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Publications

The following is a list of publications for the Huber group.




2010



Anders S. and Huber W. (2010)
Differential expression analysis for sequence count data.
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Bourgon R., Gentleman R. and Huber W. (2010)
Independent filtering increases detection power for high-throughput experiments
PNAS 2010 (in press)
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Fuchs F., Pau, G., Kranz, D., Sklyar, O., Budjan, C., Steinbrink, S., Horn, T., Pedal, A., Huber, W. and Boutros, M. (2010)
Clustering phenotype populations by genome-wide RNAi and multiparametric imaging.
Molecular Systems Biology 6.
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Granovskaia M.V., Jensen L.J., Ritchie M.E., Toedling J., Ning Y., Bork P., Huber W. and Steinmetz L.M. (2010)
High-resolution transcription atlas of the mitotic cell cycle in budding yeast.
Genome Biology 2010, 11: R24.
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Karp N.A., Huber W., Sadowski P.G., Charles P.D., Hester SV, Lilley K.S. (2010)
Addressing accuracy and precision issues in iTRAQ quantitation.
Mol Cell Proteomics. 2010 Apr 10. [Epub ahead of print]
abstract full-text PDF

Kasowski M., Grubert F., Heffelfinger C., Hariharan M., Asabere A., Waszak S.M., Habegger L., Rozowsky J., Shi M., Urban A.E., Hong M., Karczewski K.J., Huber W., Weissman S.M., Gerstein M.B., Korbel J.O., SnyderM. (2010)
Variation in Transcription Factor Binding Among Humans.
Science 328(5975): 232-235.
abstract full-text PDF

Kauffmann A., Huber W. (2010)
Microarray data quality control improves the detection of differentially expressed genes.
Genomics. 2010 Mar;95(3): 138-142.
abstract full-text PDF

Kuttenkeuler D., Pelte N, Ragab A., Gesellchen V., Schneider L., Blass C., Axelsson E., Huber W., Boutros M. (2010)
A Large-Scale RNAi Screen Identifies Deaf1 as a Regulator of Innate Immune Responses in Drosophila.
Journal of Innate Immunity 2010;2: 181-194.
abstract

Lukk M., Kapushesky M., Nikkila J., Parkinson H., Goncalves A., Huber W., Ukkonen E., Brazma A. (2010)
A global map of human gene expression.
Nature Biotechnology 28: 322–324
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Neumann B., Walter T., Heriché J., Bulkescher J., Erfle H., Conrad C., Rogers P., Poser I., Held M., Liebel U., Cetin C., Sieckmann F., Pau G., Kabbe R., Wünsche A., Satagopam V., Schmitz M.H.A., Gerlich D.W., Schneider R., Eils R., Huber W., Peters J., Hyman A.A., Durbin R., Pepperkok R. and Ellenberg J. (2010)
Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes.
Nature 464(7289): 684-685.
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Pau G., Fuchs F., Sklyar O., Boutros M., Huber W. (2010)
EBImage - an R package for image processing with applications to cellular phenotypes.
Bioinformatics 26(7): 979-981.
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Schmid R, Baum P, Ittrich C, Fundel-Clemens K, Huber W, Brors B, Eils R, Weith A, Mennerich D, Quast K. (2010)
Comparison of normalization methods for Illumina BeadChip(R) HumanHT-12 v3.
BMC Genomics. 2010 Jun 2;11(1):349.
abstract



2009


Anders S. (2009)
Visualisation of genomic data with the Hilbert curve.
Bioinformatics. 2009 May 15;25(10):1231-5. Epub 2009 Mar 17.
abstract full-text PDF

Bourgon R., Mancera E., Brozzi A., Steinmetz L.M., Huber W. (2009)
Array-based genotyping in S. cerevisiae using semi-supervised clustering.
Bioinformatics. 2009 Apr 15;25(8):1056-62
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Chiang T., Scholtens D. (2009)
A general pipeline for quality and statistical assessment of protein interaction data using R and Bioconductor.
Nature Protocols 4(4): 535-546.
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Durinck S, Spellman PT, Birney E, Huber W. (2009)
Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt.
Nature Protocols 4(8): 1184-1191. Epub 2009 Jul 23.
abstract full-text PDF

