List of works - Alessandra Carbone

3D Fractal DNA Assembly from Coding, Geometry and Protection

article

A Question of Time

A combinatorial approach to detect coevolved amino acid networks in protein families of variable divergence

scientific article

A discriminative method for family-based protein remote homology detection that combines inductive logic programming and propositional models

scientific article

A multi-objective optimization approach accurately resolves protein domain architectures

scientific article published on 12 October 2015

A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling

scientific article published on 28 August 2018

A new mapping between combinatorial proofs and sequent calculus proofs read out from logical flow graphs

article

Asymptotic Cyclic Expansion and Bridge Groups of Formal Proofs

BIS2Analyzer: a server for co-evolution analysis of conserved protein families

scientific article published on 2 May 2017

Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment

scientific article published on 25 October 2019

CLAG: an unsupervised non hierarchical clustering algorithm handling biological data

scientific article

Chromosomal periodicity and positional networks of genes in Escherichia coli

scientific article

Circuits and programmable self-assembling DNA structures

scientific article

Co-evolution and Information Signals in Biological Sequences

Co-evolution and information signals in biological sequences

Codon Bias is a Major Factor Explaining Phage Evolution in Translationally Biased Hosts

article

Codon adaptation index as a measure of dominating codon bias.

scientific article published in November 2003

Codon bias signatures, organization of microorganisms in codon space, and lifestyle

scientific article published on 10 November 2004

Coevolution analysis of Hepatitis C virus genome to identify the structural and functional dependency network of viral proteins

scientific article published on 20 May 2016

Coevolution analysis of amino-acids reveals diversified drug-resistance solutions in viral sequences: a case study of hepatitis B virus

scientific article published on 01 January 2020

Combinatorics of chromosomal rearrangements based on synteny blocks and synteny packs

Computability in Europe 2010

Computational prediction of genomic functional cores specific to different microbes.

scientific article published on 10 November 2006

Decrypting protein surfaces by combining evolution, geometry, and molecular docking

scientific article published on 26 June 2019

Diatom Phytochromes Reveal the Existence of Far-Red-Light-Based Sensing in the Ocean.

scientific article published on 3 March 2016

Dissecting protein architecture with communication blocks and communicating segment pairs

scientific article published on 20 January 2016

Environmental and Physiological Insights from Microbial Genome Sequences

Extracting Coevolving Characters from a Tree of Species

article published in 2013

From complete cross-docking to partners identification and binding sites predictions

scientific article published on 28 January 2022

Functional labels and syntactic entropy on DNA strings and proteins

Great Interactions: Binding Incorrect Partners to Learn about Protein Recognition and Function

Great interactions: How binding incorrect partners can teach us about protein recognition and function

scientific article published on 10 June 2016

Group Cancellation and Resolution

Histone H1 protects telomeric repeats from H3K27me3 invasion in Arabidopsis

scientific article published in 2023

INTerface Builder: a fast protein-protein interface reconstruction tool

scientific article published on 9 October 2017

Identification of Plasmodium falciparum nuclear proteins by mass spectrometry and proposed protein annotation

scientific article published in PLoS ONE

Identification of Protein Interaction Partners from Shape Complementarity Molecular Cross-Docking

Identification of protein interaction partners and protein-protein interaction sites

scientific article published on 7 August 2008

Improvement in Protein Domain Identification Is Reached by Breaking Consensus, with the Agreement of Many Profiles and Domain Co-occurrence

scientific article

Information Content of Sets of Biological Sequences Revisited

Insights on the evolution of metabolic networks of unicellular translationally biased organisms from transcriptomic data and sequence analysis

scientific article

JET2 Viewer: a database of predicted multiple, possibly overlapping, protein-protein interaction sites for PDB structures

scientific article published on 28 November 2016

JET2 Viewer: a database of predicted multiple, possibly overlapping, protein-protein interaction sites for PDB structures

scientific article published on 7 December 2016

Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence sampling

scientific article

Large scale chromosomal mapping of human microRNA structural clusters

scientific article

Local Geometry and Evolutionary Conservation of Protein Surfaces Reveal the Multiple Recognition Patches in Protein-Protein Interactions

scientific article

Local Geometry and Evolutionary Conservation of Protein Surfaces Reveal the Multiple Recognition Patches in Protein-Protein Interactions

Logical structures and genus of proofs

article

MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data

scientific article

Marine diatoms change their gene expression profile when exposed to microscale turbulence under nutrient replete conditions

scientific article

Meet-U: Educating through research immersion.

scientific article published on 15 March 2018

Modelling macromolecular networks: two meetings in Paris, July, 2002

scholarly article by François Képès & Alessandra Carbone published 22 November 2002 in BioEssays

Much shorter proofs: A bimodal investigation

Multiple protein-DNA interfaces unravelled by evolutionary information, physico-chemical and geometrical properties

scientific article published on 03 February 2020

MyCLADE: a multi-source domain annotation server for sequence functional exploration

scientific article published on 01 July 2021

New highly divergent rRNA sequence among biodiverse genotypes of Enterocytozoon bieneusi strains isolated from humans in Gabon and Cameroon.

scientific article

Pattern Formation in Biology, Vision and Dynamics

article

Pattern Formation in Biology, Vision and Dynamics

Periodic distributions of hydrophobic amino acids allows the definition of fundamental building blocks to align distantly related proteins.

scientific article published in May 2007

Plasmobase: a comparative database of predicted domain architectures for Plasmodium genomes

scientific article published on 7 June 2017

Predicting substitutions to modulate disorder and stability in coiled-coils

scientific article published on 21 December 2020

Preface

Protein fragments: functional and structural roles of their coevolution networks

scientific article

Protein social behavior makes a stronger signal for partner identification than surface geometry

scientific article (publication date: 2017)

Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information

scientific article (publication date: 2013)

Provable Fixed Points

Provable fixed points in ${\rm I}\Delta_0+\Omega_1$

Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus

scientific article published on 31 May 2016

Rosser Orderings in Bimodal Logics

SPoRE: a mathematical model to predict double strand breaks and axis protein sites in meiosis

scientific article published on 11 December 2014

Streams and strings in formal proofs

SynChro: a fast and easy tool to reconstruct and visualize synteny blocks along eukaryotic chromosomes

scientific article

The complexity of protein interactions unravelled from structural disorder

scientific article published on 08 January 2021

The diversity of small non-coding RNAs in the diatom Phaeodactylum tricornutum

scientific article

List of works by Alessandra Carbone

3D Fractal DNA Assembly from Coding, Geometry and Protection

A Question of Time

A combinatorial approach to detect coevolved amino acid networks in protein families of variable divergence

A discriminative method for family-based protein remote homology detection that combines inductive logic programming and propositional models

A multi-objective optimization approach accurately resolves protein domain architectures

A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling

A new mapping between combinatorial proofs and sequent calculus proofs read out from logical flow graphs

Asymptotic Cyclic Expansion and Bridge Groups of Formal Proofs

BIS2Analyzer: a server for co-evolution analysis of conserved protein families

Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment

CLAG: an unsupervised non hierarchical clustering algorithm handling biological data

Chromosomal periodicity and positional networks of genes in Escherichia coli

Circuits and programmable self-assembling DNA structures

Co-evolution and Information Signals in Biological Sequences

Co-evolution and information signals in biological sequences

Codon Bias is a Major Factor Explaining Phage Evolution in Translationally Biased Hosts

Codon adaptation index as a measure of dominating codon bias.

Codon bias signatures, organization of microorganisms in codon space, and lifestyle

Coevolution analysis of Hepatitis C virus genome to identify the structural and functional dependency network of viral proteins

Coevolution analysis of amino-acids reveals diversified drug-resistance solutions in viral sequences: a case study of hepatitis B virus

Combinatorics of chromosomal rearrangements based on synteny blocks and synteny packs

Computability in Europe 2010

Computational prediction of genomic functional cores specific to different microbes.

Decrypting protein surfaces by combining evolution, geometry, and molecular docking

Diatom Phytochromes Reveal the Existence of Far-Red-Light-Based Sensing in the Ocean.

Dissecting protein architecture with communication blocks and communicating segment pairs

Environmental and Physiological Insights from Microbial Genome Sequences

Extracting Coevolving Characters from a Tree of Species

From complete cross-docking to partners identification and binding sites predictions

Functional labels and syntactic entropy on DNA strings and proteins

Great Interactions: Binding Incorrect Partners to Learn about Protein Recognition and Function

Great interactions: How binding incorrect partners can teach us about protein recognition and function

Group Cancellation and Resolution

Histone H1 protects telomeric repeats from H3K27me3 invasion in Arabidopsis

INTerface Builder: a fast protein-protein interface reconstruction tool

Identification of Plasmodium falciparum nuclear proteins by mass spectrometry and proposed protein annotation

Identification of Protein Interaction Partners from Shape Complementarity Molecular Cross-Docking

Identification of protein interaction partners and protein-protein interaction sites

Improvement in Protein Domain Identification Is Reached by Breaking Consensus, with the Agreement of Many Profiles and Domain Co-occurrence

Information Content of Sets of Biological Sequences Revisited

Insights on the evolution of metabolic networks of unicellular translationally biased organisms from transcriptomic data and sequence analysis

JET2 Viewer: a database of predicted multiple, possibly overlapping, protein-protein interaction sites for PDB structures

JET2 Viewer: a database of predicted multiple, possibly overlapping, protein-protein interaction sites for PDB structures

Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence sampling

Large scale chromosomal mapping of human microRNA structural clusters

Local Geometry and Evolutionary Conservation of Protein Surfaces Reveal the Multiple Recognition Patches in Protein-Protein Interactions

Local Geometry and Evolutionary Conservation of Protein Surfaces Reveal the Multiple Recognition Patches in Protein-Protein Interactions

Logical structures and genus of proofs

MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data

Marine diatoms change their gene expression profile when exposed to microscale turbulence under nutrient replete conditions

Meet-U: Educating through research immersion.

Modelling macromolecular networks: two meetings in Paris, July, 2002

Much shorter proofs: A bimodal investigation

Multiple protein-DNA interfaces unravelled by evolutionary information, physico-chemical and geometrical properties

MyCLADE: a multi-source domain annotation server for sequence functional exploration

New highly divergent rRNA sequence among biodiverse genotypes of Enterocytozoon bieneusi strains isolated from humans in Gabon and Cameroon.

Pattern Formation in Biology, Vision and Dynamics

Pattern Formation in Biology, Vision and Dynamics

Periodic distributions of hydrophobic amino acids allows the definition of fundamental building blocks to align distantly related proteins.

Plasmobase: a comparative database of predicted domain architectures for Plasmodium genomes

Predicting substitutions to modulate disorder and stability in coiled-coils

Preface

Protein fragments: functional and structural roles of their coevolution networks

Protein social behavior makes a stronger signal for partner identification than surface geometry

Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information

Provable Fixed Points

Provable fixed points in ${\rm I}\Delta_0+\Omega_1$

Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus

Rosser Orderings in Bimodal Logics

SPoRE: a mathematical model to predict double strand breaks and axis protein sites in meiosis

Streams and strings in formal proofs

SynChro: a fast and easy tool to reconstruct and visualize synteny blocks along eukaryotic chromosomes

The complexity of protein interactions unravelled from structural disorder

The diversity of small non-coding RNAs in the diatom Phaeodactylum tricornutum