Relevant bibliographies by topics / Pseudotime

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  2. Dissertations / Theses
  3. Book chapters
  4. Conference papers

Academic literature on the topic 'Pseudotime'

Author: Grafiati
Published: 4 June 2021
Last updated: 26 July 2025

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Journal articles on the topic "Pseudotime"

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Lee, Hyunjong, Hojoong Kim, Young Soo Choi, Hong Ryul Pyo, Myung-Ju Ahn, and Joon Young Choi. "Prognostic Significance of Pseudotime from Texture Parameters of FDG PET/CT in Locally Advanced Non-Small-Cell Lung Cancer with Tri-Modality Therapy." Cancers 14, no. 15 (2022): 3809. http://dx.doi.org/10.3390/cancers14153809.

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Texture analysis provides image parameters from F-18 fluorodeoxyglucose positron emission tomography/computed tomography (FDG PET/CT). Although some parameters are associated with tumor biology and clinical features, the types and implications of these parameters are complicated. We applied pseudotime analysis, which has recently been used to estimate changes in individual sample characteristics, to texture parameters from FDG PET/CT images of locally advanced non-small-cell lung cancer (NSCLC) patients undergoing neoadjuvant concurrent chemoradiation therapy (CCRT) followed by surgery. Our su
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Mao, Shuainan, Jiajia Liu, Weiling Zhao, and Xiaobo Zhou. "LVPT: Lazy Velocity Pseudotime Inference Method." Biomolecules 13, no. 8 (2023): 1242. http://dx.doi.org/10.3390/biom13081242.

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The emergence of RNA velocity has enriched our understanding of the dynamic transcriptional landscape within individual cells. In light of this breakthrough, we embarked on integrating RNA velocity with cellular pseudotime inference, aiming to improve the prediction of cell orders along biological trajectories beyond existing methods. Here, we developed LVPT, a novel method for pseudotime and trajectory inference. LVPT introduces a lazy probability to indicate the probability that the cell stays in the original state and calculates the transition matrix based on RNA velocity to provide the pro
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Lapborisuth, Kalsuda, Colin Farrell, and Matteo Pellegrini. "Pseudotime Analysis Reveals Exponential Trends in DNA Methylation Aging with Mortality Associated Timescales." Cells 11, no. 5 (2022): 767. http://dx.doi.org/10.3390/cells11050767.

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The epigenetic trajectory of DNA methylation profiles has a nonlinear relationship with time, reflecting rapid changes in DNA methylation early in life that progressively slow with age. In this study, we use pseudotime analysis to determine the functional form of these trajectories. Unlike epigenetic clocks that constrain the functional form of methylation changes with time, pseudotime analysis orders samples along a path, based on similarities in a latent dimension, to provide an unbiased trajectory. We show that pseudotime analysis can be applied to DNA methylation in human blood and brain t
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Haghverdi, Laleh, Maren Büttner, F. Alexander Wolf, Florian Buettner, and Fabian J. Theis. "Diffusion pseudotime robustly reconstructs lineage branching." Nature Methods 13, no. 10 (2016): 845–48. http://dx.doi.org/10.1038/nmeth.3971.

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Zhai, Jingyi, Hongkai Ji, and Hui Jiang. "Reconstruction of Single-Cell Trajectories Using Stochastic Tree Search." Genes 14, no. 2 (2023): 318. http://dx.doi.org/10.3390/genes14020318.

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The recent advancement in single-cell RNA sequencing technologies enables the understanding of dynamic cellular processes at the single-cell level. Using trajectory inference methods, pseudotimes can be estimated based on reconstructed single-cell trajectories which can be further used to gain biological knowledge. Existing methods for modeling cell trajectories, such as minimal spanning tree or k-nearest neighbor graph, often lead to locally optimal solutions. In this paper, we propose a penalized likelihood-based framework and introduce a stochastic tree search (STS) algorithm aiming at the
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Zhang, Miao, and Luis F. Ayala H. "Gas-Production-Data Analysis of Variable-Pressure-Drawdown/Variable-Rate Systems: A Density-Based Approach." SPE Reservoir Evaluation & Engineering 17, no. 04 (2014): 520–29. http://dx.doi.org/10.2118/172503-pa.