Gagneur J., Sinha H., Perocchi F., Bourgon R., Huber W., Steinmetz L.M. (2009)
Genome-wide allele- and strand-specific expression profiling.
Mol Syst Biol. 2009;5:274. Epub 2009 Jun 16.
abstract full-text PDF

Kauffmann A., Gentleman R., Huber W. (2009)
arrayQualityMetrics - a Bioconductor package for quality assessment of microarray data.
Bioinformatics 25(3): 415-416.
abstract full-text PDF

Kauffmann A., Rayner T.F., Parkinson H., Kapushesky M., Lukk M., Brazma A., Huber W. (2009)
Importing ArrayExpress datasets into R/Bioconductor.
Bioinformatics. 2009 Aug 15;25(16):2092-4. Epub 2009 Jun 8.
abstract full-text PDF

Morgan M., Anders S., Lawrence M., Aboyoun P., Pagès H., Gentleman R. (2009)
Bioinformatics. 2009 Oct 1;25(19):2607-8. Epub 2009 Aug 3.
ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data.
abstract full-text PDF

Sarkar D., Parkin R., Wyman S., Bendoraite A., Sather C., Delrow J., Godwin A., Drescher C., Huber W., Gentleman R. and Tewari M. (2009)
Quality Assessment and Data Analysis for microRNA Expression Arrays.
Nucleic Acids Research 37(2): e17.
abstract full-text PDF

Xu Z., Wei W., Gagneur J., Perocchi F., Clauder-Münster S., Camblong J., Guffanti E., Stutz F., Huber W., Steinmetz L.M. (2009)
Bidirectional promoters generate pervasive transcription in yeast.
Nature 457(7232): 1033-1037.
abstract full-text PDF



2008


Mancera E., Bourgon R., Brozzi A., Huber W., Steinmetz L.M. (2008)
High-resolution mapping of meiotic crossovers and non-crossovers in yeast.
Nature 454(7203): 479-485.
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Chiang T., Li N., Orchard S., Kerrien S., Hermjakob H., Gentleman R., Huber W. (2008)
Rintact: Enabling computational analysis of molecular interaction data from the IntAct repository.
Bioinformatics 24: 1100-1101.
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Hahne F., Huber W., Gentleman R., Falcon S. (2008)
Bioconductor Case Studies (Use R series).
Springer
more info

Lin S.M., Du P., Huber W., Kibbe W.A. (2008)
Model-based variance-stabilizing transformation for Illumina microarray data.
Nucleic Acids Research 36(2): e11.
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Sarasin A., and Kauffmann A. (2008)
Overexpression of DNA repair genes is associated with metastasis: A new hypothesis.
Mutation Research 659(1-2): 49-55.
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Scholtens D., Chiang T., Huber W., Gentleman R. (2008)
Estimating node degree in bait-prey graphs.
Bioinformatics 24(2): 218-224.
abstract full-text PDF

Toedling J, Huber W. (2008)
Analyzing ChIP-chip data using bioconductor.
PLoS Computational Biology 2008 Nov;4(11): e1000227.
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2007


Casneuf T., Van de Peer Y., Huber W. (2007)
In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation.
BMC Bioinformatics 8: 461.
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Chiang T., Scholtens D., Sarkar D., Gentleman R., Huber W. (2007)
Coverage and error models of protein-protein interaction data by directed graph analysis.
Genome Biology 8(9): R186.
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Girardot C., Sklyar O., Grosz S., Huber W., Furlong E.E. (2007)
CoCo: A web application to display, store and curate ChIP-on-chip data integrated with diverse types of gene expression data.
Bioinformatics 23(6): 771-773.
abstract full-text PDF

Gentleman R., Huber W. (2007)
Making the most of high-throughput protein-interaction data.
Genome Biology 8(10): 112-112. [Epub ahead of print]
abstract full-text PDF

Huber W., Carey V.J., Long L., Falcon S., Gentleman R. (2007)
Graphs in molecular biology.
BMC Bioinformatics 8 Suppl 6: S8.
abstract full-text PDF

