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Revisiting the Training of Logic Models of Protein Signaling Networks with ASP [chapter]

Santiago Videla, Carito Guziolowski, Federica Eduati, Sven Thiele, Niels Grabe, Julio Saez-Rodriguez, Anne Siegel
2012 Lecture Notes in Computer Science  
Logic formalisms have become very popular to model signaling networks because their simplicity allows us to model large systems encompassing hundreds of proteins.  ...  We illustrate the application of ASP with in silico cases based on realistic networks and data.  ...  Acknowledgements The work of the first author was supported by the project ANR-10-BLANC-0218. The work of the second author was financed by the BMBF MEDSYS 0315401B.  ... 
doi:10.1007/978-3-642-33636-2_20 fatcat:fjkopvyhyrhi3c36izu2uglsx4

Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming

Carito Guziolowski, Santiago Videla, Federica Eduati, Sven Thiele, Thomas Cokelaer, Anne Siegel, Julio Saez-Rodriguez
2013 Computer applications in the biosciences : CABIOS  
Logic models can be generated by training a network containing the prior knowledge to phospho-proteomics data.  ...  We illustrate the usefulness of caspo by revisiting a model of pro-growth and inflammatory pathways in liver cells.  ...  Gonc¸alves for help plotting the networks and A. MacNamara and C. Chancellor for reading the manuscript. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btt393 pmid:23853063 pmcid:PMC3753570 fatcat:gl5sat62zjed7mseduqubunejq

Learning Boolean logic models of signaling networks with ASP

Santiago Videla, Carito Guziolowski, Federica Eduati, Sven Thiele, Martin Gebser, Jacques Nicolas, Julio Saez-Rodriguez, Torsten Schaub, Anne Siegel
2015 Theoretical Computer Science  
Towards the construction of predictive models, one can convert the generic prior knowledge (canonical cell signaling networks) into a mathematical model (e.g. a set of differential equations or a set of  ...  Further, it has been shown that, if the inherent experimental noise is considered, many different logical networks can be compatible with a set of experimental observations [52] .  ...  Acknowledgements The work of the first author was supported by the project ANR-10-BLANC-0218.  ... 
doi:10.1016/j.tcs.2014.06.022 fatcat:abcdo6ua3bgctlurhsywb6ki4u

Reasoning on the Response of Logical Signaling Networks with ASP [chapter]

Torsten Schaub, Anne Siegel, Santiago Videla
2014 Logical Modeling of Biological Systems  
Nonetheless, a large majority of the authors working with (Boolean) logic-based models, rely on ad-hoc methods to build their models.  ...  That is, signaling networks by no means could function in isolation from metabolic and regulatory 14 Logical Modeling of Biological Systems processes.  ...  This work was partially funded by the projects ANR-10-BLANC-0218 and DFG grant SCHA 550/10-1.  ... 
doi:10.1002/9781119005223.ch2 fatcat:sbrmukr6zbapfier77sfp4zkx4

Inductive logic programming at 30 [article]

Andrew Cropper, Sebastijan Dumančić, Richard Evans, Stephen H. Muggleton
2021 arXiv   pre-print
Inductive logic programming (ILP) is a form of logic-based machine learning. The goal is to induce a hypothesis (a logic program) that generalises given training examples.  ...  As ILP turns 30, we review the last decade of research.  ...  A key difference between ASP and Prolog is semantics. A definite logic program has only one model (the least Herbrand model).  ... 
arXiv:2102.10556v2 fatcat:kv7ktjbajng6jjfae3sq3ubbmu

A method to identify and analyze biological programs through automated reasoning

Boyan Yordanov, Sara-Jane Dunn, Hillel Kugler, Austin Smith, Graziano Martello, Stephen Emmott
2016 npj Systems Biology and Applications  
To address these limitations, we present a methodology based on automated formal reasoning, which permits the synthesis and analysis of the complete set of logical models consistent with experimental observations  ...  Current approaches tend to construct and examine static interaction network models, which are descriptively rich but often lack explanatory and predictive power, or dynamic models that can be simulated  ...  With no prior knowledge of how such signals could input to the network, we included a possible positive and negative interaction from each signal to every component of the network, while again considering  ... 
doi:10.1038/npjsba.2016.10 pmid:27668090 pmcid:PMC5034891 fatcat:3n2ahtmyjjetpgsvlbwo5kgzg4

Completing causal networks by meta-level abduction

Katsumi Inoue, Andrei Doncescu, Hidetomo Nabeshima
2013 Machine Learning  
Case studies of meta-level abduction are presented in p53 signaling networks, in which causal relations are abduced to suppress a tumor with a new protein and to stop DNA synthesis when damage has occurred  ...  Effects of our method are also analyzed through experiments of completing networks randomly generated with both positive and negative links.  ...  colleagues of the Systems Resilience project for discussions on robustness, Philip Reiser for his early attempt to complete biological networks by SOLAR, and the reviewers of this paper for their many  ... 
doi:10.1007/s10994-013-5341-z fatcat:w2i25sbowfadrldsjukgdp65ia

The AnnoLite and AnnoLyze programs for comparative annotation of protein structures

