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\LARGE {\bf Schriftenverzeichnis}
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%\begin{thebibliography}{99}
\subsection*{Publikationen in internationalen Journalen}
\vspace{0.2cm}
\begin{enumerate}

\bibitem{ebhese83}
W.~Ebeling, H.~Herzel, and E.~E. Selkov.
 The influence of noise on an oscillating glycolytic model.
 {\em studia biophysica}, 98, 147-154 (1983).


\bibitem{ebheen85}
W.~Ebeling, H.~Herzel, and H.~Engel-Herbert.
 On the entropy of dissipative structures.
 {\em Z. phys. Chem.}, 266, 253-256 (1985).

\bibitem{heeb85}
H.~Herzel and W.~Ebeling.
 The decay of correlations in chaotic maps.
 {\em Phys. Lett. A}, 111, 1-4 (1985).


\bibitem{kuhe86}
J.~Kurths and H.~Herzel.
 Can a solar pulsation event be characterized by a low-dimensional chaotic attractor?
 {\em Solar Physics}, 107, 39-45 (1986).

\bibitem{ebherisc86}
W.~Ebeling, H.~Herzel, W.~Richert, and L.~Schimansky-Geier.
 Influence of noise on {D}uffing - van der {P}ol oscillators.
 {\em Z. Angew. Math. Mech.}, 66, 141-146 (1986).

\bibitem{ebenhe86a}
W.~Ebeling, H.~Engel-Herbert, and H.~Herzel.
 On the entropy of dissipative and turbulent structures.
 {\em Ann. der Physik}, 43, 187-195 (1986).

\bibitem{sche86}
Th.~Schulmeister and H.~Herzel.
 Chaos in forced {S}elkov systems.
 {\em Z. Angew. Math. Mech.}, 66, 375-378 (1986).

\bibitem{kuhe87}
J.~Kurths and H.~Herzel.
 An attractor in a solar time series.
 {\em Physica D}, 25, 165-172 (1987).

\bibitem{hesc87a}
H.~Herzel and Th. Schulmeister.
 Quantitative description of chaos in a biochemical model.
 {\em Sys. Anal. Mod. Sim.}, 4, 113-124 (1987).

\bibitem{heebsc87}
H.~Herzel, W.~Ebeling, and Th. Schulmeister.
 Nonuniform chaotic dynamics and effects of noise in biochemical
  systems.
 {\em Zeitschr. Naturf.}, 42a, 136-142 (1987).


\bibitem{hepo87}
H.~Herzel and B.~Pompe.
 Effects of noise on a nonuniform chaotic map.
 {\em Phys. Lett. A}, 122, 121-125 (1987).

\bibitem{ebfehe87}
W.~Ebeling, R.~Feistel, and H.~Herzel.
 Dynamics and complexity of biomolecules.
 {\em Physica Scripta}, 35, 761-768 (1987).


\bibitem{anhe88}
A.S. Anishchenko and H.~Herzel.
 Noise-induced chaos in a system with homoclinic points.
 {\em Z. Angew. Math. Mech.}, 68, 317-318 (1988).

\bibitem{he88a}
H.~Herzel.
 Complexity of symbol sequences.
 {\em Sys. Anal. Mod. Sim.}, 5, 435-444 (1988).

\bibitem{he88b}
H.~Herzel.
 Stabilization of chaotic orbits by random noise.
 {\em Z. Angew. Math. Mech.}, 68, 582-583 (1988).

\bibitem{heeb90}
H.~Herzel and W.~Ebeling.
 Effects of noise and inhomogeneous attractors in biochemical systems.
 {\em Biomed. Biochem. Acta}, 49, 941-949 (1990).

\bibitem{mehewe90}
W.~Mende, H.~Herzel, and K.~Wermke.
 Bifurcations and chaos in newborn infant cries.
 {\em Phys. Lett. A}, 145, 418-424 (1990).

\bibitem{heplsv91}
H.~Herzel, P.~Plath, and P.~Svensson.
 Experimental evidence of homoclinic chaos and type {II} intermittency
  during the oxidation of methanol.
 {\em Physica D}, 48, 340-352 (1991).


\bibitem{gohegr92}
M.~G"ober, H.~Herzel, and H.~Graf.
 Dimension-analysis of {E}l {N}ino-{S}outhern {O}scillation time
  series.
 {\em Ann. Geophys.}, 10, 729-734 (1992).

\bibitem{he92}
H.~Herzel.
 Bifurcations and chaos in voice signals.
  {\em Appl. Mech. Rev.}. 46, 399-413 (1993).

\bibitem{sche93}
L.~Schimansky-Geier and H.~Herzel.
 Positive {L}yapunov-exponents in the {K}ramers- oscillator.
 {\em J. Stat. Phys.}, 70, 141-147 (1993).

\bibitem{scheeb93}
A.~Schmitt, H.~Herzel, and W.~Ebeling.
 A new method to calculate higher-order entropies from finite samples.
 {\em Europhys. Lett.}, 23, 303-309 (1993).

\bibitem{hebetisa93}
H.~Herzel, D.~Berry, I.~Titze, and M.~Saleh.
 Analysis of vocal disorders with methods from nonlinear dynamics.
 {\em J. Speech Hearing Research}, 37, 1008-1019 (1994).

\bibitem{hesceb93}
H.~Herzel, A.~Schmitt, and W.~Ebeling.
 Finite sample effects in sequence analysis.
 {\em Chaos, Solitons, and Fractals}, 4, 97-113 (1994).

\bibitem{behetikr93}
D.~A. Berry, H.~Herzel, I.~R. Titze, and K.~Krischer.
 Interpretation of biomechanical simulations of normal and chaotic
  vocal fold oscillations with empirical eigenfunctions.
 {\em J. Acoust. Soc. Am.}, 95, 3595-3604 (1994).

\bibitem{hemehesc94}
O.~Hess, D.~Merbach, H.~Herzel, and E.~Sch"oll.
  Bifurcations of a 3-torus in twin-stripe
semiconductor lasers.
 {\em Phys. Lett. A}, 195, 289-294 (1994).

\bibitem{heebsc94}
H.~Herzel, W.~Ebeling, and A.~O.~Schmitt.
 Entropies of biosequences - the role of repeats.
 {\em Phys. Rev. E}, 50, 5061-5071 (1994).

\bibitem{hegrhe94}
M.~M.~Hess, M.~Gross, and H.~Herzel.
 Hochgeschwindigkeitsaufnahmen von Schwingungsmoden der Stimmlippen.
 {\em Otorhinolaryngologia NOVA}, 4, 307-312 (1994).

\bibitem{hekn93}
H.~Herzel and C.~Knudsen.
 Bifurcations in a vocal fold model.
 {\em Nonlinear Dynamics}, 7, 53-64 (1995).


\bibitem{sthe95}
I.~Steinecke and H.~Herzel.
 Bifurcations in an asymmetric  vocal fold model.
  {\em J. Acoust. Soc. Am.}, 97, 1874-1884 (1995).

\bibitem{hebetist94}
H.~Herzel, D.~Berry, I.~Titze, and I.~Steinecke.
 Nonlinear Dynamics of the Voice: Signal Analysis and
Biomechanical Modeling.
 {\em CHAOS}, 5, 30-34 (1995).

\bibitem{hegr95}
H.~Herzel and I.~Gro"se.
 Measuring correlations in symbolic sequences.
{\em Physica A}, 216, 518-542 (1995).

\bibitem{mehe95}
D.~Merbach, O.~Hess, H.~Herzel, and E.~Sch"oll.
 Injection-induced bifurcations of transverse spatio-temporal patterns
 in semiconductor laser arrays.
 {\em Phys. Rev. E}, 52, 1571-1578 (1995).

\bibitem{hefr5}
H.~Herzel and J.~Freund.
Chaos, noise, and synchronization reconsidered.
   {\em Phys. Rev. E} 52, 3238-3241 (1995).

\bibitem{frhe94}
J.~Freund and H.~Herzel.
 The limit entropy for sequences constructed from composites.
 {\em Chaos, Solitons, and Fractals}, 7, 49-60 (1996).

