Filters








9,019 Hits in 5.6 sec

Qualitative Reasoning on Systematic Gene Perturbation Experiments [chapter]

Francesco Sambo, Barbara Di Camillo
2011 Lecture Notes in Computer Science  
For this purpose, we present a novel Qualitative Reasoning approach, based on a qualitative abstraction of DNA-microarray data and on a set of IF-THEN inference rules.  ...  Observations of systematic gene perturbation experiments have been proven the most informative for the identification of regulatory relations between genes.  ...  Acknowledgments We would like to thank Professor Silvana Badaloni and Professor Gianna Toffolo of the Department of Information Engineering, University of Padova, for the precious advice and suggestions  ... 
doi:10.1007/978-3-642-21946-7_11 fatcat:najkctvwyveknj7gjouekbl4ky

Perturbation Biology: Inferring Signaling Networks in Cellular Systems

Evan J. Molinelli, Anil Korkut, Weiqing Wang, Martin L. Miller, Nicholas P. Gauthier, Xiaohong Jing, Poorvi Kaushik, Qin He, Gordon Mills, David B. Solit, Christine A. Pratilas, Martin Weigt (+5 others)
2013 PLoS Computational Biology  
The experiments are systematic series of perturbations of cancer cell lines by targeted drugs, singly or in combination.  ...  We present a new experimental-computational technology of inferring network models that predict the response of cells to perturbations and that may be useful in the design of combinatorial therapy against  ...  pathways from systematic perturbation experiments.  ... 
doi:10.1371/journal.pcbi.1003290 pmid:24367245 pmcid:PMC3868523 fatcat:veovpdsvyzep3pkusq5kdrdi3i

Principles and Strategies for Developing Network Models in Cancer

Dana Pe'er, Nir Hacohen
2011 Cell  
The key underlying assumption frequently used for inferring networks from genomic data is that influences and interactions between biological entities generate statistical relations in the observed data  ...  In the end, a "good" model of biological networks should be able to predict the behavior of the network under different conditions and perturbations and, ideally, even help us to engineer a desired response  ...  D.P. holds a Career Award at the Scientific Interface from the Burroughs Wellcome Fund and Packard Fellowship for Science and Engineering.  ... 
doi:10.1016/j.cell.2011.03.001 pmid:21414479 pmcid:PMC3082135 fatcat:pfb4lxzgdzh5fjcd75uk5yyaui

Identifying Gene Regulatory Networks from Gene Expression Data [chapter]

Vladimir Filkov
2005 Chapman & Hall/CRC Computer & Information Science Series  
Extending Bayesian Networks Bayesian networks offer an intuitive, probabilistic framework in which to model and reason about qualitative properties of gene networks.  ...  The inference problem, then, is to find a network consistent with expression data resulting from genetic perturbations.  ... 
doi:10.1201/9781420036275.ch27 fatcat:n57gltun7nbdpajuuk3zjqtj4m

Personalized signaling models for personalized treatments

Julio Saez‐Rodriguez, Nils Blüthgen
2020 Molecular Systems Biology  
Dynamic mechanistic models that are based on biological knowledge have great potential for modeling specific systems, because they require less data for training to provide biological insight in particular  ...  such as Boolean networks or systems of differential equations.  ...  Acknowledgements The authors apologize for all the colleagues whose work could not be cited due to the limitations in the number of citations.  ... 
doi:10.15252/msb.20199042 pmid:32129942 pmcid:PMC6951359 fatcat:clbhjyazlzempaykta7hentria

The cognitive phenotype of Down syndrome: Insights from intracellular network analysis

Avi Ma'ayan, Katheleen Gardiner, Ravi Iyengar
2006 NeuroRx  
Networks can be assembled from highthroughput experiments or by text-mining of experimental literature.  ...  Systematic approaches such as intracellular network construction and analysis have not been generally applied in DS research.  ...  Research in the Iyengar Laboratory is supported by Grants GM-072853 and GM-54508 from NIH and an advanced center grant from NYSTAR. Research in the Gardiner Laboratory is  ... 
doi:10.1016/j.nurx.2006.05.036 pmid:16815222 pmcid:PMC3032589 fatcat:pvaheiy3djbghfluhgiljzieci

The cognitive phenotype of Down syndrome: Insights from intracellular network analysis

Avi Ma'ayan, Katheleen Gardiner, Ravi Iyengar
2006 Neurotherapeutics  
Networks can be assembled from highthroughput experiments or by text-mining of experimental literature.  ...  Systematic approaches such as intracellular network construction and analysis have not been generally applied in DS research.  ...  Research in the Iyengar Laboratory is supported by Grants GM-072853 and GM-54508 from NIH and an advanced center grant from NYSTAR. Research in the Gardiner Laboratory is  ... 
doi:10.1007/bf03206662 fatcat:dzxzwzldzjc3liq37j53quskba

Reverse Engineering of Molecular Networks from a Common Combinatorial Approach [article]

Bhaskar DasGupta and Paola Vera-Licona and Eduardo Sontag
2011 arXiv   pre-print
We will explore the ultimate impact that the alternative algorithms have on the inference of published in silico biological networks.  ...  Thus, the "reverse-engineering" of networks from data has emerged as one of the central concern of systems biology research.  ...  Acknowledgments The authors would like to thank Joe Dundas for the implementation and maintenance of the web tool for Ideker et. al. method. We would like to thank as well Dr.  ... 
arXiv:1102.4904v1 fatcat:r4bfdx5rozhqfpsy5o2ltypnte

