Ziv Shkedy

Ziv Shkedy
Hasselt University · Research Institute Center for Statistics (CENSTAT)

About

267
Publications
25,156
Reads
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2,796
Citations
Citations since 2017
60 Research Items
1506 Citations
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2017201820192020202120222023050100150200250
2017201820192020202120222023050100150200250
2017201820192020202120222023050100150200250

Publications

Publications (267)
Article
Aims: There has been an increased interest in studying the association between microbial communities and different diseases and in discovering microbiome biomarkers. This association is pivotal to discover such biomarkers. In this paper, we present a unified modelling approach that can be used to detect and develop microbiome biomarkers for differ...
Article
Several major global challenges, including climate change and water scarcity, warrant a scientific approach to generating solutions. Developing high quality and robust capacity in (bio)statistics is key to ensuring sound scientific solutions to these challenges, so collaboration between academic and research institutes should be high on university...
Article
Full-text available
Background In resource-limited settings, changes in CD4 counts constitute an important component in patient monitoring and evaluation of treatment response as these patients do not have access to routine viral load testing. In this study, we quantified trends on CD4 counts in patients on highly active antiretroviral therapy (HAART) in a comprehensi...
Article
Full-text available
Research on the microbiome has boomed recently, which resulted in a wide range of tools, packages, and algorithms to analyze microbiome data. Here we investigate and map currently existing tools that can be used to perform visual analysis on the microbiome, and associate the including methods, visual representations and data features to the researc...
Article
Full-text available
Technological advances now make it possible to generate diverse, complex and varying sizes of data in a wide range of applications from business to engineering to medicine. In the health sciences, in particular, data are being produced at an unprecedented rate across the full spectrum of scientific inquiry spanning basic biology, clinical medicine,...
Article
Full-text available
Background Previous work has shown differential predominance of certain Mycobacterium tuberculosis (M . tb) lineages and sub-lineages among different human populations in diverse geographic regions of Ethiopia. Nevertheless, how strain diversity is evolving under the ongoing rapid socio-economic and environmental changes is poorly understood. The p...
Article
Full-text available
Background Previous work has shown differential predominance of certain Mycobacterium tuberculosis (M. tb) lineages and sub-lineages among different human populations in diverse geographic regions of Ethiopia. Nevertheless, how strain diversity is evolving under the ongoing rapid socio-economic and environmental changes is poorly understood. The pr...
Article
Full-text available
Tuberculosis (TB) is a chronic communicable bacterial disease caused by Mycobacterium tuberculosis complex (MTBC) species. M. tuberculosis is the main causative agent of human TB, and cattle are the primary host of Mycobacterium bovis; due to close interaction between cattle and humans, M. bovis poses a zoonotic risk. This review summarizes and est...
Article
Parameter estimation is often considered as a post model selection problem, i.e., the parameters of interest are often estimated based on “the best” model. However, this approach does not take into account that “the best” model was selected from a set of possible models. Ignoring this uncertainty may lead to bias in estimation. In this paper, we pr...
Preprint
Our aim in this study is to develop predictive microbiome biomarkers for intestinal IgA levels. In this article, a operational taxonomic units(OTU)-specific (family-specific) and time-specific joint model is presented as a tool to model the association between OTU (or family) and biological response (measured by IgA level) taking into account the t...
Article
Full-text available
Bayesian inference for generalized linear mixed models (GLMM) is appealing, but its widespread use has been hampered by the lack of a fast implementation tool and the difficulty in specifying prior distributions. In this paper, we conduct an extensive simulation study to evaluate the performance of INLA for estimation of the hierarchical Poisson re...
Article
Full-text available
The extraordinary global growth of digital connectivity has generated optimism that mobile technologies can help overcome infrastructural barriers to development, with ‘mobile health’ (mhealth) being a key component of this. However, while ‘formal’ (top-down) mhealth programmes continue to face challenges of scalability and sustainability, we know...
Article
Full-text available
Introduction In contrast to most tuberculosis (TB) high burden countries, Ethiopia has for a long time reported a very high percentage of extra pulmonary TB (EPTB), which is also reflected in population based estimations reported by the World Health Organization (WHO). Particularly a steadily higher proportion of cervical tuberculous lymphadenitis...
Preprint
Full-text available
