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1

Human DNA methylomes at base resolution show widespread epigenomic differences

Lister, Ryan, Pelizzola, Mattia, Dowen, Robert H., Hawkins, R. David, Hon, Gary, Tonti-Filippini, Julian, Nery, Joseph R., Lee, Leonard, Ye, Zhen, Ngo, Que-Minh

Journal:

Année:

2009

Langue:

english

Fichier:

PDF, 1.42 MB

english, 2009

2

Degradation dynamics of microRNAs revealed by a novel pulse-chase approach

Marzi, Matteo J, Ghini, Francesco, Cerruti, Benedetta, de Pretis, Stefano, Bonetti, Paola, Giacomelli, Chiara, Gorski, Marcin G, Kress, Theresia, Pelizzola, Mattia, Muller, Heiko, Amati, Bruno, Nicass

Journal:

Genome Research

Année:

2016

Langue:

english

Fichier:

PDF, 5.84 MB

english, 2016

3

Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis

Chang, Katherine Noelani, Zhong, Shan, Weirauch, Matthew T, Hon, Gary, Pelizzola, Mattia, Li, Hai, Huang, Shao-shan Carol, Schmitz, Robert J, Urich, Mark A, Kuo, Dwight, Nery, Joseph R, Qiao, Hong, Ya

Journal:

Année:

2013

Langue:

english

Fichier:

PDF, 1.15 MB

english, 2013

4

A critical role for lipophosphoglycan in proinflammatory responses of dendritic cells to Leishmania mexicana

Toni Aebischer, Clare L. Bennett, Mattia Pelizzola, Caterina Vizzardelli, Norman Pavelka, Matteo Urbano, Monica Capozzoli, Alessandra Luchini, Thomas Ilg, Francesca Granucci, C. Clare Blackburn, Paola

Journal:

European Journal of Immunology

Année:

2005

Langue:

english

Fichier:

PDF, 424 KB

english, 2005

5

Effects of dexamethazone on LPS-induced activationand migration of mouse dendritic cells revealed by a genome-wide transcriptional analysis

Caterina Vizzardelli, Norman Pavelka, Alessandra Luchini, Ivan Zanoni, Lee Bendickson, Mattia Pelizzola, Ottavio Beretta, Maria Foti, Francesca Granucci, Marit Nilsen-Hamilton, Paola Ricciardi-Castagn

Journal:

European Journal of Immunology

Année:

2006

Langue:

english

Fichier:

PDF, 558 KB

english, 2006

6

Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

Lister, Ryan, Pelizzola, Mattia, Kida, Yasuyuki S., Hawkins, R. David, Nery, Joseph R., Hon, Gary, Antosiewicz-Bourget, Jessica, O’Malley, Ronan, Castanon, Rosa, Klugman, Sarit

Journal:

Année:

2011

Langue:

english

Fichier:

PDF, 1.56 MB

english, 2011

7

Temporal gene expression profile of the hippocampus following trace fear conditioning

Alessandra Sirri, Veronica Bianchi, Mattia Pelizzola, Manuel Mayhaus, Paola Ricciardi-Castagnoli, Daniela Toniolo, Patrizia D'Adamo

Journal:

Année:

2010

Langue:

english

Fichier:

PDF, 678 KB

english, 2010

8

The DNA methylome

Mattia Pelizzola, Joseph R. Ecker

Journal:

Année:

2011

Langue:

english

Fichier:

PDF, 473 KB

english, 2011

9

A power law global error model for the identification of differentially expressed genes in microarray data

Norman Pavelka, Mattia Pelizzola, Caterina Vizzardelli, Monica Capozzoli, Andrea Splendiani, Francesca Granucci, Paola Ricciardi-Castagnoli

Journal:

BMC Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 1.62 MB

english, 2004

10

AMDA: an R package for the automated microarray data analysis

Mattia Pelizzola, Norman Pavelka, Maria Foti, Paola Ricciardi-Castagnoli

Journal:

BMC Bioinformatics

Année:

2006

Langue:

english

Fichier:

PDF, 733 KB

english, 2006

11

The Genopolis Microarray Database

Andrea Splendiani, Marco Brandizi, Gael Even, Ottavio Beretta, Norman Pavelka, Mattia Pelizzola, Manuel Mayhaus, Maria Foti, Giancarlo Mauri, Paola Ricciardi-Castagnoli

Journal:

BMC Bioinformatics

Année:

2007

Langue:

english

Fichier:

PDF, 1.02 MB

english, 2007

12

Distinct Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells

R. David Hawkins, Gary C. Hon, Leonard K. Lee, QueMinh Ngo, Ryan Lister, Mattia Pelizzola, Lee E. Edsall, Samantha Kuan, Ying Luu, Sarit Klugman, Jessica Antosiewicz-Bourget, Zhen Ye, Celso Espinoza,

Journal:

Année:

2010

Langue:

english

Fichier:

PDF, 2.23 MB

english, 2010

13

Patterns of population epigenomic diversity

Schmitz, Robert J., Schultz, Matthew D., Urich, Mark A., Nery, Joseph R., Pelizzola, Mattia, Libiger, Ondrej, Alix, Andrew, McCosh, Richard B., Chen, Huaming, Schork, Nicholas J., Ecker, Joseph R.

