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Information- and Communication Theory in Molecular Biology pp 3–81Cite as

Introduction

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Part of the book series: Lecture Notes in Bioengineering ((LNBE))

Abstract

The present book describes a broad variety of interdisciplinary results, which have been achieved within the priority program headed as “Information- and Communication Theory in Molecular Biology (InKoMBio, SPP 1395)”, that has been funded by the German Research Foundation DFG. In all projects there were at least two principle investigators from at least two fields, namely biology and information theory. The main results of almost all projects funded in InKoMBio are described in this book. By InKoMBio not only many interdisciplinary results have been created but also many ongoing interdisciplinary research activities. First a very compact shelving of the projects is given, with the objective to outline all the ventures in a condensed manner, reduced to their essential goals and obtained results, as abstracts, supported by the most important publications that have been released in the funding period. Afterwards a detailed descriptions of all specific projects can be found, which includes some administrative data, e.g., the applicants, their scientific staff and affiliation, national and international cooperations, and a summary of all publications and educational qualifications that has been supported and facilitated by project subtopics. The core element of the descriptive parts give background information about the investigated topic and the starting point of the research, as well as the actual work performed in the project. Each detailed report is finalized by concluding remarks about the essential results of the interdisciplinary work and possible future perspectives.

This compendium was authored by the individual project contributers of Part II starting p. 83.

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Notes

  1. 1.

    A finite random variable is a discrete random variable with finite symbol alphabet.

References

  • Abendroth C et al (2015) The CENP-T C-Terminus is exclusively proximal to H3. 1 and not to H3. 2 or H3. 3. Int J Mol Sci 16(3):5839–5863

    Article  Google Scholar 

  • Abraham U et al (2010) Coupling governs entrainment range of circadian clocks. Mol Syst Biol 6(1):438. http://www.ncbi.nlm.nih.gov/pubmed/21119632, http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC3010105

  • Alirezaei G, Mathar R, (2015a) Optimum one-bit quantizatio. IEEE information theory workshop (ITW, (2015) vol 2015. Jeju Island, Korea, pp 357–361

    Google Scholar 

  • Alirezaei G, Mathar R (2015b) An upper bound on the capacity of censored channels. In: The 9th international conference on signal processing and communication systems (ICSPCS’15). Australia, Cairns, p 6

    Google Scholar 

  • Anders A, Breunig KD (2011) Evolutionary aspects of a genetic network: studying the lactose/galactose regulon of Kluyveromyces lactis. In: Becskei A (ed) Yeast genetic networks: methods and protocols. Humana Press, Totowa, pp 259–277. doi:10.1007/978-1-61779-086-7_13

  • Arts M et al (2013) Modelling biological systems using a parallel quantized MIMO channel. In: The tenth international symposium on wireless communication systems (ISWCS 2013). Ilmenau, Germany, pp 385–389

    Google Scholar 

  • Arts M et al (2016) A discontinuous neural network for non-negative sparse approximation. In: ArXiv e-prints arXiv:1603.06353 [cs.NE]

  • Behrisch M et al (2013) Visual comparison of orderings and rankings. In: Pohl M, Schumann H (eds) EuroVis workshop on visual analytics. The Eurographics Association, pp 7–11. http://diglib.eg.org/EG/DL/PE/EuroVAST/EuroVA13/007-011.pdf

  • Bhargava A, Herzel H, Ananthasubramaniam B (2015) Mining for novel candidate clock genes in the circadian regulatory network. BMC Syst Biol 9:78. doi:10.1186/s12918-015-0227-2. Accessed 29 June 2016

  • Bruggeman FJ, Blüthgen N, Westerhoff HV (2009) Noise management by molecular networks. PLoS Comput Biol 5(9):e1000506. http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000506

  • Bui M et al (2012) Cell-cycle-dependent structural transitions in the human CENP-A nucleosome in vivo. Cell 150(2):317–326

    Article  Google Scholar 

  • Busch W et al (2016) Transcriptional control of a plant stem cell niche. Develop Cell 5:841–853

    Google Scholar 

  • Caydasi AK et al (2012) A dynamical model of the spindle position checkpoint. Mol Syst Biol 8:582

    Article  Google Scholar 

  • Covert MW et al (2004) Integrating high-throughput and computational data elucidates bacterial networks. Nature 429(6987):92–96

    Article  Google Scholar 

  • Dornblut C et al (2014) A CENP-S/X complex assembles at the centromere in S and G2 phases of the human cell cycle. Open Biol 4(2):130229

