Anna Górska

Anna Górska
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Anna verified their affiliation via an institutional email.
Verified
Anna verified their affiliation via an institutional email.
University of Verona | UNIVR · Dept. of Infectious Diseases

Ph.D.
all described in details: aniagorska.me

About

58
Publications
9,352
Reads
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2,608
Citations
Additional affiliations
April 2019 - present
University of Verona
Position
  • PostDoc Position
September 2011 - September 2013
University of Warsaw
Position
  • Master's Student
September 2013 - March 2019
University of Tübingen
Position
  • PhD Student
Education
September 2013 - June 2016
October 2011 - June 2013
University of Warsaw
Field of study
  • Bioinformatics and systems biology
October 2008 - June 2011
University of Warsaw
Field of study
  • Bioinformatics and systems bioilogy

Publications

Publications (58)
Article
Full-text available
Several studies reported alterations of the human gut microbiota (GM) during COVID-19. To evaluate the potential role of the GM as an early predictor of COVID-19 at disease onset, we analyzed gut microbial samples of 315 COVID-19 patients that differed in disease severity. We observed significant variations in microbial diversity and composition as...
Article
Full-text available
COVID-19 pandemic brought chemosensory impairment to the forefront of medicine, revealing gaps in the knowledge of pathophysiological mechanisms, true prevalence and preventive/therapeutic alternatives. This is a sub-study of the ORCHESTRA cohort focusing on post-COVID-19 chemosensory symptoms. Risk factors for neurosensorial cluster of post-COVID-...
Article
The motivation behind this research is to perform a privacy-preserving analysis of data located at remote sites and in different jurisdictions with no possibility of sharing individual-level information. Here, we present key findings from requirements analysis and a resulting federated data analysis workflow built using open-source research softwar...
Article
Systematic review and meta-analysis constitute a staple of evidence-based medicine, an obligatory step in developing the guideline and recommendation document. It is a formalized process aiming at extracting and summarizing knowledge from the published work, grading, and considering the quality of the included studies. It is very laborious and time...
Article
Full-text available
COVID-19 has been associated with having a negative impact on patients’ gut microbiome during both active disease and in the post-acute phase. In acute COVID-19, rapid alteration of the gut microbiome composition was observed, showing on one side a reduction in beneficial symbionts (e.g., Roseburia, Lachnospiraceae) and on the other side an increas...
Chapter
Full-text available
Within the HORIZON 2020 project ORCHESTRA, patient data from numerous clinical studies in Europe related to COVID-19 were harmonized to create new knowledge on the disease. In this article, we describe the ecosystem that was established for the management of data collected and contributed by project partners. Study protocols elements were mapped to...
Article
Background: Lack of specific definitions of clinical characteristics, disease severity, and risk and preventive factors of post-COVID-19 syndrome (PCS) severely impacts research and discovery of new preventive and therapeutics drugs. Methods: This prospective multicenter cohort study was conducted from February 2020 to June 2022 in 5 countries,...
Article
Full-text available
Objective: Several studies showed the substantial use of antibiotics and increased risk of antimicrobial resistant infections in patients with COVID-19. The impact of COVID-19-related treatments and antibiotics on gut dysbiosis has not been clarified. Design: The prospective cohort study included hospitalized COVID-19 patients (April-December 20...
Article
Main aim of this systematic review is to quantify the risk and identify predictors of clinical evolution of SARS-CoV-2 in hematological patients compared to different control populations. Two independent reviewers screened the literature assessing clinical outcomes of SARS-CoV-2 infection in adult patients with active hematological malignancies pub...
Article
Full-text available
The COVID-19 pandemic saw a massive investment into collaborative research projects with a focus on producing data to support public health decisions. We relay our direct experience of four projects funded under the Horizon2020 programme, namely ReCoDID, ORCHESTRA, unCoVer and SYNCHROS. The projects provide insight into the complexities of sharing...
Article
Full-text available
Background International travel has been recognized as a risk factor contributing to the spread of antimicrobial resistance (AMR). However, tools focused on AMR in the context of international travel and designed to guide decision making are limited. We aimed at developing an evidence-based educational tool targeting both healthcare professionals (...
Article
Background A significant increased risk of complications and mortality in immunocompromised patients affected by COVID-19 has been described. However, the impact of COVID-19 in solid organ transplant (SOT) recipients is an issue still on debate, due to conflicting evidence emerged from different observational studies. Objective We performed a syst...
