Welcome to CSB

The capability of biological systems to respond to environmental changes is realized by a complex dynamic adjustment of the interplay between genes, proteins and metabolites. For a deeper understanding at the systems level, we need to study the structure and dynamics of cellular and organismal functions rather than the characteristics of isolated parts of a cell or an organism.

Research

What our research is aiming for

The main focus of our group is the application and development of computational methods to process and integrate quantitative biological data from modern high-throughput measurements in order to gain novel insights into biological responses to environment changes. The main challenge is the rigorous integration of different system level analyses and present knowledge into biological interpretable models. Therefore, we want to drive theory and technology forward with a combination of biological science, applied informatics, statistical and machine learning approaches.

Team

Our research team on CSB

Timo Mühlhaus (Junior Professor)

Timo Mühlhaus

Junior Professor
David Zimmer (PhD Student)

David Zimmer

PhD Student
Benedikt Venn (PhD Student)

Benedikt Venn

PhD Student
Lukas Weil (PhD Student)

Lukas Weil

PhD Student
Kevin Schneider (PhD Student)

Kevin Schneider

PhD Student
Oliver Maus (PhD Student)

Oliver Maus

PhD Student
Jonathan Ott (PhD Student)

Jonathan Ott

PhD Student
CL

Christopher Lux

KF

Kevin Frey

Nn

none

  • 2020

    Lukas Weil (Master Student)

    Kevin Schneider (Master Student)

    Jonathan Ott (Master Student)

  • 2019

    Patrick Blume (Master Student)

    Marc Gottlieb (Bachelor Student)

  • 2018

    Benedikt Venn (Master Student)

    Esther Wieczorek (Master Student)

    Isabella Christina Capilla Navarro (Master Student)

  • 2017

    David Zimmer (Master Student)

    Kevin Schneider (Bachelor Student)

  • 2016

    Sabrina Gödel (Master Student)

    Lukas Weil (Bachelor Student)

  • 2015

    Esther Wieczorek (Bachelor Student)

    Paul Menges (Bachelor Student)

