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Towards a whole-cell modeling approach for synthetic biology

Oliver Purcell, Bonny Jain, Jonathan R. Karr, Markus W. Covert, Timothy K. Lu
2013 Chaos  
To address this problem, we present a modeling approach for the design of synthetic circuits in the context of cellular networks.  ...  This reliance on experimental tuning is because current modeling approaches are unable to make reliable predictions about the in vivo behavior of synthetic circuits.  ...  Towards a whole-cell modeling approach for synthetic biology, we investigate a critically important question: How do synthetic gene circuits affect the host cell?  ... 
doi:10.1063/1.4811182 pmid:23822510 pmcid:PMC3695969 fatcat:qtufba5jvfhfxf5l3lmkbbjdvy

A hidden Markov model approach for determining expression from genomic tiling micro arrays

Kasper Munch, Paul P Gardner, Peter Arctander, Anders Krogh
2006 BMC Bioinformatics  
We present a probabilistic procedure, ExpressHMM, that adaptively models tiling data prior to predicting expression on genomic sequence.  ...  A hidden Markov model (HMM) is used to model the distributions of tiling array probe scores in expressed and non-expressed regions.  ...  training, however, produces a starting point that allows the model to reach a desirable local optimum.  ... 
doi:10.1186/1471-2105-7-239 pmid:16672042 pmcid:PMC1481622 fatcat:3r27wbqao5e4nnogbubhpxw5iu

Plant development: new models and approaches bring progress

J. A. Long
2006 Development  
The model also accurately reproduced the changes in PIN1 subcellular localization and concentration that occur as primordia are established.  ...  These 'computable' plant meristems should allow researchers to predict how live meristems will react to perturbations introduced into the computer model.  ... 
doi:10.1242/dev.02676 pmid:17079267 fatcat:usq4y6ugone5jbt3vhbup4xfam

A practical guide to mechanistic systems modeling in biology using a logic-based approach

Anna Niarakis, Tomáš Helikar
2020 Briefings in Bioinformatics  
The protocol provides a framework that includes defining the model scope, choosing validation criteria, selecting the appropriate modeling approach, constructing a model and simulating the model.  ...  Aimed at those who are new to computational modeling, we present here a practical hands-on protocol breaking down the process of mechanistic modeling of biological systems in a succession of precise steps  ...  CAP site of DNA (depicted with a green box with a cross).  ... 
doi:10.1093/bib/bbaa236 pmid:33064138 pmcid:PMC8293813 fatcat:xm75t5rawvew5fbdrarfyjiu5u

A Multi-Scale Approach to Modeling E. coli Chemotaxis

Eran Agmon, Ryan K. Spangler
2020 Entropy  
Vivarium's approach is demonstrated by combining severalsub-models of biophysical processes into a model of chemotactic E. coli that exchange molecules withtheir environment, express the genes required  ...  membrane boundary and metabolism converting them to useful metabolites, (2) transcription,translation, complexation, and degradation, with stochastic mechanisms that read real gene sequencedata and consume  ...  Each promoter has a number of binding sites that can be occupied by a number of different transcription factors (or sigma factors, which are treated similarly).  ... 
doi:10.3390/e22101101 pmid:33286869 pmcid:PMC7597207 fatcat:7qbzshymk5bynhwiiv4cdismci

Vocabulon: a dictionary model approach for reconstruction and localization of transcription factor binding sites

C. Sabatti, L. Rohlin, K. Lange, J. C. Liao
2004 Bioinformatics  
On one hand, the dictionary model specifies a probability for the entire sequence taking simultaneously into account all the possible binding sites.  ...  Results: We describe the first implementation of dictionary-style models to the study of transcription factors binding sites in an entire genome.  ...  INTRODUCTION The identification of binding sites for regulatory proteins in the upstream region of genes is an important step toward understanding transcription regulation.  ... 
doi:10.1093/bioinformatics/bti083 pmid:15509602 fatcat:hag36no2brdedn5dgwwrniz32q

A proteogenomic approach to understand splice isoform functions through sequence and expression-based computational modeling

Hong-Dong Li, Gilbert S. Omenn, Yuanfang Guan
2016 Briefings in Bioinformatics  
Integrative analysis of these data at different molecular levels enables a proteogenomic approach to systematically interrogate isoform functions.  ...  Notably, RNA-seq technology generates quantitative profiling of transcript expression at the genome scale, with an unprecedented amount of expression data available for developing isoform function prediction  ...  Their method involves refining of exon-intron boundaries, clustering of ESTs by common splice sites and finding a minimal set of full-length transcript isoforms.  ... 
doi:10.1093/bib/bbv109 pmid:26740460 pmcid:PMC5142014 fatcat:fn3irxjnnra5rbui47q2iqck6q

Evolutionary Context Improves Regulatory Network Predictions

Jonathan L. Gordon, Brigida Gallone, Steven Maere, Kevin J. Verstrepen
2017 Cell Systems  
, let alone predict how they are affected by mutations.  ...  Moreover, unlike coding regions, binding sites are small, largely unstructured stretches of DNA with a variable base composition, making it difficult to even identify them based on their sequence alone  ...  network inference than approaches that do not include phylogenetic information, and allows more accurate prediction of regulatory networks for non-model systems starting from only a limited dataset.  ... 
doi:10.1016/j.cels.2017.05.004 pmid:28544878 pmcid:PMC5467721 fatcat:qlghaypnxzddrinpaczbf6psyi