Supervised Inference of Gene Regulatory Networks by Linear Programming [chapter]

Yong Wang, Trupti Joshi, Dong Xu, Xiang-Sun Zhang, Luonan Chen
2006 Lecture Notes in Computer Science  
In this paper we propose a novel method to combine timecourse microarray dataset and documented or potential known transcription regulators for inferring gene regulatory networks.  ...  The development of algorithms for reverse-engineering gene regulatory networks is boosted by microarray technologies, which enable the simultaneous measurement of all RNA transcripts in a cell.  ...  A wide variety of approaches have been proposed to infer gene regulatory networks from time-course data [3, 4, 5] or perturbation experiments [6] , such as discrete models of Boolean networks and Bayesian  ... 
doi:10.1007/11816102_59 fatcat:v2kxadlqpnan5nekp7sehmsfxa

Reverse Engineering of Molecular Networks from a Common Combinatorial Approach [chapter]

Bhaskar Dasgupta, Paola Vera-licona, Eduardo Sontag
2010 Algorithms in Computational Molecular Biology  
Acknowledgments The authors would like to thank Joe Dundas for the implementation and maintenance of the web tool for Ideker et. al. method. We would like to thank as well Dr.  ...  Brandilyn Stigler for useful discussions on different aspects of this book chapter.  ...  [13] This paper introduces a method for the inference of the network topology from gene expression data, from which one extracts state transition measurements of wild-type and perturbation data.  ... 
doi:10.1002/9780470892107.ch40 fatcat:j5s6j24a7bh4dgt3vd7hrwl7j4

How Difficult Is Inference of Mammalian Causal Gene Regulatory Networks?

Djordje Djordjevic, Andrian Yang, Armella Zadoorian, Kevin Rungrugeecharoen, Joshua W. K. Ho, Frank Emmert-Streib
2014 PLoS ONE  
Nonetheless, if we have expression profiling data from genetic or molecular perturbation experiments, such as gene knock-out or signalling stimulation, it is possible to use the set of differentially expressed  ...  Our result supports the importance of using perturbation experimental data in causal network reconstruction.  ...  Conceived and designed the experiments: JWKH. Performed the experiments: DD. Analyzed the data: DD AY. Contributed reagents/ materials/analysis tools: AY AZ KR. Wrote the paper: DD JWKH.  ... 
doi:10.1371/journal.pone.0111661 pmid:25369032 pmcid:PMC4219746 fatcat:q2lcsoz53bgndme4w2d2k7p2wq

Reconstructing Gene Regulatory Networks from Homozygous and Heterozygous Deletion Data Using Gaussian Noise Model

Faridah Hani Mohamed Salleh, Shereena Mohd Arif, Suhaila Zainuddin, Mohd Firdaus Raih
2013 2013 1st International Conference on Artificial Intelligence, Modelling and Simulation  
In this research study, we propose an algorithm for inferring the regulatory interactions from homozygous and heterozygous deletion data using a Gaussian model.  ...  The analysis of the experiment results reveals that our method can reconstruct networks and predict signed edges with a wide range of network types, connectivity, and noise levels with a reasonable error  ...  Over the last decade, numerous methods have been developed for the inference of regulatory networks from gene expression data.  ... 
doi:10.1109/aims.2013.19 fatcat:jbdqslbm7zgjvazcvrxhylsk5m

Biological feature validation of estimated gene interaction networks from microarray data: a case study on MYC in lymphomas

U. Mansmann, V. Jurinovic
2011 Briefings in Bioinformatics  
databases to support the derived findings and (v) a strategy for biological experiments derived from the findings in steps (i^iv).  ...  A major goal in systems biology/medicine is to reconstruct the network of components from microarray data.  ...  Acknowledgements We thank Khadija ElAmrani for providing the software to visualize the comparison of graphs. We also thank three anonymous reviewers for their constructive and helpful comments.  ... 
doi:10.1093/bib/bbr007 pmid:21498549 fatcat:5ztt4uc7v5ccneatfxh74rwxge

Unravelling gene networks from noisy under-determined experimental perturbation data

A. de la Fuente, D.P. Makhecha
2006 IEE Proceedings - Systems Biology  
Previously, an algorithm for gene network inference from gene expression perturbation data was proposed. Here, the algorithm is extended by using regression with subset selection.  ...  The first step in this modelling process is to unravel the interaction structure of biological systems from experimental data.  ...  Acknowledgment We would like to thank Valerie and Edwin Robinson for their continuing moral support.  ... 
doi:10.1049/ip-syb:20050061 pmid:16986627 fatcat:d7guaynhd5fnfgmpyh24wxt4ku

Checking consistency between expression data and large scale regulatory networks: a case study

C Guziolowski
2007 Journal of Biological Physics and Chemistry  
We study the response of E.coli regulatory network to nutritional stress, and compare it to publicly available DNA microarray experiments.  ...  We proposed in previous articles a qualitative approach to check the compatibility between a model of interactions and gene expression data.  ...  ACKNOWLEDGMENTS The authors would like to kindly thank the chilean "National Commission for Scientific and Technological Research" (Conicyt) for supporting the work of the first author.  ... 
doi:10.4024/20701.jbpc.07.02 fatcat:ir5a5x2qbvcxxlhwicclljyoky
« Previous Showing results 1 — 15 out of 9,019 results