\bibitem{sch95}
A.~O.~Schmitt, W.~Ebeling, and H.~Herzel.
 The modular structure of informational sequences.
{\em BioSystems}, 37, 199-210 (1996).

\bibitem{crepeau}
J.~C.~Crepeau and H.~Herzel.
  Comparison of Spectral Entropy with Statistical Entropy
  in Selected Physical Systems.
{\em J. Non-Equilib. Thermodyn.}, 21, 169-174 (1996).

\bibitem{be95}
D.~Berry, H.~Herzel, I.~Titze, and B.~Story.
  Bifurcations in excised larynx experiments.
  {\em J. of Voice}, 10, 129-138 (1996).

\bibitem{HNO}
M.~M.~Hess, H.~Herzel, O.~K"oster, F.~Scheurich und M.~Gross.
  Endoskopische Darstellung von Stimmlippenschwingungen:
  Digitale Hochgeschwindigkeitsaufnahmen mit verschiedenen Systemen.
  {\em HNO}, 44, 685-693 (1996).

\bibitem{AJP}
H.~Seidel, H.~Herzel, and D.~L.~Eckberg.
  Phase Dependences of the Human Baroreflex.
  {\em Am. J. Physiol.}, 41, H 2040-2053 (1997). 

\bibitem{coding}
H.~Herzel and I.~Gro"se.
  Correlations in DNA Sequences -- the Role of Protein Coding Segments.
  {\em Phys. Rev. E}, 55, 800-810 (1997).

\bibitem{tigges}
M.~Tigges, P.~Mergell, H.~Herzel, Th.~Wittenberg, and U.~Eysholdt.
  Observation and Modelling of Glottal Biphonation.
  {\em Acustica}, 83, 707-714 (1997).

\bibitem{son}
H.~Herzel and R.~Reuter.
  Whistle Register and Biphonation in a Child`s Voice.
  {\em Folia phoniatrica}, 49, 216-224 (1997).

\bibitem{eof}
J.~Arndt, H.~Herzel, S.~Bose, M.~Falcke, and E.~Sch"oll.
  Quantification of Transients using Empirical Orthogonal Functions.
  {\em Chaos, Solit. \& Fractals}, 8, 1911-1920 (1997).

\bibitem{spco}
P.~Mergell and H.~Herzel.
  Modelling Biphonation - The Role of the Vocal Tract.
  {\em Speech Communication}, 22, 141-154 (1997).

\bibitem{armin}
A.~O.~Schmitt and H.~Herzel.
  Estimating the Entropy of DNA Sequences.
  {\em J. theor. Biol.}, 188, 369-377 (1997).

\bibitem{olaf1}
O.~Weiss and H.~Herzel.
  Measuring Correlations in Protein Sequences.
  {\em Z. Phys. Chem.}, 204, 183-197 (1998).

\bibitem{inka}
I.~Wilden, H.~Herzel, G.~Peters, and G.~Tembrock.
  Subharmonics, Biphonation, and Deterministic Chaos in Mammal Vocalization.
  {\em Bioacoustics}, 9, 171-196 (1998).

\bibitem{phdIII}
H.~Seidel and H.~Herzel.
Bifurcations in a Nonlinear Model of the Baro\-receptor-Cardiac Reflex.
{\em Physica D}, 115, 145-160 (1998).

\bibitem{JTBII}
O.~Weiss and H.~Herzel.
  Correlations in Protein Sequences and Property Codes.
  {\em J. theor. Biol.}, 190, 341-353 (1998).

\bibitem{phaII}
H.~Herzel, E.~N.~Trifonov, O.~Weiss, and I.~Gro{\ss}e.
  Interpreting Correlations in Biosequences. 
  {\em Physica A}, 249, 449-459 (1998).

\bibitem{dirk}
D.~Holste, H.~Herzel, and I.~Gro{\ss}e.
  Bayes Estimators of Generalized Entropies.
  {\em J. Phys. A}, 31, 20551-20566 (1998).

\bibitem{onset}
P.~Mergell, H.~Herzel, Th.~Wittenberg, M.~Tigges, and U.~Eysholdt.
  Phonation Onset: Modelling and High Speed Glottography.
  {\em J. Acoust. Soc. Am.}, 104, 464-470 (1998).

\bibitem{IEEE0}
D.~Hoyer, B.~Pompe, H.~Herzel, and U.~Zwiener.
  Nonlinear Coordination of the Cardiovascular Autonomic Control.
  {\em IEEE Eng. Med. Biol.}, 17, 17-21 (1998).

\bibitem{strogatz}
H.~Herzel.
  How to quantify `small-world networks' ?.
  {\em Fractals}, 6, 301-303 (1998).

\bibitem{IEEE1}
H.~Seidel and H.~Herzel.
  Analyzing Entrainment of Heartbeat and Respiration with
  Surrogates.
  {\em IEEE Eng. Med. Biol.}, 17, 54-57 (1998).

\bibitem{IEEE2}
H.~Seidel and H.~Herzel.
  Modeling Wenckebach Rhythms and the Influence of the
  Baroreceptor-Cardiac Reflex.
  {\em IEEE Eng. Med. Biol.}, 17, 22-25 (1998).

\bibitem{JBSD}
H.~Herzel, O.~Weiss, and E.~N.~Trifonov.
  Sequence Periodicity in Complete Genomes of Archaea
  Suggests Positive Supercoiling.
  {\em J. Biomol. Struc. Dyn.}, 16, 341-345 (1998).

\bibitem{reviewvoice}
H.~Herzel.
  Nonlinear Dynamics of the Voice: Time Series Analysis,
  Modeling, and Experiments. 
  {\em Curr. Topics Acoust. Res.}, 2, 17-30 (1998).

\bibitem{bifchaos}
R.~Reuter, H.~Herzel, and R.~Orgelmeister.
  Simulations of Vocal Fold Vibrations with an Analog Circuit.
  {\em Int. J. Bifurc. \& Chaos}, 9, 1075-1088 (1999).

\bibitem{VM}
P.~Mergell, W.~T.~Fitch, and H.~Herzel.
  Modeling the Role of Non-Human Vocal Membranes on Phonation.
  {\em J. Acoust. Soc. Am.}, 105, 2020-2028 (1999).

\bibitem{bioinf}
H.~Herzel, O.~Weiss, and E.~N.~Trifonov.
  10--11 bp Periodicities in Complete Genomes Reflect Protein
  Structure and DNA Folding.
  {\em Bioinformatics}, 15, 187--193 (1999).

\bibitem{acustica}
H.~Herzel and R.~Reuter.
  Quantifying Correlations in Pitch- and Amplitude 
  Contours of Sustained Phonation.
  {\em Acustica \& Acta Acustica}, 86, 129--135 (2000).

\bibitem{ivoPRE}
I.~Grosse, H.~Herzel, S.~V.~Buldyrev, H.~E.~Stanley.
  Species Independence of Mutual Information
  in Coding and Noncoding DNA.
  {\em Phys. Rev. E}, 61, 5624--5629 (2000).

\bibitem{toJASA} 
T.~Riede, H.~Herzel, D.~Mehwald, W.~Seidner, E.~Trumler, G.~B"ohme,
and G.~Tembrock.
  Nonlinear Phenomena in the Natural Howling of a Dog-Wolf Breed.
  {\em J. Acoust. Soc. Am.}, 108, 1435--1442 (2000).

\bibitem{NAR}
J.~Schuchhardt, D.~Beule, A.~Malik, E.~Wolski, H.~Eickhoff,
H.~Lehrach, and H.~Herzel. 
  Normalization Strategies for cDNA-Arrays.
  {\em Nucl. Acids Res.}, 28:~e47~i--v (2000).

\bibitem{H}
O.~Weiss, M.~Jimenez-Montano, H.~Herzel.
  Information content of protein sequences.
  {\em J. theor. Biol.}, 206, 379--386 (2000).

\bibitem{JME}
D.~Holste, O.~Weiss, I.~Gro{\ss}e, and H.~Herzel.
  Are non--coding sequences of {\it Rickettsia prowazekii}
  remnants of `neutralized' genes ?
  {\em J. Mol. Evol.}, 51, 353--362 (2000). 

