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List of works by Tomasz Burzykowski

A "Refined Hydrogen Rule" and a "Refined Hydrogen and Halogen Rule" for Organic Molecules

scientific article published on 21 November 2019

A Bayesian Markov-chain-based heteroscedastic regression model for the analysis of 18O-labeled mass spectra

scientific article published on 15 January 2011

A Comparison of Procedures for Controlling the False Discovery Rate in the Presence of Small Variance Genes: A Simulation Study

article

A Conceptual Framework for Abundance Estimation of Genomic Targets in the Presence of Ambiguous Short Sequencing Reads

scientific article published on 31 December 2019

A Markov-chain model for the analysis of high-resolution enzymatically 18O-labeled mass spectra

scientific article published on 6 January 2011

A Markov-chain-based regression model with random effects for the analysis of18O-labelled mass spectra

A Multivariate Negative-Binomial Model with Random Effects for Differential Gene-Expression Analysis of Correlated mRNA Sequencing Data

scientific article published on 17 July 2019

A Poisson approach to the validation of failure time surrogate endpoints in individual patient data meta-analyses

scientific article

A bayesian model averaging approach to the quantification of overlapping peptides in an maldi-tof mass spectrum

scientific article published on 23 May 2011

A cross-validation study to select a classification procedure for clinical diagnosis based on proteomic mass spectrometry.

scientific article published on 24 March 2008

A hidden Markov-model for gene mapping based on whole-genome next generation sequencing data.

scientific article

A model-based method for the prediction of the isotopic distribution of peptides

scientific article

A modeling approach to the analysis of nerve regenerative experiments

scientific article published in January 2006

A multivariate linear model for investigating the association between gene-module co-expression and a continuous covariate

scientific article published on 15 March 2019

A nonhomogeneous hidden markov model for gene mapping based on next-generation sequencing data.

scientific article

A perspective on surrogate endpoints in controlled clinical trials

scientific article published on June 2004

A statistical approach to central monitoring of data quality in clinical trials

scientific article

A strategy for the prior processing of high-resolution mass spectral data obtained from high-dimensional combined fractional diagonal chromatography

scientific article

A unified framework for the evaluation of surrogate endpoints in mental-health clinical trials

scientific article published on 16 July 2009

A version of the EM algorithm for proportional hazard model with random effects

scientific article published in December 2005

ARMD Trial: Linear Model with Heterogeneous Variance

ARMD Trial: Linear Model with Homogeneous Variance

article

ARMD Trial: Modeling Correlated Errors for Visual Acuity

ARMD Trial: Modeling Visual Acuity

Abstract LB-004: Molecular hallmarks of cancer: Stemness

Abstract P3-10-24: Fibroblast Growth Factor Receptor 1 Amplification and Overexpression in Breast Cancer Tissue Microarrays Using Chromogenic In Situ Hybridization and Immunohistochemistry

Adoption of Pathologic Complete Response as a Surrogate End Point in Neoadjuvant Trials in HER2-Positive Breast Cancer Still an Open Question

scientific article published on 17 November 2016

An efficient method to calculate the aggregated isotopic distribution and exact center-masses

scientific article published on 15 February 2012

An information-theoretic approach for the evaluation of surrogate endpoints based on causal inference

scientific article

An investigation on performance of Significance Analysis of Microarray (SAM) for the comparisons of several treatments with one control in the presence of small-variance genes

scientific article published in October 2008

An open label phase II study evaluating first-line EGFR tyrosine kinase inhibitor erlotinib in non-small cell lung cancer patients with tumors showing high EGFR gene copy number

scientific article published on 04 December 2016

Analysis of photon count data from single-molecule fluorescence experiments

Are prostate-specific antigen changes valid surrogates for survival in hormone-refractory prostate cancer? A meta-analysis is needed!

scientific article published in December 2007

Axillary sentinel node and tumour-related factors associated with non-sentinel node involvement in breast cancer

scientific article published in September 2004

BRAIN: a universal tool for high-throughput calculations of the isotopic distribution for mass spectrometry.

