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Graph analytics for phenome-genome associations inference [article]

Davide Cirillo, Dario Garcia-Gasulla, Ulises Cortés, Alfonso Valencia
2019 bioRxiv   pre-print
We utilized human physical protein-protein interactions experimentally verified by colocalization, co-purification, FRET, and two-hybrid assays (Cirillo et al. Nucleic Acids Res. 2015) .  ... 
doi:10.1101/682229 fatcat:pj44bi5hozb2pc7h7trpusfoqe

Quantum Coherence in Loopless Superconductive Networks [article]

Massimiliano Lucci, Davide Cassi, Vittorio Merlo, Francesco Romeo, Gaetano Salina, Matteo Cirillo
2022 arXiv   pre-print
Measurements indicating that planar networks of superconductive islands connected by Josephson junctions display long range quantum coherence are reported. The networks consist of superconducting islands connected by Josephson junctions and have a tree-like topological structure containing no loops. Enhancements of superconductive gap over specific branches of the networks and sharp increases of pair currents are the main signatures of the coherent states and, in order to unambiguously
more » ... the observed effects to branches being embedded in the networks, comparisons with geometrically equivalent, but isolated, counterparts are reported. Tuning the Josephson coupling energy by an external magnetic field generates increases of the Josephson currents, along the above mentioned specific branches, which follow a functional dependence typical of phase transitions. Results are presented for double comb and star geometry networks and in both cases the observed effects provide positive quantitative evidence of the predictions of existing theoretical models.
arXiv:2203.05895v1 fatcat:i7sx3c5qeverzof3o2omejkdjm

Discovery of protein–RNA networks

Davide Cirillo, Carmen Maria Livi, Federico Agostini, Gian Gaetano Tartaglia
2014 Molecular Biosystems  
We review the latest advances and future challenges in experimental and computational investigation of protein–RNA networks.
doi:10.1039/c4mb00099d pmid:24756571 fatcat:hmdr6ox7yjdybgthvcqvf5i3k4

The multilayer community structure of medulloblastoma

Iker Núñez-Carpintero, Marianyela Petrizzelli, Andrei Zinovyev, Davide Cirillo, Alfonso Valencia
2021 iScience  
Resource availability Lead contact Further information and requests for resources and reagents should be directed to and will be fulfilled by the lead contact, Davide Cirillo (davide.cirillo@bsc.es).  ... 
doi:10.1016/j.isci.2021.102365 pmid:33889829 pmcid:PMC8050854 fatcat:6se42hrzebgg5p52xtoc472vmm

Neurodegeneration and Cancer: Where the Disorder Prevails

Petr Klus, Davide Cirillo, Teresa Botta Orfila, Gian Gaetano Tartaglia
2015 Scientific Reports  
It has been reported that genes up-regulated in cancer are often down-regulated in neurodegenerative disorders and vice versa. The fact that apparently unrelated diseases share functional pathways suggests a link between their etiopathogenesis and the properties of molecules involved. Are there specific features that explain the exclusive association of proteins with either cancer or neurodegeneration? We performed a large-scale analysis of physico-chemical properties to understand what
more » ... ristics differentiate classes of diseases. We found that structural disorder significantly distinguishes proteins up-regulated in neurodegenerative diseases from those linked to cancer. We also observed high correlation between structural disorder and age of onset in Frontotemporal Dementia, Parkinson's and Alzheimer's diseases, which strongly supports the role of protein unfolding in neurodegenerative processes. It has been reported that tumor suppressor p53 has physico-chemical features that are typical of prionoid proteins associated with neurodegenerative diseases 1 . This finding is particularly interesting because it suggests that common molecular properties can be linked to relatively distant diseases. As a matter of fact, a recent study by Ibáñez et al. 2 shows that transcripts up-regulated in cancer are down-regulated in central nervous system (CNS) diseases and vice versa. In line with this finding, a risk reduction for some cancer types has been observed in patients affected by Parkinson's 3 and Alzheimer's diseases 4 . Are there common physico-chemical determinants behind comorbidities? We re-analysed the data published by Ibáñez et al. 2 to understand if differential regulation of genes can be associated with specific protein features. While the original study by Ibáñez et al. 2 focused on transcripts that are exclusively up-regulated in cancer and down-regulated in CNS diseases and vice versa 2 , our analysis deals with genes that are exclusively associated with either CNS diseases or cancer (Fig. 1 ). In agreement with recent experimental findings 5 and theoretical analyses 6-9 , we investigated the physico-chemical properties of gene products assuming a proportionality between transcript and protein abundances.
doi:10.1038/srep15390 pmid:26493371 pmcid:PMC4615981 fatcat:fogi353a4ngatdnxv2ord6vewq

