77 research outputs found
MuLaN: a MultiLayer Networks Alignment Algorithm
A Multilayer Network (MN) is a system consisting of several topological
levels (i.e., layers) representing the interactions between the system's
objects and the related interdependency. Therefore, it may be represented as a
set of layers that can be assimilated to a set of networks of its own objects,
by means inter-layer edges (or inter-edges) linking the nodes of different
layers; for instance, a biological MN may allow modeling of inter and intra
interactions among diseases, genes, and drugs, only using its own structure.
The analysis of MNs may reveal hidden knowledge, as demonstrated by several
algorithms for the analysis. Recently, there is a growing interest in comparing
two MNs by revealing local regions of similarity, as a counterpart of Network
Alignment algorithms (NA) for simple networks. However, classical algorithms
for NA such as Local NA (LNA) cannot be applied on multilayer networks, since
they are not able to deal with inter-layer edges. Therefore, there is the need
for the introduction of novel algorithms. In this paper, we present MuLaN, an
algorithm for the local alignment of multilayer networks. We first show as
proof of concept the performances of MuLaN on a set of synthetic multilayer
networks. Then, we used as a case study a real multilayer network in the
biomedical domain. Our results show that MuLaN is able to build high-quality
alignments and can extract knowledge about the aligned multilayer networks.
MuLaN is available at https://github.com/pietrocinaglia/mulan
A novel Network Science Algorithm for Improving Triage of Patients
Patient triage plays a crucial role in healthcare, ensuring timely and
appropriate care based on the urgency of patient conditions. Traditional triage
methods heavily rely on human judgment, which can be subjective and prone to
errors. Recently, a growing interest has been in leveraging artificial
intelligence (AI) to develop algorithms for triaging patients. This paper
presents the development of a novel algorithm for triaging patients. It is
based on the analysis of patient data to produce decisions regarding their
prioritization. The algorithm was trained on a comprehensive data set
containing relevant patient information, such as vital signs, symptoms, and
medical history. The algorithm was designed to accurately classify patients
into triage categories through rigorous preprocessing and feature engineering.
Experimental results demonstrate that our algorithm achieved high accuracy and
performance, outperforming traditional triage methods. By incorporating
computer science into the triage process, healthcare professionals can benefit
from improved efficiency, accuracy, and consistency, prioritizing patients
effectively and optimizing resource allocation. Although further research is
needed to address challenges such as biases in training data and model
interpretability, the development of AI-based algorithms for triaging patients
shows great promise in enhancing healthcare delivery and patient outcomes
Extracting Dense and Connected Subgraphs in Dual Networks by Network Alignment
The use of network based approaches to model and analyse large datasets is
currently a growing research field. For instance in biology and medicine,
networks are used to model interactions among biological molecules as well as
relations among patients. Similarly, data coming from social networks can be
trivially modelled by using graphs. More recently, the use of dual networks
gained the attention of researchers. A dual network model uses a pair of graphs
to model a scenario in which one of the two graphs is usually unweighted (a
network representing physical associations among nodes) while the other one is
edge-weighted (a network representing conceptual associations among nodes). In
this paper we focus on the problem of finding the Densest Connected sub-graph
(DCS) having the largest density in the conceptual network which is also
connected in the physical network. The problem is relevant but also
computationally hard, therefore the need for introducing of novel algorithms
arises. We formalise the problem and then we map DCS into a graph alignment
problem. Then we propose a possible solution. A set of experiments is also
presented to support our approach
BioPAX-Parser: parsing and enrichment analysis of BioPAX pathways
Abstract
Summary
Biological pathways are fundamental for learning about healthy and disease states. Many existing formats support automatic software analysis of biological pathways, e.g. BioPAX (Biological Pathway Exchange). Although some algorithms are available as web application or stand-alone tools, no general graphical application for the parsing of BioPAX pathway data exists. Also, very few tools can perform pathway enrichment analysis (PEA) using pathway encoded in the BioPAX format. To fill this gap, we introduce BiP (BioPAX-Parser), an automatic and graphical software tool aimed at performing the parsing and accessing of BioPAX pathway data, along with PEA by using information coming from pathways encoded in BioPAX.
