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1

[Methods in Molecular Biology] RNA Editing Volume 2181 (Methods and Protocols) || RNA Editing in Neurological and Neurodegenerative Disorders

Picardi, Ernesto, Pesole, Graziano

Year:

2021

File:

PDF, 386 KB

2021

2

[Methods in Molecular Biology] RNA Editing Volume 2181 (Methods and Protocols) ||

Picardi, Ernesto, Pesole, Graziano

Year:

2021

File:

PDF, 9.06 MB

2021

3

Differences in Gene Expression and Cytokine Release Profiles Highlight the Heterogeneity of Distinct Subsets of Adipose Tissue-Derived Stem Cells in the Subcutaneous and Visceral Adipose Tissue in Humans

Perrini, Sebastio, Ficarella, Romina, Picardi, Ernesto, Cignarelli, Angelo, Barbaro, Maria, Nigro, Pasquale, Peschechera, Alessandro, Palumbo, Orazio, Carella, Massimo, De Fazio, Michele, Natalicchio,

Journal:

Year:

2013

Language:

english

File:

PDF, 813 KB

english, 2013

4

REDIdb 3.0: A Comprehensive Collection of RNA Editing Events in Plant Organellar Genomes

Lo Giudice, Claudio, Pesole, Graziano, Picardi, Ernesto

Journal:

Frontiers in Plant Science

Year:

2018

Language:

english

File:

PDF, 2.93 MB

english, 2018

5

Investigating RNA editing in deep transcriptome datasets with REDItools and REDIportal

Lo Giudice, Claudio, Tangaro, Marco Antonio, Pesole, Graziano, Picardi, Ernesto

Journal:

Nature Protocols

Year:

2020

Language:

english

File:

PDF, 1.14 MB

english, 2020

6

[Methods in Molecular Biology] RNA Bioinformatics Volume 1269 || Analysis of Alternative Splicing Events in Custom Gene Datasets by AStalavista

Picardi, Ernesto

Year:

2015

Language:

english

File:

PDF, 595 KB

english, 2015

7

[Methods in Molecular Biology] RNA Editing Volume 2181 (Methods and Protocols) || High-Throughput Sequencing to Detect DNA-RNA Changes

Picardi, Ernesto, Pesole, Graziano

Year:

2021

File:

PDF, 309 KB

2021

8

Tissue-specific mtDNA abundance from exome data and its correlation with mitochondrial transcription, mass and respiratory activity

D'Erchia, Anna Maria, Atlante, Anna, Gadaleta, Gemma, Pavesi, Giulio, Chiara, Matteo, De Virgilio, Caterina, Manzari, Caterina, Mastropasqua, Francesca, Prazzoli, Gian Marco, Picardi, Ernesto, Gissi,

Journal:

Year:

2015

Language:

english

File:

PDF, 1.12 MB

english, 2015

9

Elucidating the editome: bioinformatics approaches for RNA editing detection

Diroma, Maria Angela, Ciaccia, Loredana, Pesole, Graziano, Picardi, Ernesto

Journal:

Briefings in Bioinformatics

Year:

2017

Language:

english

File:

PDF, 514 KB

english, 2017

10

Characterization of Epstein–Barr virus genotypes in multiple sclerosis through next generation sequencing approaches

Coarelli, Giulia, Manzari, Caterina, Annese, Anita, Anastasiadou, Eleni, Policano, Claudia, D'erchia, Anna Maria, Picardi, Ernesto, Buscarinu, Maria Chiara, Annibali, Viviana, Ricigliano, Vito Ag, Tul

Journal:

Journal of Neuroimmunology

Year:

2014

Language:

english

File:

PDF, 61 KB

english, 2014

11

[Methods in Molecular Biology] RNA Bioinformatics Volume 1269 || RIP-Seq Data Analysis to Determine RNA–Protein Associations

Picardi, Ernesto

Year:

2015

Language:

english

File:

PDF, 280 KB

english, 2015

12

REDIportal: a comprehensive database of A-to-I RNA editing events in humans

Picardi, Ernesto, D'Erchia, Anna Maria, Lo Giudice, Claudio, Pesole, Graziano

Journal:

Nucleic Acids Research

Year:

2016

Language:

english

File:

PDF, 3.09 MB

english, 2016

13

Genome-Wide Analysis of Differentially Expressed Genes and Splicing Isoforms in Clear Cell Renal Cell Carcinoma

Valletti, Alessio, Gigante, Margherita, Palumbo, Orazio, Carella, Massimo, Divella, Chiara, Sbisà, Elisabetta, Tullo, Apollonia, Picardi, Ernesto, D’Erchia, Anna Maria, Battaglia, Michele, Gesualdo, L