New Nanocatalyst for Vocs Removal from Recycled Plastics

Maria Sarno, Davide Scarpa, Claudia Cirillo, Carmela Scudieri
2019 Chemical Engineering Transactions  
Graphene-based supports for catalysis are currently attracting great attention due to their unique and advantageous properties. However, their application in gas-phase thermal catalysis including catalytic oxidation of volatile organic compounds (VOCs) remains a theoretical research stage. Here, a new use of a graphene-based material as a catalyst support for 2-ethyl-1-hexanol (2-EH) oxidation was developed. The design of CuO/Ag catalyst incorporated into the porous structure of reduced
more » ... oxide aerogel (rGOA) exposes more active surface for catalysis. Therefore, this hybrid design enables great performance enhancements in 2-EH oxidation, displaying a ( 99% removal at a temperature of 350 °C. Highly stable performance and excellent recycling ability are observed over CuO/Ag-rGOA dual function adsorbent-catalyst material. The high activity and good stability of CuO/Ag-rGOA make it an excellent candidate for the development of 2-EH oxidation catalysis.
doi:10.3303/cet1973020 doaj:c9302483c02844b9b48f0c976e0650ff fatcat:efb7x6pvezedtmoqrbiyxjhpra

Algorithmic complexity in computational biology: basics, challenges and limitations [article]

Davide Cirillo, Miguel Ponce-de-Leon, Alfonso Valencia
2021 arXiv   pre-print
Computational problems can be classified according to their algorithmic complexity, which is defined based on how the resources needed to solve the problem, e.g. the execution time, scale with the problem size. Many problems in computational biology are computationally infeasible in the sense that the exhaustive search for the optimal solution is prohibitive in practical terms. As a consequence, these problems are tackled through heuristics and approximations aiming to overcome the exceeding
more » ... putational requirements at the cost of providing suboptimal solutions. The importance of defining the computational complexity of computational biology algorithms is a topic rarely surveyed for broad audiences of bioinformaticians and users of bioinformatics tools. However, recognizing the underlying complexity of any algorithm is essential for understanding their potential and limitations. Thus, the aim of this review is to survey the main algorithmic solutions to intractable problems in computational biology, highlighting the importance of High-Performance Computing in this area.
arXiv:1811.07312v2 fatcat:f6qnbrilnrh3zomveqptsjbbju

Predictions of protein-RNA interactions

Davide Cirillo, Federico Agostini, Gian Gaetano Tartaglia
2012 Wiley Interdisciplinary Reviews. Computational Molecular Science  
Ribonucleoprotein interactions play important roles in a wide variety of cellular processes, ranging from transcriptional and posttranscriptional regulation of gene expression to host defense against pathogens. High throughput experiments to identify RNA-protein interactions provide information about the complexity of interaction networks, but require time and considerable efforts. Thus, there is need for reliable computational methods for predicting ribonucleoprotein interactions. In this
more » ... w, we discuss a number of approaches that have been developed to predict the ability of proteins and RNA molecules to associate.
doi:10.1002/wcms.1119 fatcat:czvefpj6nrfelhgwyfe4a64oui

SeAMotE: a method for high-throughput motif discovery in nucleic acid sequences

Federico Agostini, Davide Cirillo, Riccardo Ponti, Gian Tartaglia
2014 BMC Genomics  
The large amount of data produced by high-throughput sequencing poses new computational challenges. In the last decade, several tools have been developed for the identification of transcription and splicing factor binding sites. Results: Here, we introduce the SeAMotE (Sequence Analysis of Motifs Enrichment) algorithm for discovery of regulatory regions in nucleic acid sequences. SeAMotE provides (i) a robust analysis of high-throughput sequence sets, (ii) a motif search based on pattern
more » ... nces and (iii) an easy-to-use web-server interface. We applied our method to recently published data including 351 chromatin immunoprecipitation (ChIP) and 13 crosslinking immunoprecipitation (CLIP) experiments and compared our results with those of other well-established motif discovery tools. SeAMotE shows an average accuracy of 80% in finding discriminative motifs and outperforms other methods available in literature. Conclusions: SeAMotE is a fast, accurate and flexible algorithm for the identification of sequence patterns involved in protein-DNA and protein-RNA recognition. The server can be freely accessed at http://s.tartaglialab.com/ new_submission/seamote.
doi:10.1186/1471-2164-15-925 pmid:25341390 pmcid:PMC4223730 fatcat:ywfaywlgmjfgfjhpu3hyivbufi

omiXcore: a web server for prediction of protein interactions with large RNA

Alexandros Armaos, Davide Cirillo, Gian Gaetano Tartaglia, Ivo Hofacker
2017 Bioinformatics  
., 2011) , we developed the uniform fragmentation procedure to predict interaction propensities between protein and RNA fragments (Cirillo et al., 2017) .  ...  The uniform fragmentation approach is based on the division of protein and RNA sequences into overlapping segments [100 fragments for each molecule] (Cirillo et al., 2013) .  ... 
doi:10.1093/bioinformatics/btx361 pmid:28637296 pmcid:PMC5870566 fatcat:drqnf7nfmbdchjweepm6zxk6tq

Josephson Currents and Gap Enhancement in Graph Arrays of Superconductive Islands