Availability and implementation
BiP is freely available for academic and non-profit organizations at https://gitlab.com/giuseppeagapito/bip under the LGPL 2.1, the GNU Lesser General Public License.
Supplementary information
Supplementary data are available at Bioinformatics online
A System for the Analysis of Snore Signals
AbstractSleep apnoea syndrome (SAS) is a disease consisting in the nocturnal cessation of oronasal airflow at least 10 seconds in duration. The standard method for SAS diagnosis is the polysomnographic exam (PSG). However it does not permit a mass screening because it has high cost and requires long term monitoring.This paper presents a preliminary software system prototype for snoring signal analysis, whose main goal is to support the doctor in SAS diagnosis and patient follow-up. The design of the system is modular to allow a future hardware implementation in a portable device for personal snore collection and monitoring
Genetic variants associated with gastrointestinal symptoms in Fabry disease.
Gastrointestinal symptoms (GIS) are often among the earliest presenting events in Fabry disease (FD), an X-linked lysosomal disorder caused by the deficiency of α-galactosidase A. Despite recent advances in clinical and molecular characterization of FD, the pathophysiology of the GIS is still poorly understood. To shed light either on differential clinical presentation or on intervariability of GIS in FD, we genotyped 1936 genetic markers across 231 genes that encode for drug-metabolizing enzymes and drug transport proteins in 49 FD patients, using the DMET Plus platform. All nine single nucleotide polymorphisms (SNPs) mapped within four genes showed statistically significant differences in genotype frequencies between FD patients who experienced GIS and patients without GIS: ABCB11 (odd ratio (OR) = 18.07, P = 0,0019; OR = 8.21, P = 0,0083; OR=8.21, P = 0,0083; OR = 8.21, P = 0,0083),SLCO1B1 (OR = 9.23, P = 0,0065; OR = 5.08, P = 0,0289; OR = 8.21, P = 0,0083), NR1I3 (OR = 5.40, P = 0,0191) and ABCC5 (OR = 14.44, P = 0,0060). This is the first study that investigates the relationships between genetic heterogeneity in drug absorption, distribution, metabolism and excretion (ADME) related genes and GIS in FD. Our findings provide a novel genetic variant framework which warrants further investigation for precision medicine in FD
Single nucleotide polymorphisms of ABCC5 and ABCG1 transporter genes correlate to irinotecan-associated gastrointestinal toxicity in colorectal cancer patients: a DMET microarray profiling study.
Abstract Recent findings have disclosed the role of UDP-glucuronosyltransferase (UGT) 1A1*28 on the haematological toxicity induced by irinotecan (CPT-11), a drug commonly used in the treatment of metastatic colorectal cancer (mCRC). We investigated the pharmacogenomic profile of irinotecan-induced gastrointestinal (GI) toxicity by the novel drug-metabolizing enzyme and transporter (DMET) microarray genotyping platform. Twenty-six mCRC patients who had undergone to irinotecan-based chemotherapy were enrolled in a case (patients experiencing > grade 3 gastrointestinal, (GI) toxicity) - control (matched patients without GI toxicity) study. A statistically significant difference of SNP genotype distribution was found in the case versus control group. The homozygous genotype C/C in the (rs562) ABCC5 gene occurred in 6/9 patients with GI toxicity versus 1/17 patients without GI toxicity (P=0.0022). The homozygous genotype G/G in the (rs425215) ABCG1 was found in 7/9 patients with GI toxicity versus 4/17 patients without GI toxicity (P=0.0135). The heterozygous genotype G/A in the 388G>A (rs2306283) OATP1B1/SLCO1B1 was found in 3/9 patients with grade > 3 GI toxicity versus 14/17 patients without GI toxicity (P=0.0277). DNA extracted from peripheral blood cells was genotyped by DMET Plus chip on Affymetrix array system. Genotype association was calculated by Fisher's exact test (two tailed) and relevant SNPs were further analyzed by direct sequencing. We have identified 3 SNPs mapping in ABCG1, ABCC5 and OATP1B1/SLCO1B1 transporter genes associated with GI toxicity induced by irinotecan in mCRC patients expanding the available knowledge of irinogenomics. The DMET microarray platform is an emerging technology for easy identification of new genetic variants for personalized medicine
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