Journal:

Année:

2013

Langue:

english

Fichier:

PDF, 2.70 MB

english, 2013

14

Microarray-based analysis of recombinant protein production inE. coli

Ronan O'Dwyer, Xuejun Hu, Mattia Pelizzola, Olga Kolaj…

Journal:

Microbial Cell Factories

Année:

2006

Langue:

english

Fichier:

PDF, 741 KB

english, 2006

15

Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis

Sabò, Arianna, Kress, Theresia R., Pelizzola, Mattia, de Pretis, Stefano, Gorski, Marcin M., Tesi, Alessandra, Morelli, Marco J., Bora, Pranami, Doni, Mirko, Verrecchia, Alessandro, Tonelli, Claudia,

Journal:

Année:

2014

Langue:

english

Fichier:

PDF, 6.20 MB

english, 2014

16

Corrigendum: Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

Lister, Ryan, Pelizzola, Mattia, Kida, Yasuyuki S., Hawkins, R. David, Nery, Joseph R., Hon, Gary, Antosiewicz-Bourget, Jessica, O’Malley, Ronan, Castanon, Rosa, Klugman, Sarit, Downes, Michael, Yu, R

Journal:

Année:

2014

Langue:

english

Fichier:

PDF, 28 KB

english, 2014

17

DOTS-Finder: a comprehensive tool for assessing driver genes in cancer genomes

Melloni, Giorgio EM, Ogier, Alessandro GE, de Pretis, Stefano, Mazzarella, Luca, Pelizzola, Mattia, Pelicci, Pier, Riva, Laura

Journal:

Genome Medicine

Année:

2014

Langue:

english

Fichier:

PDF, 1.75 MB

english, 2014

18

Computational epigenomics: challenges and opportunities

Robinson, Mark D., Pelizzola, Mattia

Journal:

Frontiers in Genetics

Année:

2015

Langue:

english

Fichier:

PDF, 180 KB

english, 2015

19

Computational and experimental methods to decipher the epigenetic code

de Pretis, Stefano, Pelizzola, Mattia

Journal:

Frontiers in Genetics

Année:

2014

Langue:

english

Fichier:

PDF, 1.87 MB

english, 2014

20

Selective transcriptional regulation by Myc: Experimental design and computational analysis of high-throughput sequencing data

Pelizzola, Mattia, Morelli, Marco J., Sabò, Arianna, Kress, Theresia R., de Pretis, Stefano, Amati, Bruno

Journal:

Année:

2015

Langue:

english

Fichier:

PDF, 198 KB

english, 2015

21

Ontology-based annotations and semantic relations in large-scale (epi)genomics data

Galeota, Eugenia, Pelizzola, Mattia

Journal:

Briefings in Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 783 KB

english, 2016

22

methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data

Kishore, Kamal, de Pretis, Stefano, Lister, Ryan, Morelli, Marco J., Bianchi, Valerio, Amati, Bruno, Ecker, Joseph R., Pelizzola, Mattia

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 2.25 MB

english, 2015

23

LowMACA: exploiting protein family analysis for the identification of rare driver mutations in cancer

Melloni, Giorgio E. M., de Pretis, Stefano, Riva, Laura, Pelizzola, Mattia, Céol, Arnaud, Costanza, Jole, Müller, Heiko, Zammataro, Luca

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.42 MB

english, 2016

24

Mycobacterium tuberculosis exploits the formation of new blood vessels for its dissemination

Polena, Helena, Boudou, Frédéric, Tilleul, Sylvain, Dubois-Colas, Nicolas, Lecointe, Cécile, Rakotosamimanana, Niaina, Pelizzola, Mattia, Andriamandimby, Soa Fy, Raharimanga, Vaomalala, Charles, Patri

Journal:

Scientific Reports

Année:

2016

Langue:

english

Fichier:

PDF, 2.08 MB

english, 2016

25

Integrative classification of human coding and noncoding genes through RNA metabolism profiles

Mukherjee, Neelanjan, Calviello, Lorenzo, Hirsekorn, Antje, de Pretis, Stefano, Pelizzola, Mattia, Ohler, Uwe

Journal:

Nature Structural and Molecular Biology

Année:

2016

Langue:

english

Fichier:

PDF, 3.54 MB

english, 2016

26

Integrative analysis of RNA polymerase II and transcriptional dynamics upon MYC activation

de Pretis, Stefano, Kress, Theresia R., Morelli, Marco J., Sabò, Arianna, Locarno, Chiara, Verrecchia, Alessandro, Doni, Mirko, Campaner, Stefano, Amati, Bruno, Pelizzola, Mattia

Journal:

Genome Research

Année:

2017

Langue:

english

Fichier:

PDF, 5.80 MB

english, 2017

27

Probing Host Pathogen Cross-Talk by Transcriptional Profiling of Both Mycobacterium tuberculosis and Infected Human Dendritic Cells and Macrophages

Tailleux, Ludovic, Waddell, Simon J., Pelizzola, Mattia, Mortellaro, Alessandra, Withers, Michael, Tanne, Antoine, Castagnoli, Paola Ricciardi, Gicquel, Brigitte, Stoker, Neil G., Butcher, Philip D.,

Journal:

Année:

2008

Langue:

english

Fichier:

PDF, 871 KB

english, 2008

28

Integrative Analysis of Epigenetic Modulation in Melanoma Cell Response to Decitabine: Clinical Implications

Halaban, Ruth, Krauthammer, Michael, Pelizzola, Mattia, Cheng, Elaine, Kovacs, Daniela, Sznol, Mario, Ariyan, Stephan, Narayan, Deepak, Bacchiocchi, Antonella, Molinaro, Annette, Kluger, Yuval, Deng,

Journal:

Année:

2009

Langue:

english

Fichier:

PDF, 1.85 MB

english, 2009

29

DNA methylation dynamics during embryonic development and postnatal maturation of the mouse auditory sensory epithelium

Yizhar-Barnea, Ofer, Valensisi, Cristina, Jayavelu, Naresh Doni, Kishore, Kamal, Andrus, Colin, Koffler-Brill, Tal, Ushakov, Kathy, Perl, Kobi, Noy, Yael, Bhonker, Yoni, Pelizzola, Mattia, Hawkins, R.

Journal:

Scientific Reports

Année:

2018

Langue:

english

Fichier:

PDF, 5.54 MB

english, 2018

30

An early Myc‐dependent transcriptional program orchestrates cell growth during B‐cell activation

Tesi, Alessandra, Pretis, Stefano, Furlan, Mattia, Filipuzzi, Marco, Morelli, Marco J, Andronache, Adrian, Doni, Mirko, Verrecchia, Alessandro, Pelizzola, Mattia, Amati, Bruno, Sabò, Arianna

Journal:

Année:

2019

Langue:

english

Fichier:

PDF, 2.88 MB

english, 2019

31

An early Myc‐dependent transcriptional program orchestrates cell growth during B‐cell activation

Tesi, Alessandra, Pretis, Stefano, Furlan, Mattia, Filipuzzi, Marco, Morelli, Marco J, Andronache, Adrian, Doni, Mirko, Verrecchia, Alessandro, Pelizzola, Mattia, Amati, Bruno, Sabò, Arianna

Journal:

Année:

2019

Fichier:

PDF, 2.88 MB

2019

32

A dual role of dLsd1 in oogenesis: regulating developmental genes and repressing transposons

Lepesant, Julie M J, Iampietro, Carole, Galeota, Eugenia, Augé, Benoit, Aguirrenbengoa, Marion, Mercé, Clemèntine, Chaubet, Camille, Rocher, Vincent, Haenlin, Marc, Waltzer, Lucas, Pelizzola, Mattia,

Journal:

Nucleic Acids Research

Année:

2019

Fichier:

PDF, 6.64 MB

2019

33

Ontology-driven integrative analysis of omics data through Onassis

Galeota, Eugenia, Kishore, Kamal, Pelizzola, Mattia

Journal:

Scientific Reports

Année:

2020

Langue:

english

Fichier:

PDF, 3.00 MB

english, 2020

34

Direct RNA Sequencing for the Study of Synthesis, Processing, and Degradation of Modified Transcripts

Furlan, Mattia, Tanaka, Iris, Leonardi, Tommaso, de Pretis, Stefano, Pelizzola, Mattia

Journal:

Frontiers in Genetics

Année:

2020

Fichier:

PDF, 1.51 MB

2020

35

INSPEcT-GUI Reveals the Impact of the Kinetic Rates of RNA Synthesis, Processing, and Degradation, on Premature and Mature RNA Species

de Pretis, Stefano, Furlan, Mattia, Pelizzola, Mattia

Journal:

Frontiers in Genetics

Année:

2020

Fichier:

PDF, 1.86 MB

2020

36

Genome-wide dynamics of RNA synthesis, processing, and degradation without RNA metabolic labeling

Furlan, Mattia, Galeota, Eugenia, Gaudio, Nunzio Del, Dassi, Erik, Caselle, Michele, de Pretis, Stefano, Pelizzola, Mattia

Journal:

Genome Research

Année:

2020

Fichier:

PDF, 12.48 MB

2020

37

Editorial: Computational Epitranscriptomics: Bioinformatic Approaches for the Analysis of RNA Modifications

Dassi, Erik, Baranov, Pavel V., Pelizzola, Mattia

Journal:

Frontiers in Genetics

Année:

2020

Fichier:

PDF, 105 KB

2020

38

Dynamics of transcriptional and post-transcriptional regulation

Furlan, Mattia, de Pretis, Stefano, Pelizzola, Mattia

Journal:

Briefings in Bioinformatics

Année:

2020

Fichier:

PDF, 795 KB

2020