Massimiliano Lucci, Davide Cassi, Vittorio Merlo, Roberto Russo, Gaetano Salina, Matteo Cirillo
2021 Entropy  
The Nobel prize awarded in 2016 to David J. Thouless, F. Duncan M. Haldane, and J.  ... 
doi:10.3390/e23070811 fatcat:jgbdzqbth5a5jlmzrsk27jocbu

Artificial Intelligence in Cancer Research: learning at different levels of data granularity

Davide Cirillo, Iker Núñez-Carpintero, Alfonso Valencia
2021 Molecular Oncology  
Cirillo et al. Molecular Oncology (2021) ª 2021 The Authors. Molecular Oncology published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.  ... 
doi:10.1002/1878-0261.12920 pmid:33533192 pmcid:PMC8024732 fatcat:likwa6lztnfe3kqlkeqfqzlaje

Constitutive patterns of gene expression regulated by RNA-binding proteins

Davide Cirillo, Domenica Marchese, Federico Agostini, Carmen Livi, Teresa Botta-Orfila, Gian Tartaglia
2014 Genome Biology  
RNA-binding proteins regulate a number of cellular processes, including synthesis, folding, translocation, assembly and clearance of RNAs. Recent studies have reported that an unexpectedly large number of proteins are able to interact with RNA, but the partners of many RNA-binding proteins are still uncharacterized. Results: We combined prediction of ribonucleoprotein interactions, based on catRAPID calculations, with analysis of protein and RNA expression profiles from human tissues. We found
more » ... trong interaction propensities for both positively and negatively correlated expression patterns. Our integration of in silico and ex vivo data unraveled two major types of protein-RNA interactions, with positively correlated patterns related to cell cycle control and negatively correlated patterns related to survival, growth and differentiation. To facilitate the investigation of protein-RNA interactions and expression networks, we developed the catRAPID express web server. Conclusions: Our analysis sheds light on the role of RNA-binding proteins in regulating proliferation and differentiation processes, and we provide a data exploration tool to aid future experimental studies.
doi:10.1186/gb-2014-15-1-r13 pmid:24401680 pmcid:PMC4054784 fatcat:p77jtib3ybcxbo24vthhxd53uq

Functionalized carbon nanotubes as transporters for antisense oligodeoxynucleotides

Anika Kaufmann, David Kunhardt, Giuseppe Cirillo, Silke Hampel, Bernd Schwenzer
2014 Journal of materials chemistry. B  
The use of DNA-based therapeutics requires efficient delivery systems to transport the DNA to their place of action within the cell. To accomplish this, we investigated multiwalled carbon nanotubes (pristine MWCNT, p-MWCNT) functionalized with hydroxyl groups via 1,3-dipolar cycloaddition. In this way, we have obtained MWCNT-f-OH with improved stability in aqueous dispersions which is an advantageous property for their use in cellular environments. Afterwards, a carrier strand
more » ... de (CS-ODN) was adsorbed to MWCNT-f-OH followed by hybridization with a therapeutic antisense oligodeoxynucleotide (AS-ODN). The amount of adsorbed CS-ODN, as well as the complementary AS-ODN and a non-complementary oligodeoxynucleotide (NS-ODN) as reference, was directly measured by radionuclide labeling of ODNs. We show that subsequent release of AS-ODNs and NS-ODNs was possible for MWCNT-f-OH above the melting temperature of AS-ODNs at 80 °C and under physiological conditions at different pH values at 37 °C. We also show a very low influence of p-MWCNT and MWCNT-f-OH on the cell viability of the bladder carcinoma (BCa) cell line EJ28 and that both MWCNT types were internalized by EJ28. Therefore, MWCNT-f-OH represents a promising carrier able to transport and release AS-ODNs inside cells.
doi:10.1039/c4tb00915k pmid:32262110 fatcat:2trihcynuzdjrixb4c46lyogbi

Vox2Vox: 3D-GAN for Brain Tumour Segmentation [article]

Marco Domenico Cirillo and David Abramian and Anders Eklund
2020 arXiv   pre-print
Gliomas are the most common primary brain malignancies, with different degrees of aggressiveness, variable prognosis and various heterogeneous histological sub-regions, i.e., peritumoral edema, necrotic core, enhancing and non-enhancing tumour core. Although brain tumours can easily be detected using multi-modal MRI, accurate tumor segmentation is a challenging task. Hence, using the data provided by the BraTS Challenge 2020, we propose a 3D volume-to-volume Generative Adversarial Network for
more » ... gmentation of brain tumours. The model, called Vox2Vox, generates realistic segmentation outputs from multi-channel 3D MR images, segmenting the whole, core and enhancing tumor with mean values of 87.20%, 81.14%, and 78.67% as dice scores and 6.44mm, 24.36mm, and 18.95mm for Hausdorff distance 95 percentile for the BraTS testing set after ensembling 10 Vox2Vox models obtained with a 10-fold cross-validation.
arXiv:2003.13653v3 fatcat:l7r32mkujvc2voxct5fxeypfji
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