scientific article published on 31 January 2013

Bayesian biomarker-driven outcome-adaptive randomization with an imperfect biomarker assay

scientific article published on 24 November 2020

Benefit of adjuvant chemotherapy for resectable gastric cancer: a meta-analysis

scientific article published on May 2010

CXCL5 as a potential novel prognostic factor in early stage non-small cell lung cancer: results of a study of expression levels of 23 genes.

scientific article

Choice of units of analysis and modeling strategies in multilevel hierarchical models

Chronological Trends in Progression-Free, Overall, and Post-Progression Survival in First-Line Therapy for Advanced NSCLC

scientific article published on 01 June 2019

Circulating tumor cell biomarker panel as an individual-level surrogate for survival in metastatic castration-resistant prostate cancer

scientific article published on 23 March 2015

Comparative assessment of trial-level surrogacy measures for candidate time-to-event surrogate endpoints in clinical trials

Comparison of different estimation procedures for proportional hazards model with random effects

Comparison of the Mahalanobis distance and Pearson's χ² statistic as measures of similarity of isotope patterns.

scientific article published on 19 November 2013

Computational methods and challenges in hydrogen/deuterium exchange mass spectrometry.

scientific article published on 7 September 2016

Correcting for the Absence of a Gold Standard Improves Diagnostic Accuracy of Biomarkers in Alzheimer's Disease

scientific article

Data Exploration

article published in 2012

Data-driven risk identification in phase III clinical trials using central statistical monitoring

scientific article

De novo prediction of the elemental composition of peptides and proteins based on a single mass

scientific article published on 29 April 2019

Design and analysis of drug combination experiments

scientific article published in June 2005

Design-based analysis of surveys: a bovine herpesvirus 1 case study.

scientific article

Detection of atypical data in multicenter clinical trials using unsupervised statistical monitoring

scientific article published on 23 July 2019

Development of a diagnostic test based on multiple continuous biomarkers with an imperfect reference test.

scientific article published on 21 September 2015

Differences in the Elemental Isotope Definition May Lead to Errors in Modern Mass-Spectrometry-Based Proteomics

scientific article published on 22 October 2015

Disease-free survival as a surrogate for overall survival in adjuvant trials of gastric cancer: a meta-analysis

scientific article

Disease-free survival as a surrogate for overall survival in patients with HER2-positive, early breast cancer in trials of adjuvant trastuzumab for up to 1 year: a systematic review and meta-analysis

scientific article published on 29 January 2019

Effect of the number of uninvolved nodes on survival in early breast cancer

scientific article published on 01 March 2003

Efficacy of oral adjuvant therapy after resection of colorectal cancer: 5-year results from three randomized trials

scientific article published in February 2004

Estimation of diagnostic accuracy of a combination of continuous biomarkers allowing for conditional dependence between the biomarkers and the imperfect reference-test

scientific article

Evaluation of Continuous Tumor-Size-Based End Points as Surrogates for Overall Survival in Randomized Clinical Trials in Metastatic Colorectal Cancer

scientific article published on 04 September 2019

Evaluation of Laplace distribution-based ANOVA models applied to microarray data

scientific article

Evaluation of disease-free survival (DFS) as a surrogate for overall survival (OS) in the adjuvant therapy of HER2-positive early breast cancer (EBC) calls for individual-patient data (IPD)

Evaluation of normalization methods to pave the way towards large-scale LC-MS-based metabolomics profiling experiments

scientific article published on 29 June 2013

Evaluation of tumor response, disease control, progression-free survival, and time to progression as potential surrogate end points in metastatic breast cancer.