\bibitem{chi}
D.~Holste, I.~Grosse, S.~V.~Buldyrev, H.~E.~Stanley, H.~Herzel.
  Optimization of Protein Coding Measures using Positional
  Dependence of Nucleotide Frequencies.
  {\em J. theor. Biol.}, 206, 525--537 (2000).

\bibitem{JASA4}
P.~Mergell, H.~Herzel, and I.~R.~Titze.
  Irregular Vocal Fold Vibration -- High-Speed Observation
  and Modeling.
  {\em J. Acoust. Soc. Am.}, 108, 2996--3002 (2000).

\bibitem{boston}
D.~Holste, I.~Grosse, and H.~Herzel.
  Entropy Estimation from Finite Data Samples.
  {\em InterJournal}, 267, 1--8 (2000).

\bibitem{chaos}
H.~Herzel, D.~Beule, S.~Kielbasa, J.~Korbel, C.~Sers,
A.~Malik, H.~Eickhoff, H.~Lehrach, and J.~Schuchhardt.
  Extracting Information from cDNA Arrays.
  {\em CHAOS}, 11, 98--107 (2001).

\bibitem{chr22}
D.~Holste, I.~Grosse, and H.~Herzel.
  Statistical Analysis of the DNA Sequence of Human Chromosome 22.
  {\em Phys. Rev. E}, 64:~041917 (2001).

\bibitem{szymon}
Sz.~M.~Kie{\l}basa, J.~O.~Korbel, D.~Beule, J.~Schuchhardt, and H.~Herzel.
    Combining frequency and positional information to predict 
    transcription factor binding sites.
    {\em Bioinformatics}, 17, 1019--1026 (2001).

\bibitem{tobias2}
T.~Riede, H.~Herzel, K.~Hammerschmidt, L.~Brunnberg, and G.~Tembrock.
   The harmonics-to-noise ratio applied to dog barks.
   {\em J.~Acoust. Soc.~Am.}, 110, 2191--2197 (2001).

\bibitem{Juergen}
J.~Neubauer, H.~Herzel, P.~Mergell, and U.~Eysholdt.
   Spatio--temporal analysis of irregular vocal fold oscillations:
   Biphonation due to desynchronization of spatial modes.
   {\em J.~Acoust.~Soc.~Am.}, 110, 3179--3192 (2001).

\bibitem{ralph}
R.~Mrowka, A.~Patzak, and H.~Herzel.
   Is there a bias in proteome research?
   {\em Genome Research}, 11, 1971--1973 (2001).

\bibitem{tecAB}
W.~T.~Fitch, J.~Neubauer, and H.~Herzel.
Calls out of Chaos: The Adaptive Significance of Nonlinear Phenomena
in Mammalian Vocal Production.
  {\em Animal Behav.}, 63, 407--418 (2002).

\bibitem{CZ}
C.~Zemlin, E.~Storch, and H.~Herzel.
   Alternans and 2:1 rhythms in an ionic model of heart cells.
   {\em Biosystems}, 66, 1--10 (2002).

\bibitem{peptides}
U.~Reineke, C.~Ivascu, M.~Schlief, C.~Landgraf, S.~Gericke, G.~Zahn, 
   H.~Herzel, R.~Volkmer-Engert, J.~Schneider-Mergener.
   Identification of distinct antibody epitopes and mimotopes from a 
   peptide array of 5520 randomly generated sequences.
   {\em J.~ Immunological Methods}, 267, 37--51 (2002).

\bibitem{isao}
I.~Tokuda, T.~Riede, J.~Neubauer, M.~J.~Owren, and H.~Herzel.
   Nonlinear analysis of irregular animal vocalizations.
   {\em J.~Acoust.~Soc.~Am.}, 111, 2908--2919 (2002).

\bibitem{ilkaNAR}
J.~Vogel, I.~Axmann, H.~Herzel, W.~Hess.
   Experimental and computational analysis of transcriptional start
   sites in the cyanobacterium.
   {\em Nucleic Acids Research}, 31, 2890--2899 (2003).

\bibitem{nilsJTB}
   N.~Bluethgen, H.~Herzel.
   How robust are switches in intracellular signaling
   cascades?
   {\em J.~theor.~Biol.}, 225, 293--300 (2003).

\bibitem{dirkPRE}
   D.~Holste, I.~Grosse, S.~Beirer, P.~Schieg, H.~Herzel.
   Repeats and correlations in human DNA sequences.
   {\em Phys. Rev. E}, 67:~061913 (2003). 

\bibitem{michael2}
M.~Edgerton, J.~Neubauer, and H.~Herzel.
   Nonlinear Phenomena in Contemporary Vocal Musical
   Composition and Performance.
   {\em Perspectives of New Music}, 41, 30--65 (2003).

\bibitem{peters}
   G.~Peters, M.~L.~East, H.~Herzel, J.~R.~Henschel,
   M.~G.~L.~Mills, K.~Wilhelm, and H.~Hofer.
   Spotted hyaena whoops: frequent incidence of vocal
   instabilities in a mammalian loud call.
   {\em Bioacoustics}, 14, 99--109 (2004).

\bibitem{homGL}
   N.~Bluethgen, S.~M.~Kielbasa, B.~Cajavec, and H.~Herzel.
   HOMGL -- comparing genelists across species and with
   different accession numbers.
   {\em Bioinformatics}, 20, 125--126 (2004).

\bibitem{jvoice2}
   J.~Neubauer, M.~Edgerton, and H.~Herzel.
   Nonlinear Phenomena in Contemporary Vocal Music.
   {\em J. of Voice}, 18, 1--12 (2004).

\bibitem{G1S}
   M.~Swat, A.~Kel, and H.~Herzel.
   Bifurcation Analysis of the Regulatory Modules
   of the Mammalian G1/S Transition.
   {\em Bioinformatics}, 20, 1506--1511 (2004).

\bibitem{kyotoSzy}
S.~M.~Kielbasa, N.~Bluethgen, C.~Sers, R.~Schaefer, and H.~Herzel.
   Prediction of cis-regulatory elements of coregulated genes.
   {\em Genome Informatics}, 15, 117--124 (2004).

\bibitem{kiran}
   K.~K.~Challapalli, C.~Zabel, J.~Schuchhardt, A.~M.~Kaindl, J.~Klose, H.~Herzel.
   High reproducibility of large gel two dimensional electrophoresis.
   {\em Electrophoresis}, 25, 3040--3047 (2004).

\bibitem{mrowka2}
   R.~Mrowka, A.~Patzak, H.~Herzel, and D.~Holste.
   Sequence-related human protein cluster by degree of
   evolutionary conservation.
   {\em Phys. Rev. E}, 70:~051908 (2004).

\bibitem{schieg}
   P.~Schieg and H.~Herzel.
   Periodicities of 10--11 bp as Indicators of the Supercoiled State
   of Genomic DNA.
   {\em J. Mol. Biol.}, 343, 891--901 (2004).

\bibitem{sabine}
   S.~Becker-Weimann, J.~Wolf, H.~Herzel, and A.~Kramer.
   Modeling Feedback Loops of the Mammalian Circadian Oscillator.
   {\em Biophys. J.}, 87, 3023--3034 (2004).

\bibitem{kyotoSab}
S.~Becker--Weimann, J.~Wolf, A.~Kramer, and H.~Herzel.
   A model of the mammalian circadian oscillator including
   the REV-ERB$\alpha$ module.
   {\em Genome Informatics}, 15, 3--12 (2004).

\bibitem{florian}
   F.~Geier, S.~Becker-Weimann, A.~Kramer, and H.~Herzel.
   Entrainment in a Model of the Mammalian Circadian Oscillator.
   {\em J. Biol. Rhythms}, 20, 83--93 (2005).

\bibitem{siRNA}
   M.~Truss, M.~Swat, S.~M.~Kielbasa, R.~Schafer, H.~Herzel, and C.~Hagemeier.
   HuSiDa -- the human siRNA database: an open--access database for published
   functional siRNA sequences and technical details of efficient transfer into
   recipient cells. 
   {\em Nucleic Acids Research}, 33, D108--D111 (2005).