Background In resource-limited settings, changes in CD4 counts constitute an important component in patient monitoring and evaluation of treatment response as these patients do not have access to routine viral load testing. In this study, we quantified trends on CD4 counts in patients on highly active antiretroviral therapy (HAART) in a comprehensi...
Preprint
Full-text available
Background: The current outbreak of COVID-19 is a major pandemic that has adversely affected the world economies, societies and also an increase in health burdens within a short time. South Africa has the highest number of confirmed COVID-19 cases in Africa and is the fourteenth most affected country in the world. Understanding the country’s COVID-...
Article
Full-text available
Background The rising burden of the ongoing COVID-19 epidemic in South Africa has motivated the application of modeling strategies to predict the COVID-19 cases and deaths. Reliable and accurate short and long-term forecasts of COVID-19 cases and deaths, both at the national and provincial level, are a key aspect of the strategy to handle the COVID...
Article
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Educational stakeholders are keen to know the magnitude and importance of different interventions. However, the way evidence is communicated to support understanding of the effectiveness of an intervention is controversial. Typically studies in education have used the standardised mean difference as a measure of the impact of interventions. This me...
Article
Full-text available
Several studies have demonstrated that the metabolite composition of plasma may indicate the presence of lung cancer. The metabolism of cancer is characterized by an enhanced glucose uptake and glycolysis which is exploited by 18F-FDG positron emission tomography (PET) in the work-up and management of cancer. This study aims to explore relationship...
Article
Identification of genomic biomarkers is an important area of research in the context of drug discovery experiments. These experiments typically consist of several high dimensional datasets that contain information about a set of drugs (compounds) under development. This type of data structure introduces the challenge of multi-source data integratio...
Article
Full-text available
Background: CD4 cell counts is widely used as a biomarker for treatment progression when studying the efficacy of drugs to treat HIV-infected patients. In the past, it had been also used in determining eligibility to initiate antiretroviral therapy. The main aim of this was to model the evolution of CD4 counts over time and use this model for an e...
Article
A way to enhance our understanding of the development and progression of complex diseases is to investigate the influence of cellular environments on gene co-expression (i.e. gene-pair correlations). Often, changes in gene co-expression are investigated across two or more biological conditions defined by categorizing a continuous covariate. However...
Code
Description Functions to identify the pattern of a dose-response curve. Then fit a set of appropriate models to it according to the identified pattern, followed by model averaging to estimate the effective dose.
Article
Full-text available
Background: Pulmonary imaging often identifies suspicious abnormalities resulting in supplementary diagnostic procedures. This study aims to investigate whether the metabolic fingerprint of plasma allows to discriminate between patients with lung inflammation and patients with lung cancer. Methods: Metabolic profiles of plasma from 347 controls,...
Article
Full-text available
Alternative gene splicing is a common phenomenon in which a single gene gives rise to multiple transcript isoforms. The process is strictly guided and involves a multitude of proteins and regulatory complexes. Unfortunately, aberrant splicing events have been linked to genetic disorders. Therefore, understanding mechanisms of alternative splicing r...
Article
Background: Progress in immunotherapy has revolutionized the treatment landscape for advanced lung cancer, with emerging evidence of patients experiencing long-term survivals. The goal of this study was to explore the existence of short- and long-term survival populations and to assess the effect of immunotherapy on them. Methods: Data from two ran...
Article
Full-text available
Dissolved oxygen is an essential controlling factor in the performance of facultative and maturation ponds since both take many advantages of algal photosynthetic oxygenation. The rate of this photosynthesis strongly depends on the time during the day and the location in a pond system, whose roles have been overlooked in previous guidelines of pond...
Article
Full-text available
Background: Alzheimer's disease (AD) is a progressive neurodegenerative disorder and the most common cause of dementia in the elderly population. In this study, we used the APP/PS1 transgenic mouse model to explore the feasibility of using diffusion kurtosis imaging (DKI) as a tool for the early detection of microstructural changes in the brain du...
Article
Full-text available
Background The effectiveness of antiretroviral therapy (ART) depends on the choice of regimens during initiation. Most evidences from developed countries indicated that there is difference between efavirenz (EFV) and nevirapine (NVP). However, the evidences are limited in resource poor countries particularly in Africa. Thus, this systematic review...
Article
Full-text available
