Research

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2024

CSF-1R in Cancer: More than a Myeloid Cell Receptor
CSF-1R in Cancer: More than a Myeloid Cell Receptor
Francesca Cersosimo, Silvia Lonardi, Cristina Ulivieri, Paolo Martini, Andrea Morrione, William Vermi, Antonio Giordano, Emanuele Giurisato
Cancers  ·  09 Jan 2024  ·  doi:10.3390/cancers16020282

2023

Protocol for generation of a time-resolved cellular interactome during tissue remodeling in adult mice
Protocol for generation of a time-resolved cellular interactome during tissue remodeling in adult mice
Elena Groppa, Lin Wei Tung, Stefania Mattevi, Morten Ritso, Fabio M.V. Rossi, Paolo Martini
STAR Protocols  ·  01 Dec 2023  ·  doi:10.1016/j.xpro.2023.102638
Polygenic scores of subcortical brain volumes as possible modulators of treatment response in depression
Polygenic scores of subcortical brain volumes as possible modulators of treatment response in depression
Vincenzo Oliva, Alfonso Martone, Giuseppe Fanelli, Katharina Domschke, Alessandra Minelli, …, Julien Mendlewicz, Diana De Ronchi, Bernhard T Baune, Alessandro Serretti, Chiara Fabbri
Cold Spring Harbor Laboratory  ·  28 Aug 2023  ·  doi:10.1101/2023.08.26.23294659
Transcriptional Profiling of Rat Prefrontal Cortex after Acute Inescapable Footshock Stress
Transcriptional Profiling of Rat Prefrontal Cortex after Acute Inescapable Footshock Stress
Paolo Martini, Jessica Mingardi, Giulia Carini, Stefania Mattevi, Elona Ndoj, …, Massimo Gennarelli, Isabella Russo, Maurizio Popoli, Laura Musazzi, Alessandro Barbon
Genes  ·  17 Mar 2023  ·  doi:10.3390/genes14030740
signifinder enables the identification of tumor cell states and cancer expression signatures in bulk, single-cell and spatial transcriptomic data
signifinder enables the identification of tumor cell states and cancer expression signatures in bulk, single-cell and spatial transcriptomic data
Stefania Pirrotta, Laura Masatti, Anna Corrà, Fabiola Pedrini, Giovanni Esposito, Paolo Martini, Davide Risso, Chiara Romualdi, Enrica Calura
Cold Spring Harbor Laboratory  ·  10 Mar 2023  ·  doi:10.1101/2023.03.07.530940
Chemical conversion of human conventional scp PSCs scp to scp TSCs scp following transient naive gene activation
Chemical conversion of human conventional PSCs to TSCs following transient naive gene activation
Irene Zorzan, Riccardo Massimiliano Betto, Giada Rossignoli, Mattia Arboit, Andrea Drusin, Clelia Corridori, Paolo Martini, Graziano Martello
EMBO reports  ·  27 Feb 2023  ·  doi:10.15252/embr.202255235
Defective excitation-contraction coupling and mitochondrial respiration precede mitochondrial Ca2 accumulation in spinobulbar muscular atrophy skeletal muscle
Defective excitation-contraction coupling and mitochondrial respiration precede mitochondrial Ca2+ accumulation in spinobulbar muscular atrophy skeletal muscle
Caterina Marchioretti, Giulia Zanetti, Marco Pirazzini, Gaia Gherardi, Leonardo Nogara, …, Gopal J. Babu, Marco Sandri, Bert Blaauw, Manuela Basso, Maria Pennuto
Nature Communications  ·  06 Feb 2023  ·  doi:10.1038/s41467-023-36185-w

