Tokuda, Isao T., Herzel, Hanspeter
APSIPA ASC 2009: Asia-Pacific Signal and Information Processing Association, 2009 Annual Summit and Conference. 4-7 October 2009. Sapporo, Japan. Oral session: Synthesis of Various Affective Speech...
der Mathematisch-Naturwissenschaftlichen Fakultät (2008)
Carsten O. Daub, Dekan Prof, Dr. Robert Seckler, Gutachter Prof, Dr. Hanspeter Herzel, Prof Dr, ...
Analysis of integrated transcriptomics and metabolomics data — a systems biology approach
Small RNAs Establish Delays and Temporal Thresholds in Gene Expression (2008)
Legewie, Stefan, Dienst, Dennis, Wilde, Annegret, Herzel, Hanspeter, Axmann, Ilka M.
Non-coding RNAs are crucial regulators of gene expression in prokaryotes and eukaryotes, but it remains poorly understood how they affect the dynamics of transcriptional networks. We analyzed the...
Mathematical models in mammalian cell biology (2008)
Herzel, Hanspeter, Blüthgen, Nils
A report on the Conference on Systems Biology of Mammalian Cells, Dresden, Germany, 22-24 May 2008.
Gautam Chaurasia, Yasir Iqbal, Christian Hänig, Hanspeter Herzel, Erich E. Wanker, Matthias E. Futschik
web-based integration of distributed large-scale
Functional and Transcriptional Coherency of Modules in the Human Protein Interaction Network (2008)
Matthias E. Futschik, Gautam Chaurasia, Anna Tschaut, Jenny Russ, M. Madan Babu, Hanspeter Herzel
Modularity is a major design principle in interaction networks. Various studies have shown that protein interaction networks in prokaryotes and eukaryotes display a modular structure. A majority of...
Genome-wide Analysis of Functions Regulated by Sets of Transcription Factors (2008)
Szymon M. Kiełbasa, Nils Blüthgen, Hanspeter Herzel
∗ both authors contributed equally Abstract: We present a pipeline for inferring biological functions regulated by a combinatorial interaction of transcription factors. Using a robust statistical...
Global parameter search reveals design principles of the mammalian circadian clock (2008)
Locke, James CW, Westermark, Pål O, Kramer, Achim, Herzel, Hanspeter
Abstract Background Virtually all living organisms have evolved a circadian (~24 hour) clock that controls physiological and behavioural processes with exquisite precision throughout the day/night...
Global parameter search reveals design principles of the mammalian circadian clock (2008)
Locke, James C. W., Westermark, Pål O., Kramer, Achim, Herzel, Hanspeter
Background: Virtually all living organisms have evolved a circadian (~24 hour) clock that controls physiological and behavioural processes with exquisite precision throughout the day/night cycle. The...
Global parameter search reveals design principles of the mammalian circadian clock (2008)
Locke, James C. W., Westermark, Pål O., Kramer, Achim, Herzel, Hanspeter
Background: Virtually all living organisms have evolved a circadian (~24 hour) clock that controls physiological and behavioural processes with exquisite precision throughout the day/night cycle. The...
Futschik, Matthias E., Herzel, Hanspeter
Motivation: Periodic processes play fundamental roles in organisms. Prominent examples are the cell cycle and the circadian clock. Microarray array technology has enabled us to screen complete sets...
BMC Systems Biology BioMed Central (2008)
James Cw Locke, Pål O Westermark, Achim Kramer, Hanspeter Herzel, Achim Kramer, Hanspeter Herzel
Research article Global parameter search reveals design principles of the mammalian circadian clock
Anddwain L. Eckberg, Hunter Holmes Mcguire, Henrik Seidel, Henrik Seidel, Hanspeter Herzel, ...
Seidel et al. Phase dependencies of the baroreflex H0836-5 MIP REV2 Page 1 Phase dependencies of the human baroreceptor reflex
W. Tecumseh Fitch, Ju Rgen Neubauer, Hanspeter Herzel
Calls out of chaos: the adaptive significance of nonlinear phenomena in mammalian vocal production
Jürgen Neubauer, Patrick Mergell, Ulrich Eysholdt, Hanspeter Herzel, Typeset Revtex
Spatio-temporal analysis of irregular vocal fold oscillations:
Mrowka, Ralf, Steege, Andreas, Kaps, Charlotte, Herzel, Hanspeter, Thiele, Bernd J., Persson, Pontus B., ...
