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Jacobberger JW, Sramkoski RM, Stefan T, Bray C, Bagwell CB. Analysis of the multiparametric cell cycle data. Methods Cell Biol 2024; 186:271-309. [PMID: 38705604 DOI: 10.1016/bs.mcb.2024.02.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
This chapter was originally written in 2011. The idea was to give some history of cell cycle analysis before and after flow cytometry became widely accessible; provide references to educational material for single parameter DNA content analysis, introduce and discuss multiparameter cell cycle analysis in a methodological style, and in a casual style, discuss aspects of the work over the last 40years that we have given thought, performing some experiments, but didn't publish. It feels like there is a linear progression that moves from counting cells for growth curves, to counting labeled mitotic cells by autoradiography, to DNA content analysis, to cell cycle states defined by immunofluorescence plus DNA content analysis, to extraction of cell cycle expression profiles, and finally to probability state modeling, which should be the "right" way to analyze cytometric cell cycle data. This is the sense of this chapter. In 2023, we have updated it, but the exciting, expansive aspects brought about by spectral and mass cytometry are still young and developing, and thus have not been vetted, reviewed, and presented in mature form.
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Affiliation(s)
| | | | - Tammy Stefan
- Case Comprehensive Cancer Center, Cleveland, OH, United States
| | - Chris Bray
- Verity Software House, Topsham, ME, United States
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Ullah M, Hadi F, Song J, Yu DJ. PScL-2LSAESM: bioimage-based prediction of protein subcellular localization by integrating heterogeneous features with the two-level SAE-SM and mean ensemble method. Bioinformatics 2023; 39:6839969. [PMID: 36413068 PMCID: PMC9947927 DOI: 10.1093/bioinformatics/btac727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/02/2022] [Accepted: 11/21/2022] [Indexed: 11/23/2022] Open
Abstract
MOTIVATION Over the past decades, a variety of in silico methods have been developed to predict protein subcellular localization within cells. However, a common and major challenge in the design and development of such methods is how to effectively utilize the heterogeneous feature sets extracted from bioimages. In this regards, limited efforts have been undertaken. RESULTS We propose a new two-level stacked autoencoder network (termed 2L-SAE-SM) to improve its performance by integrating the heterogeneous feature sets. In particular, in the first level of 2L-SAE-SM, each optimal heterogeneous feature set is fed to train our designed stacked autoencoder network (SAE-SM). All the trained SAE-SMs in the first level can output the decision sets based on their respective optimal heterogeneous feature sets, known as 'intermediate decision' sets. Such intermediate decision sets are then ensembled using the mean ensemble method to generate the 'intermediate feature' set for the second-level SAE-SM. Using the proposed framework, we further develop a novel predictor, referred to as PScL-2LSAESM, to characterize image-based protein subcellular localization. Extensive benchmarking experiments on the latest benchmark training and independent test datasets collected from the human protein atlas databank demonstrate the effectiveness of the proposed 2L-SAE-SM framework for the integration of heterogeneous feature sets. Moreover, performance comparison of the proposed PScL-2LSAESM with current state-of-the-art methods further illustrates that PScL-2LSAESM clearly outperforms the existing state-of-the-art methods for the task of protein subcellular localization. AVAILABILITY AND IMPLEMENTATION https://github.com/csbio-njust-edu/PScL-2LSAESM. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Matee Ullah
- School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Fazal Hadi
- School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | | | - Dong-Jun Yu
- To whom correspondence should be addressed. or
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Shao W, Liu M, Xu YY, Shen HB, Zhang D. An Organelle Correlation-Guided Feature Selection Approach for Classifying Multi-Label Subcellular Bio-Images. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:828-838. [PMID: 28278481 DOI: 10.1109/tcbb.2017.2677907] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Nowadays, with the advances in microscopic imaging, accurate classification of bioimage-based protein subcellular location pattern has attracted as much attention as ever. One of the basic challenging problems is how to select the useful feature components among thousands of potential features to describe the images. This is not an easy task especially considering there is a high ratio of multi-location proteins. Existing feature selection methods seldom take the correlation among different cellular compartments into consideration, and thus may miss some features that will be co-important for several subcellular locations. To deal with this problem, we make use of the important structural correlation among different cellular compartments and propose an organelle structural correlation regularized feature selection method CSF (Common-Sets of Features) in this paper. We formulate the multi-label classification problem by adopting a group-sparsity regularizer to select common subsets of relevant features from different cellular compartments. In addition, we also add a cell structural correlation regularized Laplacian term, which utilizes the prior biological structural information to capture the intrinsic dependency among different cellular compartments. The CSF provides a new feature selection strategy for multi-label bio-image subcellular pattern classifications, and the experimental results also show its superiority when comparing with several existing algorithms.