Publications

View our selected publications

CSBJ
2021
Identifying the minimum amplicon sequence depth to adequately predict classes in eDNA-based marine biomonitoring using supervised machine learning
Dully V, Wilding TA, Mühlhaus T, Stoeck T
Nat Chem Biol
2021
Peroxiredoxins couple metabolism and cell division in an ultradian cycle
Amponsah P S, Yahya G, Zimmermann J, Mai M, Mergel S, Mühlhaus T, Storchova Z, Morgan B
Cell Reports
2021
The chaperone-binding activity of the mitochondrial surface receptor Tom70 protects the cytosol against mitoprotein-induced stress
Backes S, Bykov Y S, Flohr T, Räschle M, Zhou J, Lenhard S, Krämer L, Mühlhaus T, Bibi C, Jann C, Smith J D, Steinmetz L M, Rapaport D, Storchová Z, Schuldiner M, Boos F, Herrmann J M
Plant J.
2021
Acclimation in plants - the Green Hub consortium
Kleine T, Nägele T, Neuhaus H E, Schmitz-Linneweber C, Fernie A R, Geigenberger P, Grimm B, Kaufmann K, Klipp E, Meurer J, Möhlmann T, Mühlhaus T, Naranjo B, Nickelsen J, Richter A, Ruwe H, Schroda M, Schwenkert S, Trentmann O, Willmund F, Zoschke R, Leister D
iScience
2020
Translational Components Contribute to Acclimation Responses to High Light, Heat, and Cold in Arabidopsis
Garcia-Molina A, Kleine T, Schneider K, Mühlhaus T, Lehmann M, Leister D
The Plant cell
2020
Vernalization Alters Sink and Source Identities and Reverses Phloem Translocation from Taproots to Shoots in Sugar Beet (Beta vulgaris)
Martins Rodrigues C, Müdsam C, Keller I, Zierer W, Czarnecki O, Corral J M, Reinhardt F, Nieberl P, Fiedler-Wieschers K, Sommer F K, Schroda M, Mühlhaus T, Harms K, Flügge U I, Sonnewald U, Koch W, Ludewig F, Neuhaus H E, and Pommerrenig B
BMC plant biology
2020
Identification of small RNAs during cold acclimation in Arabidopsis thaliana
Tiwari B, Habermann K, Arif M A, Weil H L, Garcia-Molina A, Kleine T, Mühlhaus T, and Frank W
ADBIS 2020
2020
A Bloom Filter-Based Framework for Interactive Exploration of Large-Scale Research Data
Doniparthi G, Mühlhaus T, and Deßloch S
Front. Plant Sci.
2020
Overexpression of Sedoheptulose-1,7-Bisphosphatase Enhances Photosynthesis in Chlamydomonas reinhardtii and Has No Effect on the Abundance of Other Calvin-Benson Cycle Enzymes
Hammel A, Sommer F, Zimmer D, Stitt M, Mühlhaus T, and Schroda M
BBA Bioenergetics
2020
Clingy genes: Why were genes for ribosomal proteins retained in many mitochondrial genomes?
Bertgen L, Mühlhaus T, and Herrmann J M
Mol. Cell.
2020
The NADH Dehydrogenase Nde1 Executes Cell Death after Integrating Signals from Metabolism and Proteostasis on the Mitochondrial Surface
Saladi S, Boos F, Poglitsch M, Meyer H, Sommer F, Mühlhaus T, Schroda M, Schuldiner M, Madeo F, and Herrmann JM
J Neurochem.
2019
Poor transcript-protein correlation in the brain: negatively correlating gene products reveal neuronal polarity as a potential cause
Moritz CP, Mühlhaus T, Tenzer S, Schulenborg T, and Friauf E
Plant physiology
2019
The Role of Plastidic Trigger Factor Serving Protein Biogenesis in Green Algae and Land Plants
Rohr M, Ries F, Herkt C, Gotsmann VL, Westrich LD, Gries K, Trösch R, Christmann J, Chaux-Jukic F, Jung M, Zimmer D, Mühlhaus T, Sommer F, Schroda M, Keller S, Möhlmann T, Willmund F
18th ECC
2019
Curve form-based quantization of short time series data
Leifeld T, Venn B, Cui S, Zhang Z, Mühlhaus T*, Zhang P*
Biotechnol J.
2019
Metabolic engineering of Corynebacterium glutamicum for high-level ectoine production - design, combinatorial assembly and implementation of a transcriptionally balanced heterologous ectoine pathway
Gießelmann G, Dietrich D, Jungmann L, Kohlstedt M, Jeon E J, Yim SS, Sommer F, Zimmer D, Mühlhaus T, Schroda M, Jeong KJ, Becker J, Wittmann C
Plant Physiology
2019
The Chlamydomonas deg1c Mutant Accumulates Proteins Involved in High Light Acclimation
Theis J, Lang J, Spaniol B, Ferté S, Niemeyer J, Sommer F, Zimmer D, Venn B, Mehr SF, Mühlhaus T, Wollman F-A, Schroda M
J. Cell Biol.
2018
Tom70 enhances mitochondrial preprotein import efficiency by binding to internal targeting sequences
Backes S, Hess S, Boos F, Woellhaf M W, Gödel S, Jung M, Mühlhaus T*, and Herrmann J M*
Frontiers in Plant Science
2018
Absolute Quantification of Major Photosynthetic Protein Complexes in Chlamydomonas reinhardtii Using Quantification Concatamers (QconCATs)
Hammel A, Zimmer D, Sommer F, Mühlhaus T* and Schroda M*
BIO-PROTOCOL
2018
Detection of Internal Matrix Targeting Signal-like Sequences (iMTS-Ls) in Mitochondrial Precursor Proteins Using the TargetP Prediction Tool
Boos F*, Mühlhaus T*, and Herrmann J
New Phytologist
2018
Investigations on VELVET regulatory mutants confirm the role of host tissue acidification and secretion of proteins in the pathogenesis of Botrytis cinerea
