Luigi Cerulo

Luigi Cerulo
Università degli Studi del Sannio | UniSannio · Department of Science and Technology (DST)

PhD

About

117
Publications
33,182
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2,760
Citations
Citations since 2016
50 Research Items
1534 Citations
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2016201720182019202020212022050100150200250
2016201720182019202020212022050100150200250
2016201720182019202020212022050100150200250

Publications

Publications (117)
Article
Full-text available
In addition to being novel biomarkers for poor cancer prognosis, members of Lymphocyte antigen-6 (Ly6) gene family also play a crucial role in avoiding immune responses to tumors. However, it has not been possible to identify the underlying mechanism of how Ly6 gene regulation operates in human cancers. Transcriptome, epigenome and proteomic data f...
Article
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Gene-set enrichment analysis is the key methodology for obtaining biological information from transcriptomic space’s statistical result. Since its introduction, Gene-set Enrichment analysis methods have obtained more reliable results and a wider range of application. Great attention has been devoted to global tests, in contrast to competitive metho...
Article
Full-text available
Brain-derived neurotrophic factor (BDNF) plays a pivotal role in neuronal growth and differentiation, neuronal plasticity, learning and memory. Using CRISPR/Cas9 technology, we generated a vital Bdnf null mutant line in zebrafish and carried out its molecular and behavioural characterization. Although no defects are evident on a morphological inspe...
Article
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It is currently unknown how many RNA transcripts are able to induce degradation of microRNAs (miRNA) via the mechanism known as target-directed miRNA degradation (TDMD). We developed TDMDfinder, a computational pipeline that identifies ‘high confidence’ TDMD interactions in the Human and Mouse transcriptomes by combining sequence alignment and feat...
Preprint
Full-text available
Background: Colorectal cancer (CRC) represents a significant and ever-increasing societal threat and burden. Activation of Lymphocyte antigen 6G6D could induce anti-tumor specific immunity unique to CRC, but factors regulating its activation remain obscure. Methods: Transcriptome, epigenome and proteomic data from TCGA and independent database were...
Article
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Metastasis is a process by which cancer cells escape from the location of the primary tumor invading normal tissues at distant organs. Chromosomal instability (CIN) is a hallmark of human cancer, associated with metastasis and therapeutic resistance. The centrosome plays a major role in organizing the microtubule cytoskeleton in animal cells regula...
Article
Background Breast carcinoma with extensive peritumoral vascular invasion (ePVI-BC) is a cancer with massive vascular invasion (>10) detected in more than one slide. This neoplasm shows clinic-pathological affinity with inflammatory breast carcinoma (IBC). In this paper we evaluate their biological relationship through the study of surrogate markers...
Article
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The stratification of patients at risk of progression of COVID-19 and their molecular characterization is of extreme importance to optimize treatment and to identify therapeutic options. The bioinformatics community has responded to the outbreak emergency with a set of tools and resource to identify biomarkers and drug targets that we review here....
Article
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Small non-coding RNAs (ncRNAs) are short non-coding sequences involved in gene regulation in many biological processes and diseases. The lack of a complete comprehension of their biological functionality, especially in a genome-wide scenario, has demanded new computational approaches to annotate their roles. It is widely known that secondary struct...
Article
Motivation The cost of drug development has dramatically increased in the last decades, with the number new drugs approved per billion US dollars spent on R&D halving every year or less. The selection and prioritization of targets is one the the most influential decisions in drug discovery. Here we present a Gaussian Process model for the prioritiz...
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Background Single-cell RNA sequencing is the reference technique for characterizing the heterogeneity of the tumor microenvironment. The composition of the various cell types making up the microenvironment can significantly affect the way in which the immune system activates cancer rejection mechanisms. Understanding the cross-talk signals between...
Article
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Background: Glioblastoma (GBM) is a complex disease with extensive molecular and transcriptional heterogeneity. GBM can be subcategorized into four distinct subtypes; tumors that shift towards the mesenchymal phenotype upon recurrence are generally associated with treatment resistance, unfavorable prognosis, and the infiltration of pro-tumorigenic...
Preprint
Full-text available
Non-coding RNAs (ncRNAs) are small non-coding sequences involved in gene regulation in many biological processes and diseases. The lack of a complete comprehension of their biological functionality, especially in a genome-wide scenario, has demanded new computational approaches to annotate their roles. It is widely known that secondary structure is...
Article
Full-text available
Embryonic stem cells (ESCs) are derived from inner cell mass (ICM) of the blastocyst. In serum/LIF culture condition, they show variable expression of pluripotency genes that mark cell fluctuation between pluripotency and differentiation metastate. The ESCs subpopulation marked by zygotic genome activation gene (ZGA) signature, including Zscan4, re...
Article
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Background: Human microsatellite-stable (MSS) colorectal cancers (CRCs) are immunologically "cold" tumour subtypes characterized by reduced immune cytotoxicity. The molecular linkages between immune-resistance and human MSS CRC is not clear. Methods: We used transcriptome profiling, in silico analysis, immunohistochemistry, western blot, RT-qPCR an...
Preprint
Single-cell RNA sequencing is the reference technique to characterize the heterogeneity of tumor microenvironment and can be efficiently used to discover cross-talk mechanisms between immune cells and cancer cells. We present a novel method, single cell Tumor-Host Interaction tool (scTHI), to identify significantly activated ligand-receptor interac...
Article
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Background Long non-coding RNAs (lncRNAs) represent a novel class of non-coding RNAs having a crucial role in many biological processes. The identification of long non-coding homologs among different species is essential to investigate such roles in model organisms as homologous genes tend to retain similar molecular and biological functions. Align...
Article
