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Studying Bioinformatics in Saarbrücken

Bioinformatik III - Suggested Reading

Winter Term 04/05

Lecture 1, October 19

Barabási, A.-L. and Oltvai, Z.N. (2004) Nature Reviews Genetics, Vol. 5, 101-113, Network biology: understanding the cell´s functional organization

Jeong, H., Tombor, B., Albert, R. Oltvai, Z.N., and Barabási, A.-L. (2000) Nature, Vol. 407, 651-654, The large-scale organization of metabolic networks

Jeong, H., Mason, S.P., Barabási, A.-L., and Oltvai, Z.N., (2001) Nature, Vol. 411, 41-42, Lethality and centrality in protein networks

Lecture 2, October 21

Przulj, N. (2003) Graph theory approaches to protein interaction data analysis

Amoutzias, G.D., Robertson, D.L., Oliver, S.G., and Bornberg-Bauer, E. (2004) EMBO reports, Vol. 5, 1-6, Convergent evolution of gene networks by single-gene duplications in higher eukarycotes

Wuchty, S. (2001) Molecular Biology and Evolution, Vol. 18, 1694-1702, Scale-free behavior in protein domain networks

Lecture 3, October 26

Matys, V., Fricke, E., Geffers, R., (2003) Nucleic Acids Research, Vol. 31, 374-378, TRANSFAC®: transcriptional regulation, from patterns to profiles

Ohler, U. and Niemann, H. (2001) Trends in Genetics, Vol. 17, 56-60, Identification and analysis of eukaryotic promoters: recent computational approaches

Lecture 4, October 28

Madan Babu, M. and Teichmann, S. (2003) Nucleic Acids Research, Vol. 31, 1234-1244, Evolution of transcription factors and the gene regulatory network in Escherichia coli

Shen-Orr, S., Milo, R., Mangan, S., and Alon, U. (2002) Nature Genetics, Vol. 31, 64-68, Network motifs in the transcriptional regulation network of Escherichia coli

Luscombe, N.M., Madan Babu, M., Yu, H., Snyder, M., Teichmann, S., and Gerstein, M. (2004) Nature, Vol. 431, 308-312, Genomic analysis of regulatory network dynamics reveals large topological changes

Lecture 5, November 2

Russel, R.B., Alber, F., Aloy, P., Davis, F.P., Korkin, D., Pichaud, M., Topf, M., and Sali, A. (2004) Current Opinion in Structural Biology, Vol. 14, 313-324, A structural perspective on protein-protein interactions

Lecture 6, November 4

Bork, P., Jensen, L.J., von Mering, C., Ramani, A.K., Lee, I., and Marcotte, E.M. (2004) Current Opinion in Structural Biology, Vol. 14, 292-299, Protein interaction networks from yeast to human

Lecture 7, November 9

Wu, X., Milne, J.L.S., Borgnia, M.J., Rostapshov, A.V., Subramaniam, S., and Brooks, B.R. (2003) Journal of Structural Biology, Vol. 141, 63-76, A core-weighted fitting method for docking atomic structures into low-resolution maps: Application to cryo-electron microscopy

Wriggers, W. and Chacón, P. (2001) Structure, Vol. 9, 779-788, Modeling Tricks and Fitting Techniques for Multiresolution Structures

Lecture 8, November 11

Middendorf, M., Ziv, E., and Wiggins, C. (2004), Inferring network mechanisms: The drosophila melanogaster protein interaction network

Giot, L. Bader, J.S., Brouwer, C., et al. (2003) Science, Vol. 302, 1727-1736, A protein interaction map of drosophila melanogaster

Amaral, L.A.N., Barrat, L., Barabási, A.-L., et. al. (2004) Eur. Phys. J. B, Vol. 38, 143-145, Virtual round table on ten leading questions for network research

Lecture 9, November 16

Adai, A.T., Date, S.V., Wieland, S., and Marcotte, E.M. (2004) Journal of Molecular Biology, Vol. 340, 179-190, LGL: Creating a map of protein function with an algorithm for visualizing very large biological networks

Ju, B.-H., Park, B., Park, J.H., and Han, K. (2003) Bioinformatics, Vol. 19, 317-318, Visualization and analysis of protein interactions

Spirin, V. and Mirny, L.A. (2003) PNAS, Vol. 100, 12123-12128, Protein complexes and functional modules in molecular networks