Müller N, Leroch M, Schumacher J, Zimmer D, Könnel A, Klug K, Leisen T, Scheuring D, Sommer F, Mühlhaus T, Schroda M, and Hahn M
Nature PLANTS
2018
Commonalities and differences of chloroplast translation in a green alga and land plants
Trösch R, Barahimipour R, Gao Y, Badillo-Corona J A, Gotsmann V L, Zimmer D, Mühlhaus T, Zoschke R, and Willmund F
Plant molecular biology
2017
Substrates of the chloroplast small heat shock proteins 22E/F point to thermolability as a regulative switch for heat acclimation in Chlamydomonas reinhardtii
Rütgers M, Muranaka L S, Mühlhaus T, Sommer F, Thoms S, Schurig J, Willmund F, Schulz-Raffelt M, and Schroda M
Proceedings of the National Academy of Sciences of the United States of America
2016
A repeat protein links Rubisco to form the eukaryotic carbon-concentrating organelle
Mackinder L C M, Meyer M T, Mettler-Altmann T, Chen V K, Mitchell M C, Caspari O Freeman Rosenzweig E S, Pallesen L, Reeves G, Itakura A, Roth R, Sommer F, Geimer S, Mühlhaus T, Schroda M, Goodenough U, Stitt M, Griffiths H, Jonikas M C
Plant Physiology
2016
GUN1 controls accumulation of the plastid ribosomal protein S1 at the protein level and interacts with proteins involved in plastid protein homeostasis
Tadini L, Pesaresi P, Kleine T, Rossi F, Guljamow A, Sommer F, Mühlhaus T, Schroda M, Masiero S, Pribil M, Rothbart M, Hedtke B, Grimm B and Leister D
The Plant Journal for Cell and Molecular Biology
2015
The Chlamydomonas heat stress response
Schroda M, Hemme D, and Mühlhaus T
Nature PLANTS
2015
Identification of the transporter responsible for sucrose accumulation in sugar beet taproots
Jung B, Ludewig F, Schulz A, Meißner G, Wöstefeld N, Flügge U-I, Pommerrenig B, Wirsching P, Sauer N, Koch W, Sommer F, Mühlhaus T, Schroda M, Cuin TA, Graus D, Marten I, Hedrich R and Eckkehard HE
Biochimica et biophysica acta
2015
ATP-dependent molecular chaperones in plastids - More complex than expected
Trösch R, Mühlhaus T, Schroda M, and Willmund F
The Plant Cell
2014
Systems Analysis of the Response of Photosynthesis, Metabolism, and Growth to an Increase in Irradiance in the Photosynthetic Model Organism Chlamydomonas reinhardtii
Mettler T, Mühlhaus, T.*, Hemme D, Schöttler M-A, Rupprecht J, Idoine A, Veyel D, Pal S K, Yaneva-Roder L, and Winck F V, Sommer F, Vosloh D, Seiwert B, Erban A, Burgos A, Arvidsson S, Schönfelder S, Arnold A, Günther M, Krause U, Lohse M, Kopka J, Nikoloski Z, Mueller-Roeber B, Willmitzer L, Bock R, Schroda M and Stitt M
The Plant Cell
2014
Nitrogen-Sparing Mechanisms in Chlamydomonas Affect the Transcriptome, the Proteome, and Photosynthetic Metabolism
Schmollinger S*, Mühlhaus T*, Boyle N R*, Blaby I K, Casero D, Mettler T, Moseley J L, Kropat J, Sommer F, Strenkert D, Hemme D, Pellegrini M, Grossman RA, Stitt M, Schroda M and Merchant
The Plant Cell
2014
Conditional Depletion of the Chlamydomonas Chloroplast ClpP Protease Activates Nuclear Genes Involved in Autophagy and Plastid Protein Quality Control
Ramundo S, Casero D, Mühlhaus T, Hemme D, Sommer F, Crèvecoeur M, Rahire M, Schroda M, Rusch J, Goodenough U, Pellegrini M, Perez-Perez ME, Crespo JL, Schaad O, Civic N, Rochaix JD
Methods in molecular biology (Clifton, N.J.)
2014
Identification and validation of protein-protein interactions by combining co-immunoprecipitation, antigen competition, and stable isotope labeling
Sommer F, Mühlhaus T, Hemme D, Veyel D, and Schroda M
The Plant Cell
2012
Evidence for a role of VIPP1 in the structural organization of the photosynthetic apparatus in Chlamydomonas
Nordhues A, Schöttler M A, Unger A-K, Geimer S, Schönfelder S, Schmollinger S, Rütgers M, Finazzi G, Soppa B, Sommer F, Mühlhaus T, Roach T, Krieger-Liszkay A, Lokstein H, Crespo JL and Schroda M
Systembiologie.de
2010
Wie Pflanzen auf Umweltveränderungen reagieren
Hemme D*, Weiss J*, Mühlhaus T*, Sommer F, and Schroda M
International review of cell and molecular biology
2010
New insights into the roles of molecular chaperones in Chlamydomonas and Volvox
Nordhues A, Miller S M, Mühlhaus T, and Schroda M
Plant signaling & behavior
2009
A 'foldosome' in the chloroplast?
Schroda M, and Mühlhaus T
The Journal of biological chemistry
2008
Assistance for a chaperone: Chlamydomonas HEP2 activates plastidic HSP70B for cochaperone binding
Willmund F, Hinnenberger M, Nick S, Schulz-Raffelt M, Mühlhaus T, and Schroda M
The Journal of biological chemistry
2007
The NH2-terminal domain of the chloroplast GrpE homolog CGE1 is required for dimerization and cochaperone function in vivo
Willmund F, Mühlhaus T*, Wojciechowska M, and Schroda M