    Article  Google Scholar 

  • Eggeling R et al (2012) Gibbs sampling for parsimonious Markov models with latent variables. In: The sixth European workshop on probabilistic graphical models

    Google Scholar 

  • Eggeling R et al (2013) Inhomogeneous parsimonious Markov models. In: Blockeel H et al (eds) Machine learning and knowledge discovery in databases: European conference, ECML PKDD 2013, Prague, Czech Republic, 23–27 September, Proceedings, Part I. Springer, Berlin, pp 321–336. doi:10.1007/978-3-642-40988-2_21

  • Eggeling R et al (2014) On the value of intra-motif dependencies of human insulator protein CTCF. PLoS One 9(1):1–12. doi:10.1371/journal.pone.0085629

    Article  Google Scholar 

  • Eggeling R et al (2015a) Inferring intra-motif dependencies of DNA binding sites from ChIP-seq data. BMC Bioinform 16(1):375. doi:10.1186/s12859-015-0797-4

    Article  Google Scholar 

  • Eggeling R, Koivisto M, Grosse I (2015b) Dealing with small data: on the generalisation of context trees. In: Proceedings of the 32nd international conference on machine learning, Lille, France

    Google Scholar 

  • Elowitz MB et al (2002) Stochastic gene expression in a single cell. Science (New York) 297(5584):1183–6. http://science.sciencemag.org/content/297/5584/1183.abstract

  • Eskat A et al (2012) Step-wise assembly, maturation and dynamic behavior of the human CENP-P/O/R/Q/U kinetochore sub-complex. PLoS One 7(9):e44717

    Article  Google Scholar 

  • Fellner L et al (2014) Phenotype of htgA (mbiA), a recently evolved orphan gene of Escherichia coli and Shigella, completely overlapping in antisense to yaaW. FEMS Microbiol Lett 350(1):57–64. doi:10.1111/1574-6968.12288

    Article  Google Scholar 

  • Fellner L et al (2015) Evidence for the recent origin of a bacterial proteincoding, overlapping orphan gene by evolutionary overprinting. BMC Evol Biol 15(1):1–14

    Article  MathSciNet  Google Scholar 

  • Fellner L et al (2016, in print) Draft genome sequence of three European lab-derivates from the enterohemorrhagic E. coli O157:H7 strain EDL933, including two plasmids. Genome Announc

    Google Scholar 

  • Feuer R et al (2012), Model-based analysis of an adaptive evolution experiment with Escherichia coli in a pyruvate limited continuous culture with glycerol. ENG TS - PubMed. EURASIP J Bioinform Syst Biol 1:14

    Google Scholar 

  • Fischer S et al (2012) Assigning a function to a conserved archaeal metallo-\(\beta \)-lactamase from Haloferax volcanii. Extremophiles 16(2):333–343 Epub 18 Feb 2012

    Article  Google Scholar 

  • Granada AE et al (2013) Human chronotypes from a theoretical perspective. PLoS One 8(3):e59464. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3609763%7B%5C&%7Dtool=pmcentrez%7B%5C&%7Drendertype=abstract

  • Gorin M et al (2016) Interdependent conductances drive infraslow intrinsic rhythmogenesis in a subset of accessory olfactory bulb. J Neurosci 36(11):3127–3144

    Article  Google Scholar 

  • Görlich D et al (2014) Molecular codes in the human inner-kinetochore model: relating CENPs to function. Biosemiotics 7(2):223–247

    Article  Google Scholar 

  • Hellwig D et al (2011) Dynamics of CENP-N kinetochore binding during the cell cycle. J Cell Sci 124(22):3871–3883

    Article  Google Scholar 

  • Henze R et al (2015) Structural analysis of in silico mutant experiments of human inner-kinetochore structure. BioSystems 127:47–59

    Article  Google Scholar 

  • Heyer R et al (2012) High throughput sequencing reveals a plethora of small RNAs including tRNA derived fragments in Haloferax volcanii. RNA Biol 9:1011–1018

    Article  Google Scholar 

  • Heyne S et al (2012) GraphClust: alignment-free structural clustering of local RNA secondary structures. Bioinformatics 28(12):i224–i232

    Article  Google Scholar 

  • Hölzle A et al (2012) tRNA-like elements in Haloferax volcanii. Biochimie 94(4):940–946 Epub 8 Dec 2011

    Article  Google Scholar 

  • Illner K, Fuchs C, Theis FJ (2014) Bayesian blind source separation for data with network structure. J Comput Biol 21(11):855–865

    Article  MathSciNet  Google Scholar 

  • Janzing D et al (2011) Detecting low-complexity unobserved causes. In: Proceedings of the 27th conference on uncertainty in artificial intelligence (UAI 2011)