Purmann A., Toedling J., Schueler M., Carninci P., Lehrach H., Hayashizaki Y., Huber W., Sperling S. (2007)
Genomic organization of transcriptomes in mammals: Coregulation and cofunctionality.
Genomics 89(5): 580-587.
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Sauermann M., Hahne F., Schmidt C., Majety M., Rosenfelder H., Bechtel S., Huber W., Poustka A., Arlt D., Wiemann S. (2007)
High-Throughput Flow Cytometry-Based Assay to Identify Apoptosis-Inducing Proteins.
Journal of Biomolecular Screening 12(4): 510-520.
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Steigele S., Huber W., Stocsits C., Stadler P.F., Nieselt K. (2007)
Comparative analysis of structured RNAs in S. cerevisiae indicates a multitude of different functions.
BioMed Central Biology 5: 25-25.
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Toedling J., Sklyar O., Huber W. (2007)
Ringo--an R/Bioconductor package for analyzing ChIP-chip readouts.
BMC Bioinformatics 8: 221.
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2006


Boutros M, Bras L, Huber W.(2006)
Analysis of cell-based RNAi screens.
Genome Biology 25;7(7): R66.
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David L., Huber W., Granovskaia M., Toedling J., Palm C.J., Bofkin L., Jones T., Davis R.W., Steinmetz L.M. (2006)
A high-resolution map of transcription in the yeast genome.
The Proceedings of the National Academy of Sciences Online (US) 103(14): 5320-5325. (Epub 2006 Mar 28).
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Gentleman R., Hahne F., and Huber, W. (2006)
Visualizing Genomic Data.
Bioconductor Project Working Papers. Working Paper 10.
abstract full-text PDF

Hahne F., Arlt D., Sauermann M., Majety M., Poustka A., Wiemann S., Huber W. (2006)
Statistical methods and software for the analysis of high throughput reverse genetic assays using flow cytometry readouts.
Genome Biology 17;7(8): R77 [Epub ahead of print]
abstract full-text PDF

Huber W. and Murrell P. (2006)
Several articles from EBI.
R News Special Issue on Bioinformatics Dec 2006 Vol 6/5.
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Huber W., Toedling J., Steinmetz L. M. (2006)
Transcript mapping with high-density oligonucleotide tiling arrays.
Bioinformatics 22(16): 1963-1970.
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Mansmann, U., Ruschhaupt, M., Huber, W. (2006)
Reproducible statistical analysis in microarray profiling studies.
Methods of Information in Medicine 45(2): 139-145.
abstract

Mehrle A., Rosenfelder H., Schupp I., del Val C., Arlt D, Hahne F., Bechtel S., Simpson J., Hofmann O., Hide W., Glatting K.H., Huber W., Pepperkok R., Poustka A., Wiemann S. (2006)
The LIFEdb database in 2006.
Nucleic Acids Research 34: D415-D418.
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Quackenbush J., Stoeckert C., Ball C., Brazma A., Gentleman R., Huber W., Irizarry R., Salit M., Sherlock G., Spellman P., Winegarden N. (2006)
Top-down standards will not serve systems biology
Nature 440 (7080): 24.
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Toedling J., Rhein P., Ratei R., Karawajew L., Spang R. (2006).
Automated in-silico detection of cell populations in flow cytometry readouts and its application to leukemia disease monitoring.
BMC Bioinformatics 7: 282.
abstract full-text PDF



2005


Arlt D., Huber W., Liebel U., Schmidt C., Majety M., Sauermann M., Rosenfelder H., Bechtel S., Mehrle A., Bannasch D., Schupp I., Seiler M., Simpson J.C., Hahne F., Moosmayer P., Ruschhaupt M., Guilleaume B., Wellenreuther R., Pepperkok R., Sültmann H., Poustka A. and Wiemann S. (2005)
Functional profiling: from microarrays via cell-based assays to novel tumor relevant modulators of the cell cycle.
Cancer Research 65(17): 7733-7742.
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Durinck S., Y. Moreau, A. Kasprzyk, S. Davis, B. De Moor, A. Brazma (EBI) & W. Huber (2005)
BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis.
Bioinformatics 21: 3439-3440.
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Gentleman R., Carey V., Huber W., Irizarry R. and Dudoit S. (2005)
Bioinformatics and Computational Biology Solutions Using R and Bioconductor.
Published by Springer.
abstract

