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Daniel Remondini

Daniel Remondini
University of Bologna, Bologna, Italy · DIFA Department of Physics and Astronomy

Professor

About

277
Publications
26,646
Reads
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3,114
Citations
Introduction
Systems Biology approaches based on Network Theory and Statistical Mechanics for multiple omics data analysis and biological systems modelling. Cell mechanisms, cancer and ageing are the most targeted topics of my research.
Additional affiliations
September 2014 - present
University of Bologna
Position
  • Lecturer
Description
  • Applied Physics for Radiologist; Applied Physics for Nursing
September 2008 - present
University of Bologna
Position
  • Lecturer
Description
  • Complex Networks for Master Degree in Physics
October 2007 - September 2014
University of Bologna
Position
  • Research Assistant

Publications

Publications (277)
Preprint
One of the main objectives of high-throughput genomics studies is to obtain a low-dimensional set of observables - a signature - for sample classification purposes (diagnosis, prognosis, stratification). We propose DNetPRO, Discriminant Analysis with Network PROcessing, a supervised network-based signature identification method. The algorithm is ea...
Article
Full-text available
Background: Radiomics is a field of research medicine and data science in which quantitative imaging features are extracted from medical images and successively analyzed to develop models for providing diagnostic, prognostic, and predictive information. The purpose of this work was to develop a machine learning model to predict the survival probabi...
Article
Full-text available
Campylobacter spp. are a leading and increasing cause of gastrointestinal infections worldwide. Source attribution, which apportions human infection cases to different animal species and food reservoirs, has been instrumental in control- and evidence-based intervention efforts. The rapid increase in whole-genome sequencing data provides an opportun...
Preprint
The characterization of bacterial communities that colonize a biological ecosystem is crucial for both the monitoring of infections and epidemics and the study of the health of organisms that live in a symbiotic relationship with bacteria. This is the case of humans, for which the connection between health and microbiota is now well established. To...
Article
Full-text available
Purpose: In this work, we propose an implementation of the Bienenstock–Cooper–Munro (BCM) model, obtained by a combination of the classical framework and modern deep learning methodologies. The BCM model remains one of the most promising approaches to modeling the synaptic plasticity of neurons, but its application has remained mainly confined to n...
Article
Full-text available
Background: Rectal cancer is a malignant neoplasm of the large intestine resulting from the uncontrolled proliferation of the rectal tract. Predicting the pathologic response of neoadjuvant chemoradiotherapy at an MRI primary staging scan in patients affected by locally advanced rectal cancer (LARC) could lead to significant improvement in the sur...
Article
Full-text available
Aim: The aim of this study was to develop robust prognostic models for mortality prediction of COVID-19 patients, applicable to different sets of real scenarios, using radiomic and neural network features extracted from chest X-rays (CXRs) with a certified and commercially available software. Methods: 1816 patients from 5 different hospitals in the...
Article
Magnetic resonance fingerprinting (MRF) is a rapidly developing approach for fast quantitative MRI. A typical drawback of dictionary-based MRF is an explosion of the dictionary size as a function of the number of reconstructed parameters, according to the "curse of dimensionality", which determines an explosion of resource requirements. Neural netw...
Article
WISDoM (Wishart Distributed Matrices) is a framework for the quantification of symmetric positive-definite matrices such as covariance or correlation matrices, with respect to ones governed by the Wishart distribution. WISDoM can be applied to tasks of supervised learning also starting from data of different dimensionality (e.g., time series with s...
Article
It is important that antibiotics prescriptions are based on antimicrobial susceptibility data to ensure effective treatment outcomes. The increasing availability of next-generation sequencing, bacterial whole genome sequencing (WGS) can facilitate a more reliable and faster alternative to traditional phenotyping for the detection and surveillance o...
Article
Full-text available
COVID-19 represents the most severe global crisis to date whose public conversation can be studied in real time. To do so, we use a data set of over 350 million tweets and retweets posted by over 26 million English speaking Twitter users from January 13 to June 7, 2020. We characterize the retweet network to identify spontaneous clustering of users...
