Francesco Oteri

Papers

Selected publications in computational biology, bioinformatics, and machine learning

Nucleotide Transformer: building and evaluating robust foundation models for human genomics

Hugo Dalla-Torre,Liam Gonzalez,Javier Mendoza-Revilla,Nicolas Lopez Carranza,Adam Henryk Grzywaczewski,Francesco Oteri,et al.

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iBIS2Analyzer: a web server for a phylogeny-driven coevolution analysis of protein families

Francesco Oteri,Edoardo Sarti,Francesca Nadalin,Alessandra Carbone

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Thumbnail for A large disordered region confers a wide spanning volume to vertebrate Suppressor of Fused as shown in a trans-species solution study

A large disordered region confers a wide spanning volume to vertebrate Suppressor of Fused as shown in a trans-species solution study

Staëlle Makamte,Aurélien Thureau,Amira Jabrani,Annick Paquelin,Anne Plessis,Matthieu Sanial,et al.

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

Riccardo Vicedomini,Clémence Blachon,Francesco Oteri,Alessandra Carbone

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A global metagenomic map of urban microbiomes and antimicrobial resistance

David Danko,Daniela Bezdan,Evan E Afshin,Sofia Ahsanuddin,Chandrima Bhattacharya,Daniel J Butler,et al.

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Phylogenetic reconstruction based on synteny block and gene adjacencies

Guénola Drillon,Raphaël Champeimont,Francesco Oteri,Gilles Fischer,Alessandra Carbone

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COVTree: Coevolution in OVerlapped sequences by Tree analysis server

Elin Teppa,Diego J Zea,Francesco Oteri,Alessandra Carbone

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

Francesco Oteri,Francesca Nadalin,Raphaël Champeimont,Alessandra Carbone

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Residues of alpha helix H3 determine distinctive features of transforming growth factor β3

Shahid M Nayeem,Francesco Oteri,Marc Baaden,Shashank Deep

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Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by direct coupling analysis

Guido Uguzzoni,Shalini John Lovis,Francesco Oteri,Alexander Schug,Hendrik Szurmant,Martin Weigt

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Direct coevolutionary couplings reflect biophysical residue interactions in proteins

Alice Coucke,Guido Uguzzoni,Francesco Oteri,Simona Cocco,Remi Monasson,Martin Weigt

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Molecular mechanism of statin-mediated LOX-1 inhibition

Silvia Biocca,Federico Iacovelli,Sara Matarazzo,Giulia Vindigni,Francesco Oteri,Alessandro Desideri,et al.

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Thumbnail for Multiscale Simulations Give Insight into the Hydrogen In and Out Pathways of [NiFe]-Hydrogenases from Aquifex aeolicus and Desulfovibrio fructosovorans

Multiscale Simulations Give Insight into the Hydrogen In and Out Pathways of [NiFe]-Hydrogenases from Aquifex aeolicus and Desulfovibrio fructosovorans

Francesco Oteri,Marc Baaden,Elisabeth Lojou,Sophie Sacquin-Mora

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Thumbnail for Influence of the single‐strand linker composition on the structural/dynamical properties of a truncated octahedral DNA nano‐cage family

Influence of the single‐strand linker composition on the structural/dynamical properties of a truncated octahedral DNA nano‐cage family

Federico Iacovelli,Cassio Alves,Mattia Falconi,Francesco Oteri,Cristiano LP de Oliveira,Alessandro Desideri

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High warfarin sensitivity in carriers of CYP2C9* 35 is determined by the impaired interaction with P450 oxidoreductase

MY Lee,P Borgiani,I Johansson,F Oteri,S Mkrtchian,M Falconi,et al.

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Thumbnail for The weak, fluctuating, dipole moment of membrane-bound hydrogenase from Aquifex aeolicus accounts for its adaptability to charged electrodes

The weak, fluctuating, dipole moment of membrane-bound hydrogenase from Aquifex aeolicus accounts for its adaptability to charged electrodes

Francesco Oteri,Alexandre Ciaccafava,Anne De Poulpiquet,Marc Baaden,Elisabeth Lojou,Sophie Sacquin-Mora

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Simulative and experimental investigation on the cleavage site that generates the soluble human LOX-1

Silvia Biocca,Tania Arcangeli,Elisa Tagliaferri,Barbara Testa,Giulia Vindigni,Francesco Oteri,et al.

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Thumbnail for Mapping multiple potential ATP binding sites on the matrix side of the bovine ADP/ATP carrier by the combined use of MD simulation and docking

Mapping multiple potential ATP binding sites on the matrix side of the bovine ADP/ATP carrier by the combined use of MD simulation and docking

Daniele Di Marino,Francesco Oteri,Blasco Morozzo della Rocca,Ilda D’Annessa,Mattia Falconi

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Thumbnail for Simulative analysis of a truncated octahedral DNA nanocage family indicates the single-stranded thymidine linkers as the major player for the conformational variability

Simulative analysis of a truncated octahedral DNA nanocage family indicates the single-stranded thymidine linkers as the major player for the conformational variability

Francesco Oteri,Mattia Falconi,Giovanni Chillemi,Felicie F Andersen,Cristiano LP Oliveira,Jan S Pedersen,et al.

