A5031461537- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- SARS-CoV-2 and COVID-19 Research
- Cancer Immunotherapy and Biomarkers
- Gene Regulatory Network Analysis
- Single-cell and spatial transcriptomics
- Trace Elements in Health
- MicroRNA in disease regulation
- Genomics and Chromatin Dynamics
- COVID-19 Clinical Research Studies
- Cancer Genomics and Diagnostics
- Computational Drug Discovery Methods
- RNA modifications and cancer
- interferon and immune responses
- Neuroblastoma Research and Treatments
- Ferroptosis and cancer prognosis
- Epigenetics and DNA Methylation
- Plant Stress Responses and Tolerance
- Plant Molecular Biology Research
- Radiopharmaceutical Chemistry and Applications
- Cancer-related molecular mechanisms research
- Plant Gene Expression Analysis
- Protein Degradation and Inhibitors
- Histone Deacetylase Inhibitors Research
- Immune cells in cancer
University of Bologna
2018-2025
Max Planck Institute of Molecular Plant Physiology
2009-2024
University of Cambridge
2017-2024
Cancer Research UK
2017-2024
Scripps Research Institute
2023
University of Rome Tor Vergata
2023
Children's Cancer Institute Australia
2020
UNSW Sydney
2020
University of Namur
2020
Zambon (Italy)
2019
The novel respiratory disease COVID-19 has reached the status of worldwide pandemic and large efforts are currently being undertaken in molecularly characterizing virus causing it, SARS-CoV-2. genomic variability SARS-CoV-2 specimens scattered across globe can underly geographically specific etiological effects. In present study, we gather 48,635 complete genomes available thanks to collection endeavor GISAID consortium thousands contributing laboratories. We analyzed annotated all mutations...
Next Generation Sequencing is having an extremely strong impact in biological and medical research diagnostics, with applications ranging from gene expression quantification to genotyping genome reconstruction. data often provided as raw reads which are processed prior analysis 1 of the most used preprocessing procedures read trimming, aims at removing low quality portions while preserving longest high part a NGS read. In current work, we evaluate nine different trimming algorithms four...
There is a rising global concern for the recently emerged novel coronavirus (2019-nCoV). Full genomic sequences have been released by worldwide scientific community in last few weeks to understand evolutionary origin and molecular characteristics of this virus. Taking advantage all information currently available, we constructed phylogenetic tree including also representatives other coronaviridae, such as Bat (BCoV) severe acute respiratory syndrome. We confirm high sequence similarity...
The accurate reconstruction of gene regulatory networks from large scale molecular profile datasets represents one the grand challenges Systems Biology. Algorithm for Reconstruction Accurate Cellular Networks (ARACNe) most effective tools to accomplish this goal. However, initial Fixed Bandwidth (FB) implementation is both inefficient and unable deal with sample sets providing largely uneven coverage probability density space. Here, we present a completely new algorithm, based on an Adaptive...
The AP2/ERF protein family contains transcription factors that play a crucial role in plant growth and development response to biotic abiotic stress conditions plants. Grapevine (Vitis vinifera) is the only woody crop whose genome has been fully sequenced. So far, no detailed expression profile of AP2/ERF-like genes available for grapevine. An exhaustive search was carried out on Vitis vinifera their analyzed by Real-Time quantitative PCR (qRT-PCR) different vegetative reproductive tissues...
Abstract The model organism Arabidopsis thaliana is readily used in basic research due to resource availability and relative speed of data acquisition. A major goal transfer acquired knowledge from crop species. However, the identification functional equivalents well-characterized genes other plants a nontrivial task. It well documented that transcriptionally coordinated tend be functionally related such relationships may conserved across different species even kingdoms. To exploit...
Abstract Therapeutic checkpoint antibodies blocking programmed death receptor 1/programmed ligand 1 (PD-L1) signaling have radically improved clinical outcomes in cancer. However, the regulation of PD-L1 expression on tumor cells is still poorly understood. Here we show that intratumoral copper levels influence cancer cells. Deep analysis The Cancer Genome Atlas database and tissue microarrays showed strong correlation between major influx transporter (CTR-1) across many cancers but not...
The recent epidemic outbreak of a novel human coronavirus called SARS-CoV-2 causing the respiratory tract disease COVID-19 has reached worldwide resonance and global effort is being undertaken to characterize molecular features evolutionary origins this virus. In paper, we set out shed light on SARS-CoV-2/host receptor recognition, crucial factor for successful virus infection. Based current knowledge interactome between host cell proteins, performed Master Regulator Analysis detect which...
Several severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have emerged, posing a renewed threat to disease 2019 containment and vaccine drug efficacy. In this study, we analyzed more than 1,000,000 SARS-CoV-2 genomic sequences deposited up April 27, 2021, on the GISAID public repository, identified novel T478K mutation located Spike protein. The is structurally in region of interaction with human receptor ACE2 was detected 11,435 distinct cases. We show that has appeared...
The COVID-19 virus has spread worldwide in a matter of few months, while healthcare systems struggle to monitor and report current cases. Testing results have struggled with the relative capabilities, testing policies preparedness each affected country, making their comparison non-trivial task. Since severe cases, which more likely lead fatal outcomes, are detected at higher rate than mild reported mortality is inflated most countries. Lockdowns changes human behavior modulate underlying...
MYCN regulates polyamines in neuroblastoma, and combined inhibition of polyamine synthesis transport has therapeutic effects mouse models.
Abstract Motivation: Coexpression networks are data-derived representations of genes behaving in a similar way across tissues and experimental conditions. They have been used for hypothesis generation guilt-by-association approaches inferring functions previously unknown genes. So far, the main platform expression data has DNA microarrays; however, recent development RNA-seq allows higher accuracy coverage transcript populations. It is therefore important to assess potential biological...
The avalanche of genomic data generated from the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus requires development tools to detect and monitor its mutations across world. Here, we present a webtool, coronapp, dedicated easily processing user-provided SARS-CoV-2 sequences visualizing current worldwide status mutations. webtool allows users highlight categorize them by frequency, country, location effect on protein sequences, their presence in population over time. tool...
SARS-CoV-2 entry in human cells is mediated by the interaction between viral Spike protein and ACE2 receptor. This mechanism evolved from ancestor bat coronavirus currently one of main targets for antiviral strategies. However, there exist several variants population as result mutations, it unclear if these may exert a specific effect on affinity with which, turn, also characterized multiple alleles population. In current study, GBPM analysis, originally developed highlighting host-guest...
The Mpox (formerly named Monkeypox) virus is the etiological cause of a recent multi-country outbreak, with thousands distinct cases detected outside endemic areas Africa as December 2023. In this article, we analyze sequences full genomes from Europe and compare them all available historical relevance, annotated by year geographic origin, well related Cowpox Variola (smallpox) sequences. Our results show that outbreak most likely originating West African clade Mpox, >99 % sequence identity...
Abstract The wide application of high-throughput transcriptomics using microarrays has generated a plethora technical platforms, data repositories, and sophisticated statistical analysis methods, leaving the individual scientist with problem choosing appropriate approach to address biological question. Several software applications that provide rich environment for microarray storage are available (e.g. GeneSpring, EMMA2), but these mostly commercial or require an advanced informatics...
While Brachypodium distachyon (Brachypodium) is an emerging model for grasses, no expression atlas or gene coexpression network available. Such tools are of high importance to provide insights into the function genes. We present a detailed atlas, capturing in its major organs at different developmental stages. The data were integrated large-scale database ( www.gene2function.de), enabling identification duplicated pathways and conserved processes across 10 plant species, thus allowing...