\bibitem{isao2}
   I.~Tokuda and H.~Herzel.
   Detecting synchronizations in an asymmetric vocal fold model from time
   series data.
   {\em Chaos}, 15:~013702 (2005).

\bibitem{TFgossip}
   N.~Bluethgen, S.~M.~Kielbasa, and H.~Herzel.
   Infering combinatorial regulation of transcription in silico.
   {\em Nucleic Acids Research}, 33, 272--279 (2005).

\bibitem{synchro}
   D.~Gonze, S.~Bernard, C.~Waltermann, A.~Kramer and H.~Herzel.
   Spontaneous synchronization of coupled circadian oscillators.
   {\em Biophys. J.}, 89, 120--129 (2005).

\bibitem{branka1}
   N.~Bluethgen, K.~Brand, B.~Cajavec, M.~Swat, H.~Herzel, and D.~Beule.
   Biological profiling of Gene Groups Utilizing Gene Ontology.
   {\em Genome Informatics}, 16, 106--115 (2005).

\bibitem{stefan1} 
   S.~Legewie, N.~Bluethgen, and H.~Herzel.
   Quantitative Analysis of Ultrasensitive Responses.
   {\em FEBS J.}, 272, 4071--4079 (2005).

\bibitem{branka1}
   B.~Cajavec, S.~Bernard, and H.~Herzel.
   Aggregation in Huntington's Disease: Insights Through Modelling.
   {\em Genome Informatics}, 16, 262--271 (2005).

\bibitem{philipp}
   I.~M.~Axmann, P.~Kensche, J.~Vogel, S.~Kohl, H.~Herzel, and W.~R.Hess.
   Identification of cyanobacterial non--coding RNAs by comparative genome analysis.
   {\em Genome Biology}, 6:~R73 (2005).

\bibitem{szyBMC} 
   S.~Kielbasa, D.~Gonze, and H.~Herzel.
   Measuring similarities between transcription factor binding sites.
   {\em BMC Bioinformatics}, 6:~237 (2005).

\bibitem{stefanPLoS}
   S.~Legewie, N.~Bluethgen, R.~Schafer, and H.~Herzel.
   ULTRASENSITIZATION Switch--like Regulation of Cellular Signalling by Transcriptional Induction.
   {\em PLoS Computational Biology}, 1:~e54 (2005). 

\bibitem{brand}
   O.~R.~Bandapalli, M.~Geheeb, D.~Kobelt, K.~Kuehnle, S.~Elezkurtaj,
   J.~Herrmann, A.~M.~Gressner, R.~Weisskirchen, D.~Beule, N.~Bluethgen,
   H.~Herzel, C.~Franke, and K.~Brand.
   Global analysis of host tissue gene expression in the invasive
   front of colorectal liver metastases.
   {\em Int. J. of Cancer}, 118, 74--89 (2006).

\bibitem{hes1}
   S.~Bernard, B.~Cajavec, L.~Pujo--Menjouet, M.~C.~Mackey, and H.~Herzel.
   Modeling transcriptional feedback loops: The role of Gro/TLE1 in
   Hes1 oscillations. {\em Phil. Trans. Royal Soc.}, 364, 1155--1170 (2006).

\bibitem{AO}
   B.~Cajavec, H.~Herzel, and S.~Bernard.
   Clustered neuronal death contributes to variance of age at onset in
   Huntington's disease. {\em Neurogenetics}, 7, 21--25 (2006).

\bibitem{PH}
   P.~Hammerstein, E.~H.~Hagen, A.~V.~M.~Herz, and H.~Herzel.
   Robustness: A key to evolutionary design.
   {\em Biological Theory}, 1, 90--93 (2006).

\bibitem{sequestr}
   N.~Bluethgen, F.~J.~Bruggemann, S.~Legewie, H.~Herzel, H.~V.~Westerhoff, and B.~N.~Kholodenko.
   Effects of Sequestration on Signal Transduction Cascades. 
   {\em FEBS J.}, 273, 895--906 (2006).

\bibitem{babis}
   H.~Hatzikirou, W.~T.~Fitch, and H.~Herzel. Voice instabilities due to source-tract
   interactions. {\em Acustica}, 92, 468--475 (2006).

\bibitem{lokesh}
   L.~Kumar, M.~Futschik, and H.~Herzel. DNA Motifs and Sequence Periodicities.
   {\em In Silico Biology}, 6: 71--78 (2006). 

\bibitem{lund}
   P.~Lund, K.~Weisshaupt, T.~Mikeska, D.~Jammas, X.~Chen, R.-J.~Kuban,
   U.~Ungethuem, U.~Krapfenbauer, H.~Herzel, R.~Schaefer, J.~Walter, and C.~Sers.
   Oncogenic HRAS suppresses clusterin cxpression through promoter hypermethylation.
   {\em Oncogene}, 25, 4880--4893 (2006).

\bibitem{apoptPLoS}
   S.~Legewie, N.~Bluethgen, and H.~Herzel.
   Mathematical Modeling Identifies Inhibitors of Apoptosis (IAPs) as 
   Mediators of Positive Feedback and Bistability.
   {\em PLoS Computational Biology}, 9, e120 (2006).
   \newline
   [highlighted in {\em Science} 314, 389 (2006)and in {\em Nature} 445, 823 (2007)]

\bibitem{riccardo}
   R.~Zaccarelli, C.~Elemans, W.~T.~Fitch, and H.~Herzel.
   Modelling Bird Songs: Voice Onset, Overtones and Registers.
   {\em Acustica}, 92, 741--748 (2006).

\bibitem{gautam}
   G.~Chaurasia, H.~Herzel, E.~Wanker, and M.~Futschik.
   Systematic Functional Assessment of Human Protein-Protein
   Interaction Maps. {\em Genome Informatics}, 17, 36--45 (2006).

\bibitem{FASPS}
   K.~Vanselow, J.~T.~Vanselow, P.~O.Westermark, S.~Reischl, B.~Maier, T.~Korte,
   A.~Herrmann, H.~Herzel, A.~Schlosser, and A.~Kramer.
   Differential effects of PER2 phosphorylation: molecular basis for the human
   familial advanced sleep phase syndrome (FASPS).
   {\em Genes and Development}, 20, 2660--2672 (2006).

\bibitem{24h}
   S.~Bernard and H.~Herzel.
   Why do cells cycle with a 24 hour period?
   {\em Genome Informatics}, 17, 72--79 (2006).

\bibitem{MaFuNAR}
   G.~Chaurasia, Y.~Iqbal, C.~Haenig, H.~Herzel, E.~E.~Wanker, and M.~E.~Futschik.
   UniHI: An Entry Gate to the Human Protein Interactome.
   {\em Nucleic Acids Research}, 35, D590--D594 (2007).

\bibitem{cyano}
   S.~Clodong, U.~Duehring, L.~Kronk, A.~Wilde, I.~Axmann, H.~Herzel,
   and M.~Kollmann. Functioning and robustness of a bacterial circadian
   clock. {\em Molecular Systems Biology}, 3:90 (2007).

\bibitem{mfuBioinf}
   M.~E.~Futschik, G.~Chaurasia, E.~Wanker, and H.~Herzel.
   Comparison of Human Protein-Protein Interaction Maps.
   {\em Bioinformatics}, 23, 605--611 (2007).

\bibitem{syncSamuel}
   S.~Bernard, D.~Gonze, B.~Cajavec, H.~Herzel, and A.~Kramer.
   Synchronization-Induced Rhythmicity of Circadian Oscillators
   in the Suprachiasmatic Nucleus. 
   {\em PLoS Computational Biology}, 3:e68 (2007).

\bibitem{gautamIB}
   G.~Chaurasia, Y.~Iqbal, C.~Haenig, H.~Herzel, E.~E.~Wanker, and M.~E.~Futschik.
   Flexible web-based integration of distributed large-scale human protein
   interaction maps.
   {\em J. Integrative Bioinformatics}, 4:51 (2007).

