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Unsupervised image segmentation for microarray spots with irregular contours and inner holes

Bogdan Belean, Monica Borda, Jörg Ackermann, Ina Koch, Ovidiu Balacescu
2015 BMC Bioinformatics  
To date, no gold-standard for the analysis of microarray images has been established. Due to the lack of a standard approach there is a strong need to identify new processing algorithms.  ...  Results: We evaluated the approach for a data set of microarray images taken from the Stanford Microarray Database (SMD).  ...  Previously, preferable features of the PDE approach for the initial step of automatic grid alignment have been demonstrated [23] .  ... 
doi:10.1186/s12859-015-0842-3 pmid:26698293 pmcid:PMC4690322 fatcat:nvc56a52erfp3hl2harhdt3qcm

Microarray image analysis: from image processing methods to gene expression levels estimation

Bogdan Belean, Robert Gutt, Carmen Costea, Ovidiu Balacescu
2020 IEEE Access  
Microarray image processing leads to the characterization of gene expression levels simultaneously, for all cellular transcripts (mRNAs) in a single experiment.  ...  We propose a density based spatial clustering procedure driven by a level-set approach for microarray spot segmentation together with a complete set of quality measures used to evaluate the proposed method  ...  Our proposed image processing techniques for automatic microarray image processing were implemented in Matlab and they are presented further on. A.  ... 
doi:10.1109/access.2020.3019844 fatcat:stopwx2o3nhsdmpo2wcki2djpe

FSL-based Hardware Implementation for Parallel Computation of cDNA Microarray Image Segmentation

Bogdan Bot, Simina Emerich, Sorin Martoiu, Bogdan Belean
2015 International Journal of Advanced Computer Science and Applications  
The present paper proposes a FPGA based hardware implementations for microarray image processing algorithms in order eliminate the shortcomings of the existing software platforms: user intervention, increased  ...  Hardware architectures for logarithm based image enhancement, profile computation and image segmentation are described.  ...  Future work aims to develop application-specific hardware architecture for more complex methods for automatic microarray image processing such us, partial differential equations (PDE)-based gridding or  ... 
doi:10.14569/ijacsa.2015.060704 fatcat:5nkljcq3qrablhgfnm3mcqcflu

Computational modeling of mammalian signaling networks

Jacob J. Hughey, Timothy K. Lee, Markus W. Covert
2009 Wiley Interdisciplinary Reviews: Systems Biology and Medicine  
Next, we review the mathematical approaches that are used to model signaling network behavior.  ...  These modeling approaches generally lack the detail of ODE-or PDE-based models.  ...  automatically.  ... 
doi:10.1002/wsbm.52 pmid:20836022 pmcid:PMC3105527 fatcat:hdwhbddq2je5ljd2tcwzmsswey

Edge Detection in Satellite Image Using Cellular Neural Network

Osama Basil, Dr. Mohamed, Dr. Hala
2014 International Journal of Advanced Computer Science and Applications  
The present paper proposes a novel approach for edge detection in satellite images based on cellular neural networks.  ...  CNN based edge detector in used conjunction with image enhancement and noise removal techniques, in order to deliver accurate edge detection results, compared with state of the art approaches.  ...  types.              ; ) , ( , ) ) , ( ( 4 ; ) , ( , 2 ) ) , ( ( 4 ) PDE-based image processing techniques are mainly used for smoothing and restoration purposes.  ... 
doi:10.14569/ijacsa.2014.051010 fatcat:c5htb7bqwfcaxnscfkzp62bwey

Proteomics and Extracellular Vesicles as Novel Biomarker Sources in Peritoneal Dialysis in Children