Elucidating the mechanisms of the human transcriptional regulatory network is a major challenge of the post-genomic era. One important aspect is the identification and functional analysis of...
Synchronization-Induced Rhythmicity of Circadian Oscillators in the Suprachiasmatic Nucleus (2007)
Samuel Bernard, Didier Gonze, Branka Čajavec, Hanspeter Herzel, Achim Kramer
The suprachiasmatic nuclei (SCN) host a robust, self-sustained circadian pacemaker that coordinates physiological rhythms with the daily changes in the environment. Neuronal clocks within the SCN...
Comparison of human protein-protein interaction maps (2007)
Futschik, Matthias E., Chaurasia, Gautam, Herzel, Hanspeter
Motivation: Large-scale mappings of protein–protein interactions have started to give us new views of the complex molecular mechanisms inside a cell. After initial projects to systematically map...
Synchronization-Induced Rhythmicity of Circadian Oscillators in the Suprachiasmatic Nucleus (2007)
Samuel Bernard, Didier Gonze, Branka Cajavec, Hanspeter Herzel, Achim Kramer
The suprachiasmatic nuclei (SCN) host a robust, self-sustained circadian pacemaker that coordinates physiological rhythms with the daily changes in the environment. Neuronal clocks within the SCN...
Functional and Transcriptional Coherency of Modules in the Human Protein Interaction Network (2007)
Futschik, Matthias E., Chaurasia, Gautam, Tschaut, Anna, Russ, Jenny, Babu, M. Madan, Herzel, Hanspeter
Modularity is a major design principle in interaction networks. Various studies have shown that protein interaction networks in prokaryotes and eukaryotes display a modular structure. A majority of...
Flexible web-based integration of distributed large-scale human protein interaction maps (2007)
Chaurasia, Gautam, Iqbal, Yasir, Hänig, Christian, Herzel, Hanspeter, Wanker, Erich E., Futschik, Matthias E.
Protein-protein interactions constitute the backbone of many molecular processes. This has motivated the recent construction of several large-scale human protein-protein interaction maps [1-10]....
Comparison of human protein-protein interaction maps (2007)
Matthias E. Futschik, Gautam Chaurasia, Erich Wanker, Hanspeter Herzel
Abstract: Large-scale mappings of protein-protein interactions have started to give us new views of the complex molecular mechanisms inside a cell. After initial projects to systematically map...
Synchronization-induced rhythmicity of circadian oscillators in the suprachiasmatic nucleus (2007)
Bernard, Samuel, Gonze, Didier, Cajavec, Branka, Herzel, Hanspeter, Kramer, Achim
The suprachiasmatic nuclei (SCN) host a robust, self-sustained circadian pacemaker that coordinates physiological rhythms with the daily changes in the environment. Neuronal clocks within the SCN...
Synchronization-induced rhythmicity of circadian oscillators in the suprachiasmatic nucleus (2007)
Bernard, Samuel, Gonze, Didier, Cajavec, Branka, Herzel, Hanspeter, Kramer, Achim
The suprachiasmatic nuclei (SCN) host a robust, self-sustained circadian pacemaker that coordinates physiological rhythms with the daily changes in the environment. Neuronal clocks within the SCN...
UniHI: an entry gate to the human protein interactome (2007)
Chaurasia, Gautam, Iqbal, Yasir, Hänig, Christian, Herzel, Hanspeter, Wanker, Erich E., Futschik, Matthias E.
Systematic mapping of protein–protein interactions has become a central task of functional genomics. To map the human interactome, several strategies have recently been pursued. The generated...
Stefan Legewie, Nils Blüthgen, Hanspeter Herzel
The intrinsic, or mitochondrial, pathway of caspase activation is essential for apoptosis induction by various stimuli including cytotoxic stress. It depends on the cellular context, whether...