\bibitem{isaoSvec}
   I.~Tokuda, J.~Horacek, J.~G.~Svec, and H.~Herzel.
   Comparison of biomechanical modeling of register transitions and voice instabilities 
   with excised larynx experiments.
   {\em J. Acoust. Soc. Am.}, 122, 519--531 (2007).

\bibitem{futschikIBSB}
   M.~Futschik, G.~Chaurasia, and H.~Herzel.
   Graph theoretical comparison reveals structural divergence of human protein interaction networks.
   {\em Genome Informatics}, 18, 141--151 (2007).

\bibitem{MEK}
   S.~Legewie, B.~Schoeberl, N.~Bluethgen, and H.~Herzel.
   Competing docking interactions can bring about bistability
   in the MAPK cascade.
   {\em Biophys. J.}, 93, 2279--2288 (2007).

\bibitem{szymanIBSB}
   S.~Kielbasa, H.~Herzel, and I.~Axmann.
   Regulatory elements of marine cyanobacteria.
   {\em Genome Informatics}, 18, 1--11 (2007).

\bibitem{mrowkanils}
   R.~Mrowka, A.~Steege, C.~Kaps, H.~Herzel, B.~J.~Thiele, P.~B.~Persson, and N.~Bluethgen.
   Dissecting the action of an evolutionary conserved non-coding region
   on renin promoter activity.
   {\em Nucleic Acids Research}, 35, 5120--5129 (2007).

\bibitem{ilkaIBSB}
   I.~Axmann, S.~Legewie, and H.~Herzel.
   A minimal circadian clock model.
   {\em Genome Informatics}, 18, 54--64 (2007).

\bibitem{reischl}
   S.~Reischl, K.~Vanselow, P.~O.~Westermark, N.~Thierfelder, B.~Maier, H.~Herzel,
   and A.~Kramer.  beta-TrCP1 mediated degradation of PERIOD2 is essential for
   circadian dynamics. {\em J. Biol. Rhythms}, 22, 375--386 (2007).

\bibitem{kasia}
   Promoter analysis of mammalian clock controlled genes.
   K.~Bozek, S.~Kielbasa, A.~Kramer, and H.~Herzel.
   {\em Genome Informatics}, 18, 65--74 (2007).

\bibitem{coen}
   C.~Elemans, R.~Zaccarelli, and H.~Herzel.
   Biomechanics and control of vocalisation in a non-songbird.
   {\em J. Royal Soc. Interface}, 5, 691--703 (2008).

\bibitem{isaoChaosregisters}
   I.~Tokuda, J.~Horacek, J.~G.~Svec, and H.~Herzel.
   Bifurcations and chaos in register transitions of excised larynx experiments.
   {\em Chaos}, 18:013102 (2008).

\bibitem{stevePNAS}
   S.~A.~Brown, D.~Kunz, A.~Dumas, P.~O.~Westermark, K.~Vanselow,
   A.~Tilmann-Wahnschaffe, H.~Herzel, and A.~Kramer.
   Molecular Insights into Human Daily Behavior.
   {\em Proc. Nat. Acad. Sci. USA}, 105, 1602--1607 (2008).

\bibitem{AR}
   M.~Futschik and H.~Herzel. Are we overestimating the number of cell-cycling genes?   
   The impact of background models on time series analysis.
   {\em Bioinformatics}, 24, 1063--1069 (2008).

\bibitem{jetlag}
   J.~C.~W.~Locke, P.~O.~Westermark, A.~Kramer, and H.~Herzel.
   Global parameter search reveals design principles of the mammalian circadian clock.
   {\em BMC Systems Biology}, 2:22 (2008).

\bibitem{liverG1S}
    A.~Chauhan, S.~Legewie, P.~O.~Westermark, S.~Lorenzen, and H.~Herzel.
    A mesoscale model for G1/S phase transition in liver regeneration.
    {\em J. Theor. Biol.}, 252, 465--473 (2008).

\bibitem{nilsMSB}
   S.~Legewie, H.~Herzel, H.~V.~Westerhoff, and N.~Bluethgen.
   Recurrent design patterns in the feedback regulation of the mammalian
   signalling network.
   {\em Mol. Syst. Biol.}, 4:190 (2008).

\bibitem{manu08}
   M.~Benary, H.~Bendfeldt, R.~Baumgrass, and H.~Herzel.
   Modeling IL--2 gene expression in human regulatory T--cells.
   {\em Genome Informatics}, 20, 222--230 (2008).

\bibitem{RNAilka}
   S.~Legewie, D.~Dienst, A.~Wilde, H.~Herzel, and I.~M.~Axmann.
   Small RNAs establish delays and temporal thresholds in gene expression.
   {\em Biophys. J.}, 95, 3232--3238 (2008).

\bibitem{dresden}
   H.~Herzel and N.~Bluethgen.
   Mathematical models in mammalian cell biology.
   {\em Genome Biology}, 9:316 (2008).

\bibitem{stefanTumorSupp}
   S.~Legewie, C.~Sers, and H.~Herzel.
   Kinetic mechanisms for overexpression insensitivity and oncogene cooperation.
   {\em FEBS Lett.}, 583, 93--96 (2009).

\bibitem{dusp6}
   N.~Bluethgen, S.~Legewie, S.~M.~Kielbasa, A.~Schramme, O.~Tchernitsa, J.~Keil, A.~Solf, M.~Vingron, R.~Schaefer, H.~Herzel, and C.~Sers.
   A systems biological approach suggests that transcriptional feedback regulation by dual-specificity phosphatase 6 shapes extracellular 
   signal-related kinase activity in RAS-transformed fibroblasts.
   {\em FEBS Journal}, 276, 1024--1035 (2009).

\bibitem{PRCs}
   A.~Granada, R.~M.~Hennig, B.~Ronacher, A.~Kramer, and H.~Herzel.
   Phase response curves elucidating the dynamics of coupled oscillators.
   {\em Methods Enzymol.}, 454, 1--27 (2009).

\bibitem{kasiaPONE}
   K.~Bozek, A.~Relogio, S.~M.~Kielbasa, M.~Heine, C.~Dame, A.~Kramer, and H.~Herzel.
   Regulation of clock-controlled genes in mammals. {\em PLoS ONE}, 4:e4882 (2009).

\bibitem{ow}
   O.~Wolkenhauer, D.~Fell, P. De Meyts, N.~Bluethgen, H.~Herzel, N. Le Novere, T.~Hoefer,
   K.~Schuerrle, and I. van Leeuven.
   Advancing systems biology for medical applications.
   {\em IET Systems Biology}, 3, 131--136 (2009).

\bibitem{adrian}
   A.~Granada and H.~Herzel.
   How to achieve fast entrainment? The timescale to synchronization.
   {\em PLoS ONE}, 4:e7057 (2009). 

\bibitem{pal}
   P.~Westermark, D.~K.~Welsh, H.~Okamura, and H.~Herzel.
   Quantification of circadian rhythms in single cells.
   {\em PLoS Computational Biology}, 5:e1000580 (2009).

\bibitem{yuhien}
   Y.H.~Lee, M.~Benary, R.~Baumgrass, and H.~Herzel.
   Prediction of regulatory transcription factors in T helper cell differentiation and maintenance.
   {\em Genome Informatics}, 22, 84--94 (2010).

\bibitem{olaf2}
   O.~Wolkenhauer, C.~Auffray, S.~Baltrusch, N.~Bluethgen, H.~Byrne, M.~Cascante,
   A.~Ciliberto, T.~Dale, D.~Drasdo, D.~Fell, J.~Ferrell Jr., D.~Gallahan, R.~Gatenby,
   U.~Guenther, B.~D.~Harms, H.~Herzel, C.~Junghanns, M.~Kunz, I.~van Leeuwen, P.~Lenormand,
   F.~Levi, M.~Linnebacher, J.~Lowengrub, P.~K.~Maini, A.~Malik, K.~Rateitschak, O.Sansom,
   R.~Schaefer, K.~Schuerrle, C.~Sers, S.~Schnell, D.~Shibata, J.~Tyson, J.~Vera, M.~White,
   B.~Zhivotovsky, and R.~Jaster.
   Systems biologists seek fuller integration of systems biology approaches in new cancer
   research programs.
   {\em Cancer Research}, 70, 12--13 (2010).
    