A Model-Based Approach to Identify Binding Sites in CLIP-Seq Data

Tao Wang, Beibei Chen, MinSoo Kim, Yang Xie, Guanghua Xiao, Gajendra P. S. Raghava
2014 PLoS ONE  
Here we present a novel model-based approach (MiClip) to identify high-confidence protein-RNA binding sites from CLIP-seq datasets.  ...  This approach assigns a probability score for each potential binding site to help prioritize subsequent validation experiments.  ...  MiClip is a model-based approach that can identify high-confidence binding sites using probability scores.  ... 
doi:10.1371/journal.pone.0093248 pmid:24714572 pmcid:PMC3979666 fatcat:xnnjobodqrdedg3xwazew4bafm

A Bayesian graphical modeling approach to microRNA regulatory network inference

Francesco C. Stingo, Yian A. Chen, Marina Vannucci, Marianne Barrier, Philip E. Mirkes
2010 Annals of Applied Statistics  
In this paper we propose a Bayesian graphical modeling approach that infers the miRNA regulatory network by integrating expression levels of miRNAs with their potential mRNA targets and, via the prior  ...  We use a directed graphical model with a particular structure adapted to our data based on biological considerations.  ...  The authors would like to acknowledge discussions with David Dahl and Adarsh Joshi on a preliminary modeling approach to the data used in this paper.  ... 
doi:10.1214/10-aoas360 pmid:23946863 pmcid:PMC3740979 fatcat:xoc44ngqfnav3j6uu66m2opvt4

Prediction of Regulatory Elements [chapter]

Albin Sandelin
2008 Msphere  
In particular, the rate of falsely predicted sites is unacceptably high with current methods, due to the small and degenerate binding sites targeted by transcription factors.  ...  Computational 'in-silico' methods for the prediction of transcription factor binding sites are mature, yet critical problems remain unsolved.  ...  Source binding sites The first step towards building models for predicting TF binding sites involves collecting data. To illustrate the process we use the transcription factor MEF2 as an example.  ... 
doi:10.1007/978-1-60327-429-6_11 pmid:18712306 fatcat:ku3wqjcnmjaw5ncqdaszcpzpj4

A Functional Evolutionary Approach to Identify Determinants of Nucleosome Positioning: A Unifying Model for Establishing the Genome-wide Pattern

Amanda L. Hughes, Yi Jin, Oliver J. Rando, Kevin Struhl
2012 Molecular Cell  
Interestingly, the locations of the +1 nucleosome and RNA start sites shift in concert.  ...  We suggest a three-step model in which nucleosome remodelers, general transcription factors, and the transcriptional elongation machinery are primarily involved in generating the nucleosome positioning  ...  His experimental and conceptual contributions were a major influence on this work, and we will miss our numerous memorable and enjoyable discussions.  ... 
doi:10.1016/j.molcel.2012.07.003 pmid:22885008 pmcid:PMC3472102 fatcat:v65pxpfgezc4hpllz3osetivqi

diffBUM-HMM: a robust statistical modeling approach for detecting RNA flexibility changes in high-throughput structure probing data

Paolo Marangio, Ka Ying Toby Law, Guido Sanguinetti, Sander Granneman
2021 Genome Biology  
We present diffBUM-HMM, a noise-aware model that enables accurate detection of RNA flexibility and conformational changes from high-throughput RNA structure-probing data. diffBUM-HMM is widely compatible  ...  Our analyses of datasets generated with a variety of RNA probing chemistries demonstrate the value of diffBUM-HMM for quantitatively detecting RNA structural changes and RNA-binding protein binding sites  ...  B Overview of the RNA-binding sites detected in the Xist transcript, as shown in [23] .  ... 
doi:10.1186/s13059-021-02379-y pmid:34044851 pmcid:PMC8157727 fatcat:36uokeemw5ed7l5dkiie5qnqse

A composite approach towards a complete model of the myosin rod

E. Nihal Korkmaz, Keenan C. Taylor, Michael P. Andreas, Guatam Ajay, Nathan T. Heinze, Qiang Cui, Ivan Rayment
2015 Proteins: Structure, Function, and Bioinformatics  
In addition, a computational approach was developed to combine the sections into a contiguous model.  ...  This has been established for over 50 years and yet a molecular model for the thick filament has not been attained.  ...  such that structural information is required to accurately model these regions.  ... 
doi:10.1002/prot.24964 pmid:26573747 pmcid:PMC4715562 fatcat:pylzstchc5gtdlfekzy4d5aclm

A Model of a MAPK•Substrate Complex in an Active Conformation: A Computational and Experimental Approach

Sunbae Lee, Mangalika Warthaka, Chunli Yan, Tamer S. Kaoud, Andrea Piserchio, Ranajeet Ghose, Pengyu Ren, Kevin N. Dalby, Vladimir N. Uversky
2011 PLoS ONE  
In the present study computer modeling approaches, with restraints derived from experimentally known interactions, were used to predict how the N-terminus of Ets-1 associates with ERK2.  ...  Citation: Lee S, Warthaka M, Yan C, Kaoud TS, Piserchio A, et al. (2011) A Model of a MAPKNSubstrate Complex in an Active Conformation: A Computational and Experimental Approach.  ...  Acknowledgments RG is a member of the New York Structural Biology Center, NYSTAR facility. Author Contributions  ... 
doi:10.1371/journal.pone.0018594 pmid:21494553 pmcid:PMC3073974 fatcat:qpwmbnk3pbghxe4pi3yihupsce
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