scientific article published in April 2008

Experimental Design in Quantitative Proteomics

scientific article published on 01 January 2019

Exploring and validating surrogate endpoints in colorectal cancer

scientific article published on 20 January 2008

Expression of vascular endothelial growth factor (VEGF) in non-small cell lung cancer (NSCLC): association with p53 gene mutation and prognosis ⬇️

scientific article published on December 1, 2001

Extensions of theRTools for Linear Mixed-Effects Models

FCAT Study: Modeling Attainment-Target Scores

Factors associated with non-sentinel node involvement in breast cancer

Finding Clusters of Positive and Negative Coregulated Genes in Gene Expression Data

article

Fitting Linear Mixed-Effects Models: The lme()Function

Fitting Linear Mixed-Effects Models: The lmer() Function

Fitting Linear Models with Fixed Effects and Correlated Errors: The gls() Function

Fitting Linear Models with Heterogeneous Variance: The gls() Function

Fitting Linear Models with Homogeneous Variance: The lm() and gls() Functions

Fitting conditional survival models to meta-analytic data by using a transformation toward mixed-effects models

scientific article

Functional form of the effect of the numbers of axillary nodes on survival in early breast cancer

scientific article published on 01 March 2003

Genomic Biomarkers for a Binary Clinical Outcome in Early Drug Development Microarray Experiments

scientific article published on 01 January 2012

High prevalence of foot diseases in Europe: results of the Achilles Project.

scientific article

Individual patient data meta-analysis of randomized trials evaluating IL-2 monotherapy as remission maintenance therapy in acute myeloid leukemia

scientific article

Individual- and trial-level surrogacy in colorectal cancer

scientific article published on 19 February 2008

Is prostate-specific antigen a valid surrogate end point for survival in hormonally treated patients with metastatic prostate cancer? Joint research of the European Organisation for Research and Treatment of Cancer, the Limburgs Universitair Centrum

scientific article published in September 2005

Is there a minimum number of lymph nodes that should be histologically assessed for a reliable nodal staging of T3N0M0 colorectal carcinomas?

scientific article published on 01 October 2002

Joint modelling of a binary and a continuous outcome measured at two cycles to determine the optimal dose

Joint modelling of repeated measurements and event time: application to performance traits and survival of lambs bred in sub-humid tropics

scientific article published on March 2005

Linear Mixed-Effects Model

Linear Mixed-Effects Models Using R

Linear Model with Fixed Effects and Correlated Errors

article

Linear Models with Heterogeneous Variance

Linear Models with Homogeneous Variance

Linear mixed-effects models for central statistical monitoring of multicenter clinical trials

scientific article published on 12 September 2014

Long-term survival of high-risk melanoma patients immunized with a Hyper-IL-6-modified allogeneic whole-cell vaccine after complete resection

scientific article published on 01 June 2012

Low-dose glucose-insulin-potassium is ineffective in acute myocardial infarction: results of a randomized multicenter Pol-GIK trial

scientific article

Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation

scientific article published in April 2018

Markers for nutrition studies: review of criteria for the evaluation of markers

scientific article

Markov-chain-based heteroscedastic regression model for the analysis of high-resolution enzymatically 18O-labeled mass spectra

scientific article published in May 2010

Missing data: discussion points from the PSI missing data expert group

scientific article

Multivariate analysis of risk factors for development of duodenal ulcer in Helicobacter pylori-infected patients

scientific article published in January 2003

Neoadjuvant as Future for Drug Development in Breast Cancer--Letter

scientific article published in January 2016

No association of leukemia inhibitory factor (LIF) DNA polymorphisms with multiple sclerosis

scientific article published on 02 November 2005

Normalisation of brain spectroscopy findings in Niemann-Pick disease type C patients treated with miglustat

scientific article published on 16 March 2016

On the relationship between the causal-inference and meta-analytic paradigms for the validation of surrogate endpoints

scientific article

PLS-SEM Mediation Analysis of Gene-Expression Data for the Evaluation of a Drug Effect

article

PRT Trial: Modeling Muscle Fiber Specific-Force

PTEN Loss Is Associated with Worse Outcome in HER2-Amplified Breast Cancer Patients but Is Not Associated with Trastuzumab Resistance

scientific article published on 3 February 2015

Performance of Gene Selection and Classification Methods in a Microarray Setting: A Simulation Study