Article
Background The burden of bloodstream infections remains high worldwide and cannot be confined to short-term in-hospital mortality. We aimed to develop scores to predict short-term and long-term mortality in patients with bloodstream infections. Methods The Bloodstream Infection due to Multidrug-resistant Organisms: Multicenter Study on Risk Factor...
Article
Full-text available
Background Point-of-care tests could be essential in differentiating bacterial and viral acute community-acquired lower respiratory tract infections and driving antibiotic stewardship in community. Objectives To assess diagnostic test accuracy of point-of-care tests in community settings for acute community-acquired lower respiratory tract infecti...
Article
Full-text available
Background: A major limitation of current predictive prognostic models in patients with COVID-19 is the heterogeneity of population in terms of disease stage and duration. This study aims at identifying a panel of clinical and laboratory parameters that at day-5 of symptoms onset could predict disease progression in hospitalized patients with COVI...
Article
Full-text available
Objectives Optimal treatment of carbapenem-resistant Gram-negative (CR-GNB) infections is uncertain due to the lack of good-quality evidence and the limited effectiveness of available antibiotics. The aim of this survey was to investigate clinicians’ prescribing strategies for treating CR-GNB infections worldwide. Methods A 36-items-questionnaire...
Preprint
Full-text available
Background: A major limitation of current predictive prognostic models in patients with COVID-19 is the heterogeneity of population in terms of disease stage and duration. This study aims at identifying a panel of clinical and laboratory parameters that at day-5 of symptoms onset could predict disease progression in hospitalized patients with COVID...
Article
Background Management and control of coronavirus disease 2019 (COVID-19) relies on reliable diagnostic testing. Objectives To evaluate the diagnostic test accuracy (DTA) of nucleic acid amplification tests (NAATs) for the diagnosis of coronavirus infections. Data sources PubMed, Web of Science, the Cochrane Library, Embase, Open Grey and conferen...
Preprint
Motivation Antibiotic resistance is widely recognized as a severe threat to current medical practice. Each antibiotic therapy drives the emergence and subsequent retention of antibiotics resistance genes within the human gut microbiome. However, the details on how the resistance spreads between bacteria within the human gut remain unknown, as does...
Chapter
Full-text available
Metagenomics has become a part of the standard toolkit for scientists interested in studying microbes in the environment. Compared to 16S rDNA sequencing, which allows coarse taxonomic profiling of samples, shotgun metagenomic sequencing provides a more detailed analysis of the taxonomic and functional content of samples. Long read technologies, su...
Article
Objectives The aim of the study was to measure the impact of antibiotic exposure on the acquisition of colonization with extended-spectrum β-lactamase-producing Gram-negative bacteria (ESBL-GNB) accounting for individual- and group-level confounding using machine-learning methods. Methods Patients hospitalized between September 2010 and June 2013...
Article
Full-text available
Background Short-read sequencing technologies have long been the work-horse of microbiome analysis. Continuing technological advances are making the application of long-read sequencing to metagenomic samples increasingly feasible. Results We demonstrate that whole bacterial chromosomes can be obtained from an enriched community, by application of...
Preprint
Full-text available
Identification of modules in molecular networks is at the core of many current analysis methods in biomedical research. However, how well different approaches identify disease-relevant modules in different types of gene and protein networks remains poorly understood. We launched the “Disease Module Identification DREAM Challenge”, an open competiti...
Preprint
Full-text available
Background Short-read sequencing technologies have long been the work-horse of microbiome analysis. Continuing technological advances are making the application of long-read sequencing to metagenomic samples increasingly feasible. Results We demonstrate that whole bacterial chromosomes can be obtained from a complex community, by application of Mi...
Article
Full-text available
Background: There are numerous computational tools for taxonomic or functional analysis of microbiome samples, optimized to run on hundreds of millions of short, high quality sequencing reads. Programs such as MEGAN allow the user to interactively navigate these large datasets. Long read sequencing technologies continue to improve and produce incr...
Article
Bacterial viruses contribute to the dynamics of the microbiome communities, as they are involved in the horizontal gene transfer. Previously we studied changes in the gut microbiome of the two healthy individuals over the course of a 6-days antibiotics treatment and subsequent 28 days recovery time (Willmann et al., 2015). Now, from the same sample...
