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Journal Club

 Statistical Bioinformatics - JOURNAL CLUB [2017]

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

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


Date Lecturer Topic

10.01.        

Farhad            

Statistical Analysis of label-free SWATH-MS data

17.01.

e:Med

~ ~ ~ consortium meeting ~ ~ ~

24.01

Master Seminar

Paul Heinrich

STAR: ultrafast universal RNA_seq aligner

[talk] [paper]       

31.01.

Master Seminar

~ cancelled due to icy weather conditions ~

07.02.

Master Seminar

(1) Gunther Glehr

Sailfish enables alignment-free isoform quantification fom RNA-seq reads using lightweight algorithms [talk] [paper]

(2) Michael Huttner

Near-optimal probabilistic RNA-seq quantification [talk] [paper]

14.02

Rainer

 ~ ~ ~ Microarray course ~ ~ ~

21.02

Julia

Inferring species interactions from co-occurrence data with Markov networks [paper]

18.02

Nick

3rd Generation Sequencing Methods

07.03

Michael G

Cancer progression and metastasis in the BALB-neuT breast cancer mouse model

14.03.

Michael A

Reference point insensitive molecular data analysis

21.03.

~ cancelled ~

~ cancelled ~

28.03.

Franziska

Screen Marker Genes for Cell Deconvolution

04.04.

Thorsten

zeroSum vignette

11.04.

Easter Break

~ ~ ~ cancelled ~ ~ ~

18.04.

Easter Break

~ ~ ~ cancelled ~ ~ ~

25.04.

Claudio

Feasibility of sample size calculation for RNA-seq studies [paper]

02.05.

Rainer

~ cancelled due to RECOMB attendance ~

09.05

Paula

*.fq quality assessment and filtering

16.05.

Christian

 ~ cancelled ~

23.05.

Christian

3rd Generation Lymmml ing

30.05.

Farhad

Residual Diagnostics in Label-free proteomics

06.06.

Pentecost

~ ~ ~ cancelled ~ ~ ~

13.06.

Timo Itzel

...

20.06.

FOR2127

~ ~ ~ meeting Forschergruppe ~ ~ ~

27.06.

Nick

RNA-Seq pipeline

04.07.

Master seminar

Paul Heinrich

Quick calculation for sample size while controlling false discovery rate with application to microarray analysis [paper] [talk]

11.07.

Master seminar

Gunther Glehr

RNASeqPowerCalculator: Power analysis and sample size estimation for RNA-seq differential expression [paper] [talk]

18.07.

Master seminar

Marian Schoen

PROPER: comprehensive power evaluation for differential expression using RNA-seq [paper] [talk]

25.07.

Michael Huttner           

Modern cryptography in the lyra app

01.08.

Master seminar

Markus Eppelsheimer

Scotty: a web tool for designing RNA-seq experiments to measure differential gene expression [paper] [talk]

05.09.

Alexandra Holler

Methylation patterns in the BALB-neuT breast cancer mouse model

12.09.

Anna Kuhn

Detection of copy number variations in the human genome

19.09.

Rudi Schill

General Markov Models of Tumor Progression

26.09.

Martin Fahrenberger

Comparative Analysis of RNA Expression in five Anopheline Mosquito Species, with focus on the reproductive system

03.10.

German Unity  Day      

~ ~ ~ cancelled ~ ~ ~

05.10.

Franziska

. . .

10.10.

Rainer

~ ~ ~ Microarray course ~ ~ ~

17.10.

cancelled

~ ~ ~ cancelled ~ ~ ~

24.10.

Michael

31.10.

Reformation Day

~ ~ ~ cancelled ~ ~ ~

07.11.

Thorsten

...

14.11.

Claudio

...

21.11.

Christian

...

28.11.

Farhad

...

05.12.

...

...



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)

 

Outlook

Day Lecture Practical
1 Introduction into Microarray Analysis A gentle Introduction into R
2 Microarray Normalization Quality Control and Normalization
3 Screening Differential Geneexpressionanalysis
4 Clustering Clustering
5 Classification Classification

More informations and PDF files:

Programming with R

Literature


RNA Sequencing

Information and material for the RNA-Seq workshop

RNA-Seq Workshop

 

  Lecture Practical
Room Seminar room
Biopark I - 2.OG
check information in VVZ #57045
Tutor Julia Engelmann

 

Description

This course provides an introduction into the analysis of next-generation seqencing data for transcriptomic studies (RNA-Seq). It covers alignment algorithms, methods for finding differentially expressed genes and transcripts and retrieving annotation data from public sources. During the exercises the participants work with real sequence data and applied open source command line tools as well as work within the statistical software environment R and Bioconductor.

Please read the introduction before the course:

http://www.stat.cmu.edu/~larry/all-of-statistics/=R/Rintro.pdf

If you are a RIGeL graduate student you receive 1,5 Credit points for this course. You can find all information on the Homepage of RIGeL.

 

Schedule

Lecture  Mo-Fr  09:30h - 11:30h (st)
Practical  Mo-Fr  13:00h - 18:00h (st)

 

Outlook

Day Lecture Practical
1 Introduction into second-generation sequencing and RNA-seq First steps in sequence data analysis
2 Sequence alignment theory Sequence alignment, play with aligned data
3 Assessing differential expression DESeq2 tutorial (differential expression)
4 Genome features and annotation DEXSeq tutorial (alternative splicing) and retrieving sequence and annotation with Bioconductor
5 Detecting mutations with RNA-seq Detecting and annotating mutations with RNA-seq tutorial

  1. Department of Medicine
  2. Institute for Funtional Genomics

Teaching Statistical Bioinformatics

 

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