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Summary This study demonstrates that production-data analysis of variable-bottomhole-flowing-pressure/variable-rate gas wells under boundary-dominated flow (BDF) is possible by use of a density-based approach. In this approach, governing equations are expressed in terms of density variables and dimensionless viscosity/compressibility ratios. Previously, the methodology was successfully used to derive rescaled exponential models for gas-rate-decline analysis of wells primarily producing at constant bottomhole pressure (Ayala and Ye 2013a, b; Ayala and Zhang 2013; Ye and Ayala 2013; Zhang and Ay
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Liu, Jiajia, Mengyuan Yang, Weiling Zhao, and Xiaobo Zhou. "CCPE: cell cycle pseudotime estimation for single cell RNA-seq data." Nucleic Acids Research 50, no. 2 (2021): 704–16. http://dx.doi.org/10.1093/nar/gkab1236.

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Abstract Pseudotime analysis from scRNA-seq data enables to characterize the continuous progression of various biological processes, such as the cell cycle. Cell cycle plays an important role in cell fate decisions and differentiation and is often regarded as a confounder in scRNA-seq data analysis when analyzing the role of other factors. Therefore, accurate prediction of cell cycle pseudotime and identification of cell cycle stages are important steps for characterizing the development-related biological processes. Here, we develop CCPE, a novel cell cycle pseudotime estimation method to cha
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Mondal, Pronoy Kanti, Udit Surya Saha, and Indranil Mukhopadhyay. "PseudoGA: cell pseudotime reconstruction based on genetic algorithm." Nucleic Acids Research 49, no. 14 (2021): 7909–24. http://dx.doi.org/10.1093/nar/gkab457.

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Abstract Dynamic regulation of gene expression is often governed by progression through transient cell states. Bulk RNA-seq analysis can only detect average change in expression levels and is unable to identify this dynamics. Single cell RNA-seq presents an unprecedented opportunity that helps in placing the cells on a hypothetical time trajectory that reflects gradual transition of their transcriptomes. This continuum trajectory or ‘pseudotime’, may reveal the developmental pathway and provide us with information on dynamic transcriptomic changes and other biological processes. Existing appro
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Xu, Qian, Guanxun Li, Daniel Osorio, et al. "scInTime: A Computational Method Leveraging Single-Cell Trajectory and Gene Regulatory Networks to Identify Master Regulators of Cellular Differentiation." Genes 13, no. 2 (2022): 371. http://dx.doi.org/10.3390/genes13020371.

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Trajectory inference (TI) or pseudotime analysis has dramatically extended the analytical framework of single-cell RNA-seq data, allowing regulatory genes contributing to cell differentiation and those involved in various dynamic cellular processes to be identified. However, most TI analysis procedures deal with individual genes independently while overlooking the regulatory relations between genes. Integrating information from gene regulatory networks (GRNs) at different pseudotime points may lead to more interpretable TI results. To this end, we introduce scInTime—an unsupervised machine lea
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Turner, T. C., M. C. P. Sok, L. A. Hymel, et al. "Harnessing lipid signaling pathways to target specialized pro-angiogenic neutrophil subsets for regenerative immunotherapy." Science Advances 6, no. 44 (2020): eaba7702. http://dx.doi.org/10.1126/sciadv.aba7702.

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To gain insights into neutrophil heterogeneity dynamics in the context of sterile inflammation and wound healing, we performed a pseudotime analysis of single-cell flow cytometry data using the spanning-tree progression analysis of density-normalized events algorithm. This enables us to view neutrophil transitional subsets along a pseudotime trajectory and identify distinct VEGFR1, VEGFR2, and CXCR4 high-expressing pro-angiogenic neutrophils. While the proresolving lipid mediator aspirin-triggered resolvin D1 (AT-RvD1) has a known ability to limit neutrophil infiltration, our analysis uncovers
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Dissertations / Theses on the topic "Pseudotime"

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Ibrahim, Mazher Hassan. "History matching pressure response functions from production data." Texas A&M University, 2004. http://hdl.handle.net/1969.1/1486.

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This dissertation presents several new techniques for the analysis of the long-term production performance of tight gas wells. The main objectives of this work are to determine pressure response function for long-term production for a the slightly compressible liquid case, to determine the original gas in place (OGIP) during pseudosteady state (PSS), to determine OGIP in the transient period, and to determine the effects of these parameters on linear flow in gas wells. Several methods are available in the industry to analyze the production performance of gas wells. One common method is superp
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Lim, Chee Yee. "Understanding transcriptional regulation through computational analysis of single-cell transcriptomics." Thesis, University of Cambridge, 2017. https://www.repository.cam.ac.uk/handle/1810/267786.

