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Michal Marczyk, PhD

Assistant Professor Adjunct

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Selected Publications

miR122 and miR21 are stable components of miRNA signatures of early lung cancer after validation in three independent cohorts.Zyla J, Dziadziuszko R, Marczyk M, Sitkiewicz M, Szczepanowska M, Bottoni E, Veronesi G, Rzyman W, Polanska J, Widlak P. miR122 and miR21 are stable components of miRNA signatures of early lung cancer after validation in three independent cohorts. Journal Of Molecular Diagnostics 2023 PMID: 37865291, DOI: 10.1016/j.jmoldx.2023.09.010.
Pre‐analytical effects on whole transcriptome and targeted RNA sequencing analysis in cytology: The effects of prolonged time in storage of effusion specimens prior to preservationSura G, Tran K, Fu C, Du L, Marczyk M, Gould R, Chen E, Tasto A, Tinnirello A, Symmans W. Pre‐analytical effects on whole transcriptome and targeted RNA sequencing analysis in cytology: The effects of prolonged time in storage of effusion specimens prior to preservation. Cytopathology 2023, 34: 551-561. PMID: 37712171, DOI: 10.1111/cyt.13304.
Pathological changes or technical artefacts? The problem of the heterogenous databases in COVID-19 CXR image analysisSocha M, Prażuch W, Suwalska A, Foszner P, Tobiasz J, Jaroszewicz J, Gruszczynska K, Sliwinska M, Nowak M, Gizycka B, Zapolska G, Popiela T, Przybylski G, Fiedor P, Pawlowska M, Flisiak R, Simon K, Walecki J, Cieszanowski A, Szurowska E, Marczyk M, Polanska J, Polanska J, Marczyk M, Prazuch W, Suwalska A, Socha M, Foszner P, Tobiasz J, Nowak M, Fiedor P, Cieszanowski A, Oronowicz-Jaskowiak A, Golebiewski B, Simon K, Sliwinska M, Rataj M, Chmielarz P, Tur A, Drabik G, Popiela T, Kozub J, Przybylski G, Kozanecka A, Szurowska E, Hildebrandt S, Krutul-Walenciej K, Baron J, Gruszczynska K, Jaroszewicz J, Piotrowski D, Walecki J, Wasilewski P, Mazur S, Flisiak R, Zapolska G, Klaude K, Rataj K, Golebiewski B, Pawlowska M, Rabiko P, Rajewski P, Gizycka B, Blewaska P, Sznajder K, Plesniak R. Pathological changes or technical artefacts? The problem of the heterogenous databases in COVID-19 CXR image analysis. Computer Methods And Programs In Biomedicine 2023, 240: 107684. PMID: 37356354, PMCID: PMC10278898, DOI: 10.1016/j.cmpb.2023.107684.
POLCOVID: a multicenter multiclass chest X-ray database (Poland, 2020–2021)Suwalska A, Tobiasz J, Prazuch W, Socha M, Foszner P, Piotrowski D, Gruszczynska K, Sliwinska M, Walecki J, Popiela T, Przybylski G, Nowak M, Fiedor P, Pawlowska M, Flisiak R, Simon K, Zapolska G, Gizycka B, Szurowska E, Marczyk M, Cieszanowski A, Polanska J. POLCOVID: a multicenter multiclass chest X-ray database (Poland, 2020–2021). Scientific Data 2023, 10: 348. PMID: 37268643, PMCID: PMC10236395, DOI: 10.1038/s41597-023-02229-5.
Trends in breast cancer death by stage at diagnoses in 2000-2018.Kahn A, Marczyk M, Silber A, Rozenblit M, Sanft T, DiGiovanna M, Schellhorn S, Krop I, Lustberg M, Winer E, Pusztai L. Trends in breast cancer death by stage at diagnoses in 2000-2018. Journal Of Clinical Oncology 2023, 41: e18855-e18855. DOI: 10.1200/jco.2023.41.16_suppl.e18855.
Somatic mutations in tumor-adjacent normal breast tissue in young women with high risk family history.Rozenblit M, Suwalska A, Hofstatter E, Reisenbichler E, Harigopal M, Marczyk M, Pusztai L. Somatic mutations in tumor-adjacent normal breast tissue in young women with high risk family history. Journal Of Clinical Oncology 2023, 41: 576-576. DOI: 10.1200/jco.2023.41.16_suppl.576.
Abstract P1-04-12: Systemic immune response to a Phase I/II trial of Durvalumab concomitant with neoadjuvant chemotherapy in early stage TNBCBlenman K, Marczyk M, Foldi J, Gunasekharan V, Silber A, Pusztai L. Abstract P1-04-12: Systemic immune response to a Phase I/II trial of Durvalumab concomitant with neoadjuvant chemotherapy in early stage TNBC. Cancer Research 2023, 83: p1-04-12-p1-04-12. DOI: 10.1158/1538-7445.sabcs22-p1-04-12.
Abstract PD9-09: Molecular differences between younger versus older estrogen receptor positive/human epidermal growth factor receptor-2 negative breast cancersQing T, Karn T, Rozenblit M, Foldi J, Marczyk M, Shan N, Blenman K, Holtrich U, Kalinsky K, Meric-Bernstam F, Pusztai L. Abstract PD9-09: Molecular differences between younger versus older estrogen receptor positive/human epidermal growth factor receptor-2 negative breast cancers. Cancer Research 2023, 83: pd9-09-pd9-09. DOI: 10.1158/1538-7445.sabcs22-pd9-09.
Assessment of stained direct cytology smears of breast cancer for whole transcriptome and targeted messenger RNA sequencingMarczyk M, Fu C, Lau R, Du L, Trevarton A, Sinn B, Gould R, Pusztai L, Hatzis C, Symmans W. Assessment of stained direct cytology smears of breast cancer for whole transcriptome and targeted messenger RNA sequencing. Cancer Cytopathology 2023, 131: 289-299. PMID: 36650408, DOI: 10.1002/cncy.22679.
