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List of works by Raffaele A. Calogero

A computational approach based on the colored Petri net formalism for studying multiple sclerosis

scientific article published on 10 December 2019

A genomic view of estrogen actions in human breast cancer cells by expression profiling of the hormone-responsive transcriptome

scientific article published on June 2004

A hypoxic signature marks tumors formed by disseminated tumor cells in the BALB-neuT mammary cancer model

scientific article published on 20 April 2016

A limited autoimmunity to p185neu elicited by DNA and allogeneic cell vaccine hampers the progression of preneoplastic lesions in HER-2/NEU transgenic mice.

scientific article

A mathematical-biological joint effort to investigate the tumor-initiating ability of Cancer Stem Cells

scientific article

A novel infection- and inflammation-associated molecular signature in peripheral blood of myasthenia gravis patients

scientific article published on 15 June 2016

A regulatory microRNA network controls endothelial cell phenotypic switch during sprouting angiogenesis

scientific article published on 24 January 2020

A versatile mathematical work-flow to explore how Cancer Stem Cell fate influences tumor progression

scientific article published on June 2015

AP-2alpha regulates migration of GN-11 neurons via a specific genetic programme involving the Axl receptor tyrosine kinase

scientific journal article

ARX regulates cortical intermediate progenitor cell expansion and upper layer neuron formation through repression of Cdkn1c

scientific article

Alternative splicing detection workflow needs a careful combination of sample prep and bioinformatics analysis.

scientific article published on June 2015

Amplification of repeat-containing transcribed sequences (ARTS): a transcriptome fingerprinting strategy to detect functionally relevant microsatellite mutations in cancer

scientific article

An integrated approach of immunogenomics and bioinformatics to identify new Tumor Associated Antigens (TAA) for mammary cancer immunological prevention

scientific article published in December 2005

Apoptosis induced by piroxicam plus cisplatin combined treatment is triggered by p21 in mesothelioma

scientific article

Apoptotic Cell Exclusion and Bias-Free Single-Cell Selection Are Important Quality Control Requirements for Successful Single-Cell Sequencing Applications

scientific article published on 11 October 2019

Are oncoantigens suitable targets for anti-tumour therapy?

scientific article (publication date: September 2007)

Arx acts as a regional key selector gene in the ventral telencephalon mainly through its transcriptional repression activity

scientific article published on 21 July 2009

Atorvastatin modulates anti-proliferative and pro-proliferative signals in Her2/neu-positive mammary cancer

scientific article

BRAF mutations in non-small cell lung cancer: has finally Janus opened the door?

scientific article published on 27 February 2016

Bisphenol A effects on gene expression in adipocytes from children: association with metabolic disorders

scientific article published on 15 April 2015

Cardioprotective mIGF-1/SIRT1 signaling induces hypertension, leukocytosis and fear response in mice

scientific article published on June 2012

Cell-to-cell signaling influences the fate of prostate cancer stem cells and their potential to generate more aggressive tumors

scientific article

Characterization of RNA-binding domains of hepatitis delta antigen.

scientific article

Characterization of a genetic mouse model of lung cancer: a promise to identify Non-Small Cell Lung Cancer therapeutic targets and biomarkers

scientific article

Characterization of the str operon genes from Spirulina platensis and their evolutionary relationship to those of other prokaryotes

scientific article

Chemical synthesis and in vivo hyperexpression of a modular gene coding for Escherichia coli translational initiation factor IF1.

scientific article published in June 1987

Chimera: a Bioconductor package for secondary analysis of fusion products

scientific article published on 6 October 2014

Clonal analysis of lineage fate in native haematopoiesis

scientific article published on 3 January 2018

Community-driven ELIXIR activities in single-cell omics

scientific article published on 29 July 2022

Comparative gene expression profiling reveals partially overlapping but distinct genomic actions of different antiestrogens in human breast cancer cells

scientific article published on August 2006

Complementary information on single nucleotide variants, INDELs and functional translocations can be obtained with RNAseq using different library preparations

scholarly article published 14 April 2018

Concordant morphologic and gene expression data show that a vaccine halts HER-2/neu preneoplastic lesions ⬇️

scientific article

Concordant morphologic and gene expression data show that a vaccine halts HER-2/neu preneoplastic lesions

article

Correction: Mimicking p14ARF Phosphorylation Influences Its Ability to Restrain Cell Proliferation.

scientific article published on 30 October 2013

Correction: p190 RhoGAP promotes contact inhibition in epithelial cells by repressing YAP activity