Chiara Trincianti, Vincenzo Meleca, Edoardo La Porta, Maurizio Bruschi, Giovanni Candiano, Andrea Garbarino, Xhuliana Kajana, Alberto Preda, Francesca Lugani, Gian Marco Ghiggeri, Andrea Angeletti, Pasquale Esposito (+1 others)
2022 International Journal of Molecular Sciences  
Although several studies investigated the complex pathogenic pathways underlying peritoneal membrane alterations, these processes remain still to explore.  ...  Peritoneal dialysis (PD) represents the dialysis modality of choice for pediatric patients with end-stage kidney disease.  ...  Protein analysis of complex samples is conducted with different combined techniques like mass spectrometry (MS) [42] , two-dimensional electrophoresis (2-DE), liquid chromatography, microarrays, or protein  ... 
doi:10.3390/ijms23105655 pmid:35628461 pmcid:PMC9144397 fatcat:ctp64om4c5cqxnzonjqab2frai

Automatic clustering with multi-objective Differential Evolution algorithms

Kaushik Suresh, Debarati Kundu, Sayan Ghosh, Swagatam Das, Ajith Abraham
2009 2009 IEEE Congress on Evolutionary Computation  
Experimental results over six artificial and four real life datasets of varying range of complexities indicates that DE holds immense promise as a candidate algorithm for devising MO clustering schemes  ...  This paper applies the Differential Evolution (DE) algorithm to the task of automatic fuzzy clustering in a Multi-objective Optimization (MO) framework.  ...  The two terms at the numerator and the denominator of XB q may not attain their best values for the same partitioning when the data has complex and overlapping clusters, such as remote sensing image data  ... 
doi:10.1109/cec.2009.4983267 dblp:conf/cec/SureshKGDA09 fatcat:i6g3we56yfadxkevrcir5kpci4

Facing the challenges of multiscale modelling of bacterial and fungal pathogen–host interactions

Jana Schleicher, Theresia Conrad, Mika Gustafsson, Gunnar Cedersund, Reinhard Guthke, Jörg Linde
2016 Briefings in Functional Genomics  
We reflect on the current availability of computational approaches for multiscale modelling of host-pathogen interactions and point out current challenges.  ...  Finally, we provide an outlook for future requirements of multiscale modelling.  ...  Agent-State-Cellular based based automata- based x x x Time-independent Continuous time modelling approach modelling approach Constraint-Game ODEs PDEs based theory x x x x x  ... 
doi:10.1093/bfgp/elv064 pmid:26857943 pmcid:PMC5439285 fatcat:zsj7jtzr3zgkvpgchx7j3b6yei

Systems Biology of Fungal Infection

Fabian Horn, Thorsten Heinekamp, Olaf Kniemeyer, Johannes Pollmächer, Vito Valiante, Axel A. Brakhage
2012 Frontiers in Microbiology  
We review current efforts to integrate omics and image-based data of host-pathogen interactions into network and spatio-temporal models.  ...  The modeling will help to elucidate pathogenicity mechanisms and to identify diagnostic biomarkers and potential drug targets for therapy and could thus pave the way for novel intervention strategies based  ...  The ruleset developed for processing microscopic raw data allows fully automated and context-based analysis of image data.  ... 
doi:10.3389/fmicb.2012.00108 pmid:22485108 pmcid:PMC3317178 fatcat:zbwfkinprvf7haap4e53qerb3y

A multi-view approach to cDNA micro-array analysis

Bachar Zineddin, Zidong Wang, Yong Shi, Yurong Li, Min Du, Xiaohui Liu
2010 International Journal of Computational Biology and Drug Design  
This paper is concerned with improving the processes involved in the analysis of microarray image data. The main focus is to clarify an image's feature space in an unsupervised manner.  ...  X. (2010) 'A multi-view approach to cDNA micro-array analysis', Int.  ...  computational platform for kernel-based algorithms and image processing (Chua, 1997) .  ... 
doi:10.1504/ijcbdd.2010.035237 pmid:20852335 fatcat:ruts65qtvjek3pxf64lei36d3u