\bibitem{registers2}
   I.T.~Tokuda, M.~Zemke, M.~Kob, and H.~Herzel.
   Biomechanical modeling of registertransitions and the role of vocal tract resonators.
   {\em J. Acoust. Soc. Am.}, 127, 1528--1536 (2010).

\bibitem{chrono}
   S.~Bernard, B.~Cajavec Bernard, F.~Levi, and H.~Herzel.
   Tumor growth rate determines the timing of optimal chronomodulated treatment schedules.
   {\em PLoS Computational Biology}, 6:~e1000712 (2010).

\bibitem{agnes}
   K.~Bozek, A.~L.~Rosahl, S.~Gaub, S.~Lorenzen, and H.~Herzel.
   Circadian transcription in liver.
   {\em Biosystems}, 102, 61--69 (2010).

\bibitem{MSB}
   U.~Abraham, A.~E.~Granada, P.~O.~Westermark, M.~Heine, A.~Kramer, and H.~Herzel.
   Coupling governs entrainment range of circadian clocks.
   {\em Molecular Systems Biology}, 6:~438 (2010).

\bibitem{karsten}
   K.~Juerchott, R.~J.~Kuban, T.~Krech, N.~Bluethgen, U.~Stein, W.~Walther, C.~Friese, S.~M.~Kielbasa, 
   U.~Ungethuem, P.~Lund, T.~Knoesel, W.~Kemmner, M.~Morkel, J.~Fritzmann, P.~M.~Schlag, W.~Birchmeier,
   T.~Krueger, S.~Sperling, C.~Sers, H.~D.~Royer, H.~Herzel, and R.~Schaefer.
   Identification of Y-box binding protein 1 as a core regulator of MEK/ERK pathway-dependent
   gene signatures in colorectal cancer. 
   {\em PLoS Genet.}, 6:~e1001231 (2010). 

\bibitem{rats}
   A.~E.~Granada, T.~Cambras, A.~Diez-Noguera, and H.~Herzel.
   Circadian desynchronization. {\em J. Royal Society Interface Focus},
   1, 153--166 (2011).

\bibitem{malte}
   M.~Kob, N.~Henrich, D.~Howard, H.~Herzel, I.~Tokuda, and J.~Wolfe.
   Analysing and understanding the singing voice: recent progress and open questions.
   {\em Current Bioinformatics}, 6, 362--374 (2011). 

\bibitem{anu2}
   A.~Chauhan, S.~Lorenzen, H.~Herzel, and S.~Bernard.
   Regulation of mammalian cell cycle progression in the regenerating liver.
   {\em J. Theor. Biol.}, 283, 103--112 (2011). 

\bibitem{joern}
   K.~L.~Jost, S.~Haase, D.~Smeets, N.~Schrode, J.~M.~Schmiedel, B.~Bertulat, H.~Herzel, M.~Cremer, M.~C.~Cardoso.
   3D-Image analysis platform monitoring relocation of pluripotency genes during reprogramming.
   {\em Nucleic Acids Res.}, 39:e113 (2011).

\bibitem{angela}
   A.~Relogio, P.~O.~Westermark, T.~Wallach, K.~Schellenberg, A.~Kramer, and H.~Herzel.
   Tuning the Mammalian Circadian Clock: Robust Synergy of Two Loops.
   {\em PLoS Computational Biology}, 7:e100230 (2011).

\bibitem{manu1}
   H.~Bendfeldt, M.~Benary, T.~Scheel, S.~Frischbutter, A.~Abajyan, A.~Radbruch, H.~Herzel, and R.~Baumgrass.
   Stable IL-2 decision making by endogenous c-Fos amounts in peripheral memory T-helper cells.
   {\em J. Biol. Chem.}, 287, 18386-18397 (2012). 

\bibitem{iwona}
   I.~Stelniec-Klotz, S.~Legewie, O.~Tchernitsa, F.~Witzel, B.~Klinger, C.~Sers, H.~Herzel, N.~Bluethgen, and R.~Schafer.
   Reverse engineering a hierarchical regulatory network downstream of oncogenic KRAS. {\em Molecular Systems Biology}, 8:601 (2012).

\bibitem{manu2}
   H.~Bendfeldt, M.~Benary, T.~Scheel, K.~Steinbrink, A.~Radbruch, H.~Herzel, and R.~Baumgrass.
   IL-2 Expression in Activated Human Memory FOXP3(+) Cells Critically Depends on the Cellular Levels of FOXP3 as Well as of Four 
   Transcription Factors of T Cell Activation.
   {\em Front. Immunol.}, 3:264 (2012).

\bibitem{anja}
   A.~Koren\v{c}i\v{c}, G.~Bordyugov, R. Ko\v{s}ir, D.~Rozman, M. Goli\v{c}nik, and H.~Herzel.
   The Interplay of \textit{cis}-regulatory Elements Rules Circadian Rhythms in Mouse Liver.
   {\em PLoS One}, 7:e46835 (2012).

\end{enumerate}

\subsection*{Publikationen in Sammelb"anden}

\begin{enumerate}
%\bibitem{he84}
%H.~Herzel.
% Zur quantitativen {B}eschreibung chaotischer {D}ynamik.
% In {\em Tagungsband {S}chule junger {W}issenschaftler}, 1984, pp. 82--89.

\bibitem{ebhesc84}
W.~Ebeling, H.~Herzel, and L.~Schimansky-Geier.
Stochastic description of a biochemical oscillator.
 In {\em Proc. 10th Intern. Conf. on Nonlinear Oscillations}. Varna, 1984.

\bibitem{enebhe84}
H.~Engel-Herbert, W.~Ebeling, and H.~Herzel.
 The influence of fluctuations on sustained oscillations.
 In {\em Temporal Order}. Springer-Verlag, 1984, pp. 144--152.

\bibitem{heebscse85}
H.~Herzel, W.~Ebeling, L.~Schimansky-Geier, and E.~E. Selkov.
 The influence of noise on a biochemical oscillator of {V}olterra
  type.
 In {\em Methods and Applications in Connection with Lotka-Volterra
  Equations in Systems Analysis}. Akademie-Verlag, 1985.

\bibitem{ebhese85}
W.~Ebeling, H.~Herzel, and E.~E. Selkov.
 Theory of stochastic biochemical oscillations.
 In {\em Proc. 16th FEBS--Congress Part C}. VNU Science Presss, 1985, pp. 443--449.

\bibitem{heebsc85}
H.~Herzel, W.~Ebeling, and Th. Schulmeister.
 Quantitative description of chaos in a biochemical system.
 In {\em Systems Analysis and Simulation}. Akademie--Verlag,
  1985, pp. 474--477.

\bibitem{ebenhe86b}
W.~Ebeling, H.~Engel-Herbert, and H.~Herzel.
 Thermodynamic as\-pects of selforganization.
 In {\em Selforganization by Nonlinear Irreversible Processes}.
  Springer-Verlag, 1986, pp. 2--16.

\bibitem{he87a}
H.~Herzel.
 Beschreibung von deterministischem {C}haos mit informa\-tions-
  theoretischen {M}ethoden.
 {\em Wiss. Zeitschr. Humb. Univ. Math.-Nat. Reihe}, 35, 440--449 (1987).

\bibitem{he87b}
H.~Herzel.
 Deterministisches {C}haos in biologischen {S}ystemen.
 {\em Wiss. Zeitschr. Humb. Univ. Math.-Nat. Reihe}, 36, 633--641 (1987).

\bibitem{hesc87b}
H.~Herzel and Th. Schulmeister.
 Chaotic dynamics and fluctuations in a biochemical system.
 In {\em Dynamical Systems and Environmental Models}. Akademie--Verlag,
  1987, pp. 85--94.

\bibitem{ebhesc88}
W.~Ebeling, H.~Herzel, and L.~Schimansky-Geier.
 Stochastic and chaotic processes in biochemical systems.
 In {\em From Chemical to Biological Organization}. Springer-Verlag,
  1988, pp. 166--176.

