List of works - Giovanni Chillemi

A coupled molecular dynamics and XANES data analysis investigation of aqueous cadmium(II).

scientific article

A gene expression atlas for different kinds of stress in the mouse brain

scientific article published on 16 December 2020

A molecular dynamics simulation study decodes the early stage of the disassembly process abolishing the human SAMHD1 function

scientific article published on March 2017

A single mutation in the 729 residue modulates human DNA topoisomerase IB DNA binding and drug resistance.

scientific article published on 4 September 2008

A specific transcriptional response of yeast cells to camptothecin dependent on the Swi4 and Mbp1 factors

scientific article published on 09 December 2008

A tool for sheep product quality: custom microarrays from public databases.

scientific article published on February 2009

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 mutant

scientific article published on 3 August 2010

Analysis of co-receptor usage of circulating viral and proviral HIV genome quasispecies by ultra-deep pyrosequencing in patients who are candidates for CCR5 antagonist treatment.

scientific article published on 5 November 2010

Anti-Inflammatory Potential of Cow, Donkey and Goat Milk Extracellular Vesicles as Revealed by Metabolomic Profile

scientific article published on 23 September 2020

Antisense transcripts enhanced by camptothecin at divergent CpG-island promoters associated with bursts of topoisomerase I-DNA cleavage complex and R-loop formation

scientific article published on 2 September 2013

Archived HIV-1 minority variants detected by ultra-deep pyrosequencing in provirus may be fully replication competent

scientific article published in November 2009

Assembly and characterization of pandemic influenza A H1N1 genome in nasopharyngeal swabs using high-throughput pyrosequencing.

scientific article

Assignment of UV-vis spectrum of (3,3')-diindolylmethane, a Leishmania donovani topoisomerase IB inhibitor and a candidate DNA minor groove binder.

scientific article published in July 2010

Biallelic Mutations in TBCD, Encoding the Tubulin Folding Cofactor D, Perturb Microtubule Dynamics and Cause Early-Onset Encephalopathy

scientific journal article

Binding of an Indenoisoquinoline to the topoisomerase-DNA complex induces reduction of linker mobility and strengthening of protein-DNA interaction

scientific article

Carbon monoxide binding to the heme group at the dimeric interface modulates structure and copper accessibility in the Cu,Zn superoxide dismutase from Haemophilus ducreyi: in silico and in vitro evidences

scientific article published on 11 June 2012

Clinical and functional characterization of a novel RASopathy-causing SHOC2 mutation associated with prenatal-onset hypertrophic cardiomyopathy

scientific article published on 06 May 2019

CoVaCS: a consensus variant calling system

scientific article

Coding-Gene Coevolution Analysis of Rotavirus Proteins: A Bioinformatics and Statistical Approach

scientific article published on 24 December 2019

Computational Evidence for a Variable First Shell Coordination of the Cadmium(II) Ion in Aqueous Solution

article

Conformational Dynamics of Lysine Methyltransferase Smyd2. Insights into the Different Substrate Crevice Characteristics of Smyd2 and Smyd3.

scientific article

DROPA: DRIP-seq optimized peak annotator ⬇️

scientific article published on 06 August 2019

Deciphering the structural properties that confer stability to a DNA nanocage.

scientific article

Detection of Second Hydration Shells in Ionic Solutions by XANES: Computed Spectra for Ni2+in Water Based on Molecular Dynamics

scientific article published on 01 February 2006

Development and validation of an integrated computational approach for the study of ionic species in solution by means of effective two-body potentials. The case of Zn2+, Ni2+, and Co2+ in aqueous solutions.

scientific article published in March 2002

Dynamic Investigation of Protein Metal Active Sites: Interplay of XANES and Molecular Dynamics Simulations

scientific article published on 01 October 2010

Dynamic changes in gene expression profiles of 22q11 and related orthologous genes during mouse development

scientific article published on 19 January 2007

Dynamic multiple-scattering treatment of X-ray absorption: Parameterization of a new molecular dynamics force field for myoglobin

scientific article published on 12 September 2018

Effect of the Zn2+and Hg2+Ions on the Structure of Liquid Water

scientific article published on 19 April 2011

Effects of dutasteride on the expression of genes related to androgen metabolism and related pathway in human prostate cancer cell lines.

scientific article

Effects of the pathological Q212P mutation on human prion protein non-octarepeat copper-binding site

scientific article published on 27 July 2012

Elite Food Between the Late Middle Ages and Renaissance: Some Case Studies from Latium