Chapter 3 Single-cell transcriptomicsMarczyk M, Kujawa T, Papiez A, Polanska J. Chapter 3 Single-cell transcriptomics. 2023, 67-84. DOI: 10.1016/b978-0-323-91810-7.00015-7.
Evaluation of zero counts to better understand the discrepancies between bulk and single-cell RNA-Seq platformsZyla J, Papiez A, Zhao J, Qu R, Li X, Kluger Y, Polanska J, Hatzis C, Pusztai L, Marczyk M. Evaluation of zero counts to better understand the discrepancies between bulk and single-cell RNA-Seq platforms. Computational And Structural Biotechnology Journal 2023, 21: 4663-4674. DOI: 10.1016/j.csbj.2023.09.035.
Molecular differences between younger versus older ER-positive and HER2-negative breast cancersQing T, Karn T, Rozenblit M, Foldi J, Marczyk M, Shan N, Blenman K, Holtrich U, Kalinsky K, Meric-Bernstam F, Pusztai L. Molecular differences between younger versus older ER-positive and HER2-negative breast cancers. Npj Breast Cancer 2022, 8: 119. PMID: 36344517, PMCID: PMC9640562, DOI: 10.1038/s41523-022-00492-0.
Influence of single-cell RNA sequencing data integration on the performance of differential gene expression analysisKujawa T, Marczyk M, Polanska J. Influence of single-cell RNA sequencing data integration on the performance of differential gene expression analysis. Frontiers In Genetics 2022, 13: 1009316. PMCID: PMC9663917, DOI: 10.3389/fgene.2022.1009316.
Influence of single-cell RNA sequencing data integration on the performance of differential gene expression analysisKujawa T, Marczyk M, Polanska J. Influence of single-cell RNA sequencing data integration on the performance of differential gene expression analysis. Frontiers In Genetics 2022, 13: 1009316. PMID: 36386846, PMCID: PMC9663917, DOI: 10.3389/fgene.2022.1009316.
Molecular testing opportunities on cytology effusion specimens: the pre-analytic effects of various body fluid cytology preparation methods on RNA extraction quality and targeted sequencingSura G, Tran K, Fu C, Du L, Marczyk M, Martinez Y, Tinnirello A, Gould R, Lau R, Symmans W. Molecular testing opportunities on cytology effusion specimens: the pre-analytic effects of various body fluid cytology preparation methods on RNA extraction quality and targeted sequencing. Journal Of The American Society Of Cytopathology 2022, 12: 10-19. PMID: 36270909, DOI: 10.1016/j.jasc.2022.09.003.
Tumor immune microenvironment of self-identified African American and non-African American triple negative breast cancerMarczyk M, Qing T, O’Meara T, Yagahoobi V, Pelekanou V, Bai Y, Reisenbichler E, Cole KS, Li X, Gunasekharan V, Ibrahim E, Fanucci K, Wei W, Rimm DL, Pusztai L, Blenman KRM. Tumor immune microenvironment of self-identified African American and non-African American triple negative breast cancer. Npj Breast Cancer 2022, 8: 88. PMID: 35869114, PMCID: PMC9307813, DOI: 10.1038/s41523-022-00449-3.
Quantifying Spatial Heterogeneity of Tumor-Infiltrating Lymphocytes to Predict Survival of Individual Cancer PatientsSuwalska A, Zientek L, Polanska J, Marczyk M. Quantifying Spatial Heterogeneity of Tumor-Infiltrating Lymphocytes to Predict Survival of Individual Cancer Patients. Journal Of Personalized Medicine 2022, 12: 1113. PMID: 35887610, PMCID: PMC9317291, DOI: 10.3390/jpm12071113.
Investigating Sources of Zeros in 10× Single-Cell RNAseq DataSlowik H, Zyla J, Marczyk M. Investigating Sources of Zeros in 10× Single-Cell RNAseq Data. 2022, 13347: 71-80. DOI: 10.1007/978-3-031-07802-6_6.
Finding Significantly Enriched Cells in Single-Cell RNA Sequencing by Single-Sample ApproachesMrukwa A, Marczyk M, Zyla J. Finding Significantly Enriched Cells in Single-Cell RNA Sequencing by Single-Sample Approaches. 2022, 13347: 33-44. DOI: 10.1007/978-3-031-07802-6_3.
Treatment Efficacy Score—continuous residual cancer burden-based metric to compare neoadjuvant chemotherapy efficacy between randomized trial arms in breast cancer trialsMarczyk M, Mrukwa A, Yau C, Wolf D, Chen Y, Balassanian R, Nanda R, Parker B, Krings G, Sattar H, Zeck J, Albain K, Boughey J, Liu M, Elias A, Clark A, Venters S, Shad S, Basu A, Asare S, Buxton M, Asare A, Rugo H, Perlmutter J, DeMichele A, Yee D, Berry D, Veer L, Symmans W, Esserman L, Pusztai L, Consortium I. Treatment Efficacy Score—continuous residual cancer burden-based metric to compare neoadjuvant chemotherapy efficacy between randomized trial arms in breast cancer trials. Annals Of Oncology 2022, 33: 814-823. PMID: 35513244, DOI: 10.1016/j.annonc.2022.04.072.
Cancer Relevance of Human Genes.Qing T, Mohsen H, Cannataro VL, Marczyk M, Rozenblit M, Foldi J, Murray M, Townsend J, Kluger Y, Gerstein M, Pusztai L. Cancer Relevance of Human Genes. Journal Of The National Cancer Institute 2022, 114: 988-995. PMID: 35417011, PMCID: PMC9275765, DOI: 10.1093/jnci/djac068.
