Introduction to Systems Biology

Introduction to Systems Biology

Language: English

Pages: 542

ISBN: 1588297063

Format: PDF / Kindle (mobi) / ePub

This book provides an introductory text for undergraduate and graduate students who are interested in comprehensive biological systems. The authors offer a broad overview of the field using key examples and typical approaches to experimental design. The volume begins with an introduction to systems biology and then details experimental omics tools. Other sections introduce the reader to challenging computational approaches. The final sections provide ideas for theoretical and modeling optimization in systemic biological researches. The book is an indispensable resource, providing a first glimpse into the state-of-the-art in systems biology.















protein–protein and protein– DNA information. Based on the observations, new hypotheses were generated, tested, and used to improve the regulatory model. The galactose utilization pathway in S. cerevisiae is a relatively wellcharacterized metabolic/regulatory system. However, many signaling and regulatory mechanisms cannot be easily reconstructed from literature because experimental “low-throughput” information is often incomplete. Several approaches have been proposed to model signal

perturbed metabolic network. Science 2001; 292(5518):929–934. 33. Ideker T, Ozier O, Schwikowski B, et al. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 2002;18 Suppl 1:S233–S240. 61 62 Oliveira, Jewett, and Nielsen 34. Steffen M, Petti A, Aach J, et al. Automated modelling of signal transduction networks. BMC Bioinformatics 2002;3:34. 35. Yeang CH, Ideker T, Jaakkola T. Physical network models. J Comput Biol 2004;11(2–3):243–262. 36. Lee TI,

next step of analysis of a co-regulated gene group is the prediction of transcription factors controlling expression of the genes. In this process, nucleotide sequences expected to contain regulatory regions of the genes (promoters) are predicted, extracted, and searched for putative transcription factor binding sites. The motifs that are recognized by the transcription factors are similar to their surroundings and, consequently, difficult to detect by computational methods. Because it is believed

Biol 2005;6:103. 36. Mata J, Lyne R, Burns G, et al. The transcriptional program of meiosis and sporulation in fission yeast. Nat Genet 2002;32:143–147. 37. Chen D, Toone WM, Mata J, et al. Global transcriptional responses of fission yeast to environmental stress. Mol Biol Cell 2003;14:214–229. 38. Chu S, DeRisi J, Eisen M, et al. The transcriptional program of sporulation in budding yeast. Science 1998;282:699–705. 39. Gasch AP, Spellman PT, Kao CM, et al. Genomic expression programs in the

7. Rigaut G, Shevchenko A, Rutz B, et al. A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol 1999;17:1030–1032. 8. Caspary F, Shevchenko A, Wilm M, et al. Partial purification of the yeast U2 snRNP reveals a novel yeast pre-mRNA splicing factor required for prespliceosome assembly. EMBO J 1999;18:3463–3474. 9. Chen CY, Gherzi R, Ong SE, et al. AU binding proteins recruit the exosome to degrade ARE-containing mRNAs. Cell

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