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479 results on '"Polanska, Joanna"'

53. Machine learning techniques combined with dose profiles indicate radiation response biomarkers

Author

Papiez Anna, Badie Christophe, and Polanska Joanna

Subjects
machine learning, gene profiling, radiation response, multiple random validation, transcription, Mathematics, QA1-939, Electronic computers. Computer science, QA75.5-76.95
Abstract

The focus of this research is to combine statistical and machine learning tools in application to a high-throughput biological data set on ionizing radiation response. The analyzed data consist of two gene expression sets obtained in studies of radiosensitive and radioresistant breast cancer patients undergoing radiotherapy. The data sets were similar in principle; however, the treatment dose differed. It is shown that introducing mathematical adjustments in data preprocessing, differentiation and trend testing, and classification, coupled with current biological knowledge, allows efficient data analysis and obtaining accurate results. The tools used to customize the analysis workflow were batch effect filtration with empirical Bayes models, identifying gene trends through the Jonckheere–Terpstra test and linear interpolation adjustment according to specific gene profiles for multiple random validation. The application of non-standard techniques enabled successful sample classification at the rate of 93.5% and the identification of potential biomarkers of radiation response in breast cancer, which were confirmed with an independent Monte Carlo feature selection approach and by literature references. This study shows that using customized analysis workflows is a necessary step towards novel discoveries in complex fields such as personalized individual therapy.

Published
2019
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55. Novel Method of Identifying DNA Methylation Fingerprint of Acute Myeloid Leukaemia

Author

Cecotka, Agnieszka, Polanska, Joanna, Kacprzyk, Janusz, Series editor, Pal, Nikhil R., Advisory editor, Bello Perez, Rafael, Advisory editor, Corchado, Emilio S., Advisory editor, Hagras, Hani, Advisory editor, Kóczy, László T., Advisory editor, Kreinovich, Vladik, Advisory editor, Lin, Chin-Teng, Advisory editor, Lu, Jie, Advisory editor, Melin, Patricia, Advisory editor, Nedjah, Nadia, Advisory editor, Nguyen, Ngoc Thanh, Advisory editor, Wang, Jun, Advisory editor, Fdez-Riverola, Florentino, editor, Mohamad, Mohd Saberi, editor, Rocha, Miguel, editor, De Paz, Juan F., editor, and Pinto, Tiago, editor

Published
2017
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56. Reproducibility of Finding Enriched Gene Sets in Biological Data Analysis

Author

Zyla, Joanna, Marczyk, Michal, Polanska, Joanna, Kacprzyk, Janusz, Series editor, Pal, Nikhil R., Advisory editor, Bello Perez, Rafael, Advisory editor, Corchado, Emilio S., Advisory editor, Hagras, Hani, Advisory editor, Kóczy, László T., Advisory editor, Kreinovich, Vladik, Advisory editor, Lin, Chin-Teng, Advisory editor, Lu, Jie, Advisory editor, Melin, Patricia, Advisory editor, Nedjah, Nadia, Advisory editor, Nguyen, Ngoc Thanh, Advisory editor, Wang, Jun, Advisory editor, Fdez-Riverola, Florentino, editor, Mohamad, Mohd Saberi, editor, Rocha, Miguel, editor, De Paz, Juan F., editor, and Pinto, Tiago, editor

Published
2017
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57. Multidimensional Feature Selection and Interaction Mining with Decision Tree Based Ensemble Methods

Author

Krol, Lukasz, Polanska, Joanna, Kacprzyk, Janusz, Series editor, Pal, Nikhil R., Advisory editor, Bello Perez, Rafael, Advisory editor, Corchado, Emilio S., Advisory editor, Hagras, Hani, Advisory editor, Kóczy, László T., Advisory editor, Kreinovich, Vladik, Advisory editor, Lin, Chin-Teng, Advisory editor, Lu, Jie, Advisory editor, Melin, Patricia, Advisory editor, Nedjah, Nadia, Advisory editor, Nguyen, Ngoc Thanh, Advisory editor, Wang, Jun, Advisory editor, Fdez-Riverola, Florentino, editor, Mohamad, Mohd Saberi, editor, Rocha, Miguel, editor, De Paz, Juan F., editor, and Pinto, Tiago, editor

Published
2017
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64. A Novel Divisive iK-Means Algorithm with Region-Driven Feature Selection as a Tool for Automated Detection of Tumour Heterogeneity in MALDI IMS Experiments

Author

Mrukwa, Grzegorz, Drazek, Grzegorz, Pietrowska, Monika, Widlak, Piotr, Polanska, Joanna, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Ortuño, Francisco, editor, and Rojas, Ignacio, editor

Published
2016
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65. Comparative Analysis of microRNA-Target Gene Interaction Prediction Algorithms - The Attempt to Compare the Results of Three Algorithms

Author

Krawczyk, Anna, Polańska, Joanna, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Ortuño, Francisco, editor, and Rojas, Ignacio, editor

Published
2016
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66. Multigene P-value Integration Based on SNPs Investigation for Seeking Radiosensitivity Signatures

Author

Zyla, Joanna, Badie, Christophe, Alsbeih, Ghazi, Polanska, Joanna, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Ortuño, Francisco, editor, and Rojas, Ignacio, editor

Published
2016
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69. Transcriptional Inflammatory Signature in Healthy Donors and Different Radiotherapy Cancer Patients.