Unique Reporter-Based Sensor Platforms to Monitor Signalling in Cells

Meesbah Jiwaji, Rónán Daly, Abdullah Gibriel, Gráinne Barkess, Pauline McLean, Jingli Yang, Kshama Pansare, Sarah Cumming, Alisha McLauchlan, Piotr J. Kamola, Musab S. Bhutta, Adam G. West (+5 others)
2012 PLoS ONE  
The methodology uses two robust and easily accessible detection platforms; quantitative real-time PCR for quantitative analysis and DNA microarrays for parallel, higher throughput analysis.  ...  Methods: Here we describe a sensitive, plasmid-based RNA reporter methodology to study transcription factor activation in mammalian cells, and apply this technology to profiling 60 transcription factors  ...  [7] reported an array-based approach for the analysis of the binding activities of TFs.  ... 
doi:10.1371/journal.pone.0050521 pmid:23209767 pmcid:PMC3510088 fatcat:b5gisnh2dffjfbpts3fjwvhlti

Transcriptome profiling of aSaccharomyces cerevisiaemutant with a constitutively activated Ras/cAMP pathway

D. L. Jones, J. Petty, D. C. Hoyle, A. Hayes, E. Ragni, L. Popolo, S. G. Oliver, L. I. Stateva
2003 Physiological Genomics  
Pde2p (the high-affinity cAMP-dependent PDE) is an Mg 2ϩ -requiring, zinc-binding enzyme with a K m for cAMP of 170 nM (66, 73, 88) .  ...  We investigated the effect of applying a purely statistical approach to microarray analysis and demonstrated that small changes in gene expression have biological significance.  ...  Microarray hybridization and image analysis.  ... 
doi:10.1152/physiolgenomics.00139.2003 pmid:14570984 fatcat:kiitblowkjanpm6ndz7tvsol2y

The Transcriptomics of Secondary Growth and Wood Formation in Conifers

Ana Carvalho, Jorge Paiva, José Louzada, José Lima-Brito
2013 Molecular Biology International  
Gymnosperms, in particular, the conifers, are ecologically and economically important, namely, for the production of wood and other forestry end products.  ...  In the last years, forestry scientists have adapted genomics and next-generation sequencing (NGS) technologies to the search for candidate genes related to the transcriptomics of secondary growth and wood  ...  The candidate genes approach based on QTL mapping [48] and gene modification have been useful for wood formation and quality studies.  ... 
doi:10.1155/2013/974324 pmid:24288610 pmcid:PMC3830773 fatcat:ayfzju4au5dbzegsa7et2xtynm

Systems Biology in Immunology: A Computational Modeling Perspective

Ronald N. Germain, Martin Meier-Schellersheim, Aleksandra Nita-Lazar, Iain D.C. Fraser
2011 Annual Review of Immunology  
create computational models and conduct simulations of immune function, We provide descriptions of the key data gathering techniques employed to generate the quantitative and qualitative data required for  ...  spectrometry) or on signal amplification with antibodies (ELISA-based assays, protein microarrays, flow cytometry, confocal imaging).  ...  Protein microarrays are similar to DNA microarrays. Proteins are automatically spotted and immobilized on a solid surface of various compositions.  ... 
doi:10.1146/annurev-immunol-030409-101317 pmid:21219182 pmcid:PMC3164774 fatcat:my2czdrjajd5ldhrm52k2fzd5a

IEEE Access Special Section Editorial: Big Data Learning and Discovery

Zhong-Ke Gao, An-An Liu, Yanhui Wang, Michael Small, Xiaojun Chang, Jurgen Kurths
2021 IEEE Access  
The SCF method was evaluated on five open gene microarray datasets and three low-dimensional datasets.  ...  The experimental results showed that in the process of feature selection, twofold CV and leave-one-out-CV were more suitable for the model evaluation of low-dimensional and small sample datasets, while  ...  His research interests include complex systems, complex networks, chaos and nonlinear dynamics, nonlinear time series analysis, and computational modeling.  ... 
doi:10.1109/access.2021.3127335 fatcat:apph47tuffblnp2dkcc7lezffy
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