Stefan Legewie, Nils Blüthgen, Hanspeter Herzel
The intrinsic, or mitochondrial, pathway of caspase activation is essential for apoptosis induction by various stimuli including cytotoxic stress. It depends on the cellular context, whether...
Why do cells cycle with a 24 hour period? (2006)
Bernard, Samuel, Herzel, Hanspeter
A typical proliferating human cell divides on average every 24 h. This division timing allows cells to synchronize with other physiological processes and with the environment. The circadian clock,...
Why do cells cycle with a 24 hour period? (2006)
Bernard, Samuel, Herzel, Hanspeter
A typical proliferating human cell divides on average every 24 h. This division timing allows cells to synchronize with other physiological processes and with the environment. The circadian clock,...
UniHI: an entry gate to the human protein interactome (2006)
Chaurasia, Gautam, Iqbal, Yasir, Hänig, Christian, Herzel, Hanspeter, Wanker, Erich E., Futschik, Matthias E.
Systematic mapping of protein–protein interactions has become a central task of functional genomics. To map the human interactome, several strategies have recently been pursued. The generated...
Vanselow, Katja, Vanselow, Jens T., Westermark, Pål O., Reischl, Silke, Maier, Bert, Korte, Thomas, ...
PERIOD (PER) proteins are central components within the mammalian circadian oscillator, and are believed to form a negative feedback complex that inhibits their own transcription at a particular...
UniHI: an entry gate to the human protein interactome (2006)
Chaurasia, Gautam, Iqbal, Yasir, Hänig, Christian, Herzel, Hanspeter, Wanker, Erich E., Futschik, Matthias E.
Systematic mapping of protein–protein interactions has become a central task of functional genomics. To map the human interactome, several strategies have recently been pursued. The generated...
Ultrasensitization: Switch-Like Regulation of Cellular Signaling by Transcriptional Induction (2005)
Stefan Legewie, Nils Blüthgen, Reinhold Schäfer, Hanspeter Herzel
Cellular signaling networks are subject to transcriptional and proteolytic regulation under both physiological and pathological conditions. For example, the expression of proteins subject to covalent...
Measuring similarities between transcription factor binding sites (2005)
Kielbasa, Szymon M, Gonze, Didier, Herzel, Hanspeter
Abstract Background Collections of transcription factor binding profiles (Transfac, Jaspar) are essential to identify regulatory elements in DNA sequences. Subsets of highly similar profiles...
ULTRASENSITIZATION Switch-like Regulation of Cellular Signalling by Transcriptional Induction (2005)
Stefan Legewie, Nils Blüthgen, Reinhold Schäfer, Hanspeter Herzel
Cellular signalling networks are subject to transcriptional and proteolytic regulation under both physiological and pathological conditions. For example, the expression of proteins subject to...
Identification of cyanobacterial non-coding RNAs by comparative genome analysis (2005)
Axmann, Ilka M, Kensche, Philip, Vogel, Jörg, Kohl, Stefan, Herzel, Hanspeter, Hess, Wolfgang R
Abstract Background Whole genome sequencing of marine cyanobacteria has revealed an unprecedented degree of genomic variation and streamlining. With a size of 1.66 megabase-pairs, Prochlorococcus sp....
Identification of cyanobacterial non-coding RNAs by comparative genome analysis (2005)
Axmann, Ilka M., Kensche, Philip, Vogel, Jörg, Kohl, Stefan, Herzel, Hanspeter, Hess, Wolfgang R.
Background Whole genome sequencing of marine cyanobacteria has revealed an unprecedented degree of genomic variation and streamlining. With a size of 1.66 megabase-pairs, Prochlorococcus sp. MED4 has...
Truss, Matthias, Swat, Maciej, Kielbasa, Szymon M., Schäfer, Reinhold, Herzel, Hanspeter, Hagemeier, Christian
Small interfering RNAs (siRNAs) have become a standard tool in functional genomics. Once incorporated into the RNA-induced silencing complex (RISC), siRNAs mediate the specific recognition of...
Inferring combinatorial regulation of transcription in silico (2005)
Blüthgen, Nils, Kielbasa, Szymon M., Herzel, Hanspeter
In this paper, we propose a functional view on the in silico prediction of transcriptional regulation. We present a method to predict biological functions regulated by a combinatorial interaction of...