Critical roles for Rictor/Sin1 complexes in interferon-dependent gene transcription and generation of antiproliferative responses

scientific article published on 27 January 2014

Cross platform microarray analysis for robust identification of differentially expressed genes

scientific article

DNA damage and transcriptional regulation in iPSC-derived neurons from Ataxia Telangiectasia patients

scientific article published in Scientific Reports

Deletion in a (T)8 microsatellite abrogates expression regulation by 3'-UTR.

scientific article

Deregulation of MicroRNAs mediated control of carnitine cycle in prostate cancer: molecular basis and pathophysiological consequences

scientific article

Development, function and clinical significance of plasmacytoid dendritic cells in chronic myeloid leukemia

article

Differential Expression Analysis in Single-Cell Transcriptomics

scientific article published on 01 January 2019

Dissecting an alternative splicing analysis workflow for GeneChip Exon 1.0 ST Affymetrix arrays

scientific article

Docker4Circ: A Framework for the Reproducible Characterization of circRNAs from RNA-Seq Data

scientific article published on 31 December 2019

Dual RNA-seq of Nontypeable Haemophilus influenzae and Host Cell Transcriptomes Reveals Novel Insights into Host-Pathogen Cross Talk

scientific article

ERCC1 and RRM1 gene expressions but not EGFR are predictive of shorter survival in advanced non-small-cell lung cancer treated with cisplatin and gemcitabine

article

Early gene expression profiling through a macro-array approach on non-apoptotic human monocytes fed with hemozoin (malarial pigment).

scientific article

Endothelial progenitor cell derived microvesicles activate an angiogenic program in endothelial cells by a horizontal transfer of mRNA.

scientific article

Epidermal growth factor ligand/receptor loop and downstream signaling activation pattern in completely resected nonsmall cell lung cancer

Erratum for Baddal et al., Dual RNA-seq of Nontypeable Haemophilus influenzae and Host Cell Transcriptomes Reveals Novel Insights into Host-Pathogen Cross Talk

scientific article published on 12 April 2016

Evolution of HER2-positive mammary carcinoma: HER2 loss reveals claudin-low traits in cancer progression

scientific article published in 2021

Excision repair cross complementing-1 and topoisomerase IIalpha gene expression in small-cell lung cancer patients treated with platinum and etoposide: a retrospective study

scientific article published in June 2008

Expression in E. coli and purification of a chimeric p22-NS3 recombinant antigen of hepatitis C virus (HCV).

scientific article published in June 1993

Extracellular Vesicles Derived From Plasma of Patients With Neurodegenerative Disease Have Common Transcriptomic Profiling

scientific article published on 16 February 2022

Extracellular Vesicles Mediate Mesenchymal Stromal Cell-Dependent Regulation of B Cell PI3K-AKT Signaling Pathway and Actin Cytoskeleton

scientific article published on 12 March 2019

Frequent mutations of FBXO11 highlight BCL6 as a therapeutic target in Burkitt lymphoma

scientific article published on 01 December 2021

Functional and pharmacodynamic evaluation of metronomic cyclophosphamide and docetaxel regimen in castration-resistant prostate cancer

scientific article

Functional and physical interaction of the human ARF tumor suppressor with Tat-binding protein-1.

scientific article published on 09 December 2003

Genes regulated by hepatocyte growth factor as targets to sensitize ovarian cancer cells to cisplatin

article

Genome-wide discovery of functional transcription factor binding sites by comparative genomics: the case of Stat3.

scholarly article

Genomic and proteomic analyses of Prdm5 reveal interactions with insulator binding proteins in embryonic stem cells

scientific article published on 16 September 2013

Global gene expression profiling of human pleural mesotheliomas: identification of matrix metalloproteinase 14 (MMP-14) as potential tumour target

scientific article

HashClone: a new tool to quantify the minimal residual disease in B-cell lymphoma from deep sequencing data

scientific article published on 23 November 2017

Histone methyltransferase MMSET/NSD2 alters EZH2 binding and reprograms the myeloma epigenome through global and focal changes in H3K36 and H3K27 methylation

scientific article

Human liver stem cell-derived microvesicles accelerate hepatic regeneration in hepatectomized rats

scientific article published on 24 July 2009

Ibrutinib inhibits CD20 upregulation on CLL B cells mediated by the CXCR4/SDF-1 axis

scientific article

Immune prevention of mammary carcinogenesis in HER-2/neu transgenic mice: a microarray scenario.

scientific article

Immunotargeting of Antigen xCT Attenuates Stem-like Cell Behavior and Metastatic Progression in Breast Cancer

scientific article published on 13 November 2015

Impact of Mycobacterium tuberculosis RD1-locus on human primary dendritic cell immune functions

scientific article

Indole-3-acetic acid improves Escherichia coli’s defences to stress

scientific article published on 23 March 2006

Indole-3-acetic acid regulates the central metabolic pathways in Escherichia coli.