Lecture 10, November 18

Gagneur, J., Krause, R., Bouwmeester, T., and Casari, G. (2004) Genome Biology, Vol. 5, R57, Modular decomposition of protein-protein interaction networks

Habib, M., de Montgolfier, F., and Paul, C. (2004) A simple linear-time modular decomposition algorithm for graphs, using order extension

Lecture 11, November 23

Girvan, M. and Newman, M.E.J. (2002) PNAS, Vol. 99, 7821-7826, Community structure in social and biological networks

Radicchi, F., Castellano, C., Cecconi, F., Loreto, V., and Parisi, D. (2004) PNAS, Vol. 101, 2658-2663, Defining and identifying communities in networks

Wuchty, S., Oltvai, Z.N., and Barabási, A.-L. (2003) Nature Genetics, Vol. 35, 176-179, Evolutionary conservation of motif constituents in the yeast protein interaction network

Lecture 12, November 30

Mering, C. von, Krause, R., Snel, B., Cornell, M., Oliver, S.G., Fields, S., and Bork, P. (2002) Nature, Vol. 417, 399-403, Comparative assessment of large-scale data sets of protein-protein interactions

Jansen, R., Yu, H., Greenbaum, D., Kluger, Y., Krogan, N.J., Chung, S., Emili, A., Snyder, M., Greenblatt, J.F., and Gerstein, M. (2003) Science, Vol. 302, 449-453, A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data

Lecture 13, December 2

Rokas, A., Williams, B.L., King, N., and Carroll, S.B. (2003) Nature, Vol. 425, 798-804, Genome-scale approaches to resolving incongruence in molecular phylogenies

Lecture 15, December 9

Pevzner, P. and Tesler, G. (2003) PNAS, Vol. 100, 7672-7677, Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution

Pevzner, P. and Tesler, G. (2003) Genome Research, Vol. 13, 37-45, Genome Rearrangements in Mammalian Evolution: Lessons From Human and Mouse Genomes

Lecture 16, December 14

Bergeron, A., and Stoye, J. (2003) Report 2003-01, Technische Fakultät Universität Bielefeld, On the Similarity of Sets of Permutations and its Applications to Genome Comparison

Lecture 18, January 11

Ouzounis, C.A. and Karp, P.D. (2000) Genome Research, Vol. 10, 568-576, Global Properties of the Metabolic Map of Escherichia coli

Edwards, S. and Palsson, B.O. (2000) PNAS, Vol. 97, 5528-5533, The Escherichia Coli MG1655 in Silico Metabolic Genotype: Its Definition, Characteristics, and Capabilities

Lecture 19, January 13

Schilling, C.H., Letscher, D., and Palsson, B.Ø (2000) Journal of Theoretical Biology, Vol. 203, 229-248, Theory for the Systemic Definition of Metabolic Pathways and their use in Interpreting Metabolic Function from a Pathway-Oriented Perspective

Papin, J.A., Price, N.D., and Palsson, B.Ø (2002) Genome Research, Vol. 12, 1889-1900, Extreme Pathway Lengths and Reaction Participation in Genome-Scale Metabolic Networks

Price, N.D., Reed, J.L., and Palsson B.Ø (2004) Nature Reviews Microbiology, Vol. 2, 886 - 897, Genome-scale models of microbial cells: evaluating the consequences of constraints

Lecture 20, January 18

Segrè, D., DeLuna, A., Church, G.M., and Kishony, R. (2005) Nature Genetics, Vol. 37, 77-83, Modular epistasis in yeast metabolism

Almaas, E., Kovács, B., Vicsek, T., Oltvai, Z.N., and Barabási, A.-L. (2004) Nature, Vol. 427, 839-843, Global organization of metabolic fluxes in the bacterium Escherichia coli

Lecture 21, January 20

Klamt, S. and Stelling, J. (2003) Trends in Biotechnology, Vol. 21, 64-69, Two approaches for metabolic pathway analysis?

Ihmels, J., Levy, R., and Barkai, N. (2004) Nature Biotechnology, Vol. 22, 86-02, Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae

Lecture 24, February 1

Gagneur, J. and Klamt. S. (2004) BMC Bioinformatics, Vol. 5, 175, Computation of elementary modes: a unifying framework and the new binary approach