Predictive Markers of Response to Neoadjuvant Durvalumab with Nab-Paclitaxel and Dose-Dense Doxorubicin/Cyclophosphamide in Basal-Like Triple-Negative Breast Cancer.Blenman KRM, Marczyk M, Karn T, Qing T, Li X, Gunasekharan V, Yaghoobi V, Bai Y, Ibrahim EY, Park T, Silber A, Wolf DM, Reisenbichler E, Denkert C, Sinn BV, Rozenblit M, Foldi J, Rimm DL, Loibl S, Pusztai L. Predictive Markers of Response to Neoadjuvant Durvalumab with Nab-Paclitaxel and Dose-Dense Doxorubicin/Cyclophosphamide in Basal-Like Triple-Negative Breast Cancer. Clinical Cancer Research 2022, 28: 2587-2597. PMID: 35377948, PMCID: PMC9464605, DOI: 10.1158/1078-0432.ccr-21-3215.
Comprehensive Analysis of Metabolic Isozyme Targets in Cancer.Marczyk M, Gunasekharan V, Casadevall D, Qing T, Foldi J, Sehgal R, Shan NL, Blenman KRM, O'Meara TA, Umlauf S, Surovtseva YV, Muthusamy V, Rinehart J, Perry RJ, Kibbey R, Hatzis C, Pusztai L. Comprehensive Analysis of Metabolic Isozyme Targets in Cancer. Cancer Research 2022, 82: 1698-1711. PMID: 35247885, DOI: 10.1158/0008-5472.can-21-3983.
Abstract P5-17-01: Targeting Acetyl-CoA carboxylase in pre-clinical breast cancer modelsFoldi J, Marczyk M, Gunasekharan V, Qing T, Sehgal R, Shan N, Muthusamy V, Umlau S, Surovtseva Y, Kibbey R, Pusztai L. Abstract P5-17-01: Targeting Acetyl-CoA carboxylase in pre-clinical breast cancer models. Cancer Research 2022, 82: p5-17-01-p5-17-01. DOI: 10.1158/1538-7445.sabcs21-p5-17-01.
Author Correction: Neoadjuvant durvalumab plus weekly nab-paclitaxel and dose-dense doxorubicin/cyclophosphamide in triple-negative breast cancerFoldi J, Silber A, Reisenbichler E, Singh K, Fischbach N, Persico J, Adelson K, Katoch A, Horowitz N, Lannin D, Chagpar A, Park T, Marczyk M, Frederick C, Burrello T, Ibrahim E, Qing T, Bai Y, Blenman K, Rimm DL, Pusztai L. Author Correction: Neoadjuvant durvalumab plus weekly nab-paclitaxel and dose-dense doxorubicin/cyclophosphamide in triple-negative breast cancer. Npj Breast Cancer 2022, 8: 17. PMID: 35115541, PMCID: PMC8814070, DOI: 10.1038/s41523-022-00392-3.
Importance of SNP Dependency Correction and Association Integration for Gene Set Analysis in Genome-Wide Association StudiesMarczyk M, Macioszek A, Tobiasz J, Polanska J, Zyla J. Importance of SNP Dependency Correction and Association Integration for Gene Set Analysis in Genome-Wide Association Studies. Frontiers In Genetics 2021, 12: 767358. PMID: 34956320, PMCID: PMC8696167, DOI: 10.3389/fgene.2021.767358.
Autoencoder-based bone removal algorithm from x-ray images of the lungKalisz S, Marczyk M. Autoencoder-based bone removal algorithm from x-ray images of the lung. 2021, 00: 1-6. DOI: 10.1109/bibe52308.2021.9635451.
Analysis of the Applicability of microRNAs in Peripheral Blood Leukocytes as Biomarkers of Sensitivity and Exposure to Fractionated Radiotherapy towards Breast CancerMarczyk M, Polańska J, Wojcik A, Lundholm L. Analysis of the Applicability of microRNAs in Peripheral Blood Leukocytes as Biomarkers of Sensitivity and Exposure to Fractionated Radiotherapy towards Breast Cancer. International Journal Of Molecular Sciences 2021, 22: 8705. PMID: 34445424, PMCID: PMC8395710, DOI: 10.3390/ijms22168705.
Abstract 423: Pooled analysis of matching score and patient outcome in I-PREDICT and WINTHER studiesCasadevall D, Marczyk M, Monzonis X, Pusztai L, Albanell J. Abstract 423: Pooled analysis of matching score and patient outcome in I-PREDICT and WINTHER studies. Cancer Research 2021, 81: 423-423. DOI: 10.1158/1538-7445.am2021-423.
Treatment scheduling effects on the evolution of drug resistance in heterogeneous cancer cell populationsPatwardhan GA, Marczyk M, Wali VB, Stern DF, Pusztai L, Hatzis C. Treatment scheduling effects on the evolution of drug resistance in heterogeneous cancer cell populations. Npj Breast Cancer 2021, 7: 60. PMID: 34040000, PMCID: PMC8154902, DOI: 10.1038/s41523-021-00270-4.
Characterization of the tumor immune microenvironment of triple-negative breast cancer (TNBC) patients who self-identify as African American (AA) or non-African American (NonAA).Blenman K, Marczyk M, Qing T, O'Meara T, Yaghoobi V, Pelekanou V, Bai Y, Reisenbichler E, Li X, Gunasekharan V, Ibrahim E, Rimm D, Pusztai L, Cole K. Characterization of the tumor immune microenvironment of triple-negative breast cancer (TNBC) patients who self-identify as African American (AA) or non-African American (NonAA). Journal Of Clinical Oncology 2021, 39: 564-564. DOI: 10.1200/jco.2021.39.15_suppl.564.