2022

Chemical conversion of human conventional Pluripotent Stem Cells to Trophoblast Stem Cells
Chemical conversion of human conventional Pluripotent Stem Cells to Trophoblast Stem Cells
Irene Zorzan, Riccardo Massimiliano Betto, Giada Rossignoli, Mattia Arboit, Andrea Drusin, Paolo Martini, Graziano Martello
Cold Spring Harbor Laboratory  ·  08 Apr 2022  ·  doi:10.1101/2022.04.07.487453
Zebrafish Mutant Lines Reveal the Interplay between nr3c1 and nr3c2 in the GC-Dependent Regulation of Gene Transcription
Zebrafish Mutant Lines Reveal the Interplay between nr3c1 and nr3c2 in the GC-Dependent Regulation of Gene Transcription
Alberto Dinarello, Annachiara Tesoriere, Paolo Martini, Camilla Maria Fontana, Davide Volpato, …, Nicola Facchinello, Chiara Romualdi, Oliana Carnevali, Luisa Dalla Valle, Francesco Argenton
International Journal of Molecular Sciences  ·  28 Feb 2022  ·  doi:10.3390/ijms23052678
Defective excitation-contraction coupling and mitochondrial respiration precede mitochondrial Ca2 accumulation in spinobulbar muscular atrophy skeletal muscle
Defective excitation-contraction coupling and mitochondrial respiration precede mitochondrial Ca2+ accumulation in spinobulbar muscular atrophy skeletal muscle
Caterina Marchioretti, Giulia Zanetti, Gaia Gherardi, Leonardo Nogara, Andreotti Roberta, …, Marco Sandri, Bert Blaauw, Manuela Basso, Marco Pirazzini, Maria Pennuto
Springer Science and Business Media LLC  ·  27 Jan 2022  ·  doi:10.21203/rs.3.rs-1261384/v1

2021

Whole Blood Transcriptome Characterization of 3xTg-AD Mouse and Its Modulation by Transcranial Direct Current Stimulation tDCS
Whole Blood Transcriptome Characterization of 3xTg-AD Mouse and Its Modulation by Transcranial Direct Current Stimulation (tDCS)
Chiara Magri, Erika Vitali, Sara Cocco, Edoardo Giacopuzzi, Marco Rinaudo, Paolo Martini, Alessandro Barbon, Claudio Grassi, Massimo Gennarelli
International Journal of Molecular Sciences  ·  16 Jul 2021  ·  doi:10.3390/ijms22147629

2020

Open collaborative writing with Manubot
Open collaborative writing with Manubot
Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, Anthony Gitter
PLOS Computational Biology  ·  04 Dec 2020  ·  doi:10.1371/journal.pcbi.1007128
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Manubot
Manuscript Source
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open-science collaboration
Allelic expression analysis of Imprinted and X-linked genes from bulk and single-cell transcriptomes
Allelic expression analysis of Imprinted and X-linked genes from bulk and single-cell transcriptomes
Paolo Martini, Gabriele Sales, Linda Diamante, Valentina Perrera, Chiara Colantuono, Sara Riccardo, Davide Cacchiarelli, Chiara Romualdi, Graziano Martello
Cold Spring Harbor Laboratory  ·  23 May 2020  ·  doi:10.1101/2020.05.20.105841
Expression profiles of PRKG1, SDF2L1 and PPP1R12A are predictive and prognostic factors for therapy response and survival in high grade serous ovarian cancer
Expression profiles of PRKG1, SDF2L1 and PPP1R12A are predictive and prognostic factors for therapy response and survival in high‐grade serous ovarian cancer
Giuseppe Benvenuto, Paola Todeschini, Lara Paracchini, Enrica Calura, Robert Fruscio, …, Franco Odicino, Maurizio D’Incalci, Eliana Bignotti, Chiara Romualdi, Sergio Marchini
International Journal of Cancer  ·  13 Mar 2020  ·  doi:10.1002/ijc.32935