Teaching

Our teaching activity for bachelor and master students

BIO-BIO-04-V-5
Theoretical(lecture)
Audience: Master students
Lecture:
Modern Methods in Biology Part II
3 CP - Sommer semester
This team-taught lecture provides an overview of a range of up-to-date methods that are currently used in the groups that are involved in the Master program.
BIO-MBP-06-V-2
Theoretical(lecture)
Audience: Bachelor students
Lecture:
Biophysics: Physical models of living systems
3 CP - Sommer semester
The lecture will introduce a model-based understanding of the dynamics and randomness in living systems to improve the knowledge of biological systems quantitatively.
BIO-BTE-12-V-4
Theoretical(lecture)
Audience: Bachelor & Master students
Lecture:
Scientific programming for biologists (lecture & excercise)
3 CP - Sommer semester
The aim of this lecture with subsequent exercises is to impart knowledge about the basics of functional and object-oriented programming and to deal with basic data structures and algorithms. Conceptual basics, methods and techniques for structuring data and for the development of algorithms are taught. Tools of scientific computing and data processing, especially for the visualization and processing of measurement data, are presented. The reference language is F# (FSharp), which is used in combination with modern software libraries and the R software environment for problem solving.
BIO-BTE-03-W-7
Theoretical(reading course)
Audience: Master students
Lecture & Reading Course:
Fundamental Concepts and Applications in Systems Biology
3 CP - Winter semester
The students will hear introductory lectures, read research and review papers, and discuss together and with the teacher the following topics:
  • Quantitative biology and Systems Biology
  • Basic concepts in bioinformatics including biostatistics, machine learning and network analysis
  • Application of quantitative methods in Plant Systems Biology research
BIO-BTE-01-W-7
Theoretical(reading course)
Audience: Master students
Lecture & Reading Course:
Plant Acclimation
3 CP - Sommer semester
The class will be a combination of lecture and reading course. In the morning, two hours of lecture introduce the different aspects of plant acclimation. Here, we will study different aspects how plant cells acclimate to changing environmental conditions (such as changes in light intensity/quality and temperature). After each lecture, literature will be provided for the intensive study of the specific aspects. The studies will be summarized in a closing discussion at the end of each day. The last two days are dedicated for literature studies addressing plant acclimation by Systems Biology approaches.
BIO-BTE-05-L-5
Practical(AP)
Audience: Bachelor students
Practical module:
Data science in biology
9 CP
Learn how to approach common and classical bioinformatics problems and implement solutions
BIO-BTE-10-L-4
Practical
Audience: Bachelor & Master students
Project work:
Non-compulsory project work in Bioinformatics
9 CP
Guided small research project with the aim to increase your bioinformatics skill set. Project topics span the range of bioinformatic application from algorithm to web service implementation. Discuss the topic your own idea or select a suggested project. For the project work it is required, that you attend the lecture Scientific Programming for Biologists (Lecture & Exercise).
BIO-BTE-06-L-7
Practical(VP)
Audience: Master students
Advanced practical module:
MS-based absolute protein quantification and computer-based data processing in mass spectrometry-based proteomics
12 CP - Winter semester
MS-based quantitative proteomics: Quantification of protein abundance and of protein complex stoichiometries in Chlamydomonas cells using label-free quantification, MRM and QconCAT approaches based on stable isotope labeling and quantitative mass spectrometry. Computational proteomics using statistical analysis of quantitative proteomics data sets.
BIO-BTE-05-L-5
Practical(VP)
Audience: Master students
Advanced practical module:
Data science in biology
12 CP
Learning data science by example: You take the steering wheel for a project and improve your bioinformatics and data science skillset by solving current research problems.
BIO-BIO-04-V-5
Theoretical(lecture)
Audience: Master students
Lecture:
Modern Methods in Biology Part II
3 CP - Sommer semester
This team-taught lecture provides an overview of a range of up-to-date methods that are currently used in the groups that are involved in the Master program.