Article
Full-text available
Identification of modules in molecular networks is at the core of many current analysis methods in biomedical research. However, how well different approaches identify disease-relevant modules in different types of gene and protein networks remains poorly understood. We launched the “Disease Module Identification DREAM Challenge”, an open competiti...
Preprint
Full-text available
Background There are numerous computational tools for taxonomic or functional analysis of microbiome samples, optimized to run on hundreds of millions of short, high quality sequencing reads. Programs such as MEGAN allow the user to interactively navigate these large datasets. Long read sequencing technologies continue to improve and produce increa...
Article
Full-text available
In this work we report a detailed analysis of the topology and phylogenetics of family 2 glycoside hydrolases (GH2). We distinguish five topologies or domain architectures based on the presence and distribution of protein domains defined in Pfam and Interpro databases. All of them share a central TIM barrel (catalytic module) with two β-sandwich do...
Data
Phylogenetic analysis of the GH2C domain. The tree was generated as described in the legend of Fig 3, but including a tag for each sequence. The tag corresponds to the GI number and a descriptive legend of the corresponding domain architecture. In most cases, where the GH2N-GH2d-GH2C tandem is conserved, only the composition of the C-terminal domai...
Data
Structural superposition of the β-galactosidases from Thermotoga. maritima (TmLac) and Kluyveromyces lactis (KlLac). The structural model of TmLac (orange) was aligned with one of the subunits of KlLac (green, PDB code 3OB8). Residues contributing to the catalytic pocket are highlighted. (TIF)
Data
Domain architectures of all GH2 sequences analyzed in this study. Sequences are classified according to DA type. Each sequence is identified by the GI number and Accession number from Genbank, EMBL or DDBJ databases. The specific domain architecture, organism of origin (source) and Genbank definition is shown. Biochemical characterization, as recor...
Data
Cluster and subcluster classification of DA type 5 proteins with unidentified C-terminal extensions. (DOCX)
Data
Pipeline followed for the analysis of GH2 domain architectures and phylogenetic tree construction. (TIF)
Data
Summary of Genbank annotations and biochemical characterization, as recorded in the CAZy database, of enzyme activity for each DA type. (DOCX)
Data
Cluster and subcluster classification of DA type 4 proteins. (DOCX)
Data
Binary vectors assigned to each sequence to describe the different domain architectures. Sheet S1.1 specifies the Pfam domain assigned to each position in the binary vector. Each Pfam code is followed by an underscore symbol and a number to indicate the presence of tandem repeats when necessary. Sheet S1.2 indicates the binary vector that correspon...
Article
The bacterial ribosome has many functional ribosomal RNA (rRNA) sites. We have computationally analyzed the rRNA regions involved in the interactions between the 30S and 50S subunits. Various properties of rRNA such as solvent accessibility, opening energy, hydrogen bonding pattern, van der Waals energy, thermodynamic stability were determined. Bas...
Preprint
Full-text available
The Tübiom project is a community-based project aimed at constructing a large, representative reference database of human gut microbiome profiles. The goal is to collect 10 000 profiles, along with detailed metadata on each participants health and lifestyle. All samples will be processed using identical sequencing and analysis protocols to ensure c...
Preprint
Full-text available
The Tübiom project is a community-based project aimed at constructing a large, representative reference database of human gut microbiome profiles. The goal is to collect 10 000 profiles, along with detailed metadata on each participants health and lifestyle. All samples will be processed using identical sequencing and analysis protocols to ensure c...
Article
Full-text available
There is increasing interest in employing shotgun sequencing, rather than amplicon sequencing, to analyze microbiome samples. Typical projects may involve hundreds of samples and billions of sequencing reads. The comparison of such samples against a protein reference database generates billions of alignments and the analysis of such data is computa...
Article
We have designed a protocol and server to aid in the search for putative binding sites in 16S ribosomal RNA (16S rRNA) that could be targeted by peptide nucleic acid oligomers. Various features of 16S rRNA were considered to score its regions as potential targets for sequence-specific binding that could result in inhibition of ribosome function. Sp...
Article
Full-text available
Structural biology experiments and structure prediction tools have provided many high-resolution three-dimensional structures of nucleic acids. Also, molecular dynamics force field parameters have been adapted to simulating charged and flexible nucleic acid structures on microsecond time scales. Therefore, we can generate the dynamics of DNA or RNA...

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