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List of works by Ernesto Picardi

A Machine Learning Approach to Parkinson’s Disease Blood Transcriptomics

scientific article published on 21 April 2022

A Novel Approach to Clustering and Assembly of Large-Scale Roche 454 Transcriptome Data for Gene Validation and Alternative Splicing Analysis

article

A high resolution A-to-I editing map in the mouse identifies editing events controlled by pre-mRNA splicing

scientific article published on 19 August 2019

A novel additional group II intron distinguishes the mitochondrial rps3 gene in gymnosperms.

scientific article published in February 2005

A novel computational strategy to identify A-to-I RNA editing sites by RNA-Seq data: de novo detection in human spinal cord tissue

scientific article

A platform independent RNA-Seq protocol for the detection of transcriptome complexity

scientific article

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

scientific article published on 10 November 2010

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

scientific article published on 12 January 2018

ASPic-GeneID: a lightweight pipeline for gene prediction and alternative isoforms detection

scientific article published on 7 November 2013

ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing

scientific article

ASPicDB: a database resource for alternative splicing analysis.

scientific article published on 3 April 2008

ASPicDB: a database web tool for alternative splicing analysis

scientific article published in January 2015

BCR/ABL1 fusion transcripts generated from alternative splicing: implications for future targeted therapies in Ph+ leukaemias.

scientific article published on June 2012

Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing

scientific article published on 27 October 2009

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

scientific article published on 16 October 2019

Clustering and Assembling Large Transcriptome Datasets by EasyCluster2

article by Vitoantonio Bevilacqua et al published 2013 in Communications in Computer and Information Science

CoVaCS: a consensus variant calling system

scientific article

Computational methods for ab initio and comparative gene finding

scientific article published on January 2010

Correction: Tusup et al. Evaluation of the Interplay between the ADAR Editome and Immunotherapy in Melanoma. Non-Coding RNA 2021, 7, 5

scientific article published on 21 November 2022

Corrigendum: Profiling RNA editing in human tissues: towards the inosinome Atlas.

scientific article published on 8 February 2016

Critical assessment of bioinformatics methods for the characterization of pathological repeat expansions with single-molecule sequencing data

scientific article published on 03 December 2019

Cumulus Cell Transcriptome after Cumulus-Oocyte Complex Exposure to Nanomolar Cadmium in an In Vitro Animal Model of Prepubertal and Adult Age

scientific article published on 4 February 2023

Cyclic AMP induces reversible EPAC1 condensates that regulate histone transcription

scientific article published on 8 September 2023

Detecting alternative gene structures from spliced ESTs: a computational approach

scientific article

Detection of post-transcriptional RNA editing events

scientific article published on January 2015

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

scientific article

Draft genome sequence ofSphingobiumsp. strain ba1, resistant to kanamycin and nickel ions

scientific article published on 01 December 2014

Dynamic inosinome profiles reveal novel patient stratification and gender-specific differences in glioblastoma

scientific article published on 13 February 2019

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

scientific article

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

scientific article

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

scientific article published on 01 February 2006

Elucidating the editome: bioinformatics approaches for RNA editing detection

scientific article published on 11 October 2017

Epstein-Barr virus genetic variants are associated with multiple sclerosis

scientific article

ExpEdit: a webserver to explore human RNA editing in RNA-Seq experiments

scientific article

Exploring the RNA editing potential of RNA-Seq data by ExpEdit

scientific article

Genome-wide analysis of differentially expressed genes and splicing isoforms in clear cell renal cell carcinoma

scientific article

Geographic Population Structure in Epstein-Barr Virus Revealed by Comparative Genomics

scientific article

Investigating Human Mitochondrial Genomes in Single Cells

scientific article published on 11 May 2020

Investigating RNA editing in deep transcriptome datasets with REDItools and REDIportal

scientific article published on 29 January 2020

Lactobacillus rossiae, a vitamin B12 producer, represents a metabolically versatile species within the Genus Lactobacillus

scientific article

Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing

scientific article published on 12 April 2010

MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing

scientific article

Massive transcriptome sequencing of human spinal cord tissues provides new insights into motor neuron degeneration in ALS

scientific article published on 30 August 2017

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

scholarly article by Renato Lupi et al published March 2010 in Mitochondrion

Mitochondrial and Nuclear DNA Variants in Amyotrophic Lateral Sclerosis: Enrichment in the Mitochondrial Control Region and Sirtuin Pathway Genes in Spinal Cord Tissue

scientific article published on 28 March 2024

Mitochondrial genomes gleaned from human whole-exome sequencing ⬇️

scientific article published on May 30, 2012

Mitofusin 2 mutation drives cell proliferation in Charcot-Marie-Tooth 2A fibroblasts

scientific article published on 22 August 2022

New Tools for Expression Alternative Splicing Validation

Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities

scientific article published on 07 December 2020

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

scientific article

Phylogenetic comparison of huntingtin homologues reveals the appearance of a primitive polyQ in sea urchin

scientific article published on 28 November 2007

Profiling RNA editing in human tissues: towards the inosinome Atlas

scientific article

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

scientific article published on June 2015

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

scientific article published on 11 April 2018

REDIdb: an upgraded bioinformatics resource for organellar RNA editing sites

scientific article published on November 6, 2010

REDIdb: the RNA editing database.

scientific article published on 14 December 2006

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

scientific article

REDItools: high-throughput RNA editing detection made easy

scientific article

RNA editing has been lost in the mitochondrial cox3 and rps13 mRNAs in Asparagales.

scientific article

RNA editing in plants: A comprehensive survey of bioinformatics tools and databases

scientific article published on 02 February 2019

RNA editing signature during myeloid leukemia cell differentiation.

scientific article published on 9 May 2017

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

scientific article published on 30 January 2018

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

scientific article

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

scientific article

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

scientific article

SpliceAid-F: a database of human splicing factors and their RNA-binding sites

scientific article

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

scientific article

Structural and Comparative Analyses of Insects Suggest the Presence of an Ultra-Conserved Regulatory Element of the Genes Encoding Vacuolar-Type ATPase Subunits and Assembly Factors

scientific article published on 13 August 2023

The ADAR1 editome reveals drivers of editing-specificity for ADAR1-isoforms

scientific article published on 7 April 2023

The cell line A-to-I RNA editing catalogue

scientific article published on 08 May 2020

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

article

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

scientific article

Transcriptional Analysis of Acinetobacter sp. neg1 Capable of Degrading Ochratoxin A.

scientific article published on January 2016

Transcriptome Assembly and Alternative Splicing Analysis

Transcriptomic analysis of nickel exposure in Sphingobium sp. ba1 cells using RNA-seq

scientific article published on 15 August 2017

UTRdb 2.0: a comprehensive, expert curated catalog of eukaryotic mRNAs untranslated regions

scientific article published on 18 November 2022

UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs

scientific article

Uncovering RNA Editing Sites in Long Non-Coding RNAs.

scientific article published on 5 December 2014

Using REDItools to Detect RNA Editing Events in NGS Datasets.

scientific article published on 9 March 2015

WEP: a high-performance analysis pipeline for whole-exome data

scientific article

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

scientific article published on 9 March 2018

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