2019

Transcriptional Characterization of Stage I Epithelial Ovarian Cancer: A Multicentric Study
Transcriptional Characterization of Stage I Epithelial Ovarian Cancer: A Multicentric Study
Enrica Calura, Matteo Ciciani, Andrea Sambugaro, Lara Paracchini, Giuseppe Benvenuto, …, Eliana Bignotti, Franco Odicino, Maurizio D’Incalci, Sergio Marchini, Chiara Romualdi
Cells  ·  01 Dec 2019  ·  doi:10.3390/cells8121554
Analysis of the circadian transcriptome of the Antarctic krill Euphausia superba
Analysis of the circadian transcriptome of the Antarctic krill Euphausia superba
Alberto Biscontin, Paolo Martini, Rodolfo Costa, Achim Kramer, Bettina Meyer, So Kawaguchi, Mathias Teschke, Cristiano De Pittà
Scientific Reports  ·  25 Sep 2019  ·  doi:10.1038/s41598-019-50282-1
MOSClip: multi-omic and survival pathway analysis for the identification of survival associated gene and modules
MOSClip: multi-omic and survival pathway analysis for the identification of survival associated gene and modules
Paolo Martini, Monica Chiogna, Enrica Calura, Chiara Romualdi
Nucleic Acids Research  ·  03 May 2019  ·  doi:10.1093/nar/gkz324
Multisite analysis of high grade serous epithelial ovarian cancers identifies genomic regions of focal and recurrent copy number alteration in 3q26.2 and 8q24.3
Multisite analysis of high‐grade serous epithelial ovarian cancers identifies genomic regions of focal and recurrent copy number alteration in 3q26.2 and 8q24.3
Sara Ballabio, Ilaria Craparotta, Lara Paracchini, Laura Mannarino, Silvia Corso, …, Antonio Pellegrino, Fabio Landoni, Maurizio D’Incalci, Luca Beltrame, Sergio Marchini
International Journal of Cancer  ·  26 Apr 2019  ·  doi:10.1002/ijc.32288
Transcriptomic Analysis of Single Isolated Myofibers Identifies miR-27a-3p and miR-142-3p as Regulators of Metabolism in Skeletal Muscle
Transcriptomic Analysis of Single Isolated Myofibers Identifies miR-27a-3p and miR-142-3p as Regulators of Metabolism in Skeletal Muscle
Francesco Chemello, Francesca Grespi, Alessandra Zulian, Pasqua Cancellara, Etienne Hebert-Chatelain, …, Chiara Romualdi, Paolo Bernardi, Luca Scorrano, Stefano Cagnin, Gerolamo Lanfranchi
Cell Reports  ·  01 Mar 2019  ·  doi:10.1016/j.celrep.2019.02.105
Transcriptome Profiles of Human Visceral Adipocytes in Obesity and Colorectal Cancer Unravel the Effects of Body Mass Index and Polyunsaturated Fatty Acids on Genes and Biological Processes Related to Tumorigenesis
Transcriptome Profiles of Human Visceral Adipocytes in Obesity and Colorectal Cancer Unravel the Effects of Body Mass Index and Polyunsaturated Fatty Acids on Genes and Biological Processes Related to Tumorigenesis
Manuela Del Cornò, Antonella Baldassarre, Enrica Calura, Lucia Conti, Paolo Martini, …, Rosaria Varì, Beatrice Scazzocchio, Massimo D’Archivio, Andrea Masotti, Sandra Gessani
Frontiers in Immunology  ·  19 Feb 2019  ·  doi:10.3389/fimmu.2019.00265
Single cell analysis reveals the involvement of the long non-coding RNA Pvt1 in the modulation of muscle atrophy and mitochondrial network
Single cell analysis reveals the involvement of the long non-coding RNA Pvt1 in the modulation of muscle atrophy and mitochondrial network
Enrico Alessio, Lisa Buson, Francesco Chemello, Caterina Peggion, Francesca Grespi, …, Chiara Romualdi, Alessandro Bertoli, Luca Scorrano, Gerolamo Lanfranchi, Stefano Cagnin
Nucleic Acids Research  ·  16 Jan 2019  ·  doi:10.1093/nar/gkz007

2018

Direct generation of human naive induced pluripotent stem cells from somatic cells in microfluidics
Direct generation of human naive induced pluripotent stem cells from somatic cells in microfluidics
Stefano Giulitti, Marco Pellegrini, Irene Zorzan, Paolo Martini, Onelia Gagliano, …, Michael Johannes Ziller, Davide Cacchiarelli, Chiara Romualdi, Nicola Elvassore, Graziano Martello
Nature Cell Biology  ·  31 Dec 2018  ·  doi:10.1038/s41556-018-0254-5

2017

lncRNAs as Novel Indicators of Patients Prognosis in Stage I Epithelial Ovarian Cancer: A Retrospective and Multicentric Study
lncRNAs as Novel Indicators of Patients' Prognosis in Stage I Epithelial Ovarian Cancer: A Retrospective and Multicentric Study
Paolo Martini, Lara Paracchini, Giulia Caratti, Maurizia Mello-Grand, Robert Fruscio, …, Costantino Mangioni, Chiara Ghimenti, Maurizio D’Incalci, Sergio Marchini, Chiara Romualdi
Clinical Cancer Research  ·  30 Apr 2017  ·  doi:10.1158/1078-0432.CCR-16-1402
NELL1, whose high expression correlates with negative outcomes, has different methylation patterns in alveolar and embryonal rhabdomyosarcoma
NELL1, whose high expression correlates with negative outcomes, has different methylation patterns in alveolar and embryonal rhabdomyosarcoma
Lucia Tombolan, Elena Poli, Paolo Martini, Angelica Zin, Chiara Romualdi, Gianni Bisogno, Gerolamo Lanfranchi
Oncotarget  ·  23 Mar 2017  ·  doi:10.18632/oncotarget.16526
Circulating miRNA landscape identifies miR-1246 as promising diagnostic biomarker in high-grade serous ovarian carcinoma: A validation across two independent cohorts
Circulating miRNA landscape identifies miR-1246 as promising diagnostic biomarker in high-grade serous ovarian carcinoma: A validation across two independent cohorts
Paola Todeschini, Elisa Salviato, Lara Paracchini, Manuela Ferracin, Marco Petrillo, …, Antonella Ravaggi, Maurizio D’Incalci, Sergio Marchini, Eliana Bignotti, Chiara Romualdi
Cancer Letters  ·  01 Mar 2017  ·  doi:10.1016/j.canlet.2016.12.017
KrillDB: A de novo transcriptome database for the Antarctic krill Euphausia superba
KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba)
Gabriele Sales, Bruce E. Deagle, Enrica Calura, Paolo Martini, Alberto Biscontin, …, So Kawaguchi, Chiara Romualdi, Bettina Meyer, Rodolfo Costa, Simon Jarman
PLOS ONE  ·  10 Feb 2017  ·  doi:10.1371/journal.pone.0171908