\bibitem{pevomewohe88}
M.~Peschel, H.M. Voigt, W.~Mende, J.~Wolf, H.~Herzel, and F.~Breitenecker.
 Chaotische {S}chalter - ein neuer {Z}ugang zur {M}odellierung von
  {N}euronennetzen.
 {\em msr}, 31, 36--38 (1988).

\bibitem{he89a}
H.~Herzel.
 Komplexit"at von {S}equenzen - statistische {A}nalyse von
  {B}iosequenzen, {S}prachen und chaotischen {S}ymbolfolgen.
 {\em Math.-Natur\-wiss. Manuskr. Humboldt Univ.}, 1, 5--28 (1989).

\bibitem{he89b}
H.~Herzel.
 Zustandsmodelle von {B}ioreaktoren.
 {\em Math.-Naturwiss. Manuskr. Humboldt Univ.}, 1, 33--40 (1989).

\bibitem{hekularo89}
H.~Herzel, J.~Kurths, P.S. Landa, and M.G. Rosenblum.
 New aspects of detecting chaos in a time series.
 In {\em Irreversible Processes and Selforganization}. Teubner-Verlag,
  1989, pp. 65--75.

\bibitem{pevohe89}
M.~Peschel, H.M. Voigt, and H.~Herzel.
 Properties of networks with chaotic neurons.
 In {\em Dynamical Networks}. Akademie-Verlag, 1989.

\bibitem{hewe91}
H.~Herzel and J.~Wendler.
 Evidence of chaos in phonatory signals.
 In {\em Proc. EUROSPEECH Genova}, 1991, pp. 263--266.

\bibitem{hestmewe91}
H.~Herzel, I.~Steinecke, W.~Mende, and K.~Wermke.
 Chaos and bifurcations during voiced speech.
 In {\em Complexity, Chaos and Biological Evolution}. Plenum Press,
  1991, pp. 41--50.

\bibitem{hesewa92}
H.~Herzel, H.~Seidel, and H.~Warzel.
 Heart rate, respiration, and baroreflex: Entrainment, bifurcations,
  and chaos.
 {\em Wiss. Zeitschr. Humboldt Univ. Reihe Medizin}, 41, 51--57 (1992).


\bibitem{wasehe92}
H.~Warzel, H.~Seidel, and H.~Herzel.
 Heart rate, respiration, and baroreflex: Motivation and experiments.
 {\em Wiss. Zeitschr. Humboldt Univ. Reihe Medizin}, 41, 59--61 (1992).


\bibitem{tibahe93}
I.R. Titze, R.~Baken, and H.~Herzel.
 Evidence of chaos in vocal fold vibration.
 In I.~R. Titze, editor, {\em Vocal Fold Physiology: New Frontiers in
  Basic Science}. Singular Publishing Group, 1993, pp. 143--188.

\bibitem{sthe93}
I.~Steinecke and H.~Herzel.
 Bifurcations in an asymmetric vocal fold model.
 In E.~Mosekilde, editor, {\em Computer Simulation in Biology, Ecology and Medicine}. Copenhagen, 1993, pp. 15--19.

\bibitem{hekebeti93}
H.~Herzel, K.~Krischer, D.~Berry, and I.~Titze.
 Analysis of spatio-temporal pattern by means of empirical orthogonal
  functions.
 In {\em Spatio-Temporal Patterns in Nonequilibrium Complex Systems}.
  Addison- Wesley, Santa Fe, 1995, pp. 505--518.

\bibitem{sehe94}
H.~Seidel and H.~Herzel.
 Modelling  Heart Rate Variability due to Respiration and
 Baroreflex.
 In {\em Modelling the Dynamics of Biological Systems}.
Springer, Berlin, 1995, pp. 205--229.

\bibitem{he93}
H.~Herzel.
 Nonlinear dynamics of voiced speech.
 In {\em Nonlinear Dynamics: New Theoretical and Applied Results}. Akademie-Verlag, Berlin, 1995, pp. 256--274.

\bibitem{braun95}
H.~Herzel, W.~Ebeling, I.~Grosse, and A.~O.~Schmitt.
  Statistical Analysis of DNA Sequences.
  In {\em Bioinformatics: From Nucleic Acids and Proteins
  to Cell Metabolism}, VCH-Verlag, Weinheim, 1995, pp. 29--43.

\bibitem{hearar93}
H.~Herzel, F.~Argoul, and A.~Arneodo.
 Type {II} intermittency in the presence of additive and
  multiplicative noise.
 In {\em Stochasticity and Quantum Chaos}. Kluwer, Dordrecht, 1995, pp. 99--113.

\bibitem{phonia}
(a) H.~Herzel. Nichtlineare Dynamik der Stimme, pp. 41--42.\\[0.2em]
(b) R.~Reuter, H.~Herzel, M.~Hess, and R.~Orglmeister.
Charakterisierung der rauhen Stimme durch Methoden aus der
Nichtlinearen Dynamik, pp. 43--45.\\[0.2em]
(c) H.~Herzel. Modellierung von Asymmetrien der Stimmlippen,
pp. 46-47.\\[0.2em]
(d) M.~Hess, M.Gross, and H.~Herzel. Desynchronisierte
Stimmlippenschwingungen, pp. 48--49.\\[0.2em]
{\em Aktuelle phoniatrisch-p"adaudiologische Aspekte},
RGV, Berlin 1995.

\bibitem{heebscji94}
H.~Herzel, W.~Ebeling, A.~O.~Schmitt, and M.~A. Jimenez-Montano,
 Entropies and Lexicographic Analysis of Biosequences.
 In {\em From Simplicity to Complexity in Chemistry and Beyond}, Eds. A.~M"uller, A.~Dress, and
F.~V"ogtle, Vieweg, Braunschweig, 1996, pp. 7--26.

\bibitem{patr}
P.~Mergell and H.~Herzel.
  Bifurcations in 2-Mass Models of the Vocal Folds -- the Role of the Vocal Tract.
  {\em Proceed. ETRW Speech Production Meeting}. Grenoble, 1996,
  pp. 189--192.

\bibitem{erlangen}
P.~Mergell and H.~Herzel.
  Analyse von Stimmlippenschwingungen und biomechanische Modelle.
  {\em Fortschritte der Untersuchungsmethoden der menschlichen
   Stimme}, Erlangen, 1996, pp. 12--15.

\bibitem{syd}
H.~Herzel.
  Possible Mechanisms of Vocal Instabilities.
  Proceed. {\em Vocal Fold Physiology: Controlling Complexity \& Chaos},
  Singular Publ. Group, San Diego, 1996, pp. 63--75.

\bibitem{mystic}
H.~Herzel and R.~Reuter.
  Biphonation in Voice Signals.
  {\em Nonlinear, Chaotic, and Advanced Signal Processing Methods
   for Engineers and Scientists},
   AIP Press, Woodbury, 1996, pp. 644--657.

\bibitem{marseille}

P.~Mergell, H.~Herzel, T.~Wittenberg, M.~Tigges and U.~Eysholdt.
Quantitative Laryngoscopy Combining High Speed
Glottography and Nonlinear Dynamics.
Proceed.{\em Larynx 97}, Marseille, 1997, pp. 47--50. 

\bibitem{erl1}
D.~A.~Berry, I.~R.~Titze, and H.~Herzel.
Normal Modes and Empirical Eigenfunctions: Tools for Interpreting
Normal and Chaotic Vocal Fold Oscillations.
  {\em Advances in Quantitative Laryngoscopy}. Erlangen 1997, pp. 126--131.

\bibitem{erl2}
R.~Reuter, R.~Orgelmeister, H.~Herzel, H.~Nguyen, and O.~Eisfeldt.
A Two-mass Model of the Vocal Folds Realized as Analog Electronical
Circuit.
  {\em Advances in Quantitative Laryngoscopy}. Erlangen 1997, pp. 136--142.

\bibitem{erl3}
P.~Mergell and H.~Herzel: 
Observation and Modelling of Pitch--Formant Resonances.
  {\em Advances in Quantitative Laryngoscopy}. Erlangen 1997, pp. 119--125.