article

Post-surgery radiation in early breast cancer: survival analysis of registry data

scientific article

Precision medicine needs randomized clinical trials

scientific article published on 7 February 2017

Predicted and observed thyroid cancer incidence in Poland after year 1986

scientific article published on 01 January 2004

Predicting treatment effect from surrogate endpoints and historical trials: an extrapolation involving probabilities of a binary outcome or survival to a specific time

scientific article published on 13 August 2011

Prentice's Approach and the Meta-Analytic Paradigm: A Reflection on the Role of Statistics in the Evaluation of Surrogate Endpoints

article

Preoperative CYFRA 21-1 level as a prognostic indicator in resected nonsmall cell lung cancer

scientific article published on 01 December 1998

Prognostic significance of p53 and bcl-2 abnormalities in operable nonsmall cell lung cancer

scientific article published on 01 April 2001

Prognostic value of serum p53 antibodies in patients with resected non-small cell lung cancer

scientific article published on 01 December 1998

Progression-free survival as a surrogate for overall survival in advanced/recurrent gastric cancer trials: a meta-analysis

scientific article published on 09 October 2013

Progression-free survival as surrogate endpoint of overall survival in patients with advanced/recurrent gastric cancer: Individual patient data analysis on 4,102 patients from 20 randomized trials

Progression-free survival is a surrogate for survival in advanced colorectal cancer

scientific article published in November 2007

Prostate-specific antigen (PSA) alone is not an appropriate surrogate marker of long-term therapeutic benefit in prostate cancer trials

scientific article

Pseudo-likelihood estimation for a marginal multivariate survival model

scientific article published in March 2004

Radiographic progression-free survival as a response biomarker in metastatic castration-resistant prostate cancer: COU-AA-302 results

scientific article

Re-induction using whole cell melanoma vaccine genetically modified to melanoma stem cells-like beyond recurrence extends long term survival of high risk resected patients - updated results

scientific article published on 29 November 2018

Re: A model to select chemotherapy regimens for phase III trials for extensive-stage small-cell lung cancer

scientific article published in March 2001

Reintroduction of Oxaliplatin Is Associated With Improved Survival in Advanced Colorectal Cancer

scientific article published on 01 August 2007

Relation between tumour response to first-line chemotherapy and survival in advanced colorectal cancer: a meta-analysis

scientific article published in The Lancet

Reply to the Comment on:

scientific article published in 2012

Resampling Plans for Frailty Models

scientific article published in 2006

Risk factors for bovine herpesvirus-1 seropositivity

scientific article published on 24 March 2005

Role of chemotherapy for advanced/recurrent gastric cancer: An individual-patient-data meta-analysis ⬇️

scientific article published on January 24, 2013

SII Project: Modeling Gains in Mathematics Achievement-Scores

Sequential double cross-validation for assessment of added predictive ability in high-dimensional omic applications ⬇️

Simplified hierarchical linear models for the evaluation of surrogate endpoints

Simplified modeling strategies for surrogate validation with multivariate failure-time data

Simultaneous mapping of multiple gene loci with pooled segregants

scientific article published on 18 February 2013

Statistical Validation of Surrogate Endpoints: Problems and Proposals

Statistical analysis of data from single molecule experiment

article published in 2003

Statistical challenges in the evaluation of surrogate endpoints in randomized trials

scientific article

Statistical evaluation of surrogate endpoints with examples from cancer clinical trials

scientific article

Statistical interaction in the survival analysis of early breast cancer using registry data: role of breast conserving surgery and radiotherapy

scientific article

Statistical monitoring of data quality and consistency in the Stomach Cancer Adjuvant Multi-institutional Trial Group Trial

scientific article

Surrogate endpoints for overall survival in locally advanced head and neck cancer: meta-analyses of individual patient data

scientific article

Surrogate endpoints in advanced sarcoma trials: a meta-analysis

scientific article published on 02 October 2018

Surrogate endpoints: wishful thinking or reality?