Article
Full-text available
Although targeting of cell metabolism is a promising therapeutic strategy in acute myeloid leukemia (AML), metabolic dependencies are largely unexplored. We aimed to classify AML patients based on their metabolic landscape and map connections between metabolic and genomic profiles. Combined serum and urine metabolomics improved AML characterization...
Article
Full-text available
Background and aim: A previously unseen body of scientific knowledge of varying quality has been produced during the ongoing COVID-19 pandemic. It has proven extremely difficult to navigate for experts and laymen alike, originating a phenomenon described as "Infodemic", a breeding ground for misinformation. This has a potential impact on vaccine h...
Article
Full-text available
Among the mechanisms leading to progression to Adult T-cell Leukaemia/Lymphoma in Human T-cell Leukaemia Virus type 1 (HTLV-1)-infected subjects, the contribution of stromal components remains poorly understood. To dissect the role of fibroblasts in HTLV-1-mediated lymphomagenesis, transcriptome studies, cytofluorimetric and qRT-PCR analyses of sur...
Article
Full-text available
MR fingerprinting (MRF) is an innovative approach to quantitative MRI. A typical disadvantage of dictionary-based MRF is the explosive growth of the dictionary as a function of the number of reconstructed parameters, an instance of the curse of dimensionality, which determines an explosion of resource requirements. In this work, we describe a deep...
Article
Many efforts have been carried out for the standardization of multiparametric Magnetic Resonance (mp-MR) images evaluation to detect Prostate Cancer (PCa), and specifically to differentiate levels of aggressiveness, a crucial aspect for clinical decision-making. Prostate Imaging—Reporting and Data System (PI-RADS) has contributed noteworthily to th...
Article
Protein structure characterization is fundamental to understand protein properties, such as folding process and protein resistance to thermal stress, up to unveiling organism pathologies (e.g., prion disease). In this chapter, we provide an overview on how the spectral properties of the networks reconstructed from the Protein Contact Map (PCM) can...
Article
Full-text available
An amendment to this paper has been published and can be accessed via the original article.
Article
Full-text available
The complex web of macromolecular interactions occurring within cells-the interactome-is the backbone of an increasing number of studies, but a clear consensus on the exact structure of this network is still lacking. Different genome-scale maps of human interactome have been obtained through several experimental techniques and functional analyses....
Article
Full-text available
Autism spectrum disorders (ASDs) are a heterogeneous group of neurodevelopmental conditions characterized by impairments in social interaction and communication and restricted patterns of behavior, interests, and activities. Although the etiopathogenesis of idiopathic ASD has not been fully elucidated, compelling evidence suggests an interaction be...
Article
Full-text available
While the SARS-CoV-2 pandemic continues to strike and collect its death toll throughout the globe, as of 31 January 2021, the vaccine candidates worldwide were 292, of which 70 were in clinical testing. Several vaccines have been approved worldwide, and in particular, three have been so far authorized for use in the EU. Vaccination can be, in fact,...
Article
Full-text available
Background Current high-throughput technologies—i.e. whole genome sequencing, RNA-Seq, ChIP-Seq, etc.—generate huge amounts of data and their usage gets more widespread with each passing year. Complex analysis pipelines involving several computationally-intensive steps have to be applied on an increasing number of samples. Workflow management syste...
Article
Full-text available
In this paper we compared taxonomic results obtained by metataxonomics (16S rRNA gene sequencing) and metagenomics (whole shotgun metagenomic sequencing) to investigate their reliability for bacteria profiling, studying the chicken gut as a model system. The experimental conditions included two compartments of gastrointestinal tracts and two sampli...
Article
PURPOSE Recurrently mutated genes and chromosomal abnormalities have been identified in myelodysplastic syndromes (MDS). We aim to integrate these genomic features into disease classification and prognostication. METHODS We retrospectively enrolled 2,043 patients. Using Bayesian networks and Dirichlet processes, we combined mutations in 47 genes w...
Article
Full-text available
WISDoM (Wishart Distributed Matrices) is a framework for the quantification of deviation of symmetric positive-definite matrices associated with experimental samples, such as covariance or correlation matrices, from expected ones governed by the Wishart distribution. WISDoM can be applied to tasks of supervised learning, like classification, in par...