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Gene expression is tightly regulated by complex transcriptional regulatory mechanisms to achieve specific expression patterns, which are essential to facilitate important biological processes such as embryonic development. Dysregulation of gene expression can lead to diseases such as cancers. A better understanding of the transcriptional regulation will therefore not only advance the understanding of fundamental biological processes, but also provide mechanistic insights into diseases. The earlier versions of high-throughput expression profiling techniques were limited to measuring average gen
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Pagliaro, Sarah Beatriz De Oliveira. "Transcriptional control induced by bcr-abl and its role in leukemic stem cell heterogeneity. Single-Cell Transcriptome in Chronic Myeloid Leukemia: Pseudotime Analysis Reveals Evidence of Embryonic and Transitional Stem Cell States Single Cell Transcriptome in Chronic Myeloid Leukemia (CML): Pseudotime Analysis Reveals a Rare Population with Embryonic Stem Cell Features and Druggable Intricated Transitional Stem Cell States A novel neuronal organoid model mimicking glioblastoma (GBM) features from induced pluripotent stem cells (iPSC) Experimental and integrative analyses identify an ETS1 network downstream of BCR-ABL in chronic myeloid leukemia (CML)." Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASQ032.

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La leucémie myéloïde chronique est une hématopoïèse maligne clonale, caractérisée par l'acquisition de la translocation t (9;22) conduisant au chromosome Ph1 et à son homologue l'oncogène BCR-ABL, dans une cellule souche hématopoïétique très primitive. La LMC est un modèle de thérapies ciblées, car il a été démontré que la preuve de la faisabilité du ciblage de l'activité tyrosine kinase (TK) BCR-ABL à l'aide d'inhibiteurs de TK (TKI) entraîne des réponses et des rémissions majeures. Cependant, les problèmes actuels rencontrés dans ces thérapies sont la résistance des cellules souches leucémiq
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Strang, Blair Lewis. "Development and characterisation of pseudotype HIV vectors." Thesis, University College London (University of London), 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.406402.

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Piccini, Giulia. "Evaluation of Influenza Lentiviral Pseudotypes as an alternative source of antigen in the Neuraminidase Inhibition Enzyme-Linked Lectin Assay." Doctoral thesis, Università di Siena, 2020. http://hdl.handle.net/11365/1096232.

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The continuously changing epidemiology of influenza viruses needs to be yearly addressed with a fast and massive production of vaccines that prevent epidemic outbreaks and occasional pandemics worldwide. Currently licensed flu vaccines are designed to elicit antibodies against the viral hemagglutinin (HA). Formulations containing standardized amounts of neuraminidase (NA) are however gaining growing interest in the influenza vaccine field, as NA‐inhibiting (NI) antibodies have been associated with resistance to disease as well as reduced severity and duration of illness. The Neuraminidase In
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Lin, Po-Yin, and 林柏吟. "Expressing dengue virus 2 E protein for pseudotype formation of murine leukemia virus with dengue virus envelope." Thesis, 2005. http://ndltd.ncl.edu.tw/handle/35241300985270384102.

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碩士<br>國立交通大學<br>生化工程研究所<br>94<br>Dengue virus (DV), a member of the family Flaviviridae, is an enveloped, single-stranded positive sense RNA virus. Dengue fever and dengue hemorrhagic fever (DF/DHF) are caused by the dengue viruses that represent a global public health problem. In the process of virus entry, the envelope protein (E protein) plays an important role. It is a glycoprotein of 495 amino acids, with a transmembrane domain at the C-terminal. The extracellular domain of E protein is thought to interact with the host cell receptor. There is no discernable change in the host cell that i
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Book chapters on the topic "Pseudotime"

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Ji, Zhicheng, and Hongkai Ji. "Pseudotime Reconstruction Using TSCAN." In Methods in Molecular Biology. Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9057-3_8.

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Mi, Dan, Jiaxin Hu, and Zhaohui Qian. "A Lentiviral Pseudotype System to Characterize SARS-CoV-2 Glycoprotein." In Methods in Molecular Biology. Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2895-9_16.