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Yang F, Xu YY, Shen HB. Many local pattern texture features: which is better for image-based multilabel human protein subcellular localization classification? ScientificWorldJournal 2014; 2014:429049. [PMID: 25050396 PMCID: PMC4094881 DOI: 10.1155/2014/429049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 05/22/2014] [Indexed: 01/14/2023] Open
Abstract
Human protein subcellular location prediction can provide critical knowledge for understanding a protein's function. Since significant progress has been made on digital microscopy, automated image-based protein subcellular location classification is urgently needed. In this paper, we aim to investigate more representative image features that can be effectively used for dealing with the multilabel subcellular image samples. We prepared a large multilabel immunohistochemistry (IHC) image benchmark from the Human Protein Atlas database and tested the performance of different local texture features, including completed local binary pattern, local tetra pattern, and the standard local binary pattern feature. According to our experimental results from binary relevance multilabel machine learning models, the completed local binary pattern, and local tetra pattern are more discriminative for describing IHC images when compared to the traditional local binary pattern descriptor. The combination of these two novel local pattern features and the conventional global texture features is also studied. The enhanced performance of final binary relevance classification model trained on the combined feature space demonstrates that different features are complementary to each other and thus capable of improving the accuracy of classification.
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Affiliation(s)
- Fan Yang
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Shanghai 200240, China
- Key Laboratory of Optic-Electronic and Communication, Jiangxi Science & Technology Normal University, Nanchang 330013, China
- Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China
| | - Ying-Ying Xu
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Shanghai 200240, China
- Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China
| | - Hong-Bin Shen
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Shanghai 200240, China
- Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China
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Yang F, Xu YY, Wang ST, Shen HB. Image-based classification of protein subcellular location patterns in human reproductive tissue by ensemble learning global and local features. Neurocomputing 2014. [DOI: 10.1016/j.neucom.2013.10.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Rosania GR, Shedden K, Zheng N, Zhang X. Visualizing chemical structure-subcellular localization relationships using fluorescent small molecules as probes of cellular transport. J Cheminform 2013; 5:44. [PMID: 24093553 PMCID: PMC3852740 DOI: 10.1186/1758-2946-5-44] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 10/01/2013] [Indexed: 12/12/2022] Open
Abstract
Background To study the chemical determinants of small molecule transport inside cells, it is crucial to visualize relationships between the chemical structure of small molecules and their associated subcellular distribution patterns. For this purpose, we experimented with cells incubated with a synthetic combinatorial library of fluorescent, membrane-permeant small molecule chemical agents. With an automated high content screening instrument, the intracellular distribution patterns of these chemical agents were microscopically captured in image data sets, and analyzed off-line with machine vision and cheminformatics algorithms. Nevertheless, it remained challenging to interpret correlations linking the structure and properties of chemical agents to their subcellular localization patterns in large numbers of cells, captured across large number of images. Results To address this challenge, we constructed a Multidimensional Online Virtual Image Display (MOVID) visualization platform using off-the-shelf hardware and software components. For analysis, the image data set acquired from cells incubated with a combinatorial library of fluorescent molecular probes was sorted based on quantitative relationships between the chemical structures, physicochemical properties or predicted subcellular distribution patterns. MOVID enabled visual inspection of the sorted, multidimensional image arrays: Using a multipanel desktop liquid crystal display (LCD) and an avatar as a graphical user interface, the resolution of the images was automatically adjusted to the avatar’s distance, allowing the viewer to rapidly navigate through high resolution image arrays, zooming in and out of the images to inspect and annotate individual cells exhibiting interesting staining patterns. In this manner, MOVID facilitated visualization and interpretation of quantitative structure-localization relationship studies. MOVID also facilitated direct, intuitive exploration of the relationship between the chemical structures of the probes and their microscopic, subcellular staining patterns. Conclusion MOVID can provide a practical, graphical user interface and computer-assisted image data visualization platform to facilitate bioimage data mining and cheminformatics analysis of high content, phenotypic screening experiments.