Gentleman R., Ruschhaupt M. and Huber W. (2005)
On the Synthesis of Microarray Experiments.
Journal de la Soci´et´e Fran¸caise de Statistique, tome 146, n◦ 1-2.
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Guilleaume B., Buness A., Schmidt C., Klimek F., Moldenhauer G., Huber W., Arlt D., Korf U., Wiemann S., Poustka A. (2005)
Systematic comparison of surface coatings for protein microarrays.
Proteomics 5(18): 4705-4712.
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Huber W., Von Heydebreck A. and Vingron M. (2005)
Low-level analysis of microarray experiments.
In Press.
[Preprint]


Sültmann H., Von Heydebreck A., Huber W., Kuner R., Buneß A., Vogt M., Gunawan B., Vingron M., Füzesí L. and Poustka A. (2005)
Gene Expression in Kidney Cancer Is Associated with Cytogenetic Abnormalities, Metastasis Formation, and Patient Survival.
Clinical Cancer Research 11: 646-655.
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2004


Buness A., Huber W., Steiner K., Sultmann H. and Poustka A. (2004)
arrayMagic: two-colour cDNA microarray quality control and preprocessing.
Bioinformatics 21(4): 554-556.
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Gentleman R.C., Carey V.J., Bates D.M., Bolstad B., Dettling M., Dudoit S., Ellis B., Gautier L., Ge Y., Gentry J., Hornik K., Hothorn T., Huber W., Iacus S., Irizarry R., Leisch F., Li C., Maechler M., Rossini A.J., Sawitzki G., Smith C., Smyth G., Tierney L., Yang J.Y. and Zhang J. (2004)
Bioconductor: open software development for computational biology and bioinformatics.
Genome Biology 5(10): R80.
abstract full-text PDF

Huber W. and Gentleman R. (2004)
matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements.
Bioinformatics 20: 1651-1652.
abstract full-text PDF

Huber W., Von Heydebreck A. and Vingron M. (2004)
Error models for microarray intensities.
to appear in: Encyclopedia of Genomics, Proteomics and Bioinformatics. John Wiley & sons.
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Rocke D.M., Huber W., Durbin B., Von Heydebreck A. and Vingron M. (2004)
Interpretability and Data Transformations for Gene Expression Microarray Data.
submitted (2004)


Ruschhaupt M., Huber W., Poustka A. and Mansmann U. (2004)
A Compendium to Ensure Computational Reproducibility in High-Dimensional Classification Tasks.
Statistical Applications in Genetics and Molecular Biology 3(1): article 37.
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Schneider J., Buness A., Huber W., Volz J., Kioschis P., Hafner M., Poustka A. and Sültmann H. (2004)
Systematic analysis of T7 RNA polymerase based in vitro linear RNA amplification for use in microarray experiments.
BMC Genomics 5: 29.
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Von Heydebreck, A., Huber W. and Gentleman R. (2004)
Differential Expression with the Bioconductor Project.
to appear in: Encyclopedia of Genomics, Proteomics and Bioinformatics. John Wiley & sons.
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Wiemann S., Arlt D., Huber W., Wellenreuther R., Schleeger S., Mehrle A., Bechtel S., Sauermann M., Korf U., Pepperkok R., Sültmann H. and Poustka A. (2004)
From ORFeome to biology: a functional genomics pipeline.
Genome Research 14(10B): 2136-2144.
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2003


Apic G., Huber W. and Teichmann S.A. (2003)
Multi-domain Protein Families and Domain Pairs: Comparison with known Structures and a Random Model of Domain Recombination
Journal of Structural and Functional Genomics 4 (2-3): 67-78.
abstract full-text PDF

Gunawan B., Von Heydebreck A., Fritsch T., Huber W., Ringert R-H., Jakse G. and Füzesi L. (2003)
Cytogenetic and Morphologic Typing of 58 papillary Renal Cell Carcinomas: Evidence for a Cytogenetic Evolution of Type 2 from Type 1 Tumors
Cancer Research 63: 6200-6205.
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Heydebreck A. V., Gunawan B., Huber W., Vingron M., Füzesi L. (2003)
Mathematical tree models for cytogenetic development in solid tumors.
Verhandlungen der Deutschen Gesellschaft fur Pathologie 87: 188-92. (2003)
abstract

Huber W., Von Heydebreck A., Sültmann H., Poustka A. and Vingron M. (2003)
Parameter estimation for the calibration and variance stabilization of microarray data.
Statistical Applications in Genetics and Molecular Biology 2(1): article3.
abstract full-text PDF