2016

Global DNA methylation profiling uncovers distinct methylation patterns of protocadherin alpha4 in metastatic and non-metastatic rhabdomyosarcoma
Global DNA methylation profiling uncovers distinct methylation patterns of protocadherin alpha4 in metastatic and non-metastatic rhabdomyosarcoma
L. Tombolan, E. Poli, P. Martini, A. Zin, C. Millino, …, B. Celegato, G. Bisogno, C. Romualdi, A. Rosolen, G. Lanfranchi
BMC Cancer  ·  14 Nov 2016  ·  doi:10.1186/s12885-016-2936-3
A prognostic regulatory pathway in stage I epithelial ovarian cancer: new hints for the poor prognosis assessment
A prognostic regulatory pathway in stage I epithelial ovarian cancer: new hints for the poor prognosis assessment
E. Calura, L. Paracchini, R. Fruscio, A. DiFeo, A. Ravaggi, …, C. Mangioni, L. Ardighieri, M. D’Incalci, S. Marchini, C. Romualdi
Annals of Oncology  ·  01 Aug 2016  ·  doi:10.1093/annonc/mdw210

2015

Profiling cancer gene mutations in longitudinal epithelial ovarian cancer biopsies by targeted next-generation sequencing: a retrospective study
Profiling cancer gene mutations in longitudinal epithelial ovarian cancer biopsies by targeted next-generation sequencing: a retrospective study
L. Beltrame, M. Di Marino, R. Fruscio, E. Calura, B. Chapman, …, A. Ravaggi, A. Zambelli, E. Ronchetti, M. D’Incalci, S. Marchini
Annals of Oncology  ·  01 Jul 2015  ·  doi:10.1093/annonc/mdv164
Pyrosequencing and i de novo i assembly of scp A scp ntarctic krill i scp E scp uphausia superba i transcriptome to study the adaptability of krill to climate induced environmental changes
Pyrosequencing andde novoassembly ofAntarctic krill (Euphausia superba)transcriptome to study the adaptability of krill to climate‐induced environmental changes
B. Meyer, P. Martini, A. Biscontin, C. De Pittà, C. Romualdi, …, S. Frickenhaus, L. Harms, U. Freier, S. Jarman, S. Kawaguchi
Molecular Ecology Resources  ·  09 Apr 2015  ·  doi:10.1111/1755-0998.12408