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Chronic myeloid leukemia (CML) is a stem cell derived malignant disorder result of translocation t(9;22)(q34;q11) called Philadelphia chromosome (Ph⁺). microRNAS (miRNAs) are involved in several biological processes, altering the progression of various pathologies, including CML. This study evaluated whether circulating miRNAs display differential...
Article
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We propose a generic framework for gene regulatory network (GRN) inference approached as a feature selection problem. GRNs obtained using Machine Learning techniques are often dense, whereas real GRNs are rather sparse. We use a Tikonov regularization inspired optimal L-curve criterion that utilizes the edge weight distribution for a given target g...
Article
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Chromosomal translocations that generate in-frame oncogenic gene fusions are notable examples of the success of targeted cancer therapies. We have previously described gene fusions of FGFR3-TACC3 (F3-T3) in 3% of human glioblastoma cases. Subsequent studies have reported similar frequencies of F3-T3 in many other cancers, indicating that F3-T3 is a...
Preprint
The transcription factors (TF) which regulate gene expressions are key determinants of cellular phenotypes. Reconstructing large-scale genome-wide networks which capture the influence of TFs on target genes are essential for understanding and accurate modelling of living cells. We propose RGBM: a gene regulatory network (GRN) inference algorithm, w...
Article
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Background: The unveiling of long non-coding RNAs as important gene regulators in many biological contexts has increased the demand for efficient and robust computational methods to identify novel long non-coding RNAs from transcripts assembled with high throughput RNA-seq data. Several classes of sequence-based features have been proposed to dist...
Article
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1 Motivation Biological networks contribute effectively to unveil the complex structure of molecular interactions and to discover driver genes especially in cancer context. It can happen that due to gene mutations, as for example when cancer progresses, the gene expression network undergoes some amount of localised re-wiring. The ability to detect...
Article
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Our understanding of the genetic and non-genetic molecular alterations associated with colorectal cancer (CRC) progression and therapy resistance has markedly expanded in recent years. In addition to their effects on tumor biology, targeted therapies can have effects on host immune responses. However, the mechanisms by which immune cells organize t...
Article
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Cancer immunotherapy is revolutionizing the clinical management of several tumors, but has demonstrated limited activity in breast cancer. The development of more effective treatments is hindered by incomplete knowledge of the genetic determinant of immune responsiveness. To fill this gap, we mined copy number alteration, somatic mutation, and expr...
Article
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This paper presents two interactive visualization tools for learning management systems (LMS) in order to improve learning and teaching in online courses. The first tool was developed at the Intelligent Information Systems Laboratory (IISLab) at the Tampere University of Technology (TUT). The tool is used to analyse students' activity from automati...
Article
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Cancer-related immune antigens in the tumor microenvironment could represent an obstacle to agents targeting EGFR “cetuximab” or VEGF “bevacizumab” in metastatic colorectal cancer (mCRC) patients. Infiltrating immune cells into tumor tissues, cancer-related expression of immune antigens (CD3, CD8, CD68, CD73, MPO, CD15/FUT4) from 102 mCRC patients...
Conference Paper
Online forums represent nowadays one of the most popular and rich repository of user generated information over the Internet. Searching information of interest in an online forum may be substantially improved by a proper organization of the forum content. With this aim, in this paper we propose an approach that enhances an existing forum by introdu...
Article
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Inflammatory Breast Cancer (IBC) is the most aggressive and highly metastatic form of breast cancer [1-3]. In a recent study [4], we analysed breast cancer with peritumoral neoplastic lymphovascular invasion (ePVI) in comparison with inflammatory breast cancer, showing that ePVI breast cancer have more clinicopathologic affinity than differences wi...
Article
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Inflammatory breast cancer (IBC) is the most rare and aggressive variant of breast cancer (BC); however, only a limited number of specific gene signatures with low generalization abilities are available and few reliable biomarkers are helpful to improve IBC classification into a molecularly distinct phenotype. We applied a network-based strategy to...
Article
Developers' communication, as contained in emails, issue trackers, and forums, is a precious source of information to support the development process. For example, it can be used to capture knowledge about development practice or about a software project itself. Thus, extracting the content of developers' communication can be useful to support seve...
Conference Paper
Large-scale genomic studies have identified a significant number of transcripts that do not code for proteins [1, 2] and only 1,5% of the human genome encodes for protein-coding genes [3]. Non-coding RNAs can be classified into two groups: small (<200 nucleotides) and long non-coding RNAs (>200 nucleotides), based on the size of their mature transc...
Conference Paper
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One of the most popular means of asynchronous communication and most rich repository of user generated information over the Internet is represented by online discussion forums. The capability of a forum to satisfy users' needs as an information source is mainly determined by its richness in information, but also by the way its content (messages and...
Article
Reverse engineering of gene regulatory relationships from genomics data is a crucial task to dissect the complex underlying regulatory mechanism occurring in a cell. From a computational point of view the reconstruction of gene regulatory networks is an undetermined problem as the large number of possible solutions is typically high in contrast to...
Article
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Embryonic Stem cells (ESCs) can be differentiated into ectoderm, endoderm, and mesoderm derivatives, producing the majority of cell types. In regular culture conditions, ESCs' self-renewal is maintained through molecules that inhibit spontaneous differentiation enabling long-term cellular expansion. This undifferentiating condition is characterized...
Conference Paper
Full-text available
Reverse engineering of regulatory relationships from genomics data is emerging as crucial to dissect the complex underlying regulatory mechanism occurring in a cell. In this paper we propose a novel reverse engineering algorithm that makes use of formal methods, usually adopted in engineering to specify and verify concurrent software and hardware s...