\bibitem{freital}
H.~Herzel, J.~Holzfuss, Z.~Kowalik,~ B.~Pompe, and R.~Reuter.
  Detecting Bifurcations in Voice Signals. 
  {\em Nonlinear Analysis of Physiological Data}. Springer, 
  Berlin, 1998, pp. 325--344.

\bibitem{contours}
R.~Reuter and H.~Herzel.
  Quantifying Correlations in Pitch-- and Amplitude Contours.
  {\em Advances in Quantitative Laryngoscopy, Voice and
   Speech Research}. Aachen, 1998, pp. 45--60.

\bibitem{greg}
T.~G.~Dewey and H.~Herzel.
  Applications of Information Theory to Biology.
  {\em Pacific Symposium on Biocomputing 2000}, pp.597--598.

\bibitem{AMIPSB}
I.~Gro{\ss}e, S.~V.~Buldyrev, H.~E.~Stanley, D.~Holste, and H.~Herzel.
  Average Mutual Information of Coding and Noncoding DNA.
  {\em Pacific Symposium on Biocomputing 2000}, pp. 611--620.

\bibitem{GCB1}
S.~Kielbasa, J.~Korbel, D.~Beule, J.~Schuchhardt,
and H.~Herzel.
  Finding Transcription Factor Binding Sites in
  Coregulated Genes by Exhaustive Sequence Search.
  {\em German Conference on Bioinformatics 2000}, pp. 55--62.

\bibitem{GCB2}
D.~Beule, J.~Schuchhardt, A.~Malik, H.~Eickhoff,
H.~Lehrach, and H.~Herzel.
  Reliability of Microarray Data and Clustering.
  {\em German Conference on Bioinformatics 2000}, pp. 167--174.

\bibitem{GCB3}
J.~Schuchhardt, L.~Dong, U.~Hofmueller, A.~Kramer,
J.~Schneider--Mergener, and H.~Herzel.
  Peptide Binding Landscapes.
  {\em German Conference on Bioinformatics 2000}, pp. 183--188.

\bibitem{CZmoskau}
C.~Zemlin, H.~Herzel, and A.~Panfilov.
  Realistic Modeling of Cardiac Arrhythmia.
  {\em Nonlinear Dynamics in Life and Social Sciences},
  IOS Press, Amsterdam, 2001, pp. 244--252.

\bibitem{Nils}
N.~Bluethgen and H.~Herzel.
  MAP-Kinase-Cascade: Switch, Amplifier or Feedback Controller?
  {\em Computation of Biochemical Pathways and Genetic Networks},
  Logos Verlag, Berlin, 2001, pp. 55--62.

\bibitem{CZfrance}
C.~Zemlin, H.~Herzel, S.~Y.~Ho, F.~R.~C.~Path and A.~Panfilov.
  A Realistic and Efficient Model of Excitation Propagation
  in the Human Atria.
  {\em Computer Simulation and Experimental Assessment of Cardiac
   Electrophysiology},
  Future Publ. Comp., Armonk, 2001, pp. 29--34.

\bibitem{arrays}
R.~Herwig, J.~Schuchhardt, H.~Eickhoff, H.~Herzel, and H.~Lehrach.
   Datenanalyse von Biochips: Von der Sequenz zum System.
   {\em Handbuch der Molekularen Medizin (Band 1).
   Molekulare und zellbiologische Grundlagen}, Springer Verlag, 
   Berlin, 2003, pp. 360--387.

\bibitem{olafAhof}
O.~Weiss, A.~Ziehe, H.~Herzel.
   Optimizing property codes in protein data reveals structural characteristics.
   {\em ICAN/ICONIP, Lecture Notes in Computer Science 2714}, 2003, pp. 245--252.
 
\bibitem{maciejGCB}
M.~Swat, A.~Kel, S.~M.~Kielbasa, and H.~Herzel.
   Modelling the G1/S transition in mammals --
   Bifurcation analysis of elementary modules.
   {\em Proceed. GCB'03}, belleville Verlag, M"unchen, 2003, pp. 147--152. 

\bibitem{heike}
J.~O.~Korbel, H.~E.~Assmus, S.~M.~Kielbasa, and H.~Herzel.
   Compositional asymmetries and predicted origins of replication
   of the {\it Saccharomyces cerevisiae} genome.
   {\em Bioinformatics of Genome Regulation and Structure}, Kluwer,
   Boston, 2004, pp. 33--38.

\bibitem{babis}
H.~Hatzikirou, W.~T.~Fitch, and H.~Herzel.
   Voice Instabilities due to Source-tract Interactions.
   {\em Voice Physiology and Biomechanics - Modeling Complexity},
   Marseille, 2004, pp.63--70.

\bibitem{isao2}
I.~Tokuda and H.~Herzel.
   Detecting Synchronizations in an Asymmetric Vocal Fold Model
   from Time Series Data.
   {\em Voice Physiology and Biomechanics - Modeling Complexity},
   Marseille, 2004, pp. 193--196.
   

\bibitem{GCB04}
S.~M.~Kielbasa, N.~Bluethgen, and H.~Herzel.
   Genome-wide analysis of functions regulated by sets of
   transcription factors. {\em Proceed. GCB'04,
   Lecture Notes in Informatics} P-53, 2004, pp. 105--113.

\bibitem{maveba}
R.~Zaccarelli, C.~Elemans, W.~T.~Fitch, and H.~Herzel.
   Two-mass model of the bird syrinx. {\em Proceed. 4th
   MAVEBA Workshop, Firenze University Press}, Firence, 2005, pp. 47--50.

\bibitem{oliver}
O.~Raudies, R.-J.~Kuban, L.~Klein-Hitpass, O.~I.~Tchernitsa, C.~Sers, H.~Herzel, R.~Schaefer.
   Functional analysis and secondary expression profiling of candidate genes deregulated 
   in conjunction with oncogenic Ras signaling. {\em Adv. Enzyme Reg.} 45, 2005, pp. 63-84.
\end{enumerate}
%\newpage
%\subsection*{Eingereichte Manuskripte}
%\vspace{0.3cm}
%Juergen VM2
%IvoPLoSCB, submitted
%I.~Gro{\ss}e, D.~Holste, H.~Herzel, S.~V.~Buldyrev, and H.~E.~Stanley.
%  Species-Independence of Tsallis Entropies in Coding and Noncoding
%  DNA.\\[0.7em]
%T.~Riede, G.~B"ohme, R.~Frey, T.~W.~Fitch, M.~L.~East,
%  H.~Hofer, and H.~Herzel.
%  Canids and hyaenas possess morphological structures that could
%  be responsible for nonlinear phenomena in the production of
%  vocalization.\\[0.7em]
%D.~Beule, J.~Schuchhardt, and H.~Herzel.
%  Clustering Gene Expression Time Series.\\[0.7em]
%\bibitem{ebhesc84}
%W.~Ebeling, H.~Herzel, and L.~Schimansky-Geier.
% Stochastic description of a biochemical oscillator.
% In {\em Proc. 10th Intern. Conf. on Nonlinear Oscillations}. Varna,
%  1984
%\newpage
\subsection*{B"ucher}
\vspace{0.1cm}
W. Ebeling, H. Engel, H. Herzel: Selbstorganisation in der Zeit.\\
Akademie-Verlag, Berlin 1990\\[0.7em]
A.~Deutsch, L.~Brusch, H.~Byrne, G.~de~Vries, and H.~Herzel (Eds.).\\
Mathematical Modeling of Biological Systems, Volume I.
Birkh"auser,\\
Boston 2007
\subsection*{Patente}
\vspace{0.1cm}

C. Albers, H. Herzel,  K.  Kricheldorff:  Verfahren  zur  Steuerung  des
Sp"ulprozesses in Haushaltswaschmaschinen (Nr. 214691)1984\\[0.4em]
C.  Albers,  H.  Herzel,  K.  Kricheldorff:  Me"szelle  f"ur  elektrische
Leitf"ahigkeitsmessungen (Nr. 218468)1985\\[0.4em]
D. Beule, J. Schuchhardt, H. Eickhoff, H. Herzel: Quantitative Messung
von Molek"ulmengen in komplexen Gemischen (Anmeldung Nr.10025384.9)
\end{document}