Marc A Marti-Renom, Andrea Rossi, Fátima Al-Shahrour, Fred P Davis, Ursula Pieper, Joaquín Dopazo, Andrej Sali
2007 BMC Bioinformatics  
Acknowledgements: This work is funded by an RO1 from the NHGRI and by a Presidential Early Career Award for Scientists and Engineers from the National Science Foundation.  ...  Our final prediction for each gap is selected, using a trained neural network, based on the predicted functional relatedness and protein-protein interaction.  ...  We chose a logic based framework for representing the rules: Inductive Logic Programming (ILP).  ... 
doi:10.1186/1471-2105-8-s4-s4 pmid:17570147 pmcid:PMC1892083 fatcat:o5p5c46emzbhxlmq27vqibskdi

Network Representation [chapter]

Zhiyuan Liu, Yankai Lin, Maosong Sun
2020 Representation Learning for Natural Language Processing  
The representations can be used as the feature of vertices and applied to many network study tasks. In this chapter, we will introduce network representation learning algorithms in the past decade.  ...  Network representation learning aims to embed the vertexes in a network into low-dimensional dense representations, in which similar vertices in the network should have "close" representations (usually  ...  of JNTM model Protein Interface Prediction.  ... 
doi:10.1007/978-981-15-5573-2_8 fatcat:2fljfkgpozhudbgqr7tgv45vxi

Voltage-Gated Proton Channels: Molecular Biology, Physiology, and Pathophysiology of the HV Family

Thomas E. DeCoursey
2013 Physiological Reviews  
The H V channel protein is strikingly similar to the voltage-sensing domain (VSD, the first four membrane-spanning segments) of voltage-gated K ϩ and Na ϩ channels.  ...  They open with membrane depolarization, but their voltage dependence is strongly regulated by the pH gradient across the membrane (⌬pH), with the result that in most species they normally conduct only  ...  The mechanisms by which Gu ϩ denatures proteins are under debate, but include replacing waters that are bound by proteins, reorganizing local water networks, and altering or disrupting hydrogen bonds between  ... 
doi:10.1152/physrev.00011.2012 pmid:23589829 pmcid:PMC3677779 fatcat:c23hljyikze45d42f7hek7rgpi

Introduction to Bioinformatics [article]

Sabu M. Thampi
2009 arXiv   pre-print
This discipline represents the convergence of genomics, biotechnology and information technology, and encompasses analysis and interpretation of data, modeling of biological phenomena, and development  ...  Bioinformatics is a new discipline that addresses the need to manage and interpret the data that in the past decade was massively generated by genomic research.  ...  Secondary Structure Prediction methods With no homologue of known structure from which to make a 3D model, a logical next step is to predict secondary structure.  ... 
arXiv:0911.4230v1 fatcat:4trytpwrw5apvkiejbwhiqmp6m

Protein-Ligand Docking in the New Millennium – A Retrospective of 10 Years in the Field

S.F. Sousa, A.J.M. Ribeiro, J.T.S. Coimbra, R.P.P. Neves, S.A. Martins, N.S.H.N. Moorthy, P.A. Fernandes, M.J. Ramos
2013 Current Medicinal Chemistry  
The emerging trends in this field are the subject of special attention, while old established docking alternatives are critically revisited.  ...  Current challenges in the field of protein-ligand docking such as the treatment of protein flexibility, the presence of structural water molecules and its effect in docking, and the entropy of binding  ...  ACKNOWLEDGEMENTS The authors would like to thank the financial support provided by FCT (PTDC/QUI-QUI/100372/2008 and grant no.  ... 
doi:10.2174/0929867311320180002 pmid:23531220 fatcat:mopdivgtp5azrhgpoab7e7vt4e

List of Abstracts from the Twenty-ninth Annual Meeting of the Association for Chemoreception Sciences

2007 Chemical Senses  
Topics include insect colonies as examples of self-organizing complex systems; deep conservation of neural mechanisms that couple experience with changes in brain structure; understanding the evolution  ...  of social behavior using the "evo-devo" paradigm, and a new perspective on the nature-nurture problem.  ...  Establishing the operational principles of networks for taste and olfaction will be critical for delineating the logic of neural coding and information processing in these senses.  ... 
doi:10.1093/chemse/bjm024 fatcat:vvc2tltr6ff2jpjf5oexocyuyy

Abstracts from the Thirty-fourth Annual Meeting of the Association for Chemoreception Sciences

2013 Chemical Senses  
I will describe experiments that have led to the identification of aggression pheromones in this species, and insights into the chemosensory "logic" by which this innate behavior is controlled.  ...  Moreover, I will present pilot data that examines whether expectation modulates patterns of neural activity at the earliest stage of the olfactory process, namely in the olfactory epithelium.  ...  In NPG, signals of WGA proteins were observed in almost all the Eya1 expressing neurons.  ... 
doi:10.1093/chemse/bjs091 pmid:23300212 fatcat:or55rqfvszfqdmmdlusi5jfrbi


2018 Seibutsu Butsuri  
to the progress of biophysics.  ...  After the first round of competitive screening based on submitted documents, the following ten applicants were selected as the young invited speakers.  ...  as a gene logic-chip.  ... 
doi:10.2142/biophys.58.s1 fatcat:6slkwnu64fen7cjixehxrcmdzm
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