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Thumbnail for Effect of the charge distribution along the “ferritin-like” pores of the proteins from the Dps family on the iron incorporation process

Effect of the charge distribution along the “ferritin-like” pores of the proteins from the Dps family on the iron incorporation process

Pierpaolo Ceci,Gisa Di Cecca,Mattia Falconi,Francesco Oteri,Carlotta Zamparelli,Emilia Chiancone

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Thumbnail for Characterization of a novel CYP2C9 gene mutation and structural bioinformatic protein analysis in a warfarin hypersensitive patient

Characterization of a novel CYP2C9 gene mutation and structural bioinformatic protein analysis in a warfarin hypersensitive patient

Cinzia Ciccacci,Mattia Falconi,Nicoletta Paolillo,Francesco Oteri,Vittorio Forte,Giuseppe Novelli,et al.

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Structural-dynamical investigation of the ZnuA histidine-rich loop: involvement in zinc management and transport

Mattia Falconi,Francesco Oteri,Francesco Di Palma,Saurabh Pandey,Andrea Battistoni,Alessandro Desideri

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Thumbnail for Conjugated eicosapentaenoic acid (cEPA) inhibits L. donovani topoisomerase I and has an antiproliferative activity against L. donovani promastigotes

Conjugated eicosapentaenoic acid (cEPA) inhibits L. donovani topoisomerase I and has an antiproliferative activity against L. donovani promastigotes

O Vassallo,S Castelli,A Biswas,S Sengupta,PK Das,I D’Annessa,et al.

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Thumbnail for ADP/ATP mitochondrial carrier MD simulations to shed light on the structural–dynamical events that, after an additional mutation, restore the function in a pathological single …

ADP/ATP mitochondrial carrier MD simulations to shed light on the structural–dynamical events that, after an additional mutation, restore the function in a pathological single …

Daniele Di Marino,Francesco Oteri,Blasco Morozzo Della Rocca,Giovanni Chillemi,Mattia Falconi

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Thumbnail for Structure of nanoscale truncated octahedral DNA cages: variation of single-stranded linker regions and influence on assembly yields

Structure of nanoscale truncated octahedral DNA cages: variation of single-stranded linker regions and influence on assembly yields

Cristiano Luis Pinto Oliveira,Sissel Juul,Hanne Lærke Jørgensen,Bjarne Knudsen,David Tordrup,Francesco Oteri,et al.

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Deciphering the structural properties that confer stability to a DNA nanocage

Mattia Falconi,Francesco Oteri,Giovanni Chillemi,Felicie F Andersen,David Tordrup,Cristiano LP Oliveira,et al.

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Conjugated eicosapentaenoic acid inhibits human topoisomerase IB with a mechanism different from camptothecin

Silvia Castelli,Alessia Campagna,Oscar Vassallo,Cinzia Tesauro,Paola Fiorani,Pietro Tagliatesta,et al.

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MD simulations of papillomavirus DNA-E2 protein complexes hints at a protein structural code for DNA deformation

M Falconi,F Oteri,T Eliseo,DO Cicero,A Desideri

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Structural biology, genomics, and bioinformatics.
Creating and applying computational tools to study biological systems.
Driven by curiosity.

Blog

Blog articles published on medium

Efficient Data Analysis: How ChatGPT Can Help Extract and Summarize Relevant Information from customer reviews

Running Alphafold2 on the serverless platform RunPod

A short guide to Slurm for Biologist transitioning to Computational Biology

Mastering Slurm Job Submissions: From Basics to Advanced Use Cases

Papers

Selected publications in computational biology, bioinformatics, and machine learning

Nucleotide Transformer: building and evaluating robust foundation models for human genomics

iBIS2Analyzer: a web server for a phylogeny-driven coevolution analysis of protein families

A large disordered region confers a wide spanning volume to vertebrate Suppressor of Fused as shown in a trans-species solution study

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

A global metagenomic map of urban microbiomes and antimicrobial resistance

Phylogenetic reconstruction based on synteny block and gene adjacencies

COVTree: Coevolution in OVerlapped sequences by Tree analysis server

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

Residues of alpha helix H3 determine distinctive features of transforming growth factor β3

Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by direct coupling analysis

Direct coevolutionary couplings reflect biophysical residue interactions in proteins

Molecular mechanism of statin-mediated LOX-1 inhibition

Multiscale Simulations Give Insight into the Hydrogen In and Out Pathways of [NiFe]-Hydrogenases from Aquifex aeolicus and Desulfovibrio fructosovorans

Influence of the single‐strand linker composition on the structural/dynamical properties of a truncated octahedral DNA nano‐cage family

