Statistical Bioinformatics - JOURNAL CLUB [2019]

 


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] [talk]

10.12.

(10:15)

Johannes Falk

           Seminar Algorithmische Bioinformatik

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

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] [talk]

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] [talk]

  1. Department of Medicine
  2. Institute of Functional Genomics