Treatment Efficacy Score (TES), a continuous residual cancer burden-based metric to compare neoadjuvant chemotherapy efficacy between trial arms in the I-SPY 2 trial.Marczyk M, Mrukwa A, Yau C, Wolf D, van 't Veer L, Esserman L, Symmans W, Pusztai L. Treatment Efficacy Score (TES), a continuous residual cancer burden-based metric to compare neoadjuvant chemotherapy efficacy between trial arms in the I-SPY 2 trial. Journal Of Clinical Oncology 2021, 39: 587-587. DOI: 10.1200/jco.2021.39.15_suppl.587.
Diverse immune response of DNA damage repair-deficient tumorsQing T, Jun T, Lindblad KE, Lujambio A, Marczyk M, Pusztai L, Huang KL. Diverse immune response of DNA damage repair-deficient tumors. Cell Reports Medicine 2021, 2: 100276. PMID: 34095878, PMCID: PMC8149377, DOI: 10.1016/j.xcrm.2021.100276.
Abstract PS19-05: Functional importance of long-tail mutations in breast cancerQing T, Mohsen H, Rozenblit M, Marczyk M, Foldi J, Blenman K, Gunasekharan V, Pusztai L. Abstract PS19-05: Functional importance of long-tail mutations in breast cancer. Cancer Research 2021, 81: ps19-05-ps19-05. DOI: 10.1158/1538-7445.sabcs20-ps19-05.
Neoadjuvant durvalumab plus weekly nab-paclitaxel and dose-dense doxorubicin/cyclophosphamide in triple-negative breast cancerFoldi J, Silber A, Reisenbichler E, Singh K, Fischbach N, Persico J, Adelson K, Katoch A, Horowitz N, Lannin D, Chagpar A, Park T, Marczyk M, Frederick C, Burrello T, Ibrahim E, Qing T, Bai Y, Blenman K, Rimm DL, Pusztai L. Neoadjuvant durvalumab plus weekly nab-paclitaxel and dose-dense doxorubicin/cyclophosphamide in triple-negative breast cancer. Npj Breast Cancer 2021, 7: 9. PMID: 33558513, PMCID: PMC7870853, DOI: 10.1038/s41523-021-00219-7.
Targeted RNAseq assay incorporating unique molecular identifiers for improved quantification of gene expression signatures and transcribed mutation fraction in fixed tumor samplesFu C, Marczyk M, Samuels M, Trevarton AJ, Qu J, Lau R, Du L, Pappas T, Sinn BV, Gould RE, Pusztai L, Hatzis C, Symmans WF. Targeted RNAseq assay incorporating unique molecular identifiers for improved quantification of gene expression signatures and transcribed mutation fraction in fixed tumor samples. BMC Cancer 2021, 21: 114. PMID: 33541297, PMCID: PMC7860187, DOI: 10.1186/s12885-021-07814-8.
Multi-Omics Investigation of Innate Navitoclax Resistance in Triple-Negative Breast Cancer CellsMarczyk M, Patwardhan GA, Zhao J, Qu R, Li X, Wali VB, Gupta AK, Pillai MM, Kluger Y, Yan Q, Hatzis C, Pusztai L, Gunasekharan V. Multi-Omics Investigation of Innate Navitoclax Resistance in Triple-Negative Breast Cancer Cells. Cancers 2020, 12: 2551. PMID: 32911681, PMCID: PMC7563413, DOI: 10.3390/cancers12092551.
Abstract 6333: Genomic, transcriptomic, and epigenetic profiling of triple-negative breast cancer cells after Navitoclax treatmentMarczyk M, Gunasekharan V, Zhao J, Qu R, Li X, Patwardhan G, Wali V, Gupta A, Pillai M, Kluger Y, Hatzis C, Pusztai L. Abstract 6333: Genomic, transcriptomic, and epigenetic profiling of triple-negative breast cancer cells after Navitoclax treatment. Cancer Research 2020, 80: 6333-6333. DOI: 10.1158/1538-7445.am2020-6333.
Technical Validity of a Customized Assay of Sensitivity to Endocrine Therapy Using Sections from Fixed Breast Cancer Tissue.Lau R, Du L, Chen E, Fu C, Gould R, Marczyk M, Sinn BV, Layman R, Bedrosian I, Valero V, Symmans WF. Technical Validity of a Customized Assay of Sensitivity to Endocrine Therapy Using Sections from Fixed Breast Cancer Tissue. Clinical Chemistry 2020, 66: 934-945. PMID: 32613237, DOI: 10.1093/clinchem/hvaa105.
Immunological Differences Between Immune-Rich Estrogen Receptor–Positive and Immune-Rich Triple-Negative Breast CancersO’Meara T, Marczyk M, Qing T, Yaghoobi V, Blenman K, Cole K, Pelekanou V, Rimm DL, Pusztai L. Immunological Differences Between Immune-Rich Estrogen Receptor–Positive and Immune-Rich Triple-Negative Breast Cancers. JCO Precision Oncology 2020, 4: po.19.00350. PMID: 32923897, PMCID: PMC7446500, DOI: 10.1200/po.19.00350.
Germline variant burden in cancer genes correlates with age at diagnosis and somatic mutation burdenQing T, Mohsen H, Marczyk M, Ye Y, O’Meara T, Zhao H, Townsend JP, Gerstein M, Hatzis C, Kluger Y, Pusztai L. Germline variant burden in cancer genes correlates with age at diagnosis and somatic mutation burden. Nature Communications 2020, 11: 2438. PMID: 32415133, PMCID: PMC7228928, DOI: 10.1038/s41467-020-16293-7.
Molecular Profiling for Predictors of Radiosensitivity in Patients with Breast or Head-and-Neck CancerDrobin K, Marczyk M, Halle M, Danielsson D, Papiez A, Sangsuwan T, Bendes A, Hong MG, Qundos U, Harms-Ringdahl M, Wersäll P, Polanska J, Schwenk JM, Haghdoost S. Molecular Profiling for Predictors of Radiosensitivity in Patients with Breast or Head-and-Neck Cancer. Cancers 2020, 12: 753. PMID: 32235817, PMCID: PMC7140105, DOI: 10.3390/cancers12030753.