    Google Scholar 

  • Janzing D et al (2012) Information-geometric approach to inferring causal directions. Artif Intell 182–183:1–31

    Article  MathSciNet  MATH  Google Scholar 

  • Jardin C et al (2012) Structural features of protein-protein interfaces analyzed with concepts of information theory. In: Proceedings of German conference on bioinformatics (GCB). Jena, Germany

    Google Scholar 

  • Jardin C et al (2013) An information-theoretic classification of amino acids for the assessment of interfaces in protein-protein docking. J Mol Model 19(9):3901–3910

    Article  Google Scholar 

  • Jiang X et al (2015) Chromosomal “Stress-Response” domains govern the spatiotemporal expression of the bacterial virulence program. mBio 6(3):e00353–15

    Google Scholar 

  • Klotz J, Bossert M, Schober S (2013a) Computing preimages of Boolean networks. BMC Bioinform 14, Suppl 1.10, p S4

    Google Scholar 

  • Klotz JG, Heckel R, Schober S (2013b) Bounds on the average sensitivity of nested canalizing functions. In: PLoS One 8(5):e64371 (Ed. by Dehmer M)

    Google Scholar 

  • Klotz JG, Bossert M, Schober S (2013c) On the noise sensitivity and mutual information of (nested-) canalizing Boolean functions. In: IEEE information theory workshop (ITW). IEEE, pp 1–5

    Google Scholar 

  • Klotz JG et al (2013d) Properties of Boolean networks and methods for their tests. EURASIP J Bioinform Syst Biol 1:1

    Google Scholar 

  • Kowarsch A et al (2011) miTALOS: analyzing the tissue-specific regulation of signaling pathways by human and mouse microRNAs. RNA (New York) 17(5):809–19

    Article  Google Scholar 

  • Kracht D (2016) Innovative Barcode-Konzepte für Sequenzierverfahren der zweiten Generation. Dissertation. Ulm University

    Google Scholar 

  • Kracht D, Schober S (2014) Using the Davey-MacKay code construction for barcodes in DNA sequencing. In: 2014 8th international symposium on Turbo codes and iterative information processing (ISTC). IEEE, pp 142–146

    Google Scholar 

  • Kracht D, Schober S (2015) Insertion and deletion correcting DNA barcodes based on watermarks. BMC Bioinform 16(1):50

    Article  Google Scholar 

  • Kreyssig P et al (2012) Cycles and the qualitative evolution of chemical systems. PLoS One 7(10):e45772

    Article  Google Scholar 

  • Kreyssig P et al (2014) Effects of small particle numbers on long-term behaviour in discrete biochemical systems. Bioinformatics 30(17):i475–i481

    Article  Google Scholar 

  • Korenčič A et al (2014) Timing of circadian genes in mammalian tissues. Sci Rep 4. http://www.nature.com/srep/2014/140722/srep05782/full/srep05782.html. Accesed 10/06/2014

  • Lampropoulos A et al (2013) GreenGate - a novel, versatile, and efficient cloning system for plant transgenesis. PLoS One 8:e83043

    Article  Google Scholar 

  • Landstorfer R et al (2014) Comparison of strand-specific transcriptomes of enterohemorrhagic Escherichia coli O157:H7 EDL933 (EHEC) under eleven different environmental conditions including radish sprouts and cattle feces. BMC Genom 15(1). Article Number: 353

    Google Scholar 

  • Lange SJ et al (2012) Global or local? Predicting secondary structure and accessibility in mRNAs. Nucleic Acids Res 40(12):5215–5226

    Article  Google Scholar 

  • Mahmood A, Islam N, Nigatu D, Henkel W (2014) DNA inspired bidirectional Lempel-Ziv-like compression algorithms. In: 2014 8th international symposium on turbo codes and iterative information processing (ISTC), pp 162–166

    Google Scholar 

  • Mathieu-Daudé F et al (1996) DNA rehybridization during PCR: the ‘C\(_{0}\)t effect’ and its consequences. Nucleic Acids Res 24(11):2080–2086

    Article  Google Scholar 

  • Maticzka D et al (2014) GraphProt: modeling binding preferences of RNA binding proteins. Genome Biol 15(1):R17

    Article  Google Scholar 

  • Mehlgarten C et al (2015) Divergent evolution of the transcriptional network controlled by Snf1-interacting protein Sip4 in budding yeasts. PLoS One 10(10):1–23. doi:10.1371/journal.pone.0139464