Equilibrium between 5- and 6-Fold Coordination in the First Hydration Shell of Cu(II).

scientific article

Erybraedin C, a natural compound from the plant Bituminaria bituminosa, inhibits both the cleavage and religation activities of human topoisomerase I.

scientific article published on 15 January 2010

Evidence for sevenfold coordination in the first solvation shell of Hg(II) aqua ion.

scientific article published on 6 April 2007

Evidence of distinct gene functional patterns in GC-poor and GC-rich isochores in Bos taurus

scientific article published on 18 February 2020

Evidence of the crucial role of the linker domain on the catalytic activity of human topoisomerase I by experimental and simulative characterization of the Lys681Ala mutant.

scientific article published on 18 September 2009

Expanding the molecular diversity and phenotypic spectrum of glycerol 3-phosphate dehydrogenase 1 deficiency.

scientific article

Experimental evidence for a variable first coordination shell of the cadmium(II) ion in aqueous, dimethyl sulfoxide, and N,N'-dimethylpropyleneurea solution

scientific article

Gallop Racing Shifts Mature mRNA towards Introns: Does Exercise-Induced Stress Enhance Genome Plasticity?

scientific article published on 09 April 2020

Genome assembly and transcriptome resource for river buffalo, Bubalus bubalis (2n = 50).

scientific article published in September 2017

Genome-Wide DNA Methylation and Gene Expression Profiles in Cows Subjected to Different Stress Level as Assessed by Cortisol in Milk

scientific article published on 25 July 2020

Global transcription regulation by DNA topoisomerase I in exponentially growing Saccharomyces cerevisiae cells: activation of telomere-proximal genes by TOP1 deletion

scientific article

HECT-Type E3 Ubiquitin Ligases in Cancer

scientific article published on 11 October 2019

Hif1α down-regulation is associated with transposition of great arteries in mice treated with a retinoic acid antagonist

scientific article

Hydrogen and Higher Shell Contributions in Zn2+, Ni2+, and Co2+Aqueous Solutions: An X-ray Absorption Fine Structure and Molecular Dynamics Study

scientific article published on 01 March 2002

Identification of a short region on chromosome 6 affecting direct calving ease in Piedmontese cattle breed

scientific article

Importance of V3 Loop Flexibility and Net Charge in the Context of Co-Receptor Recognition. A Molecular Dynamics Study on HIV gp120

scientific article published on 01 January 2012

Integrated experimental and theoretical approach for the structural characterization of Hg2+ aqueous solutions

scientific article published on 01 February 2008

Massive NGS data analysis reveals hundreds of potential novel gene fusions in human cell lines

article

Massive screening of copy number population-scale variation in Bos taurus genome

scientific article (publication date: 26 February 2013)

Massively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte sub-populations

scientific article published on 12 February 2009

Microarray gene expression profiling of neural tissues in bovine spastic paresis

scientific article

Microarrays and high-throughput transcriptomic analysis in species with incomplete availability of genomic sequences.

scientific article published on 05 April 2009

Microcephaly, intractable seizures and developmental delay caused by biallelic variants in TBCD: further delineation of a new chaperone-mediated tubulinopathy.

scientific article published on 2 November 2016

Modeling conformational transitions in kinases by molecular dynamics simulations: achievements, difficulties, and open challenges

scientific article published on 13 May 2014

Molecular Characterization of the First Ebola Virus Isolated in Italy, from a Health Care Worker Repatriated from Sierra Leone

scientific article published on 18 June 2015

Molecular Signature of the Ebola Virus Associated with the Fishermen Community Outbreak in Aberdeen, Sierra Leone, in February 2015

scientific article

Molecular dynamics recipes for genome research.

scientific article published on 18 February 2017

Multiple Recombination Events and Strong Purifying Selection at the Origin of SARS-CoV-2 Spike Glycoprotein Increased Correlated Dynamic Movements

scientific article published on 23 December 2020

Muscle transcriptome analysis identifies genes involved in ciliogenesis and the molecular cascade associated with intramuscular fat content in Large White heavy pigs

scientific article published on 19 May 2020

New hints on the Ph-driven tautomeric equilibria of the topotecan anticancer drug in aqueous solutions from an integrated spectroscopic and quantum-mechanical approach

scientific article published in November 2005

Novel and known genetic variants for male breast cancer risk at 8q24.21, 9p21.3, 11q13.3 and 14q24.1: results from a multicenter study in Italy

scientific article published on 3 August 2015

On the Solvation of the Zn2+Ion in Methanol: A Combined Quantum Mechanics, Molecular Dynamics, and EXAFS Approach

scientific article published on 29 July 2011

PeachVar-DB: a curated collection of genetic variations for the interactive analysis of peach genome data

scientific article

Protein concerted motions in the DNA-human topoisomerase I complex.