High warfarin sensitivity in carriers of CYP2C9* 35 is determined by the impaired interaction with P450 oxidoreductase

The weak, fluctuating, dipole moment of membrane-bound hydrogenase from Aquifex aeolicus accounts for its adaptability to charged electrodes

Simulative and experimental investigation on the cleavage site that generates the soluble human LOX-1

Mapping multiple potential ATP binding sites on the matrix side of the bovine ADP/ATP carrier by the combined use of MD simulation and docking

Simulative analysis of a truncated octahedral DNA nanocage family indicates the single-stranded thymidine linkers as the major player for the conformational variability

Effect of the charge distribution along the “ferritin-like” pores of the proteins from the Dps family on the iron incorporation process

Characterization of a novel CYP2C9 gene mutation and structural bioinformatic protein analysis in a warfarin hypersensitive patient

Structural-dynamical investigation of the ZnuA histidine-rich loop: involvement in zinc management and transport

Conjugated eicosapentaenoic acid (cEPA) inhibits L. donovani topoisomerase I and has an antiproliferative activity against L. donovani promastigotes

ADP/ATP mitochondrial carrier MD simulations to shed light on the structural–dynamical events that, after an additional mutation, restore the function in a pathological single …

Structure of nanoscale truncated octahedral DNA cages: variation of single-stranded linker regions and influence on assembly yields

Deciphering the structural properties that confer stability to a DNA nanocage

Conjugated eicosapentaenoic acid inhibits human topoisomerase IB with a mechanism different from camptothecin

MD simulations of papillomavirus DNA-E2 protein complexes hints at a protein structural code for DNA deformation

Structural biology, genomics, and bioinformatics.Creating and applying computational tools to study biological systems.Driven by curiosity.

Blog

Blog articles published on medium

Efficient Data Analysis: How ChatGPT Can Help Extract and Summarize Relevant Information from customer reviews

Running Alphafold2 on the serverless platform RunPod

A short guide to Slurm for Biologist transitioning to Computational Biology

Mastering Slurm Job Submissions: From Basics to Advanced Use Cases

Papers

Selected publications in computational biology, bioinformatics, and machine learning

Nucleotide Transformer: building and evaluating robust foundation models for human genomics

iBIS2Analyzer: a web server for a phylogeny-driven coevolution analysis of protein families

A large disordered region confers a wide spanning volume to vertebrate Suppressor of Fused as shown in a trans-species solution study

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

A global metagenomic map of urban microbiomes and antimicrobial resistance

Phylogenetic reconstruction based on synteny block and gene adjacencies

COVTree: Coevolution in OVerlapped sequences by Tree analysis server

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

Residues of alpha helix H3 determine distinctive features of transforming growth factor β3

Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by direct coupling analysis

Direct coevolutionary couplings reflect biophysical residue interactions in proteins

Molecular mechanism of statin-mediated LOX-1 inhibition

Multiscale Simulations Give Insight into the Hydrogen In and Out Pathways of [NiFe]-Hydrogenases from Aquifex aeolicus and Desulfovibrio fructosovorans

Influence of the single‐strand linker composition on the structural/dynamical properties of a truncated octahedral DNA nano‐cage family

High warfarin sensitivity in carriers of CYP2C9* 35 is determined by the impaired interaction with P450 oxidoreductase

The weak, fluctuating, dipole moment of membrane-bound hydrogenase from Aquifex aeolicus accounts for its adaptability to charged electrodes

Simulative and experimental investigation on the cleavage site that generates the soluble human LOX-1

Mapping multiple potential ATP binding sites on the matrix side of the bovine ADP/ATP carrier by the combined use of MD simulation and docking

Simulative analysis of a truncated octahedral DNA nanocage family indicates the single-stranded thymidine linkers as the major player for the conformational variability

Effect of the charge distribution along the “ferritin-like” pores of the proteins from the Dps family on the iron incorporation process

Characterization of a novel CYP2C9 gene mutation and structural bioinformatic protein analysis in a warfarin hypersensitive patient

Structural-dynamical investigation of the ZnuA histidine-rich loop: involvement in zinc management and transport

Conjugated eicosapentaenoic acid (cEPA) inhibits L. donovani topoisomerase I and has an antiproliferative activity against L. donovani promastigotes

ADP/ATP mitochondrial carrier MD simulations to shed light on the structural–dynamical events that, after an additional mutation, restore the function in a pathological single …

Structure of nanoscale truncated octahedral DNA cages: variation of single-stranded linker regions and influence on assembly yields

Deciphering the structural properties that confer stability to a DNA nanocage

Conjugated eicosapentaenoic acid inhibits human topoisomerase IB with a mechanism different from camptothecin

MD simulations of papillomavirus DNA-E2 protein complexes hints at a protein structural code for DNA deformation

Structural biology, genomics, and bioinformatics.
Creating and applying computational tools to study biological systems.
Driven by curiosity.