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Nehring, Dirk, Ralf Pörtner, and Peter Czermak. "Production of Retroviral Pseudotype Vectors in Fixed Bed Reactors for Use in Gene Therapy." In Cells and Culture. Springer Netherlands, 2010. http://dx.doi.org/10.1007/978-90-481-3419-9_107.

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Paniagua-Zambrana, Narel Y., Rainer W. Bussmann, Javier Echeverría, and Carolina Romero. "Senecio adenophyllus Meyen & Walp. Senecio atacamensis Phil. Senecio breviscapus DC. Senecio candollei Wedd. Senecio canescens (Bonpl.) Cuatrec Senecio chinogeton Wedd. Senecio ctenophyllus Phil. Senecio filaginoides DC. Senecio haenkeanus Cuatrec. Senecio nutans Sch. Bip. Senecio olivaceobracteatus Ricardi & Martic. Senecio pappii Ricardi & Martic. Senecio proteus J. Rémy var. proteus Senecio pseudotites Grieseb. Senecio puchii Phil. Senecio scorzonerifolius Meyen & Walp. Senecio smithioides Cabrera Senecio volckmannii Phil. Senecio xerophilus Phil. var. xerophilus Senecio zoellneri Martic. & Quezada Asteraceae." In Ethnobotany of Mountain Regions. Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-319-77093-2_265-1.

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Paniagua-Zambrana, Narel Y., Rainer W. Bussmann, Javier Echeverría, and Carolina Romero. "Senecio adenophyllus Meyen & Walp. Senecio atacamensis Phil. Senecio breviscapus DC. Senecio candollei Wedd. Senecio canescens (Bonpl.) Cuatrec Senecio chinogeton Wedd. Senecio ctenophyllus Phil. Senecio filaginoides DC. Senecio haenkeanus Cuatrec. Senecio nutans Sch. Bip. Senecio olivaceobracteatus Ricardi & Martic. Senecio pappii Ricardi & Martic. Senecio proteus J. Rémy var. proteus Senecio pseudotites Grieseb. Senecio puchii Phil. Senecio scorzonerifolius Meyen & Walp. Senecio smithioides Cabrera Senecio volckmannii Phil. Senecio xerophilus Phil. var. xerophilus Senecio zoellneri Martic. & Quezada Asteraceae." In Ethnobotany of Mountain Regions. Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-28933-1_265.

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Zhu, Jiuru, Jiaqing Chen, Peizheng Li, and Yuanze Chen. "A Performance Evaluation Model of Single-Cell Pseudotime Trajectory Inference Algorithms." In Advances in Transdisciplinary Engineering. IOS Press, 2021. http://dx.doi.org/10.3233/atde210335.

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The study on single-cell pseudotime trajectory is of great significance to the exploration of the environmental factors of life and diseases. The large scale and complexity of single-cell data make the single-cell pseudotime trajectory algorithms face great challenges. A performance evaluation model is proposed to measure the performance of existing pseudotime trajectory inference algorithms and mine the problems existing in the inference algorithms in order to promote the improvement of the inference algorithms. Under the condition of given original single-cell data, the model uses the Spearm
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"Pseudotype." In Encyclopedia of Genetics, Genomics, Proteomics and Informatics. Springer Netherlands, 2008. http://dx.doi.org/10.1007/978-1-4020-6754-9_13764.

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Wright, Edward. "Demonstration of Viral Antibodies by Pseudotype Virus Neutralization." In Current Laboratory Techniques in Rabies Diagnosis, Research and Prevention. Elsevier, 2014. http://dx.doi.org/10.1016/b978-0-12-800014-4.00015-9.

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Schenck, Douglas, and Peter Wilson. "Datatypes." In Information Modeling: The EXPRESS Way. Oxford University Press, 1994. http://dx.doi.org/10.1093/oso/9780195087147.003.0018.

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This chapter explains the EXPRESS pseudotypes and datatypes. You will also want to read about defined types and entity types, both of which are covered in Chapter 11. Datatypes represent domains of values. A domain is the set of possible values associated with an attribute, local variable or formal parameter. Datatype values can be operated upon as explained in Chapter 14. EXPRESS is fussy about the way datatypes are used. The datatypes are grouped this way: • Pseudo (Generic and Aggregate — see 10.1) • Simple (Integer, String, etc. — see 10.2) • Collection (Array, List, etc. — see 10.3) • Enu
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Schenck, Douglas, and Peter Wilson. "Symbols." In Information Modeling: The EXPRESS Way. Oxford University Press, 1994. http://dx.doi.org/10.1093/oso/9780195087147.003.0026.