Abstract P5-13-02: Neoadjuvant aromatase inhibitor therapy plus the mTOR inhibitor everolimus in postmenopausal women with hormone receptor positive/HER2 negative breast cancer and an oncotype Dx recurrence score (≤25)Abu-Khalaf M, Aderhold K, Marczyk M, Chung G, Hofstatter E, Sanft T, Silber A, DiGiovanna M, Zelterman D, Puzstai L, Hatzis C. Abstract P5-13-02: Neoadjuvant aromatase inhibitor therapy plus the mTOR inhibitor everolimus in postmenopausal women with hormone receptor positive/HER2 negative breast cancer and an oncotype Dx recurrence score (≤25). Cancer Research 2020, 80: p5-13-02-p5-13-02. DOI: 10.1158/1538-7445.sabcs19-p5-13-02.
Abstract P3-09-05: Predictive markers of response to durvalumab concurrent with nab-paclitaxel and dose dense doxorubicin cyclophosphamide (ddAC) neoadjuvant therapy for triple negative breast cancer (TNBC)Blenman K, Li X, Marczyk M, O'Meara T, Yaghoobi V, Gunasekharan V, Park T, Rimm D, Pusztai L. Abstract P3-09-05: Predictive markers of response to durvalumab concurrent with nab-paclitaxel and dose dense doxorubicin cyclophosphamide (ddAC) neoadjuvant therapy for triple negative breast cancer (TNBC). Cancer Research 2020, 80: p3-09-05-p3-09-05. DOI: 10.1158/1538-7445.sabcs19-p3-09-05.
The impact of RNA extraction method on accurate RNA sequencing from formalin-fixed paraffin-embedded tissuesMarczyk M, Fu C, Lau R, Du L, Trevarton AJ, Sinn BV, Gould RE, Pusztai L, Hatzis C, Symmans WF. The impact of RNA extraction method on accurate RNA sequencing from formalin-fixed paraffin-embedded tissues. BMC Cancer 2019, 19: 1189. PMID: 31805884, PMCID: PMC6896723, DOI: 10.1186/s12885-019-6363-0.
185PD Immunological differences between immune-rich estrogen receptor-positive and -negative breast cancersO’Meara T, Marczyk M, Blenman K, Yaghoobi V, Pelenkanou V, Rimm D, Pusztai L. 185PD Immunological differences between immune-rich estrogen receptor-positive and -negative breast cancers. Annals Of Oncology 2019, 30: v60-v61. DOI: 10.1093/annonc/mdz240.011.
Gene set enrichment for reproducible science: comparison of CERNO and eight other algorithmsZyla J, Marczyk M, Domaszewska T, Kaufmann SHE, Polanska J, Weiner J. Gene set enrichment for reproducible science: comparison of CERNO and eight other algorithms. Bioinformatics 2019, 35: 5146-5154. PMID: 31165139, PMCID: PMC6954644, DOI: 10.1093/bioinformatics/btz447.
Lung cancer survival and comorbidities in lung cancer screening participants of the Gdańsk screening cohort.Ostrowski M, Marczyk M, Dziedzic R, Jelitto-Górska M, Marjański T, Pisiak S, Jędrzejczyk T, Polańska J, Zdrojewski T, Wojtyniak B, Rzyman W. Lung cancer survival and comorbidities in lung cancer screening participants of the Gdańsk screening cohort. European Journal Of Public Health 2019, 29: 1114-1117. PMID: 31004154, DOI: 10.1093/eurpub/ckz052.
Defining Risk of Late Recurrence in Early-Stage Estrogen Receptor–Positive Breast Cancer: Clinical Versus Molecular ToolsFoldi J, O'Meara T, Marczyk M, Sanft T, Silber A, Pusztai L. Defining Risk of Late Recurrence in Early-Stage Estrogen Receptor–Positive Breast Cancer: Clinical Versus Molecular Tools. Journal Of Clinical Oncology 2019, 37: jco.18.01933. PMID: 30943126, DOI: 10.1200/jco.18.01933.
Abstract P2-06-06: Targeting loss of isoenzyme diversity as a novel therapeutic strategy in breast cancerMarczyk M, Gunasekharan V, Wali V, Shi W, Patwardhan G, Qing T, Pusztai L, Hatzis C. Abstract P2-06-06: Targeting loss of isoenzyme diversity as a novel therapeutic strategy in breast cancer. Cancer Research 2019, 79: p2-06-06-p2-06-06. DOI: 10.1158/1538-7445.sabcs18-p2-06-06.
Abstract P4-03-01: Pathway level complementarity of germline and somatic events in breast cancerQing T, Marczyk M, Wali V, Gunasekharan V, Patwardhan G, Pusztai L, Hatzis C. Abstract P4-03-01: Pathway level complementarity of germline and somatic events in breast cancer. Cancer Research 2019, 79: p4-03-01-p4-03-01. DOI: 10.1158/1538-7445.sabcs18-p4-03-01.
Abstract P4-08-20: Pre-analytical effects of FFPE extraction methods on targeted and whole transcriptome sequencing assays for endocrine sensitivity in metastatic breast cancerMarczyk M, Fu C, Lau R, Du L, Trevarton A, Sinn B, Gould R, Symmans W, Hatzis C. Abstract P4-08-20: Pre-analytical effects of FFPE extraction methods on targeted and whole transcriptome sequencing assays for endocrine sensitivity in metastatic breast cancer. Cancer Research 2019, 79: p4-08-20-p4-08-20. DOI: 10.1158/1538-7445.sabcs18-p4-08-20.