scientific article

Inflammation and breast cancer. Inflammatory component of mammary carcinogenesis in ErbB2 transgenic mice

scientific article

Intelligent informatics in biomedicine

scientific article

Interleukin 12-activated lymphocytes influence tumor genetic programs

scientific article published on 01 April 2001

Involvement of inflammatory chemokines in survival of human monocytes fed with malarial pigment

scientific article published on 23 August 2010

Kohonen neural networks and genetic classification

LSD1 mediates MYCN control of epithelial-mesenchymal transition through silencing of metastatic suppressor NDRG1 gene.

scientific article published on 22 November 2016

Large disclosing the nature of computational tools for the analysis of next generation sequencing data

scientific article

Laser capture microdissection for transcriptomic profiles in human skin biopsies.

scientific article

Learning from nature: pregnancy changes the expression of inflammation-related genes in patients with multiple sclerosis

scientific article

Live-animal imaging of native haematopoietic stem and progenitor cells

scientific article published on 05 February 2020

Long non-coding and coding RNAs characterization in Peripheral Blood Mononuclear Cells and Spinal Cord from Amyotrophic Lateral Sclerosis patients

scientific article

Look for methods, not conclusions

scientific article published on 05 December 2019

Luminal breast cancer-specific circular RNAs uncovered by a novel tool for data analysis.

scientific article published on 19 February 2018

Mechanism of translational initiation in prokaryotes

article

Mesenchymal stem cell-derived microvesicles protect against acute tubular injury

scientific article published on 23 April 2009

MicroRNA miR-34a downregulates FOXP1 during DNA damage response to limit BCR signalling in chronic lymphocytic leukaemia B cells

scientific article published on 15 August 2018

MicroRNAs from saliva of anopheline mosquitoes mimic human endogenous miRNAs and may contribute to vector-host-pathogen interactions

scientific article published on 27 February 2019

Microarray data analysis and mining approaches

scientific article

Microarray data analysis and mining.

scientific article

Microarray probe expression measures, data normalization and statistical validation

scientific article

Mimicking p14ARF phosphorylation influences its ability to restrain cell proliferation

scientific article

Multi-level model for the investigation of oncoantigen-driven vaccination effect

scientific article

Mutant SOD1 and mitochondrial damage alter expression and splicing of genes controlling neuritogenesis in models of neurodegeneration.

scientific article published on 25 January 2011

NUAK2 is a critical YAP target in liver cancer

scientific article published in Nature Communications

Neutron diffraction evidence for substrate-triggered intermolecular interactions in the ribosomal protein IF-2

article

Non-small cell lung cancer exhibits transcript overexpression of genes associated with homologous recombination and DNA replication pathways

scientific article

Novel insights into Notum and glypicans regulation in colorectal cancer

scientific article published on 20 October 2015

Oncoantigens as anti-tumor vaccination targets: the chance of a lucky strike?

article by Raffaele A. Calogero et al published 20 February 2008 in Cancer Immunology, Immunotherapy

Optimizing a massive parallel sequencing workflow for quantitative miRNA expression analysis

scientific article

Oxidative stress controls the choice of alternative last exons via a Brahma-BRCA1-CstF pathway

scientific article published on 02 September 2016

Oxysterol-induced up-regulation of MCP-1 expression and synthesis in macrophage cells

scientific article published on 11 August 2005

PIK3R1W624R Is an Actionable Mutation in High Grade Serous Ovarian Carcinoma

scientific article published on 14 February 2020

Piroxicam and cisplatin in a mouse model of peritoneal mesothelioma

scientific article published on October 2006

Prdm5 regulates collagen gene transcription by association with RNA polymerase II in developing bone

scientific article

Prdm5 suppresses Apc(Min)-driven intestinal adenomas and regulates monoacylglycerol lipase expression.

scientific article published on 22 July 2013

Purification of recombinant hepatitis delta antigen expressed in E. coli cells.