Bmc Bioinformatics, Hanspeter Herzel
Software Measuring similarities between transcription factor binding sites
Biological Profiling of Gene Groups utilizing Gene Ontology (2004)
Blüthgen, Nils, Brand, Karsten, Čajavec, Branka, Swat, Maciej, Herzel, Hanspeter, Beule, Dieter
Increasingly used high throughput experimental techniques, like DNA or protein microarrays give as a result groups of interesting, e.g. differentially regulated genes which require further biological...
Bifurcation analysis of the regulatory modules of the mammalian G1/S transition (2004)
Swat, Maciej, Kel, Alexander, Herzel, Hanspeter
Motivation: Mathematical models of the cell cycle can contribute to an understanding of its basic mechanisms. Modern simulation tools make the analysis of key components and their interactions very...
HOMGL--comparing genelists across species and with different accession numbers (2004)
Blüthgen, Nils, Kielbasa, Szymon M., Cajavec, Branka, Herzel, Hanspeter
Summary:Homology Gene List (HomGL) is a web-based tool for comparing gene lists with different accession numbers and identifiers and between different organisms. UniGene, LocusLink, HomoloGene and...
Optimizing property codes in protein data reveals structural characteristics (2003)
Olaf Weiss, Andreas Ziehe, Hanspeter Herzel
Abstract. We search for assignments of numbers to the amino acids (property codes) that maximize the autocorrelation function signal in given protein sequence data by an iterative method. Our method...
Optimizing Property Codes in Protein Data Reveals Structural Characteristics (2003)
Olaf Weiss, Andreas Ziehe, Hanspeter Herzel
We search for assignments of numbers to the amino acids (property codes) that maximize the autocorrelation function signal in given protein sequence data by an iterative method. Our method yields...
Vogel, Jörg, Axmann, Ilka M., Herzel, Hanspeter, Hess, Wolfgang R.
In contrast to certain model eubacteria, little is known as to where transcription is initiated in the genomes of cyanobacteria, which are largely distinct from other prokaryotes. In this work, 25...
Datenanalyse von Biochips: Von der Sequenz zum System (2002)
Herwig,Ralf, Schuchhardt,Johannes, Eickhoff,Holger, Herzel,Hanspeter, Lehrach,Hans
Die Zunahme unserer Kenntnisse über die molekularen Mechanismen u.a. von Wachstums-, Entwicklungs- und Differenzierungsprozessen hat die Grundlagen der molekularen Medizin innerhalb weniger Jahre...
Datenanalyse von Biochips: Von der Sequenz zum System (2002)
Herwig, Ralf, Schuchhardt, Johannes, Eickhoff, Holger, Herzel, Hanspeter, Lehrach, Hans
Die Zunahme unserer Kenntnisse über die molekularen Mechanismen u.a. von Wachstums-, Entwicklungs- und Differenzierungsprozessen hat die Grundlagen der molekularen Medizin innerhalb weniger Jahre...
Combining frequency and positional information to predict transcription factor binding sites (2001)
Kielbasa, Szymon M., Korbel, Jan O., Beule, Dieter, Schuchhardt, Johannes, Herzel, Hanspeter
Motivation: Even though a number of genome projects have been finished on the sequence level, still only a small proportion of DNA regulatory elements have been identified. Growing amounts of gene...
Average Mutual Information Of Coding And Noncoding Dna (2000)
Ivo Grosse, Sergey V. Buldyrev, H. Eugene Stanley, Dirk Holste, Hanspeter Herzel
Introduction DNA carries the genetic information of many living organisms, and one goal of genome projects is to extract that information. One basic problem in the analysis of DNA sequences is the...
Normalization strategies for cDNA microarrays (2000)
Schuchhardt, Johannes, Beule, Dieter, Malik, Arif, Wolski, Eryc, Eickhoff, Holger, Lehrach, Hans, ...
Multiple Arabidopsis thaliana clones from an experimental series of cDNA microarrays are evaluated in order to identify essential sources of noise in the spotting and hybridization process....