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Affiliation(s)
- Gus R Rosania
- Department of Pharmaceutical Sciences, University of Michigan College of Pharmacy, 428 Church Street, Ann Arbor, MI 48109, USA.
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Zheng N, Tsai HN, Zhang X, Rosania GR. The subcellular distribution of small molecules: from pharmacokinetics to synthetic biology. Mol Pharm 2011; 8:1619-28. [PMID: 21805990 DOI: 10.1021/mp200092v] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The systemic pharmacokinetics and pharmacodynamics of small molecules are determined by subcellular transport phenomena. Although approaches used to study the subcellular distribution of small molecules have gradually evolved over the past several decades, experimental analysis and prediction of cellular pharmacokinetics remains a challenge. In this review, we survey the progress of subcellular distribution research since the 1960s, with a focus on the advantages, disadvantages and limitations of the various experimental techniques. Critical review of the existing body of knowledge points to many opportunities to advance the rational design of organelle-targeted chemical agents. These opportunities include (1) development of quantitative, non-fluorescence-based, whole cell methods and techniques to measure the subcellular distribution of chemical agents in multiple compartments; (2) exploratory experimentation with nonspecific transport probes that have not been enriched with putative, organelle-targeting features; (3) elaboration of hypothesis-driven, mechanistic and modeling-based approaches to guide experiments aimed at elucidating subcellular distribution and transport; and (4) introduction of revolutionary conceptual approaches borrowed from the field of synthetic biology combined with cutting edge experimental strategies. In our laboratory, state-of-the-art subcellular transport studies are now being aimed at understanding the formation of new intracellular membrane structures in response to drug therapy, exploring the function of drug-membrane complexes as intracellular drug depots, and synthesizing new organelles with extraordinary physical and chemical properties.
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Affiliation(s)
- Nan Zheng
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
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Radulovic M, Godovac-Zimmermann J. Proteomic approaches to understanding the role of the cytoskeleton in host-defense mechanisms. Expert Rev Proteomics 2011; 8:117-26. [PMID: 21329431 DOI: 10.1586/epr.10.91] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The cytoskeleton is a cellular scaffolding system whose functions include maintenance of cellular shape, enabling cellular migration, division, intracellular transport, signaling and membrane organization. In addition, in immune cells, the cytoskeleton is essential for phagocytosis. Following the advances in proteomics technology over the past two decades, cytoskeleton proteome analysis in resting and activated immune cells has emerged as a possible powerful approach to expand our understanding of cytoskeletal composition and function. However, so far there have only been a handful of studies of the cytoskeleton proteome in immune cells. This article considers promising proteomics strategies that could augment our understanding of the role of the cytoskeleton in host-defense mechanisms.
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Affiliation(s)
- Marko Radulovic
- Division of Medicine, University College London, 5 University Street, London WC1E 6JF, UK.
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SHAMIR L. Assessing the efficacy of low-level image content descriptors for computer-based fluorescence microscopy image analysis. J Microsc 2011; 243:284-92. [DOI: 10.1111/j.1365-2818.2011.03502.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
Cytometric techniques are continually being improved, refined, and adapted to new applications. This chapter briefly outlines recent advances in the field of cytometry with the main focus on new instrumentations in flow and image cytometry as well as new probes suitable for multiparametric analyses. There is a remarkable trend for miniaturizing cytometers, developing label-free and fluorescence-free analytical approaches, and designing "intelligent" probes. Furthermore, new methods for analyzing complex data for extracting relevant information are reviewed.
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Lee YH, Tan HT, Chung MCM. Subcellular fractionation methods and strategies for proteomics. Proteomics 2010; 10:3935-56. [DOI: 10.1002/pmic.201000289] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Rittscher J. Characterization of Biological Processes through Automated Image Analysis. Annu Rev Biomed Eng 2010; 12:315-44. [DOI: 10.1146/annurev-bioeng-070909-105235] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jens Rittscher
- Visualization and Computer Vision Laboratory, GE Global Research, Niskayuna, New York, 12309;
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Ljosa V, Carpenter AE. Introduction to the quantitative analysis of two-dimensional fluorescence microscopy images for cell-based screening. PLoS Comput Biol 2009; 5:e1000603. [PMID: 20041172 PMCID: PMC2791844 DOI: 10.1371/journal.pcbi.1000603] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Vebjorn Ljosa
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Anne E. Carpenter
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
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