Preprint
Full-text available
COVID-19 represents the most severe global crisis to date whose public conversation can be studied in real time. To do so, we use a data set of over 350 million tweets and retweets posted by over 26 million English speaking Twitter users from January 13 to June 7, 2020. In characterizing the complex retweet network, we identify several stable commu...
Article
Full-text available
Photoplethysmography (PPG) measured by smartphone has the potential for a large scale, non-invasive, and easy-to-use screening tool. Vascular aging is linked to increased arterial stiffness, which can be measured by PPG. We investigate the feasibility of using PPG to predict healthy vascular aging (HVA) based on two approaches: machine learning (ML...
Article
Full-text available
In this work we propose an index to estimate the gut microbiota biodiversity using a modeling approach with the aim of describing its relationship with health and aging. The gut microbiota, a complex ecosystem that links nutrition and metabolism, has a pervasive effect on all body organs and systems, undergoes profound changes with age and life-sty...
Article
Full-text available
It is important that antibiotics prescriptions are based on antimicrobial susceptibility data to ensure effective treatment outcomes. The increasing availability of next-generation sequencing, bacterial whole genome sequencing (WGS) can facilitate a more reliable and faster alternative to traditional phenotyping for the detection and surveillance o...
Conference Paper
Lung cancer is the main cause of cancer-related mortality worldwide. Despite the availability of different therapeutic options, including chemotherapy, target therapy, and immunotherapy, prognosis for lung cancer patients remains poor. Among innovative therapeutic approaches, inhibitors of the bromodomain and extraterminal domain containing protein...
Conference Paper
Full-text available
Non-contact galvanotaxis as a way to drive the cells migration could be a promising tool for a variety of biomedical applications, such as wound healing control, avoiding the interaction between electrodes and cell cultures. To this regard, the efficacy of this electrical stimulus application has to be deeper studied to control physiological migrat...
Article
Full-text available
Salmonella enterica subspecies enterica serovar Typhimurium and its monophasic variant are among the most common Salmonella serovars associated with human salmonellosis each year. Related infections are often due to consumption of contaminated meat of pig, cattle, and poultry origin. In order to evaluate novel microbial subtyping methods for source...
Preprint
Photoplethysmography (PPG) measured by smartphone has the potential for a large scale, non-invasive, and easy-to-use screening tool. Vascular ageing is linked to increased arterial stiffness, which can be measured by PPG. We investigate the feasibility of using PPG to predict healthy vascular ageing (HVA) based on two approaches: machine learning (...
Preprint
Full-text available
Genome organization in eukaryotes during interphase stems from the delicate balance between non-random correlations present in the DNA polynucleotide linear sequence and the physico/chemical reactions which shape continuously the form and structure of DNA and chromatin inside the nucleus of the cell. It is now clear that these mechanisms have a key...
Preprint
Full-text available
Background: Current high-throughput technologies - i.e. Whole Genome Sequencing (WGS), RNA-Seq, ChIP-Seq, etc. - generate huge amounts of data and their usage gets more widespread with each passing year. Complex analysis pipelines involving several computationally-intensive steps have to be applied on an increasing number of samples. Workflow Manag...
Article
Full-text available
Paratuberculosis or Johne’s disease in cattle is a chronic granulomatous gastroenteritis caused by infection with Mycobacterium avium subspecies paratuberculosis (MAP). Paratuberculosis is not treatable; therefore, the early identification and isolation of infected animals is a key point to reduce its incidence. In this paper, we analyse RNAseq exp...
Preprint
WISDoM (Wishart Distributed Matrices) is a new framework for the characterization of symmetric positive-definite matrices associated to experimental samples, like covariance or correlation matrices, based on the Wishart distribution as a null model. WISDoM can be applied to tasks of supervised learning, like classification, even when such matrices...
Article
Background: Elevated peripheral levels of different cytokines and chemokines in subjects with Alzheimer's disease (AD), as compared with healthy controls (HC), have emphasized the role of inflammation in such a disease. Considering the cross-talking between the central nervous system and the periphery, the inflammatory analytes may provide utility...