BatchI: Batch effect Identification in high-throughput screening data using a dynamic programming algorithmPapiez A, Marczyk M, Polanska J, Polanski A. BatchI: Batch effect Identification in high-throughput screening data using a dynamic programming algorithm. Bioinformatics 2018, 35: 1885-1892. PMID: 30357412, PMCID: PMC6546123, DOI: 10.1093/bioinformatics/bty900.
GaMRed—Adaptive Filtering of High-Throughput Biological DataMarczyk M, Jaksik R, Polanski A, Polanska J. GaMRed—Adaptive Filtering of High-Throughput Biological Data. IEEE/ACM Transactions On Computational Biology And Bioinformatics 2018, 17: 149-157. PMID: 30040660, DOI: 10.1109/tcbb.2018.2858825.
Initializing the EM Algorithm for Univariate Gaussian, Multi-Component, Heteroscedastic Mixture Models by Dynamic Programming PartitionsPolanski A, Marczyk M, Pietrowska M, Widlak P, Polanska J. Initializing the EM Algorithm for Univariate Gaussian, Multi-Component, Heteroscedastic Mixture Models by Dynamic Programming Partitions. International Journal Of Computational Methods 2018, 15: 1850012. DOI: 10.1142/s0219876218500123.
P2.13-010 Five-Year-Long Follow-Up of the Low-Dose Computed Tomography Screening Program in Gdansk, PolandOstrowski M, Marjanski T, Marczyk M, Polanska J, Rzyman W. P2.13-010 Five-Year-Long Follow-Up of the Low-Dose Computed Tomography Screening Program in Gdansk, Poland. Journal Of Thoracic Oncology 2017, 12: s2168-s2169. DOI: 10.1016/j.jtho.2017.09.1357.
1713P Prognostic value of NK and T-lymphocyte markers in operable non-small cell lung cancer (NSCLC)Skrzypski M, Szymanowska-Narloch A, Kowalczyk A, Maciejewska A, Marczyk M, Polańska J, Biernat W, Rzyman W, Jassem J. 1713P Prognostic value of NK and T-lymphocyte markers in operable non-small cell lung cancer (NSCLC). Annals Of Oncology 2017, 28: v599. DOI: 10.1093/annonc/mdx391.012.
Serum lipid profile discriminates patients with early lung cancer from healthy controlsRos-Mazurczyk M, Jelonek K, Marczyk M, Binczyk F, Pietrowska M, Polanska J, Dziadziuszko R, Jassem J, Rzyman W, Widlak P. Serum lipid profile discriminates patients with early lung cancer from healthy controls. Lung Cancer 2017, 112: 69-74. PMID: 29191603, DOI: 10.1016/j.lungcan.2017.07.036.
Abstract 3700: Prognostic value of the expression of NKG2D and CD96 in early stage non-small cell lung cancer (NSCLC)Skrzypski M, Marczyk M, Szymanowska A, Kowalczyk A, Maciejewska A, Pawlowski R, Biernat W, Polańska J, Jassem J. Abstract 3700: Prognostic value of the expression of NKG2D and CD96 in early stage non-small cell lung cancer (NSCLC). Cancer Research 2017, 77: 3700-3700. DOI: 10.1158/1538-7445.am2017-3700.
Processing 2D Gel Electrophoresis Images for Efficient Gaussian Mixture ModelingMarczyk M. Processing 2D Gel Electrophoresis Images for Efficient Gaussian Mixture Modeling. 2017, 616: 35-42. DOI: 10.1007/978-3-319-60816-7_5.
Reproducibility of Finding Enriched Gene Sets in Biological Data AnalysisZyla J, Marczyk M, Polanska J. Reproducibility of Finding Enriched Gene Sets in Biological Data Analysis. 2017, 616: 146-154. DOI: 10.1007/978-3-319-60816-7_18.
Prognostic value of NK and T-lymphocytes markers in operable non-small cell lung cancer (NSCLC).Skrzypski M, Szymanowska-Narloch A, Jassem E, Marczyk M, Polanska J, Biernat W, Rzyman W, Maciejewska A, Pawlowski R, Jassem J. Prognostic value of NK and T-lymphocytes markers in operable non-small cell lung cancer (NSCLC). Journal Of Clinical Oncology 2017, 35: 11556-11556. DOI: 10.1200/jco.2017.35.15_suppl.11556.
Ranking metrics in gene set enrichment analysis: do they matter?Zyla J, Marczyk M, Weiner J, Polanska J. Ranking metrics in gene set enrichment analysis: do they matter? BMC Bioinformatics 2017, 18: 256. PMID: 28499413, PMCID: PMC5427619, DOI: 10.1186/s12859-017-1674-0.
Stage I non-small-cell lung cancer: long-term results of lobectomy versus sublobar resection from the Polish National Lung Cancer Registry.Dziedzic R, Zurek W, Marjanski T, Rudzinski P, Orlowski TM, Sawicka W, Marczyk M, Polanska J, Rzyman W. Stage I non-small-cell lung cancer: long-term results of lobectomy versus sublobar resection from the Polish National Lung Cancer Registry. European Journal Of Cardio-Thoracic Surgery 2017, 52: 363-369. PMID: 28402455, DOI: 10.1093/ejcts/ezx092.
Mixture Modeling of 2-D Gel Electrophoresis Spots Enhances the Performance of Spot DetectionMarczyk M. Mixture Modeling of 2-D Gel Electrophoresis Spots Enhances the Performance of Spot Detection. IEEE Transactions On NanoBioscience 2017, 16: 91-99. PMID: 28278480, DOI: 10.1109/tnb.2017.2676725.
Improving Peak Detection by Gaussian Mixture Modeling of Mass Spectral SignalMarczyk M, Polanska J, Polanski A. Improving Peak Detection by Gaussian Mixture Modeling of Mass Spectral Signal. 2017, 39-43. DOI: 10.1109/icfsp.2017.8097057.