Author

O'Brien, Gráinne, Kamuda, Malgorzata, Cruz-Garcia, Lourdes, Polozova, Mariia, Tichy, Ales, Markova, Marketa, Sirak, Igor, Zahradnicek, Oldrich, Widłak, Piotr, Ponge, Lucyna, Polanska, Joanna, and Badie, Christophe

Subjects
CANCER radiotherapy, CANCER patients, RADIOTHERAPY safety, GENE expression, INFLUENZA vaccines, IONIZING radiation
Abstract

Cancer and ionizing radiation exposure are associated with inflammation. To identify a set of radiation-specific signatures of inflammation-associated genes in the blood of partially exposed radiotherapy patients, differential expression of 249 inflammatory genes was analyzed in blood samples from cancer patients and healthy individuals. The gene expression analysis on a cohort of 63 cancer patients (endometrial, head and neck, and prostate cancer) before and during radiotherapy (24 h, 48 h, ~1 week, ~4–8 weeks, and 1 month after the last fraction) identified 31 genes and 15 up- and 16 down-regulated genes. Transcription variability under normal conditions was determined using blood drawn on three separate occasions from four healthy donors. No difference in inflammatory expression between healthy donors and cancer patients could be detected prior to radiotherapy. Remarkably, repeated sampling of healthy donors revealed an individual endogenous inflammatory signature. Next, the potential confounding effect of concomitant inflammation was studied in the blood of seven healthy donors taken before and 24 h after a flu vaccine or ex vivo LPS (lipopolysaccharide) treatment; flu vaccination was not detected at the transcriptional level and LPS did not have any effect on the radiation-induced signature identified. Finally, we identified a radiation-specific signature of 31 genes in the blood of radiotherapy patients that were common for all cancers, regardless of the immune status of patients. Confirmation via MQRT-PCR was obtained for BCL6, MYD88, MYC, IL7, CCR4 and CCR7. This study offers the foundation for future research on biomarkers of radiation exposure, radiation sensitivity, and radiation toxicity for personalized radiotherapy treatment. [ABSTRACT FROM AUTHOR]

Published
2024
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70. Combining Low-Dose Computer-Tomography-Based Radiomics and Serum Metabolomics for Diagnosis of Malignant Nodules in Participants of Lung Cancer Screening Studies.

Author

Zyla, Joanna, Marczyk, Michal, Prazuch, Wojciech, Sitkiewicz, Magdalena, Durawa, Agata, Jelitto, Malgorzata, Dziadziuszko, Katarzyna, Jelonek, Karol, Kurczyk, Agata, Szurowska, Edyta, Rzyman, Witold, Widłak, Piotr, and Polanska, Joanna

Subjects
LUNG cancer, RADIOMICS, EARLY detection of cancer, PULMONARY nodules, LUNGS, TUMOR classification, SERUM
Abstract

Radiomics is an emerging approach to support the diagnosis of pulmonary nodules detected via low-dose computed tomography lung cancer screening. Serum metabolome is a promising source of auxiliary biomarkers that could help enhance the precision of lung cancer diagnosis in CT-based screening. Thus, we aimed to verify whether the combination of these two techniques, which provides local/morphological and systemic/molecular features of disease at the same time, increases the performance of lung cancer classification models. The collected cohort consists of 1086 patients with radiomic and 246 patients with serum metabolomic evaluations. Different machine learning techniques, i.e., random forest and logistic regression were applied for each omics. Next, model predictions were combined with various integration methods to create a final model. The best single omics models were characterized by an AUC of 83% in radiomics and 60% in serum metabolomics. The model integration only slightly increased the performance of the combined model (AUC equal to 85%), which was not statistically significant. We concluded that radiomics itself has a good ability to discriminate lung cancer from benign lesions. However, additional research is needed to test whether its combination with other molecular assessments would further improve the diagnosis of screening-detected lung nodules. [ABSTRACT FROM AUTHOR]

Published
2024
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72. Überwachtes Lernen zur Prädiktion von Tumorwachstum

Author

Weber, Christian, Götz, Michael, Binczyck, Franciszek, Polanska, Joanna, Tarnawski, Rafal, Bobek-Billewicz, Barbara, Meinzer, Hans-Peter, Stieltjes, Bram, Maier-Hein, Klaus, Handels, Heinz, editor, Deserno, Thomas Martin, editor, Meinzer, Hans-Peter, editor, and Tolxdorff, Thomas, editor