Are Noncoding Sequences of Rickettsia prowazekii Remnants of “Neutralized ” Genes? (1999)
Dirk Holste, Olaf Weiss, Ivo Grosse, Hanspeter Herzel
Abstract. It has been hypothesized that a large fraction of 24 % noncoding DNA in R. prowazekii consists of degraded genes. This hypothesis has been based on the relatively high G+C content of...
Are Noncoding Sequences of Rickettsia prowazekii Remnants of “Neutralized ” Genes? (1999)
Dirk Holste, Olaf Weiss, Ivo Grosse, Hanspeter Herzel
Abstract. It has been hypothesized that a large fraction of 24 % noncoding DNA in R. prowazekii consists of degraded genes. This hypothesis has been based on the relatively high G+C content of...
Correlations in protein sequences and property codes (1998)
Correlation functions in large sets of nonhomologous protein sequences are analyzed. Finite size corrections are applied and fluctuations are estimated. As symbol sequences have to be mapped to...
Generalized entropies through Bayesian estimation (1998)
Dirk Holste, Ivo Grosse, Hanspeter Herzel
opy H (R) q from observed data. The Bayesian estimator yields the smallest mean-squared deviation from the true parameter as compared with any other estimator. We compare the Bayesian entropy...
Detecting Bifurcations in Voice Signals (1997)
Hanspeter Herzel, Joachim Holzfuss, Zbigniew J. Kowalik, Robert Reuter
. This chapter is concerned with the detection of bifurcations in voice signals applying several techniques of sliding signal analysis --- conventional ones as well as novel methods originating from...
Modelling Heart Rate Variability due to Respiration and Baroreflex (1995)
Henrik Seidel, Hanspeter Herzel
This chapter is devoted to the interactions of heart beat, respiration, and blood pressure oscillations. A nonlinear model is derived which describes the essential parts of the baroreceptor loop:...
Normalization strategies for cDNA microarrays
Schuchhardt, Johannes, Beule, Dieter, Malik, Arif, Wolski, Eryc, Eickhoff, Holger, Lehrach, Hans, ...
Multiple Arabidopsis thaliana clones from an experimental series of cDNA microarrays are evaluated in order to identify essential sources of noise in the spotting and hybridization process....
Vogel, Jörg, Axmann, Ilka M., Herzel, Hanspeter, Hess, Wolfgang R.
In contrast to certain model eubacteria, little is known as to where transcription is initiated in the genomes of cyanobacteria, which are largely distinct from other prokaryotes. In this work, 25...
Truss, Matthias, Swat, Maciej, Kielbasa, Szymon M., Schäfer, Reinhold, Herzel, Hanspeter, Hagemeier, Christian
Small interfering RNAs (siRNAs) have become a standard tool in functional genomics. Once incorporated into the RNA-induced silencing complex (RISC), siRNAs mediate the specific recognition of...
Inferring combinatorial regulation of transcription in silico
Blüthgen, Nils, Kiełbasa, Szymon M., Herzel, Hanspeter
In this paper, we propose a functional view on the in silico prediction of transcriptional regulation. We present a method to predict biological functions regulated by a combinatorial interaction of...
Identification of cyanobacterial non-coding RNAs by comparative genome analysis
Axmann, Ilka M, Kensche, Philip, Vogel, Jörg, Kohl, Stefan, Herzel, Hanspeter, Hess, Wolfgang R
The first genome-wide and systematic screen for non-coding RNAs (ncRNAs) in cyanobacteria. Several ncRNAs were computationally predicted and their presence was biochemically verified. These ncRNAs...
Ultrasensitization: Switch-Like Regulation of Cellular Signaling by Transcriptional Induction
Legewie, Stefan, Blüthgen, Nils, Schäfer, Reinhold, Herzel, Hanspeter
Cellular signaling networks are subject to transcriptional and proteolytic regulation under both physiological and pathological conditions. For example, the expression of proteins subject to covalent...
Modeling Feedback Loops of the Mammalian Circadian Oscillator
Becker-Weimann, Sabine, Wolf, Jana, Herzel, Hanspeter, Kramer, Achim
The suprachiasmatic nucleus governs daily variations of physiology and behavior in mammals. Within single neurons, interlocked transcriptional/translational feedback loops generate circadian rhythms...