scientific article

Purification of recombinant proteins having high isoelectric points

scientific article

Purification of recombinant proteins with high isoelectric points

scientific article published in January 2004

Quantifying entire transcriptomes by aligned RNA-seq data

scientific article

RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application

scientific article published on June 2015

RNA-Seq profiling in peripheral blood mononuclear cells of amyotrophic lateral sclerosis patients and controls

scientific article published on 05 February 2019

RRE: a tool for the extraction of non-coding regions surrounding annotated genes from genomic datasets

scientific article

Recombinant human lactoferrin induces human and mouse dendritic cell maturation via Toll-like receptors 2 and 4

scientific article published on 02 October 2013

Regulation of leukemic cell differentiation and retinoid-induced gene expression by statins

scientific article published on 24 February 2009

Reinitiation of protein synthesis in Escherichia coli can be induced by mRNA cis -elements unrelated to canonical translation initiation signals

scientific article published on 01 February 2000

Reproducible Bioinformatics Project: A community for reproducible bioinformatics analysis pipelines

SETD2 and histone H3 lysine 36 methylation deficiency in advanced systemic mastocytosis

scientific article

STRIRED: graphical analysis of string repeats ⬇️

scientific article published on January 1, 1998

Selection of suitable reference genes for accurate normalization of gene expression profile studies in non-small cell lung cancer

scientific article

SeqBox: RNAseq/ChIPseq reproducible analysis on a consumer game computer.

scientific article published in March 2018

Site-directed mutagenesis of Escherichia coli translation initiation factor IF1. Identification of the amino acid involved in its ribosomal binding and recycling.

scientific article

Small non-coding RNA profiling in human biofluids and surrogate tissues from healthy individuals: description of the diverse and most represented species

scientific article published on 14 December 2017

State of art fusion-finder algorithms are suitable to detect transcription-induced chimeras in normal tissues?

scientific article

State-of-the-art fusion-finder algorithms sensitivity and specificity

scientific article

The Hay Wells syndrome-derived TAp63alphaQ540L mutant has impaired transcriptional and cell growth regulatory activity.

scientific article published on 21 January 2006

The Hippo transducer YAP1 transforms activated satellite cells and is a potent effector of embryonal rhabdomyosarcoma formation.

scientific article published on 31 July 2014

The MET oncogene transforms human primary bone-derived cells into osteosarcomas by targeting committed osteo-progenitors

scientific article

The TRPA1 channel is a cardiac target of mIGF-1/SIRT1 signaling

scientific article published on 8 August 2014

The cellular apoptosis susceptibility CAS/CSE1L gene protects ovarian cancer cells from death by suppressing RASSF1C.

scientific article published on 2 March 2012

The effect of trans-10, cis-12 conjugated linoleic acid on gene expression profiles related to lipid metabolism in human intestinal-like Caco-2 cells.

scientific article published on 13 March 2009

The human MDM2 oncoprotein increases the transcriptional activity and the protein level of the p53 homolog p63.

scientific article

The long intergenic non-coding RNA CCR492 functions as a let-7 competitive endogenous RNA to regulate c-Myc expression

scientific article published on 23 June 2016

The noninflammatory role of high mobility group box 1/Toll-like receptor 2 axis in the self-renewal of mammary cancer stem cells

scientific article published on 22 August 2013

Towards a long-lasting immune prevention of HER2 mammary carcinomas: directions from transgenic mice.

scientific article published on 19 June 2004

Transcriptional analysis of an E2F gene signature as a biomarker of activity of the cyclin-dependent kinase inhibitor PHA-793887 in tumor and skin biopsies from a phase I clinical study

scientific article

Transcriptional analysis of the Aurora inhibitor Danusertib leading to biomarker identification in TP53 wild type cells

scientific article published on 2 September 2011

Transcriptional profiling of endometriosis tissues identifies genes related to organogenesis defects

scientific article published in September 2013

Transcriptional profiling of polycythemia vera identifies gene expression patterns both dependent and independent from the action of JAK2V617F.

scientific article published on 2 July 2010

Translational modulation in hepatitis B virus preS-S open reading frame expression

scientific article published on January 1992

Use of a constrain phage displayed-peptide library for the isolation of peptides binding to HIV-1 nucleocapsid protein (NCp7).

scientific article published on March 1995

VIRTLAB: a virtual molecular biology laboratory

scientific article published in January 1998

Xenopatients show the need for precision medicine approach to chemotherapy in ovarian cancer.

scientific article published on 24 March 2016

YAP Drives Growth by Controlling Transcriptional Pause Release from Dynamic Enhancers

scientific article

YAP-TEAD signaling promotes basal cell carcinoma development via a c-JUN/AP1 axis

article

miR-135b coordinates progression of ErbB2-driven mammary carcinomas through suppression of MID1 and MTCH2.

scientific article published on 23 April 2013

microRNA profiles in urine by next-generation sequencing can stratify bladder cancer subtypes.

scientific article

oneChannelGUI: a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language

scientific article published on 17 September 2007

rCASC: reproducible classification analysis of single-cell sequencing data

scientific article published on 01 September 2019

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