Published
2015
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74. Statistical Integration of p-values for Enhancing Discovery of Radiotoxicity Gene Signatures

Author

Papiez, Anna, Kabacik, Sylwia, Badie, Christophe, Bouffler, Simon, Polanska, Joanna, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, Series editor, Pevzner, Pavel, Series editor, Waterman, Michael S., Series editor, Ortuño, Francisco, editor, and Rojas, Ignacio, editor

Published
2015
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75. Mixture Model Based Efficient Method for Magnetic Resonance Spectra Quantification

Author

Binczyk, Franciszek, Marczyk, Michal, Polanska, Joanna, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, Series editor, Pevzner, Pavel, Series editor, Waterman, Michael S., Series editor, Ortuño, Francisco, editor, and Rojas, Ignacio, editor

Published
2015
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79. An Efficient Algorithm for Microarray Probes Re-annotation

Author

Foszner, Pawel, Gruca, Aleksandra, Polanski, Andrzej, Marczyk, Michal, Jaksik, Roman, Polanska, Joanna, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Nguyen, Ngoc-Thanh, editor, and Le-Thi, Hoai An, editor

Published
2014
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82. Multivariate piecewise linear regression model to predict radiosensitivity using the association with the genomewide copy number variation.

Author

Tobiasz, Joanna, Al-Harbi, Najla, Judia, Sara Bin, Wakil, Salma Majid, Polanska, Joanna, and Alsbeih, Ghazi

Subjects
RADIATION tolerance, REGRESSION analysis, IONIZING radiation, RADIATION exposure, DYNAMIC programming
Abstract

Introduction: The search for biomarkers to predict radiosensitivity is important not only to individualize radiotherapy of cancer patients but also to forecast radiation exposure risks. The aim of this study was to devise a machine-learning method to stratify radiosensitivity and to investigate its association with genomewide copy number variations (CNVs) as markers of sensitivity to ionizing radiation. Methods: We used the Affymetrix CytoScan HD microarrays to survey common CNVs in 129 fibroblast cell strains. Radiosensitivity was measured by the surviving fraction at 2 Gy (SF2). We applied a dynamic programming (DP) algorithm to create a piecewise (segmented) multivariate linear regression model predicting SF2 and to identify SF2 segment-related distinctive CNVs. Results: SF2 ranged between 0.1384 and 0.4860 (mean=0.3273 The DP algorithm provided optimal segmentation by defining batches of radiosensitive (RS), normally-sensitive (NS), and radio-resistant (RR) responders. The weighted mean relative errors (MRE) decreased with increasing the segments' number. The borders of the utmost segments have stabilized after partitioning SF2 into 5 subranges. Discussion: The 5-segment model associated C-3SFBP marker with the most-RS and C-7IUVU marker with the most-RR cell strains. Both markers were mapped to gene regions (MCC and SLC1A6, respectively). In addition, C-3SFBP marker is also located in enhancer and multiple binding motifs. Moreover, for most CNVs significantly correlated with SF2, the radiosensitivity increased with the copynumber decrease. In conclusion, the DP-based piecewise multivariate linear regression method helps narrow the set of CNV markers from the whole radiosensitivity range to the smaller intervals of interest. Notably, SF2 partitioning not only improves the SF2 estimation but also provides distinctive markers. Ultimately, segment-related markers can be used, potentially with tissues’ specific factors or other clinical data, to identify radiotherapy patients who are most RS and require reduced doses to avoid complications and the most RR eligible for dose escalation to improve outcomes. [ABSTRACT FROM AUTHOR]

Published
2023
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84. POLCOVID : a multicenter multiclass chest X-ray database (Poland, 2020–2021)

Author

Suwalska, Aleksandra, Tobiasz, Joanna, Prazuch, Wojciech, Socha, Marek, Foszner, Pawel, Piotrowski, Damian, Gruszczynska, Katarzyna, Sliwinska, Magdalena, Walecki, Jerzy, Popiela, Tadeusz, Przybylski, Grzegorz, Nowak, Mateusz, Fiedor, Piotr, Pawlowska, Malgorzata, Flisiak, Robert, Simon, Krzysztof, Zapolska, Gabriela, Gizycka, Barbara, Szurowska, Edyta, Marczyk, Michal, Cieszanowski, Andrzej, and Polanska, Joanna

Published
2023

89. Efficient Algorithm for Microarray Probes Re-annotation

Author

Foszner, Pawel, Gruca, Aleksandra, Polanski, Andrzej, Marczyk, Michal, Jaksik, Roman, Polanska, Joanna, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Goebel, Randy, editor, Siekmann, Jörg, editor, Wahlster, Wolfgang, editor, Jędrzejowicz, Piotr, editor, Nguyen, Ngoc Thanh, editor, and Hoang, Kiem, editor

Published
2011
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