2014

Altered Gene Transcription in Human Cells Treated with Ludox Silica Nanoparticles
Altered Gene Transcription in Human Cells Treated with Ludox® Silica Nanoparticles
Caterina Fede, Caterina Millino, Beniamina Pacchioni, Barbara Celegato, Chiara Compagnin, …, Fabrizio Mancin, Lucia Celotti, Gerolamo Lanfranchi, Maddalena Mognato, Stefano Cagnin
International Journal of Environmental Research and Public Health  ·  28 Aug 2014  ·  doi:10.3390/ijerph110908867
Decellularized Allogeneic Heart Valves Demonstrate Self-Regeneration Potential after a Long-Term Preclinical Evaluation
Decellularized Allogeneic Heart Valves Demonstrate Self-Regeneration Potential after a Long-Term Preclinical Evaluation
Laura Iop, Antonella Bonetti, Filippo Naso, Stefania Rizzo, Stefano Cagnin, …, Cristina Basso, Maurizio Marchini, Alessandro Gandaglia, Fulvia Ortolani, Gino Gerosa
PLoS ONE  ·  18 Jun 2014  ·  doi:10.1371/journal.pone.0099593
Wiring miRNAs to pathways: a topological approach to integrate miRNA and mRNA expression profiles
Wiring miRNAs to pathways: a topological approach to integrate miRNA and mRNA expression profiles
Enrica Calura, Paolo Martini, Gabriele Sales, Luca Beltrame, Giovanna Chiorino, Maurizio D’Incalci, Sergio Marchini, Chiara Romualdi
Nucleic Acids Research  ·  06 May 2014  ·  doi:10.1093/nar/gku354
timeClip: pathway analysis for time course data without replicates
timeClip: pathway analysis for time course data without replicates
Paolo Martini, Gabriele Sales, Enrica Calura, Stefano Cagnin, Monica Chiogna, Chiara Romualdi
BMC Bioinformatics  ·  01 May 2014  ·  doi:10.1186/1471-2105-15-S5-S3
Tissue-Specific Expression and Regulatory Networks of Pig MicroRNAome
Tissue-Specific Expression and Regulatory Networks of Pig MicroRNAome
Paolo Martini, Gabriele Sales, Mattia Brugiolo, Alessandro Gandaglia, Filippo Naso, …, Gino Gerosa, Francesco Chemello, Chiara Romualdi, Stefano Cagnin, Gerolamo Lanfranchi
PLoS ONE  ·  03 Apr 2014  ·  doi:10.1371/journal.pone.0089755

2013

Systems Biology Approach to the Dissection of the Complexity of Regulatory Networks in the S. scrofa Cardiocirculatory System
Systems Biology Approach to the Dissection of the Complexity of Regulatory Networks in the S. scrofa Cardiocirculatory System
Paolo Martini, Gabriele Sales, Enrica Calura, Mattia Brugiolo, Gerolamo Lanfranchi, Chiara Romualdi, Stefano Cagnin
International Journal of Molecular Sciences  ·  21 Nov 2013  ·  doi:10.3390/ijms141123160
miRNA Landscape in Stage I Epithelial Ovarian Cancer Defines the Histotype Specificities
miRNA Landscape in Stage I Epithelial Ovarian Cancer Defines the Histotype Specificities
Enrica Calura, Robert Fruscio, Lara Paracchini, Eliana Bignotti, Antonella Ravaggi, …, Sergio Pecorelli, Costantino Mangioni, Maurizio D’Incalci, Chiara Romualdi, Sergio Marchini
Clinical Cancer Research  ·  31 Jul 2013  ·  doi:10.1158/1078-0432.CCR-13-0360
Graphite Web: web tool for gene set analysis exploiting pathway topology
Graphite Web: web tool for gene set analysis exploiting pathway topology
Gabriele Sales, Enrica Calura, Paolo Martini, Chiara Romualdi
Nucleic Acids Research  ·  10 May 2013  ·  doi:10.1093/nar/gkt386

2012

Overview of Micro- and Nano-Technology Tools for Stem Cell Applications: Micropatterned and Microelectronic Devices
Overview of Micro- and Nano-Technology Tools for Stem Cell Applications: Micropatterned and Microelectronic Devices
Stefano Cagnin, Elisa Cimetta, Carlotta Guiducci, Paolo Martini, Gerolamo Lanfranchi
Sensors  ·  19 Nov 2012  ·  doi:10.3390/s121115947
Along signal paths: an empirical gene set approach exploiting pathway topology
Along signal paths: an empirical gene set approach exploiting pathway topology
Paolo Martini, Gabriele Sales, M. Sofia Massa, Monica Chiogna, Chiara Romualdi
Nucleic Acids Research  ·  21 Sep 2012  ·  doi:10.1093/nar/gks866

2011

Statistical Test of Expression Pattern STEPath : a new strategy to integrate gene expression data with genomic information in individual and meta-analysis studies
Statistical Test of Expression Pattern (STEPath): a new strategy to integrate gene expression data with genomic information in individual and meta-analysis studies
Paolo Martini, Davide Risso, Gabriele Sales, Chiara Romualdi, Gerolamo Lanfranchi, Stefano Cagnin
BMC Bioinformatics  ·  11 Apr 2011  ·  doi:10.1186/1471-2105-12-92

2009

Overview of Electrochemical DNA Biosensors: New Approaches to Detect the Expression of Life
Overview of Electrochemical DNA Biosensors: New Approaches to Detect the Expression of Life
Stefano Cagnin, Marcelo Caraballo, Carlotta Guiducci, Paolo Martini, Marty Ross, Mark SantaAna, David Danley, Todd West, Gerolamo Lanfranchi
Sensors  ·  24 Apr 2009  ·  doi:10.3390/s90403122