48. MicroRNA prognostic signature for distant relapse in early stage colon cancerBobowicz M, Skrzypski M, Czapiewski P, Marczyk M, Maciejewska A, Jankowski M, Szulgo-Paczkowska A, Zegarski W, Pawłowski R, Polańska J, Biernat W, Jaśkiewicz J, Jassem J. 48. MicroRNA prognostic signature for distant relapse in early stage colon cancer. European Journal Of Surgical Oncology 2016, 42: s85. DOI: 10.1016/j.ejso.2016.06.054.
O-093STAGE I NON-SMALL CELL LUNG CANCER: LONG-TERM RESULTS OF LOBECTOMY VERSUS SUBLOBAR RESECTION FROM THE POLISH LUNG CANCER NATIONAL REGISTRYZurek W, Rudzinski P, Orlowski T, Marczyk M, Rzyman W. O-093STAGE I NON-SMALL CELL LUNG CANCER: LONG-TERM RESULTS OF LOBECTOMY VERSUS SUBLOBAR RESECTION FROM THE POLISH LUNG CANCER NATIONAL REGISTRY. Interdisciplinary CardioVascular And Thoracic Surgery 2016, 23: i26-i26. DOI: 10.1093/icvts/ivw260.92.
Prognostic value of 5-microRNA based signature in T2-T3N0 colon cancerBobowicz M, Skrzypski M, Czapiewski P, Marczyk M, Maciejewska A, Jankowski M, Szulgo-Paczkowska A, Zegarski W, Pawłowski R, Polańska J, Biernat W, Jaśkiewicz J, Jassem J. Prognostic value of 5-microRNA based signature in T2-T3N0 colon cancer. Clinical & Experimental Metastasis 2016, 33: 765-773. PMID: 27485175, PMCID: PMC5110606, DOI: 10.1007/s10585-016-9810-1.
Serum mass profile signature as a biomarker of early lung cancerWidlak P, Pietrowska M, Polanska J, Marczyk M, Ros-Mazurczyk M, Dziadziuszko R, Jassem J, Rzyman W. Serum mass profile signature as a biomarker of early lung cancer. Lung Cancer 2016, 99: 46-52. PMID: 27565913, DOI: 10.1016/j.lungcan.2016.06.011.
Sensitivity, Specificity and Prioritization of Gene Set Analysis When Applying Different Ranking MetricsZyla J, Marczyk M, Polanska J. Sensitivity, Specificity and Prioritization of Gene Set Analysis When Applying Different Ranking Metrics. 2016, 477: 61-69. DOI: 10.1007/978-3-319-40126-3_7.
Improved Detection of 2D Gel Electrophoresis Spots by Using Gaussian Mixture ModelMarczyk M. Improved Detection of 2D Gel Electrophoresis Spots by Using Gaussian Mixture Model. 2016, 9683: 284-294. DOI: 10.1007/978-3-319-38782-6_24.
Signal Partitioning Algorithm for Highly Efficient Gaussian Mixture Modeling in Mass SpectrometryPolanski A, Marczyk M, Pietrowska M, Widlak P, Polanska J. Signal Partitioning Algorithm for Highly Efficient Gaussian Mixture Modeling in Mass Spectrometry. PLOS ONE 2015, 10: e0134256. PMID: 26230717, PMCID: PMC4521892, DOI: 10.1371/journal.pone.0134256.
Influence of genetic background and oxidative stress response on risk of mandibular osteoradionecrosis after radiotherapy of head and neck cancerDanielsson D, Brehwens K, Halle M, Marczyk M, Sollazzo A, Polanska J, Munck-Wikland E, Wojcik A, Haghdoost S. Influence of genetic background and oxidative stress response on risk of mandibular osteoradionecrosis after radiotherapy of head and neck cancer. Head & Neck 2015, 38: 387-393. PMID: 25352150, DOI: 10.1002/hed.23903.
MicroRNA (MiRNA) expression profiles in early colon cancer (CC) and lung adenocarcinoma (AC).Skrzypski M, Marczyk M, Bobowicz M, Czapiewski P, Maciejewska A, Pawlowski R, Polanska J, Jassem J. MicroRNA (MiRNA) expression profiles in early colon cancer (CC) and lung adenocarcinoma (AC). Journal Of Clinical Oncology 2015, 33: e22062-e22062. DOI: 10.1200/jco.2015.33.15_suppl.e22062.
Least Squares Estimators of Peptide Species Concentrations Based on Gaussian Mixture Decompositions of Protein Mass SpectraPolanski A, Marczyk M, Pietrowska M, Widlak P, Polanska J. Least Squares Estimators of Peptide Species Concentrations Based on Gaussian Mixture Decompositions of Protein Mass Spectra. 2015, 122: 425-432. DOI: 10.1007/978-3-319-13881-7_47.
Mixture Model Based Efficient Method for Magnetic Resonance Spectra QuantificationBinczyk F, Marczyk M, Polanska J. Mixture Model Based Efficient Method for Magnetic Resonance Spectra Quantification. 2015, 9044: 406-417. DOI: 10.1007/978-3-319-16480-9_40.
Modeling of Imaging Mass Spectrometry Data and Testing by Permutation for Biomarkers Discovery in TissuesMarczyk M, Drazek G, Pietrowska M, Widlak P, Polanska J, Polanski A. Modeling of Imaging Mass Spectrometry Data and Testing by Permutation for Biomarkers Discovery in Tissues. Procedia Computer Science 2015, 51: 693-702. DOI: 10.1016/j.procs.2015.05.186.