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EXPRESS-G has three basic kinds of symbol; defintion, relation, and composition. Definition and relation symbols are used to define the contents and structure of an information model. Composition symbols enable the diagrams to be spread across many physical pages. A definition symbol is a rectangle enclosing the name of the thing being defined. The type of the definition is denoted by the style of the box. Symbols are provided for EXPRESS simple types, defined types, entity types and schemas. The EXPRESS language offers a number of predefined simple types, namely Binary, Boolean, Integer, Logi
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Conference papers on the topic "Pseudotime"

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Aqila, Tasmia, and Ananda Mohan Mondal. "Pseudotime Based Analysis of Cancer Dynamics." In BCB '19: 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics. ACM, 2019. http://dx.doi.org/10.1145/3307339.3343253.

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Aminian, K., S. Ameri, W. E. Abbitt, and L. E. Cunningham. "Polynomial Approximations for Gas Pseudopressure and Pseudotime." In SPE Eastern Regional Meeting. Society of Petroleum Engineers, 1991. http://dx.doi.org/10.2118/23439-ms.

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Aqila, Tasmia, Abdullah Al Mamun, and Ananda Mohan Mondal. "Pseudotime Based Discovery of Breast Cancer Heterogeneity." In 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2019. http://dx.doi.org/10.1109/bibm47256.2019.8983300.

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Tabatabaie, S. Hamed, Louis Mattar, and Mehran Pooladi-Darvish. "Pseudotime Calculation in Low Permeability Gas Reservoirs." In SPE Unconventional Resources Conference Canada. Society of Petroleum Engineers, 2013. http://dx.doi.org/10.2118/167185-ms.

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E. Plessix, R., P. Milcik, C. Corcoran, H. Kuehl, and K. Matson. "Full Waveform Inversion with a Pseudotime Approach." In 74th EAGE Conference and Exhibition incorporating EUROPEC 2012. EAGE Publications BV, 2012. http://dx.doi.org/10.3997/2214-4609.20148713.

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Aanonsen, S. "Application of Pseudotime To Estimate Average Reservoir Pressure." In SPE Annual Technical Conference and Exhibition. Society of Petroleum Engineers, 1985. http://dx.doi.org/10.2118/14256-ms.

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Wu, Yunheng, and Meixue Li. "Study on fatty liver based on Pseudotime analysis." In ICBIP 2022: 2022 7th International Conference on Biomedical Signal and Image Processing. ACM, 2022. http://dx.doi.org/10.1145/3563737.3563744.

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Frey, Christian, Jan Backhaus, Graham Ashcroft, Georg Geiser, Benjamin Winhart, and Heinrich Stüer. "Using Pseudotime Marching for the Solution of Harmonic Balance Problems." In ASME Turbo Expo 2024: Turbomachinery Technical Conference and Exposition. American Society of Mechanical Engineers, 2024. http://dx.doi.org/10.1115/gt2024-127820.

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Abstract The aim of this paper is to study approaches to implement implicit pseudotime marching for the harmonic balance system in the frequency domain. We first give a motivation for using pseudotime marching as a solution technique. It turns out that, when the discretization errors of the pseudospectral time derivative and the pseudotime derivative are neglected, the harmonic balance solution converges to a stable periodic flow, provided that the initial solution is sufficiently close to a stable periodic solution. This motivates the choice of a robust pseudotime marching approach, e.g., an
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He, Bing, Shu Zhang, Shannon L. Risacher, Andrew J. Saykin, and Jingwen Yan. "Multi-modal Imaging-based Pseudotime Analysis of Alzheimer progression." In Pacific Symposium on Biocomputing 2025. WORLD SCIENTIFIC, 2024. http://dx.doi.org/10.1142/9789819807024_0047.

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Spivey, J. P., and W. J. Lee. "The Use of Pseudotime: Wellbore Storage and the Middle Time Region." In SPE Unconventional Gas Technology Symposium. Society of Petroleum Engineers, 1986. http://dx.doi.org/10.2118/15229-ms.

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