Journal:

Year:

2013

Language:

english

File:

PDF, 1.42 MB

english, 2013

14

Changes in gene expression and metabolic profile of drupes of Olea europaea L. cv Carolea in relation to maturation stage and cultivation area

Bruno, Leonardo, Picardi, Ernesto, Pacenza, Marianna, Chiappetta, Adriana, Muto, Antonella, Gagliardi, Olimpia, Muzzalupo, Innocenzo, Pesole, Graziano, Bitonti, Maria Beatrice

Journal:

BMC Plant Biology

Year:

2019

File:

PDF, 3.34 MB

2019

15

Rhodobacter sphaeroides adaptation to high concentrations of cobalt ions requires energetic metabolism changes

Volpicella, Mariateresa, Costanza, Alessandra, Palumbo, Orazio, Italiano, Francesca, Claudia, Leoni, Placido, Antonio, Picardi, Ernesto, Carella, Massimo, Trotta, Massimo, Ceci, Luigi R.

Journal:

FEMS Microbiology Ecology

Year:

2014

Language:

english

File:

PDF, 380 KB

english, 2014

16

The influence of invasive jellyfish blooms on the aquatic microbiome in a coastal lagoon (Varano, SE Italy) detected by an Illumina-based deep sequencing strategy

Manzari, Caterina, Fosso, Bruno, Marzano, Marinella, Annese, Anita, Caprioli, Rosa, D’Erchia, Anna Maria, Gissi, Carmela, Intranuovo, Marianna, Picardi, Ernesto, Santamaria, Monica, Scorrano, Simonett

Journal:

Biological Invasions

Year:

2015

Language:

english

File:

PDF, 560 KB

english, 2015

17

Whole transcriptome profiling of Late-Onset Alzheimer’s Disease patients provides insights into the molecular changes involved in the disease

Annese, Anita, Manzari, Caterina, Lionetti, Claudia, Picardi, Ernesto, Horner, David S., Chiara, Matteo, Caratozzolo, Mariano Francesco, Tullo, Apollonia, Fosso, Bruno, Pesole, Graziano, D’Erchia, Ann

Journal:

Scientific Reports

Year:

2018

Language:

english

File:

PDF, 1.74 MB

english, 2018

18

Changes in gene expression and metabolic profile of drupes of Olea europaea L. cv Carolea in relation to maturation stage and cultivation area

Bruno, Leonardo, Picardi, Ernesto, Pacenza, Marianna, Chiappetta, Adriana, Muto, Antonella, Gagliardi, Olimpia, Muzzalupo, Innocenzo, Pesole, Graziano, Bitonti, Maria Beatrice

Journal:

BMC Plant Biology

Year:

2019

Language:

english

File:

PDF, 3.34 MB

english, 2019

19

[Methods in Molecular Biology] RNA Editing Volume 2181 (Methods and Protocols) || MicroRNA Editing Detection and Function: A Combined In Silico and Experimental Approach for the Identification and Validation of Putative Oncogenic Targets

Picardi, Ernesto, Pesole, Graziano

Year:

2021

File:

PDF, 252 KB

2021

20

EdiPy: A resource to simulate the evolution of plant mitochondrial genes under the RNA editing

Ernesto Picardi, Carla Quagliariello

Journal:

Computational Biology and Chemistry

Year:

2006

Language:

english

File:

PDF, 284 KB

english, 2006

21

MitoZoa: A curated mitochondrial genome database of metazoans for comparative genomics studies

Renato Lupi, Paolo D’Onorio de Meo, Ernesto Picardi, Mattia D’Antonio, Daniele Paoletti, Tiziana Castrignanò, Graziano Pesole, Carmela Gissi

Journal:

Year:

2010

Language:

english

File:

PDF, 1.08 MB

english, 2010

22

REDIdb: An upgraded bioinformatics resource for organellar RNA editing sites

Ernesto Picardi, Teresa M.R. Regina, Daniil Verbitskiy, Axel Brennicke, Carla Quagliariello

Journal:

Year:

2011

Language:

english

File:

PDF, 1017 KB

english, 2011

23

Is plant mitochondrial RNA editing a source of phylogenetic incongruence? An answer fromin silicoandin vivodata sets

Ernesto Picardi, Carla Quagliariello

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 349 KB

english, 2008

24

EasyCluster: a fast and efficient gene-oriented clustering tool for large-scale transcriptome data

Ernesto Picardi, Flavio Mignone, Graziano Pesole

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 336 KB

english, 2009

25

A Novel Computational Strategy to Identify A-to-I RNA Editing Sites by RNA-Seq Data: De Novo Detection in Human Spinal Cord Tissue