scientific article published on 15 April 2008

Surrogate threshold effect: an alternative measure for meta-analytic surrogate endpoint validation

scientific article published on 01 July 2006

Survivin-targeted immunotherapy drives robust polyfunctional T cell generation and differentiation in advanced ovarian cancer patients

scientific article

Taxanes alone or in combination with anthracyclines as first-line therapy of patients with metastatic breast cancer.

scientific article published in April 2008

Testing for trends in dose-response microarray experiments: a comparison of several testing procedures, multiplicity and resampling-based inference

scientific article

The (generalized) hydrogen rule for organic molecules

scientific article published on 27 December 2019

The Detection of Metabolite-Mediated Gene Module Co-Expression Using Multivariate Linear Models

scientific article

The authors replied as follows:

The correlation structure of longitudinal measurements of vision in patients with macular degeneration

scientific article published on 01 March 2011

The effect of long-term water storage on the tensile strength of orthodontic brackets bonded with resin-reinforced glass-lonomer cements

scientific article published on 01 January 1999

The effects of foot disease on quality of life: results of the Achilles Project.

scientific article published in March 2005

The impact of the method of extracting metabolic signal from 1H-NMR data on the classification of samples: A case study of binning and BATMAN in lung cancer

scientific article published on 06 February 2019

The isotopic distribution conundrum

scientific article

The meta-analytic framework for the evaluation of surrogate endpoints in clinical trials

The retrospective study of 93 patients with transmigration of mandibular canine and a comparative analysis with a control group

article

The search for surrogate endpoints for immunotherapy trials

The use of background signal in the transformation of cDNA-microarray measurements

scientific article published in January 2006

The use of the isotopic distribution as a complementary quality metric to assess tandem mass spectra results

scientific article published on 31 December 2013

The validation of surrogate end points by using data from randomized clinical trials: a case-study in advanced colorectal cancer

Titrating Theileria parva: single stocks against combination of stocks

scientific article

Transferring cut-off values between assays for cerebrospinal fluid Alzheimer's disease biomarkers

scientific article published on 9 October 2015

Trial-level association between response-based endpoints (RBEs) and progression-free (PFS)/overall survival (OS) in first-line therapy for metastatic colorectal cancer (mCRC) in the ARCAD database

Unbiasedness and efficiency of non-parametric and UMVUE estimators of the probabilistic index and related statistics

scientific article published on 01 December 2020

Understanding and Communicating Measures of Treatment Effect on Survival: Can We Do Better?

scientific article published on 01 March 2018

Unveiling the Molecular Mechanism of Trastuzumab Resistance in SKBR3 and BT474 Cell Lines for HER2 Positive Breast Cancer

scientific article published in 2024

Use of the Beta-Binomial Model for Central Statistical Monitoring of Multicenter Clinical Trials

Using Linear Mixed Models for Normalization of cDNA Microarrays

scientific article published on 26 July 2007

Using a Poisson approximation to predict the isotopic distribution of sulphur-containing peptides in a peptide-centric proteomic approach

scientific article

Using the expected survival to explain differences between the results of randomized trials: a case in advanced ovarian cancer

scientific article published in May 2003

Validation of Surrogate Endpoints in Multiple Randomized Clinical Trials with Discrete Outcomes

Validation of a longitudinally measured surrogate marker for a time-to-event endpoint

Validation of surrogate end points in multiple randomized clinical trials with failure time end points

Vegetables Affect the Expression of Genes Involved in Anticarcinogenic Processes in the Colonic Mucosa of C57Bl/6 Female Mice

article

Vegetables affect the expression of genes involved in carcinogenic and anticarcinogenic processes in the lungs of female C57BL/6 mice

scientific article published in November 2005

Visualizing the agreement of peptide assignments between different search engines

scientific article published on 12 November 2019

Whole Cell Therapeutic Vaccine Modified With Hyper-IL6 for Combinational Treatment of Nonresected Advanced Melanoma

scientific article

p53 gene mutation and protein expression in operable non-small cell lung cancer in Poland

article

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