Preprint
Full-text available
A possible way to tackle the crisis of antimicrobial resistance development is a strict policy when prescribing antibiotics. Thus, it is important that prescriptions are based on antimicrobial susceptibility data to ensure effective treatment outcomes. The increasing availability of next-generation sequencing (NGS), bacterial whole genome sequencin...
Article
Full-text available
Inhibitors of BET proteins (BETi) are anti-cancer drugs that have shown efficacy in pre-clinical settings and are currently in clinical trials for different types of cancer, including non-small cell lung cancer (NSCLC). Currently, no predictive biomarker is available to identify patients that may benefit from this treatment. To uncover the mechanis...
Article
Genome organization in eukaryotes during interphase stems from the delicate balance between non-random correlations present in the DNA polynucleotide linear sequence and the physico/chemical reactions which shape continuously the form and structure of DNA and chromatin inside the nucleus of the cell. It is now clear that these mechanisms have a key...
Article
Full-text available
In this study three DNA extraction procedures, two library preparation protocols and two sequencing platforms were applied to analyse six bacterial cultures and their corresponding DNA obtained as part of a proficiency test. The impact of each variable on sequencing results was assessed using the following parameters: reads quality, assembly and al...
Preprint
Full-text available
The objective of many high-throughput "omics" studies is to obtain a relatively low-dimensional set of observables - signature - for sample classification purposes (diagnosis, prognosis, stratification). We propose DNetPRO, Discriminant Analysis with Network PROcessing, a supervised signature identification method based on a bottom-up combinatorial...
Conference Paper
Genomic and functional alterations of enzymatic activity drive cancer metabolic reprogramming along with mutations of tumor suppressors and oncogenes. IDH1/2 lesions represent a paradigmatic example in acute myeloid leukemia (AML). The study aimed to stratify AML patients based on their metabolic landscape and to map potential connections between t...
Conference Paper
Background: The genetically heterogeneous and poor survival group of Philadelphia negative (Ph-) B-ALL group that doesn’t have the most recurrent adult rearrangements (t(9;22); t(1;19); t(4;11)) is collectively referred to as “triple negative” (Ph-/-/-). is frequently altered in adult B-ALL, especially in Ph-like pts (50-75% of cases). Alterations...
Conference Paper
Genomic and functional alterations of enzymatic activity drive cancer metabolic reprogramming along with mutations of tumor suppressors and oncogenes. IDH1/2 lesions represent a paradigmatic example in acute myeloid leukemia (AML). The study aimed to stratify AML patients based on their metabolic landscape and to map potential connections between t...
Poster
The adult “triple negative” [Ph-/-/-; neg for t(9;22); t(1;19); t(4;11); 61% of adult B-ALL (Roberts KG et al., JCO. 2017)] B-ALL group is characterized by an high genetic heterogeneity and poor survival. Many very low freq subgroups have been recently distinguished in a very large international cohort of pts (Gu Z, NatGenet. 2019); identified them...
Poster
The adult “triple negative” [Ph-/-/-; neg for t(9;22); t(1;19); t(4;11); 61% of adult B-ALL (Roberts KG et al., JCO. 2017)] B-ALL group is characterized by an high genetic heterogeneity and poor survival. Many very low freq subgroups have been recently distinguished in a very large international cohort of pts (Gu Z, NatGenet. 2019); identified them...
Poster
Background Primary chemo-refractory disease and relapse are the most important causes of mortality in acute myeloid leukemia (AML) patients (Döhner et al., N. Engl. J. Med. 2015). Leukemia stem cells (LSCs) are likely responsible for disease relapse (Guzman et al., Blood 2007). Several genomic studies of newly-diagnosed and relapsed AML have reveal...
Poster
Background An expanding body of evidence indicates that targeting cell metabolism is a promising therapeutic strategy in acute myeloid leukemia (AML). Pyrimidine biosynthesis, oxidative phosphorylation, amino acid and arginine metabolism are among the most relevant actionable pathways (Sykes et al. Cell 2016; Molina et al. Nat Med 2018; Jones et al...