Spontaneous Synchronization of Coupled Circadian Oscillators
Gonze, Didier, Bernard, Samuel, Waltermann, Christian, Kramer, Achim, Herzel, Hanspeter
In mammals, the circadian pacemaker, which controls daily rhythms, is located in the suprachiasmatic nucleus (SCN). Circadian oscillations are generated in individual SCN neurons by a molecular...
Legewie, Stefan, Blüthgen, Nils, Herzel, Hanspeter
The intrinsic, or mitochondrial, pathway of caspase activation is essential for apoptosis induction by various stimuli including cytotoxic stress. It depends on the cellular context, whether...
Normalization strategies for cDNA microarrays
Schuchhardt, Johannes, Beule, Dieter, Malik, Arif, Wolski, Eryc, Eickhoff, Holger, Lehrach, Hans, ...
Multiple Arabidopsis thaliana clones from an experimental series of cDNA microarrays are evaluated in order to identify essential sources of noise in the spotting and hybridization process....
Vogel, Jörg, Axmann, Ilka M., Herzel, Hanspeter, Hess, Wolfgang R.
In contrast to certain model eubacteria, little is known as to where transcription is initiated in the genomes of cyanobacteria, which are largely distinct from other prokaryotes. In this work, 25...
Truss, Matthias, Swat, Maciej, Kielbasa, Szymon M., Schäfer, Reinhold, Herzel, Hanspeter, Hagemeier, Christian
Small interfering RNAs (siRNAs) have become a standard tool in functional genomics. Once incorporated into the RNA-induced silencing complex (RISC), siRNAs mediate the specific recognition of...
Inferring combinatorial regulation of transcription in silico
Blüthgen, Nils, Kiełbasa, Szymon M., Herzel, Hanspeter
In this paper, we propose a functional view on the in silico prediction of transcriptional regulation. We present a method to predict biological functions regulated by a combinatorial interaction of...
Identification of cyanobacterial non-coding RNAs by comparative genome analysis
Axmann, Ilka M, Kensche, Philip, Vogel, Jörg, Kohl, Stefan, Herzel, Hanspeter, Hess, Wolfgang R
The first genome-wide and systematic screen for non-coding RNAs (ncRNAs) in cyanobacteria. Several ncRNAs were computationally predicted and their presence was biochemically verified. These ncRNAs...
Ultrasensitization: Switch-Like Regulation of Cellular Signaling by Transcriptional Induction
Legewie, Stefan, Blüthgen, Nils, Schäfer, Reinhold, Herzel, Hanspeter
Cellular signaling networks are subject to transcriptional and proteolytic regulation under both physiological and pathological conditions. For example, the expression of proteins subject to covalent...
Modeling Feedback Loops of the Mammalian Circadian Oscillator
Becker-Weimann, Sabine, Wolf, Jana, Herzel, Hanspeter, Kramer, Achim
The suprachiasmatic nucleus governs daily variations of physiology and behavior in mammals. Within single neurons, interlocked transcriptional/translational feedback loops generate circadian rhythms...
Spontaneous Synchronization of Coupled Circadian Oscillators
Gonze, Didier, Bernard, Samuel, Waltermann, Christian, Kramer, Achim, Herzel, Hanspeter
In mammals, the circadian pacemaker, which controls daily rhythms, is located in the suprachiasmatic nucleus (SCN). Circadian oscillations are generated in individual SCN neurons by a molecular...
Legewie, Stefan, Blüthgen, Nils, Herzel, Hanspeter
The intrinsic, or mitochondrial, pathway of caspase activation is essential for apoptosis induction by various stimuli including cytotoxic stress. It depends on the cellular context, whether...
UniHI: an entry gate to the human protein interactome
Chaurasia, Gautam, Iqbal, Yasir, Hänig, Christian, Herzel, Hanspeter, Wanker, Erich E., Futschik, Matthias E.
Systematic mapping of protein–protein interactions has become a central task of functional genomics. To map the human interactome, several strategies have recently been pursued. The generated...
Vanselow, Katja, Vanselow, Jens T., Westermark, Pål O., Reischl, Silke, Maier, Bert, Korte, Thomas, ...