BIO-BTE-12-V-4
Theoretical(lecture)
Audience: Bachelor & Master students
Lecture:
Scientific programming for biologists (lecture & excercise)
3 CP - Sommer semester
The aim of this lecture with subsequent exercises is to impart knowledge about the basics of functional and object-oriented programming and to deal with basic data structures and algorithms. Conceptual basics, methods and techniques for structuring data and for the development of algorithms are taught. Tools of scientific computing and data processing, especially for the visualization and processing of measurement data, are presented. The reference language is F# (FSharp), which is used in combination with modern software libraries and the R software environment for problem solving.
BIO-BTE-01-W-7
Theoretical(reading course)
Audience: Master students
Lecture & Reading Course:
Plant Acclimation
3 CP - Sommer semester
The class will be a combination of lecture and reading course. In the morning, two hours of lecture introduce the different aspects of plant acclimation. Here, we will study different aspects how plant cells acclimate to changing environmental conditions (such as changes in light intensity/quality and temperature). After each lecture, literature will be provided for the intensive study of the specific aspects. The studies will be summarized in a closing discussion at the end of each day. The last two days are dedicated for literature studies addressing plant acclimation by Systems Biology approaches.
BIO-BTE-05-L-5
Practical(AP)
Audience: Bachelor students
Practical module:
Data science in biology
9 CP
Learn how to approach common and classical bioinformatics problems and implement solutions.
BIO-BTE-10-L-4
Practical
Audience: Bachelor & Master students
Project work:
Non-compulsory project work in Bioinformatics
9 CP
Guided small research project with the aim to increase your bioinformatics skill set. Project topics span the range of bioinformatic application from algorithm to web service implementation. Discuss the topic your own idea or select a suggested project. For the project work it is required, that you attend the lecture Scientific Programming for Biologists (Lecture & Exercise).
BIO-BTE-05-L-5
Practical(VP)
Audience: Master students
Advanced practical module:
Data science in biology
12 CP
Learning data science by example: You take the steering wheel for a project and improve your bioinformatics and data science skillset by solving current research problems.
BIO-BTE-03-W-7
Theoretical(reading course)
Audience: Master students
Lecture & Reading Course:
Fundamental Concepts and Applications in Systems Biology
3 CP - Winter semester
The students will hear introductory lectures, read research and review papers, and discuss together and with the teacher the following topics:
  • Quantitative biology and Systems Biology
  • Basic concepts in bioinformatics including biostatistics, machine learning and network analysis
  • Application of quantitative methods in Plant Systems Biology research
BIO-BTE-05-L-5
Practical(AP)
Audience: Bachelor students
Practical module:
Data science in biology
9 CP
Learn how to approach common and classical bioinformatics problems and implement solutions.
BIO-BTE-10-L-4
Practical
Audience: Bachelor & Master students
Project work:
Non-compulsory project work in Bioinformatics (Scientific programming for biologists)
9 CP - since 2019
Guided small research project with the aim to increase your bioinformatics skill set. Project topics span the range of bioinformatic application from algorithm to web service implementation. Discuss the topic your own idea or select a suggested project. For the project work it is required, that you attend the lecture Scientific Programming for Biologists (Lecture & Exercise).
BIO-BTE-05-L-5
Practical(VP)
Audience: Master students
Advanced practical module:
Data science in biology
12 CP
Learning data science by example: You take the steering wheel for a project and improve your bioinformatics and data science skillset by solving current research problems.

Open Source

Take a look on our public repositories on github. Feel free to contribute!

View Github

Contact

Faculty Impressum Datenschutz

Jun. Prof. Dr. Timo Mühlhaus
Computational Systems Biology

University of Kaiserslautern
Paul-Ehrlich-Str. 23 R109
67663 Kaiserslautern, Germany

+ 49 631 205 4657
+ 49 631 205 2999