Radiation-induced Changes in Levels of Selected Proteins in Peripheral Blood Serum of Breast Cancer Patients as a Potential Triage Biodosimeter for Large-scale Radiological EmergenciesDeperas-Kaminska M, Bajinskis A, Marczyk M, Polanska J, Wersäll P, Lidbrink E, Ainsbury EA, Guipaud O, Benderitter M, Haghdoost S, Wojcik A. Radiation-induced Changes in Levels of Selected Proteins in Peripheral Blood Serum of Breast Cancer Patients as a Potential Triage Biodosimeter for Large-scale Radiological Emergencies. Health Physics 2014, 107: 555-563. PMID: 25353241, DOI: 10.1097/hp.0000000000000158.
Radiation-Induced Changes in Serum Lipidome of Head and Neck Cancer PatientsJelonek K, Pietrowska M, Ros M, Zagdanski A, Suchwalko A, Polanska J, Marczyk M, Rutkowski T, Skladowski K, Clench MR, Widlak P. Radiation-Induced Changes in Serum Lipidome of Head and Neck Cancer Patients. International Journal Of Molecular Sciences 2014, 15: 6609-6624. PMID: 24747595, PMCID: PMC4013650, DOI: 10.3390/ijms15046609.
Comparison of Algorithms for Profile-Based Alignment of Low Resolution MALDI-ToF SpectraMarczyk M, Polanska J, Polanski A. Comparison of Algorithms for Profile-Based Alignment of Low Resolution MALDI-ToF Spectra. 2014, 242: 193-201. DOI: 10.1007/978-3-319-02309-0_20.
An Efficient Algorithm for Microarray Probes Re-annotationFoszner P, Gruca A, Polanski A, Marczyk M, Jaksik R, Polanska J. An Efficient Algorithm for Microarray Probes Re-annotation. 2014, 8342: 201-218. DOI: 10.1007/978-3-642-54455-2_9.
Sources of High Variance between Probe Signals in Affymetrix Short Oligonucleotide MicroarraysJaksik R, Marczyk M, Polanska J, Rzeszowska-Wolny J. Sources of High Variance between Probe Signals in Affymetrix Short Oligonucleotide Microarrays. Sensors 2013, 14: 532-548. PMID: 24385030, PMCID: PMC3926573, DOI: 10.3390/s140100532.
Adaptive filtering of microarray gene expression data based on Gaussian mixture decompositionMarczyk M, Jaksik R, Polanski A, Polanska J. Adaptive filtering of microarray gene expression data based on Gaussian mixture decomposition. BMC Bioinformatics 2013, 14: 101. PMID: 23510016, PMCID: PMC3637832, DOI: 10.1186/1471-2105-14-101.
Radiation-related Changes in Serum Proteome Profiles Detected by Mass Spectrometry in Blood of Patients Treated with Radiotherapy Due to Larynx CancerWidlak P, Pietrowska M, Rutkowski T, Wygoda A, Skladowski K, Wojtkiewicz K, Marczyk M, Polanska J. Radiation-related Changes in Serum Proteome Profiles Detected by Mass Spectrometry in Blood of Patients Treated with Radiotherapy Due to Larynx Cancer. International Journal Of Radiation Oncology • Biology • Physics 2011, 81: s161-s162. DOI: 10.1016/j.ijrobp.2011.06.1660.
Comparison of peptide cancer signatures identified by mass spectrometry in serum of patients with head and neck, lung and colorectal cancers: association with tumor progression.Pietrowska M, Polańska J, Suwiński R, Wideł M, Rutkowski T, Marczyk M, Domińczyk I, Ponge L, Marczak L, Polański A, Widłak P. Comparison of peptide cancer signatures identified by mass spectrometry in serum of patients with head and neck, lung and colorectal cancers: association with tumor progression. International Journal Of Oncology 2011, 40: 148-56. PMID: 21894432, DOI: 10.3892/ijo.2011.1186.
Radiation-related Changes in Serum Proteome Profiles Detected by Mass Spectrometry in Blood of Patients Treated with Radiotherapy Due to Larynx CancerWIDŁAK P, PIETROWSKA M, WOJTKIEWICZ K, RUTKOWSKI T, WYGODA A, MARCZAK Ł, MARCZYK M, POLAŃSKA J, WALASZCZYK A, DOMIŃCZYK I, SKŁADOWSKI K, STOBIECKI M, POLAŃSKI A. Radiation-related Changes in Serum Proteome Profiles Detected by Mass Spectrometry in Blood of Patients Treated with Radiotherapy Due to Larynx Cancer. Journal Of Radiation Research 2011, 52: 575-581. PMID: 21768750, DOI: 10.1269/jrr.11019.
Association between plasma proteome profiles analysed by mass spectrometry, a lymphocyte-based DNA-break repair assay and radiotherapy-induced acute mucosal reaction in head and neck cancer patientsPietrowska M, Polańska J, Walaszczyk A, Wygoda A, Rutkowski T, Składowski K, Marczak Ł, Stobiecki M, Marczyk M, Polański A, Widłak P. Association between plasma proteome profiles analysed by mass spectrometry, a lymphocyte-based DNA-break repair assay and radiotherapy-induced acute mucosal reaction in head and neck cancer patients. International Journal Of Radiation Biology 2011, 87: 711-719. PMID: 21351848, DOI: 10.3109/09553002.2011.556174.
Affymetrix Chip Definition Files Construction Based on Custom Probe Set Annotation DatabaseMarczyk M, Jaksik R, Polański A, Polańska J. Affymetrix Chip Definition Files Construction Based on Custom Probe Set Annotation Database. 2011, 381: 135-144. DOI: 10.1007/978-3-642-23418-7_13.
Efficient Algorithm for Microarray Probes Re-annotationFoszner P, Gruca A, Polanski A, Marczyk M, Jaksik R, Polanska J. Efficient Algorithm for Microarray Probes Re-annotation. 2011, 6923: 281-289. DOI: 10.1007/978-3-642-23938-0_29.

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Michal Marczyk, PhD

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