Picardi, Ernesto, Gallo, Angela, Galeano, Federica, Tomaselli, Sara, Pesole, Graziano, Banfi, Sandro

Journal:

Year:

2012

Language:

english

File:

PDF, 938 KB

english, 2012

26

The cell line A-to-I RNA editing catalogue

Schaffer, Amos A, Kopel, Eli, Hendel, Ayal, Picardi, Ernesto, Levanon, ErezÂ Y, Eisenberg, Eli

Journal:

Nucleic Acids Research

Year:

2020

File:

PDF, 1.98 MB

2020

27

[Methods in Molecular Biology] RNA Editing Volume 2181 (Methods and Protocols) || RNA Editing in Human and Mouse Tissues

Picardi, Ernesto, Pesole, Graziano

Year:

2021

File:

PDF, 207 KB

2021

28

Quantifying RNA Editing in Deep Transcriptome Datasets

Lo Giudice, Claudio, Silvestris, Domenico Alessandro, Roth, Shalom Hillel, Eisenberg, Eli, Pesole, Graziano, Gallo, Angela, Picardi, Ernesto

Journal:

Frontiers in Genetics

Year:

2020

Language:

english

File:

PDF, 3.68 MB

english, 2020

29

Reduced levels of protein recoding by A-to-I RNA editing in Alzheimer's disease

Khermesh, Khen, D'Erchia, Anna Maria, Barak, Michal, Annese, Anita, Wachtel, Chaim, Levanon, Erez Y., Picardi, Ernesto, Eisenberg, Eli

Journal:

Year:

2015

Language:

english

File:

PDF, 555 KB

english, 2015

30

Investigating Human Mitochondrial Genomes in Single Cells

Diroma, Maria Angela, Varvara, Angelo Sante, Attimonelli, Marcella, Pesole, Graziano, Picardi, Ernesto

Journal:

Year:

2020

File:

PDF, 534 KB

2020

31

HPC-REDItools: a novel HPC-aware tool for improved large scale RNA-editing analysis

Flati, Tiziano, Gioiosa, Silvia, Spallanzani, Nicola, Tagliaferri, Ilario, Diroma, Maria Angela, Pesole, Graziano, Chillemi, Giovanni, Picardi, Ernesto, CastrignanÃ², Tiziana

Journal:

BMC Bioinformatics

Year:

2020

File:

PDF, 2.36 MB

2020

32

A Novel Additional Group II Intron Distinguishes the Mitochondrialrps3Gene in Gymnosperms

Teresa M.R. Regina, Ernesto Picardi, Loredana Lopez, Graziano Pesole, Carla Quagliariello

Journal:

Journal of Molecular Evolution

Year:

2005

Language:

english

File:

PDF, 237 KB

english, 2005

33

Detecting Alternative Gene Structures from Spliced ESTs: A Computational Approach

Bonizzoni, Paola, Mauri, Giancarlo, Pesole, Graziano, Picardi, Ernesto, Pirola, Yuri, Rizzi, Raffaella

Journal:

Journal of Computational Biology

Year:

2009

Language:

english

File:

PDF, 429 KB

english, 2009

34

[Methods in Molecular Biology] RNA Editing Volume 2181 (Methods and Protocols) || Adenosine-to-Inosine RNA Editing Enzyme ADAR and microRNAs

Picardi, Ernesto, Pesole, Graziano

Year:

2021

File:

PDF, 805 KB

2021

35

A polygalacturonase-inhibiting protein with a role in pea defence against the cyst nematode Heterodera goettingiana

PASQUA VERONICO, M. TERESA MELILLO, CONCETTA SAPONARO, PAOLA LEONETTI, ERNESTO PICARDI, JOHN T. JONES

Journal:

Molecular Plant Pathology

Year:

2011

Language:

english

File:

PDF, 1.30 MB

english, 2011

36

EasyCluster2: an improved tool for clustering and assembling long transcriptome reads

Bevilacqua, Vitoantonio, Pietroleonardo, Nicola, Giannino, Ely, Stroppa, Fabio, Simone, Domenico, Pesole, Graziano, Picardi, Ernesto

Journal:

BMC Bioinformatics

Year:

2014

Language:

english

File:

PDF, 944 KB

english, 2014

37

Striking differences in RNA editing requirements to express the rps4 gene in magnolia and sunflower mitochondria

Teresa M.R. Regina, Loredana Lopez, Ernesto Picardi, Carla Quagliariello

Journal:

Year:

2002

Language:

english

File:

PDF, 680 KB

english, 2002

38

Profiling RNA editing in human tissues: towards the inosinome Atlas

Picardi, Ernesto, Manzari, Caterina, Mastropasqua, Francesca, Aiello, Italia, D’Erchia, Anna Maria, Pesole, Graziano