    Article  Google Scholar 

  • Mendes ND et al (2012) Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches. Bioinformatics 28(23):3034–3041

    Article  Google Scholar 

  • Mir K, Schober S (2014a) Investigation of genetic code optimality for overlapping protein coding sequences. In: Proceedings 8th international symposium on turbo codes and iterative information processing (ISTC). Ulm, Germany

    Google Scholar 

  • Mir K, Schober S (2014b) Selection pressure in alternative reading frames. PLoS One 9(10):e108768

    Article  Google Scholar 

  • Mir K et al (2012) Predicting statistical properties of open reading frames in bacterial genomes. PLoS One 7(9):e45103

    Article  Google Scholar 

  • Mir K et al (2013) Short barcodes for next generation sequencing. PLoS One 8(12):e82933

    Article  Google Scholar 

  • Muskhelishvili G, Travers A (2013) Integration of syntactic and semantic properties of the DNA code reveals chromosomes as thermodynamic machines converting energy into information. Cell Mol Life Sci, pp 1–13. doi:10.1007/s00018-013-1394-1

  • Muskhelishvili G, Travers A (2014) Order from the order: how a spatiotemporal genetic program is encoded in a 2-D genetic map of the bacterial chromosome. J Mol Microbiol Biotechnol 24(5–6):332–343

    Article  Google Scholar 

  • Müssel C et al (2012) Multi-objective parameter selection for classifiers. J Stat Softwa 46(i05) (2012)

    Google Scholar 

  • Nettling M et al (2015) DiffLogo: a comparative visualization of sequence motifs. BMC Bioinform 16:387+. doi:10.1186/s12859-015-0767-x (17 Nov 2015)

  • Nettling M et al (2016) Detecting and correcting the binding-affinity bias in ChIP-seq data using inter-species information. BMC Genomics 17(1). http://view.ncbi.nlm.nih.gov/pubmed/27165633

  • Neuhaus K et al (2016) Translatomics combined with transcriptomics and proteomics reveals novel functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC). BMC Genomics 133(17)

    Google Scholar 

  • Nigatu D, Mahmood A, Henkel W (2014a) The empirical codon mutation matrix as a communication channel. BMC Bioinform 15(80) (22 Mar 2014)

    Google Scholar 

  • Nigatu D et al (2014b) Relating digital information, thermodynamic stability, and classes of functional genes in E. coli. In: 2014 IEEE global conference on signal and information processing (GlobalSIP), pp 1338–1341

    Google Scholar 

  • Nigatu D et al (2016) Relationship between digital information and thermodynamic stability in bacterial genomes. EURASIP J Bioinform Syst Biol 2016(1):4. http://bsb.eurasipjournals.com/content/2016/1/4

  • Offermann B et al (2016) Boolean modeling reveals the necessity of transcriptional regulation for bistability in PC12 Cell Differentiation. Front Genet 7:44. http://journal.frontiersin.org/article/10.3389/fgene.2016.00044/abstract. Accessed 30 Mar 2016

  • Oelke D et al (2011) Visual boosting in pixel-based visualizations. Comput Graph Forum 30(3):871–880

    Article  Google Scholar 

  • Othersen OG et al (2012) Application of information theory to feature selection in protein docking. J Mol Model 18(4):1285–1297

    Article  Google Scholar 

  • Peters J et al (2011) Identifiability of causal graphs using functional models. In: Proceedings of the 27th conference on uncertainty in artificial intelligence (UAI 2011)

    Google Scholar 

  • Prendergast L et al (2011) Premitotic assembly of human CENPs-T and-W switches centromeric chromatin to a mitotic state. PLoS Biol 9(6):e1001082

    Article  Google Scholar 

  • Preusse M et al (2015) SimiRa: a tool to identify coregulation between microRNAs and RNA-binding proteins. RNA Biol 12(9):998–1009

    Article  Google Scholar 

  • Preusse M, Theis FJ, Mueller NS (2016) miTALOS v2: analyzing tissue specific microrna function. PLoS One (accepted)

    Google Scholar 

  • Rinck A et al (2013) The human transcriptome is enriched for miRNAbinding sites located in cooperativity-permitting distance. RNA Biol 10(6)

    Google Scholar 

  • Sancar C et al (2015a) Dawn- and dusk-phased circadian transcription rhythms coordinate anabolic and catabolic functions in Neurospora. BMC Biol 13:17. doi:10.1186/s12915-015-0126-4. Accessed 06 May 2016

  • Sancar C et al (2015b) Combinatorial control of light induced chromatin remodeling and gene activation in Neurospora. PLoS Genet 11(3):1–26. doi:10.1371/journal.pgen.1005105

