List of works - Paolo Di Tommaso

AMPA: an automated web server for prediction of protein antimicrobial regions.

scientific article published on 3 November 2011

Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee

scientific article

Approaches for containerized scientific workflows in cloud environments with applications in life science

Cloud-Coffee: implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud

scientific article published on 6 July 2010

Fast and accurate large multiple sequence alignments using root-to-leave regressive computation:

Generalized Bootstrap Supports for Phylogenetic Analyses of Protein Sequences Incorporating Alignment Uncertainty

scientific article published on 01 November 2018

Incorporating alignment uncertainty into Felsenstein’s phylogenetic bootstrap to improve its reliability

scientific article published on 06 February 2019

Large multiple sequence alignments with a root-to-leaf regressive method

scientific article published on 02 December 2019

Multiple Sequence Alignment Computation Using the T-Coffee Regressive Algorithm Implementation

scientific article published on 01 January 2021

Nextflow

Open source workflow software

Nextflow enables reproducible computational workflows

scientific article

Nextflow, an efficient tool to improve computation numerical stability in genomic analysis

scientific article published in January 2017

SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments

scientific article

Scalable Workflows and Reproducible Data Analysis for Genomics

scientific article published on 01 January 2019

T-Coffee: Tree-based consistency objective function for alignment evaluation

scientific article published in January 2014

T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension

scientific article

T-RMSD: a web server for automated fine-grained protein structural classification ⬇️

scientific article published on May 28, 2013

TCS: a new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction

scientific article (publication date: June 2014)

TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction

scientific article

The impact of Docker containers on the performance of genomic pipelines

scientific article

The impact of Docker containers on the performance of genomic pipelines

The nf-core framework for community-curated bioinformatics pipelines

scientific article published on 01 March 2020

Using the Nextflow framework for reproducible in-silico omics analyses across clusters and clouds

Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures

scientific article published on November 2011

nf-core: Community curated bioinformatics pipelines

scientific article

List of works by Paolo Di Tommaso

AMPA: an automated web server for prediction of protein antimicrobial regions.

Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee

Approaches for containerized scientific workflows in cloud environments with applications in life science

Cloud-Coffee: implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud

Fast and accurate large multiple sequence alignments using root-to-leave regressive computation:

Generalized Bootstrap Supports for Phylogenetic Analyses of Protein Sequences Incorporating Alignment Uncertainty

Incorporating alignment uncertainty into Felsenstein’s phylogenetic bootstrap to improve its reliability

Large multiple sequence alignments with a root-to-leaf regressive method

Multiple Sequence Alignment Computation Using the T-Coffee Regressive Algorithm Implementation

Nextflow

Nextflow enables reproducible computational workflows

Nextflow, an efficient tool to improve computation numerical stability in genomic analysis

SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments

Scalable Workflows and Reproducible Data Analysis for Genomics

T-Coffee: Tree-based consistency objective function for alignment evaluation

T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension

T-RMSD: a web server for automated fine-grained protein structural classification ⬇️

TCS: a new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction

TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction

The impact of Docker containers on the performance of genomic pipelines

The impact of Docker containers on the performance of genomic pipelines

The nf-core framework for community-curated bioinformatics pipelines

Using the Nextflow framework for reproducible in-silico omics analyses across clusters and clouds

Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures

nf-core: Community curated bioinformatics pipelines