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Supplemental Material

This page contains supplemental material for the publications listed below.

Katrin Madjar and Jörg Rahnenführer:
Weighted Cox regression for the prediction of heterogeneous patient subgroups
BMC Medical Informatics and Decision Making, 2021

A file containing data and R code can be downloaded [here].

Vera Rieder, Karin U. Schork, Laura Kerschke, Bernhard Blank-Landeshammer, Albert Sickmann and Jörg Rahnenführer:
Comparison and evaluation of clustering algorithms for tandem mass spectra

J. Proteome Res., 2017

A file containing R code of clustering algorithms and measures for assessment of the quality of cluster algorithms can be downloaded [here].

Our R guide related to the manuscript can be downloaded [here].

Vera Rieder, Bernhard Blank-Landeshammer, Marleen Stuhr, Tilman Schell, Karsten Biß, Laxmikanth Kollipara, Achim Meyer, Markus Pfenninger, Hildegard Westphal, Albert Sickmann and Jörg Rahnenführer:
DISMS2: A flexible algorithm for direct proteome-wide distance calculation of LC-MS/MS runs
BMC Bioinformatics, 2017

A file containing R code of DISMS2 can be downloaded [here].

Miriam Lohr, Birte Hellwig, Karolina Edlund, Johanna Mattsson, Johan Botling, Marcus Schmidt, Jan G. Hengstler, Patrick Micke, Jörg Rahnenführer:
Identification of sample annotation errors in gene expression datasets
Archives of Toxicology, 2015

A file containing the description of the algorithms used for building and applying the sex classifier can be found [here].

It contains the following three algorithms:
1. Algorithm for selection of suitable variables (genes, probe sets) for sex classification
2. Algorithm for normalization of datasets
3. Algorithm for the sex classifier

A file containing some additional tables can be found [here].

A file containing some additional figures can be found [here].

Marco Grzegorczyk, Dirk Husmeier:
Improvements in the reconstruction of time-varying gene regulatory networks: dynamic programming and regularization by information sharing among genes
Bioinformatics, 2011

Our Matlab implementation of the regularized cpBGe model can be downloaded [here].

A description and a worked example is available [here].

Marco Grzegorczyk, Dirk Husmeier and Jörg Rahnenführer:
Modelling non-stationary dynamic gene regulatory processes with the BGM model
Computational Statistics, 2011

A zip folder containing our Matlab implementation of the RJMCMC algorithm can be downloaded [here].

A supplementary paper providing details, which for space restrictions could not be included in the main paper, can be downloaded [here] .

Kai Kammers, Michel Lang, Jan G. Hengstler, Marcus Schmidt and Jörg Rahnenführer:
Survival models with preclustered gene groups as covariates
BMC Bioinformatics, 2011

A file containing R code for model selection and evaluation can be downloaded [here].

Birte Hellwig, Jan G. Hengstler, Marcus Schmidt, Mathias C. Gehrmann, Wiebke Schormann, Jörg Rahnenführer:
Comparison of scores for bimodality of gene expression distributions and genome-wide evaluation of the prognostic relevance of high-scoring genes
BMC Bioinformatics, 2010

A file containing R code for computing measures of bimodality and linking them to survival data can be downloaded [here].

Katharina Podwojski, Arno Fritsch, Daniel C. Chamrad, Wolfgang Paul, Barbara Sitek, Kai Stühler, Petra Mutzel, Christian Stephan, Helmut E. Meyer, Wolfgang Urfer, Katja Ickstadt, Jörg Rahnenführer:
Retention Time Alignment Algorithms for LC/MS Data must consider Nonlinear Shifts
Bioinformatics, 2009

A text file containing the R code for the regression-based alignment algorithms can be downloaded [here].

Please read the file [readme] for instructions on the usage of the R code.

The simulated data sets analyzed in the paper can be downloaded here: [Data10ppm] and [Data100ppm]

Location & approach

The campus of TU Dort­mund Uni­ver­sity is located close to interstate junction Dort­mund West, where the Sauerlandlinie A45 (Frankfurt-Dort­mund) crosses the Ruhrschnellweg B1 / A40. The best interstate exit to take from A45 is “Dort­mund-Eichlinghofen” (closer to South Cam­pus), and from B1 / A40 “Dort­mund-Dorstfeld” (closer to North Cam­pus). Signs for the uni­ver­si­ty are located at both exits. Also, there is a new exit before you pass over the B1-bridge leading into Dort­mund.

For travelling to the Department of Statistics, convenient parking places can be found at Vogelpothsweg (Gates 21 / 24) or alternatively at the Otto-Hahn-Straße (Gates 28 / 30 / 35).

TU Dort­mund Uni­ver­sity has its own train station (“Dort­mund Uni­ver­si­tät”). From there, suburban trains (S-Bahn) leave for Dort­mund main station (“Dort­mund Hauptbahnhof”) and Düsseldorf main station via the “Düsseldorf Airport Train Station” (take S-Bahn number 1, which leaves every 15 or 30 minutes). The uni­ver­si­ty is easily reached from Bo­chum, Essen, Mülheim an der Ruhr and Duis­burg.

You can also take the bus or subway train from Dort­mund city to the uni­ver­si­ty: From Dort­mund main station, you can take any train bound for the Station “Stadtgarten”, usually lines U41, U45, U 47 and U49. At “Stadtgarten” you switch trains and get on line U42 towards “Hombruch”. Look out for the Station “An der Palmweide”. From the bus stop just across the road, busses bound for TU Dort­mund Uni­ver­sity leave every ten minutes (445, 447 and 462). Another option is to take the subway routes U41, U45, U47 and U49 from Dort­mund main station to the stop “Dort­mund Kampstraße”. From there, take U43 or U44 to the stop “Dort­mund Wittener Straße”. Switch to bus line 447 and get off at “Dort­mund Uni­ver­si­tät S”.

The H-Bahn is one of the hallmarks of TU Dort­mund Uni­ver­sity. There are two stations on North Cam­pus. One (“Dort­mund Uni­ver­si­tät S”) is directly located at the suburban train stop, which connects the uni­ver­si­ty directly with the city of Dort­mund and the rest of the Ruhr Area. Also from this station, there are connections to the “Technologiepark” and (via South Cam­pus) Eichlinghofen. The other station is located at the dining hall at North Cam­pus and offers a direct connection to South Cam­pus every five minutes.

The AirportExpress is a fast and convenient means of transport from Dort­mund Airport (DTM) to Dort­mund Central Station, taking you there in little more than 20 minutes. From Dort­mund Central Station, you can continue to the uni­ver­si­ty campus by interurban railway (S-Bahn). A larger range of in­ter­na­tio­nal flight connections is offered at Düsseldorf Airport (DUS), which is about 60 kilometres away and can be directly reached by S-Bahn from the uni­ver­si­ty station.

Interactive map

The facilities of TU Dortmund University are spread over two campuses, the larger Campus North and the smaller Campus South. Additionally, some areas of the university are located in the adjacent "Technologiepark".

Campus Lageplan Zum Lageplan