    Article  Google Scholar 

  • Sass S et al (2013) A modular framework for gene set analysis integrating multilevel omics data. Nucleic Acids Res

    Google Scholar 

  • Sass S et al (2015) RAMONA: a web application for gene set analysis on multilevel omics data. Bioinformatics 31(1):128–130

    Article  Google Scholar 

  • Schnattinger T, Schöning U, Kestler HA, (2012) Pareto-optimal RNA sequence-structure alignments. 9th international workshop on computational systems biology, (2012) WCSB 2012. Ulm, Germany, pp 83–86

    Google Scholar 

  • Schnattinger T et al (2013a) RNA-Pareto: interactive analysis of Pareto-optimal RNA sequence-structure alignments. Bioinformatics 29(23):3102–3104 Epub 16 Sept 2013

    Google Scholar 

  • Schnattinger T, Schöning U, Kestler HA (2013b) Structural RNA alignment by multi-objective optimization. Bioinformatics 29(13):1607–1613 Epub 24 Apr 2013

    Google Scholar 

  • Schuster C et al (2014) A regulatory framework for shoot stem cell control integrating metabolic, transcriptional, and phytohormone signals. Develop Cell 4:438–449

    Article  Google Scholar 

  • Simon S et al (2011) Visual analysis of next-generation sequencing data to detect overlapping genes in bacterial genomes. In: Proceedings of IEEE symposium on biological data visualization, October 23–24, Providence, Rhode Island, USA, vol 1, pp 47–54

    Google Scholar 

  • Simon S et al (2015a) Bridging the gap of domain and visualization experts with a Liaison. In: Bertini E, Kennedy J, Puppo E (eds) Eurographics conference on visualization (EuroVis) - short papers, Cagliari, Italy, 25–29 May. The Eurographics Association, pp 127–133

    Google Scholar 

  • Simon S et al (2015b) VisExpress - visual exploration of differential gene expression data. Inf Vis

    Google Scholar 

  • Sobetzko P et al (2013) DNA thermodynamic stability and supercoil dynamics determine the gene expression program during the bacterial growth cycle. Mol BioSyst 9(7):1643–1651

    Article  Google Scholar 

  • Stefani AG et al (2012) Towards confidence intervals for the mutual information between two binary random variables. In: Proceedings of the 9th international workshop on computational systems biology, pp 105–105

    Google Scholar 

  • Stefani AG et al (2013) A lower bound for the confidence interval of the mutual information of high dimensional random variables. In: Proceedings of the 10th international workshop on computational systems biology, pp 136–136

    Google Scholar 

  • Stefani AG et al (2014a) A tight lower bound on the mutual information of a binary and an arbitrary finite random variable as a function of the variational distance. Aust Commun Theory Workshop (AusCTW) 2014:1–4

    Google Scholar 

  • Stefani AG et al (2014b) Confidence intervals for the mutual information. Int J Mach Intell Sens Signal Process 1(3):201–214. doi:10.1504/IJMISSP.2014.066430

  • Suzuki MT, Giovannoni SJ (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62(2):625–630

    Google Scholar 

  • Travers A, Muskhelishvili G, Thompson JMT (2012) DNA information: from digital code to analogue structure. Philos Trans A Math Phys Eng Sci 370(1969):2960–86

    Article  MATH  Google Scholar 

  • Tschernyschkow S et al (2013) Rule-based modeling and simulations of the inner kinetochore structure. Prog Biophys Mol Biol 113(1):33–45

    Article  Google Scholar 

  • Vens C, Costa F (2011) Random forest based feature induction. In: 2011 IEEE 11th international conference on data mining (ICDM). IEEE, pp 744–753

    Google Scholar 

  • Wend S et al (2013) A quantitative ratiometric sensor for time-resolved analysis of auxin dynamics. Sci Rep 3:2052

    Article  Google Scholar 

  • Zscheischler J, Janzing D, Zhang K (2011) Testing whether linear equations are causal: a free probability theory approach. In: Proceedings of the 27th conference on uncertainty in artificial intelligence (UAI 2011)

    Google Scholar 

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  1. Institute of Communications Engineering, Ulm University, Albert-Einstein-Allee 43, 89081, Ulm, Germany

    Martin Bossert

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    Martin Bossert

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Bossert, M. (2018). Introduction. In: Bossert, M. (eds) Information- and Communication Theory in Molecular Biology. Lecture Notes in Bioengineering. Springer, Cham. https://doi.org/10.1007/978-3-319-54729-9_1

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