Author summary Visceral leishmaniasis (VL), a disease caused by a parasite, Leishmania, belongs to the most neglected tropical diseases: they mainly occur in low-income countries and affect the poorest populations. The parasites are transmitted via the bite of an insect vector and migrate to the internal organs. When VL occurs, the patients will pr...
Data
Complete blood count of healthy controls. WBC = white blood cells; Plt = platelets; Hct = hematocrit; Hb = haemoglobin. Normal range: neutrophils (x103)/μl = 2–7.5; platelets (x103)/μl = 150–450; white blood cells (x103)/μl = 4.5–10.5; Hct (%) = 35–60; Hgb (g/dl) = 11–18. These parameters were measured in the blood of healthy non-endemic controls (...
Poster
Full-text available
Dissolved oxygen is an essential controlling factor in the operation of facultative and maturation ponds since their purification processes take many advantages from algal photosynthetic oxygenation. The rate of this photosynthesis strongly depends on the location within a pond and climatic conditions which can be extreme at high altitude, such as...
Presentation
Full-text available
Dissolved oxygen is an essential controlling factor in the operation of facultative and maturation ponds since their purification processes take many advantages from algal photosynthetic oxygenation. The rate of this photosynthesis strongly depends on the location within a pond and climatic conditions which can be extreme at high altitude, such as...
Article
Full-text available
Background Highly active antiretroviral therapy (HAART) has shown a dramatic change in controlling the burden of HIV/AIDS. However, the new challenge of HAART is to allow long-term sustainability. Toxicities, comorbidity, pregnancy, and treatment failure, among others, would result in frequent initial HAART regimen change. The aim of this study was...
Article
Early prediction of the final size of any epidemic and in particular for Zika disease outbreaks can be useful for health authorities in order to plan the response to the outbreak. The Richards model is often been used to estimate epidemiological parameters for arboviral diseases based on the reported cumulative cases in single- and multi-wave outbr...
Article
Full-text available
Background Alternative gene splicing is a common phenomenon in which a single gene gives rise to multiple transcript isoforms. The process is strictly guided and involves a multitude of proteins and regulatory complexes. Unfortunately, aberrant splicing events do occur which have been linked to genetic disorders, such as several types of cancer and...
Article
Full-text available
The analysis of transcriptomic experiments with ordered covariates, such as dose-response data, has become a central topic in bioinformatics, in particular in omics studies. Consequently, multiple R packages on CRAN and Bioconductor are designed to analyse microarray data from various perspectives under the assumption of order restriction. We intro...
Chapter
This paper discusses the relevance of surrogate marker validation method for empirical assessment of gene expression biomarkers for radiation exposure.
Article
The identification of the minimum effective dose is of high importance in the drug development process. In early stage screening experiments, establishing the minimum effective dose can be translated into a model selection based on information criteria. The presented alternative, Bayesian variable selection approach, allows for selection of the min...
Article
In recent years there has been an increased interest in using statistical models for analysis of single dengue outbreaks based on the reported cumulative cases. Sometimes this type of data is collected for all urban areas in a particular region. Modeling in order to estimate epidemiological parameters is usually performed for each area separately,...
Article
Full-text available
Background Antiretroviral therapy has shown to be effective in reducing morbidity and mortality in patients infected with HIV for the past couples of decades. However, there remains a need to better understand the characteristics of long-term treatment outcomes in resource poor settings. The main aim of this study was to determine and compare the l...
Data
Statistical methods for time to event and Immunological outcomes. (PDF)
Data
Cox PH model for sensitivity analysis. (PDF)
Data
Kaplan-Meier Survival plot for selected baseline covariates. (TIFF)
Data
Separate analysis of long-term treatment outcomes. (PDF)
Data
Kaplan-Meier Survival plot for all treatment regimens. (TIFF)
Article
Benjamini and Yekutieli () introduced the concept of the false coverage-statement rate (FCR) to account for selection when the confidence intervals (CIs) are constructed only for the selected parameters. Dose-response analysis in dose-response microarray experiments is conducted only for genes having monotone dose-response relationship, which is a...
Chapter
An important factor that affects the duration, complexity and cost of a clinical trial is the endpoint used to study the treatment's efficacy. When a true endpoint is difficult to use because of such factors as long follow-up times or prohibitive cost, it is sometimes possible to use a surrogate endpoint that can be measured in a more convenient or...
Article
Full-text available
Immunologically, active visceral leishmaniasis (VL) is characterized by profound immunosuppression, severe systemic inflammatory responses, and an impaired capacity to control parasite replication. Neutrophils are highly versatile cells, which play a crucial role in the induction as well as the resolution of inflammation, the control of pathogen re...