PERIOD (PER) proteins are central components within the mammalian circadian oscillator, and are believed to form a negative feedback complex that inhibits their own transcription at a particular...
Functioning and robustness of a bacterial circadian clock
Clodong, Sébastien, Dühring, Ulf, Kronk, Luiza, Wilde, Annegret, Axmann, Ilka, Herzel, Hanspeter, ...
Cyanobacteria are the simplest known cellular systems that regulate their biological activities in daily cycles. For the cyanobacterium Synechococcus elongatus, it has been shown by in vitro and in...
Synchronization-Induced Rhythmicity of Circadian Oscillators in the Suprachiasmatic Nucleus
Bernard, Samuel, Gonze, Didier, Čajavec, Branka, Herzel, Hanspeter, Kramer, Achim
The suprachiasmatic nuclei (SCN) host a robust, self-sustained circadian pacemaker that coordinates physiological rhythms with the daily changes in the environment. Neuronal clocks within the SCN...
Dissecting the action of an evolutionary conserved non-coding region on renin promoter activity
Mrowka, Ralf, Steege, Andreas, Kaps, Charlotte, Herzel, Hanspeter, Thiele, Bernd J., Persson, Pontus B., ...
Elucidating the mechanisms of the human transcriptional regulatory network is a major challenge of the post-genomic era. One important aspect is the identification and functional analysis of...
Global parameter search reveals design principles of the mammalian circadian clock
Locke, James CW, Westermark, Pål O, Kramer, Achim, Herzel, Hanspeter
Recurrent design patterns in the feedback regulation of the mammalian signalling network
Legewie, Stefan, Herzel, Hanspeter, Westerhoff, Hans V, Blüthgen, Nils
Biochemical networks are characterized by recurrent patterns and motifs, but the design principles underlying the dynamics of the mammalian intracellular signalling network remain unclear. We...
Molecular insights into human daily behavior
Brown, Steven A., Kunz, Dieter, Dumas, Amelie, Westermark, Pål O., Vanselow, Katja, Tilmann-Wahnschaffe, Amely, ...
Human beings exhibit wide variation in their timing of daily behavior. We and others have suggested previously that such differences might arise because of alterations in the period length of the...
Mathematical models in mammalian cell biology
Herzel, Hanspeter, Blüthgen, Nils
A report on the Conference on Systems Biology of Mammalian Cells, Dresden, Germany, 22-24 May 2008.
Competing Docking Interactions can Bring About Bistability in the MAPK Cascade
Legewie, Stefan, Schoeberl, Birgit, Blüthgen, Nils, Herzel, Hanspeter
Mitogen-activated protein kinases are crucial regulators of various cell fate decisions including proliferation, differentiation, and apoptosis. Depending on the cellular context, the Raf-Mek-Erk...
Regulation of Clock-Controlled Genes in Mammals
Bozek, Katarzyna, Relógio, Angela, Kielbasa, Szymon M., Heine, Markus, Dame, Christof, Kramer, Achim, ...
The complexity of tissue- and day time-specific regulation of thousands of clock-controlled genes (CCGs) suggests that many regulatory mechanisms contribute to the transcriptional output of the...
Biomechanics and control of vocalization in a non-songbird
Elemans, Coen P.H, Zaccarelli, Riccardo, Herzel, Hanspeter
The neuromuscular control of vocalization in birds requires complicated and precisely coordinated motor control of the vocal organ (i.e. the syrinx), the respiratory system and upper vocal tract. The...
How to Achieve Fast Entrainment? The Timescale to Synchronization
Granada, Adrián E., Herzel, Hanspeter
Entrainment, where oscillators synchronize to an external signal, is ubiquitous in nature. The transient time leading to entrainment plays a major role in many biological processes. Our goal is to...
Small RNAs Establish Delays and Temporal Thresholds in Gene Expression
Legewie, Stefan, Dienst, Dennis, Wilde, Annegret, Herzel, Hanspeter, Axmann, Ilka M.
Noncoding RNAs are crucial regulators of gene expression in prokaryotes and eukaryotes, but how they affect the dynamics of transcriptional networks remains poorly understood. We analyzed the...