Teaching

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

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

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

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

Computational Science

content of 'B.Sc./M.Sc. Studiengang Computational Science | Informatik in den Naturwissenschaften'

Journal Club

Statistical Bioinformatics - JOURNAL CLUB [2019]

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

08.01.

Michael Huttner

15.01.

cancelled

22.01.

Rainer Spang

29.01.

cancelled

05.02.

Julian Lorenz

12.02

Rudolf Schill

19.02.

Marian Schön

26.02.

Gunther Glehr

05.03.

Christian Kohler

12.03.

Stefan Hansch

19.03.

Thorsten Rehberg

26.03.

Claudio Lottaz

02.04.

workshop

09.04

Victoria-Marie Rothe

16.04

Easter Holiday

23.04

Stefan Kirsch

(ITEM, Rgbg)

30.04.

Michael Huttner

07.05.

cancelled

14.05.

Rudolf Schill

21.05.

Marian Schön

28.05.

Kevin Rupp

04.06.

Christoph Kopp

11.06.

Pentecost

18.06.

Martina Häckl

25.06.

Sibylle Wilfling

02.07.

cancelled

05.07. (Fr !)

Stefan Bentink

09.07.

Victoria-Marie Rothe

16.07.

cancelled

23.07.

Max Pichler

30.07.

Daniel Grünbaum

01.08. - 16.09.

Summer Break

17.09.

Marian Schön

24.09

Hike Weltenburg

01.10

Gunther Glehr

08.10.

cancelled

15.10