Huber W., Von Heydebreck A. and Vingron M. (2003)
Analysis of microarray gene expression data.
Handbook of Statistical Genetics, 2nd edition, Wiley.
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Langer C., Gunawan B., Schuler P., Huber W., Fuzesi L. and Becker H. (2003)
Prognostic factors influencing surgical management and outcome of gastrointestinal stromal tumours.
British Journal of Surgery 90(3): 332-399.
abstract



2002


Huber W., Von Heydebreck A., Sültmann H., Poustka A. and Vingron M. (2002)
Variance stabilization applied to microarray data calibration and to the quantification of differential expression.
Bioinformatics 18: suppl. 1 (2002), S96-S104 (ISMB 2002).
abstract full-text PDF



2001


Boer J.M., Huber W., Sültmann H., Wilmer F., Von Heydebreck A., Haas S., Korn B., Gunawan B., Vente A., Füzesi L., Vingron M. and Poustka A. (2001)
Identification and Classification of Differentially Expressed Genes in Renal Cell Carcinoma by Expression Profiling on a Global Human 31,500 Element cDNA Array.
Genome Research 11: 1861-1870.
abstract full-text PDF

Gunawan B., Huber W., Holtrup M., Von Heydebreck A., Efferth T., Poustka A., Ringert R-H., Jaske G. and Füzesi L. (2001)
Prognostic impacts of cytogenetic findings in clear cell renal cell carcinoma: Chromosome translocation der(3)t(3;5) or gain of 5q predict a distinct clinical phenotype with favourable prognosis.
Cancer Research 61: 7731-7738.
abstract full-text PDF

Pitman M.C., Huber W., Horn H., Krämer A., Rice J.E., Swope W.C. (2001)
FLASHFLOOD: A 3D Field-Based Similarity Search and Alignment Method for Flexible Molecules.
Journal of Computer-Aided Molecular Design 15 (7): 587-612.
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Von Heydebreck A., Huber W., Poustka A. and Vingron M. (2001)
Identifying splits with clear separation: a new class discovery method for gene expression data.
Bioinformatics 17: suppl. 1 (2001), S107-S114 (ISMB 2001).
abstract full-text PDF



1990-2000


Breuer H.P., Huber W. and Petruccione F. (2000)
vQuasistationary distributions of dissipative nonlinear quantum oscillators in strong periodic driving fields.
Physical Review E 61: 4883-4889.
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Huber W. (1998)
Dynamics of strongly driven open quantum systems (dissertation, in German).
Fakultät für Physik, Universität Freiburg.
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Breuer H.P., Huber W. and Petruccione F. (1997)
Stochastic wave function method versus density matrix: a numerical comparison.
Computer Physics Communications 104: 46-58.
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Mergner T., Huber W. and Becker W. (1997)
Vestibular-Neck Interaction and Transformation of Sensory Coordinates.
Journal of Vestibular Research 7(4): 347-367.
abstract

Breuer H.P., Huber W. and Petruccione F. (1996)
Fast Monte Carlo algorithm for non-equilibrium systems.
Physical Review E 53: 4232.
abstract full-text postscript full-text PDF

Breuer H.P., Huber W. and Petruccione F. (1996)
Fast nonequilibrium Monte Carlo simulations.
Proceedings of the Conference 'Physics Computing 96', Krakow, Poland.
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Huber W., Kopitzki K., Timmer J. and Warnke P. (1996)
Spatially resolved measurement and modeling of blood brain barrier permeability (in German).
Biomedizinische Technik 41 suppl. 1: 160.
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Breuer H.P., Huber W. and Petruccione F. (1995)
The macroscopic limit in a stochastic reaction-diffusion process.
Europhysics Letters 30: 69.
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Fischer B., Gezeck S. and Huber W. (1995)
The three-loop model: a neural network for the generation of saccadic reaction times.
Biological Cybernetics 72: 185-196.
abstract

Breuer H.P., Huber W. and Petruccione F. (1994)
Fluctuation effects on wave propagation in a reaction-diffusion process.
Physica D 73: 259-273.
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Huber W. (1994)
The description of reaction diffusions processes by master equations, (diploma thesis, in German).
Fakultät für Physik, Universität Freiburg.
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