Journal:

Scientific Reports

Year:

2015

Language:

english

File:

PDF, 1.69 MB

english, 2015

39

RNentropy: an entropy-based tool for the detection of significant variation of gene expression across multiple RNA-Seq experiments

Zambelli, Federico, Mastropasqua, Francesca, Picardi, Ernesto, D’Erchia, Anna Maria, Pesole, Graziano, Pavesi, Giulio

Journal:

Nucleic Acids Research

Year:

2018

Language:

english

File:

PDF, 2.58 MB

english, 2018

40

Diagnostic-driven antifungal approach in neutropenic patients at high risk for chronic disseminated candidiasis: preliminary observations on the role of 1,3-β-D-glucan antigenemia and multiphasic contrast-enhanced computed tomography

Della Pepa, Roberta, Cerchione, Claudio, Pugliese, Novella, Colicchio, Roberta, Salvatore, Paola, Sirignano, Cesare, Soscia, Ernesto, Pagano, Livio, Sanguinetti, Maurizio, Pane, Fabrizio, Picardi, Mar

Journal:

Supportive Care in Cancer

Year:

2018

Language:

english

File:

PDF, 1.65 MB

english, 2018

41

ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community

CastrignanÃ², Tiziana, Gioiosa, Silvia, Flati, Tiziano, Cestari, Mirko, Picardi, Ernesto, Chiara, Matteo, Fratelli, Maddalena, Amente, Stefano, Cirilli, Marco, Tangaro, Marco Antonio, Chillemi, Giovan

Journal:

BMC Bioinformatics

Year:

2020

File:

PDF, 1.49 MB

2020

42

Single cell transcriptomics reveals specific RNA editing signatures in the human brain

Picardi, Ernesto, Horner, David Stephen, Pesole, Graziano

Journal:

Year:

2017

Language:

english

File:

PDF, 1.03 MB

english, 2017

43

[Methods in Molecular Biology] RNA Bioinformatics Volume 1269 || Free Energy Minimization to Predict RNA Secondary Structures and Computational RNA Design

Picardi, Ernesto

Year:

2015

Language:

english

File:

PDF, 702 KB

english, 2015

44

PIntron: a fast method for detecting the gene structure due to alternative splicing via maximal pairings of a pattern and a text

Yuri Pirola, Raffaella Rizzi, Ernesto Picardi, Graziano Pesole, Gianluca Della Vedova, Paola Bonizzoni

Journal:

BMC Bioinformatics

Year:

2012

Language:

english

File:

PDF, 453 KB

english, 2012

45

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

D'Antonio, Mattia, D'Onorio De Meo, Paolo, Pallocca, Matteo, Picardi, Ernesto, D'Erchia, Anna Maria, Calogero, Raffaele A, Castrignanò, Tiziana, Pesole, Graziano

Journal:

Year:

2015

Language:

english

File:

PDF, 836 KB

english, 2015

46

REDIportal: millions of novel A-to-I RNA editing events from thousands of RNAseq experiments

Mansi, Luigi, Tangaro, Marco Antonio, LoÂ Giudice, Claudio, Flati, Tiziano, Kopel, Eli, Schaffer, Amos Avraham, CastrignanÃ², Tiziana, Chillemi, Giovanni, Pesole, Graziano, Picardi, Ernesto

Journal:

Nucleic Acids Research

Year:

2020

File:

PDF, 2.09 MB

2020

47

[Methods in Molecular Biology] RNA Bioinformatics Volume 1269 ||

Picardi, Ernesto

Year:

2015

Language:

english

File:

PDF, 22.56 MB

english, 2015

48

CoVaCS: a consensus variant calling system

Chiara, Matteo, Gioiosa, Silvia, Chillemi, Giovanni, D’Antonio, Mattia, Flati, Tiziano, Picardi, Ernesto, Zambelli, Federico, Horner, David Stephen, Pesole, Graziano, Castrignanò, Tiziana

Journal:

Year:

2018

Language:

english

File:

PDF, 919 KB

english, 2018

49

A-GAME: improving the assembly of pooled functional metagenomics sequence data

Chiara, Matteo, Placido, Antonio, Picardi, Ernesto, Ceci, Luigi Ruggiero, Horner, David Stephen, Pesole, Graziano

Journal:

Year:

2018

Language:

english

File:

PDF, 1.38 MB

english, 2018

50

Mitochondrial genomes gleaned from human whole-exome sequencing

Picardi, Ernesto, Pesole, Graziano

Journal:

Year:

2012

Language:

english

File:

PDF, 1007 KB

english, 2012

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