scientific article

Quantitative analysis of XANES spectra of disordered systems based on molecular dynamics

article

RNA-Sequencing for profiling goat milk transcriptome in colostrum and mature milk

scientific article

Revised Ionic Radii of Lanthanoid(III) Ions in Aqueous Solution

scientific article published on 15 April 2011

Role of the keratin 1 and keratin 10 tails in the pathogenesis of ichthyosis hystrix of Curth Macklin.

scientific article published on 24 April 2018

Role of the linker domain and the 203-214 N-terminal residues in the human topoisomerase I DNA complex dynamics.

scientific article published on 3 September 2004

SHOC2 subcellular shuttling requires the KEKE motif-rich region and N-terminal leucine-rich repeat domain and impacts on ERK signalling

scientific article published on 27 July 2016

Signatures of selection in five Italian cattle breeds detected by a 54K SNP panel.

scientific article published on 19 January 2014

Simulations of DNA topoisomerase 1B bound to supercoiled DNA reveal changes in the flexibility pattern of the enzyme and a secondary protein-DNA binding site

scientific article

Simulative Analysis of a Truncated Octahedral DNA Nanocage Family Indicates the Single-Stranded Thymidine Linkers as the Major Player for the Conformational Variability

Single mutation in the linker domain confers protein flexibility and camptothecin resistance to human topoisomerase I.

scientific article

Skeletal muscle transcriptional profiles in two Italian beef breeds, Chianina and Maremmana, reveal breed specific variation

scientific article published on 20 February 2016

Smyd2 conformational changes in response to p53 binding: role of the C-terminal domain.

scientific article published on 21 May 2019

Smyd3 open & closed lock mechanism for substrate recruitment: The hinge motion of C-terminal domain inferred from μ-second molecular dynamics simulations

scientific article published on 13 April 2016

Solvation structure of the halides from x-ray absorption spectroscopy.

scientific article published on July 2016

Solvent dependency of the UV-Vis spectrum of indenoisoquinolines: role of keto-oxygens as polarity interaction probes

scientific article (publication date: 2013)

Solvent effects on the valence UV-vis absorption spectra of topotecan anticancer drug in aqueous solution at room temperature: a nanoseconds time-scale TD-DFT/MD computational study

scientific article published in May 2010

Structural Evolution and Dynamics of the p53 Proteins.

scientific article published on 18 April 2016

Structural Investigation of Lanthanoid Coordination: a Combined XANES and Molecular Dynamics Study

article

Structural and Dynamic Characterization of the C313Y Mutation in Myostatin Dimeric Protein, Responsible for the "Double Muscle" Phenotype in Piedmontese Cattle.

scientific article

Structural and dynamic analysis of G558R mutation in chicken TSHR gene shows altered signal transduction and corroborates its role as a domestication gene

scientific article published on 20 November 2019

Structural and dynamical effects induced by the anticancer drug topotecan on the human topoisomerase I - DNA complex

scientific article

Structural and dynamical properties of the Hg2+ aqua ion: a molecular dynamics study

scientific article published on 27 March 2008

Structural dynamics of V3 loop in a trimeric ambiance, a molecular dynamics study on gp120-CD4 trimeric mimic.

scientific article published on 28 February 2014

Structural dynamics of V3 loop with different electrostatics: implications on co-receptor recognition: a molecular dynamics study of HIV gp120

article

Structural dynamics of the mitochondrial ADP/ATP carrier revealed by molecular dynamics simulation studies

scientific article

Structure and hydration of the DNA-human topoisomerase I covalent complex.

scientific article

The SNPs in the human genetic blueprint era.

scientific article

The different cleavage DNA sequence specificity explains the camptothecin resistance of the human topoisomerase I Glu418Lys mutant.

scientific article

The p53 tetramer shows an induced-fit interaction of the C-terminal domain with the DNA-binding domain

scientific article published on 19 October 2015

Theoretical modeling of the valence UV spectra of 1,2,3-triazine and uracil in solution.

scientific article published on 24 February 2006

Transcriptomic investigation of meat tenderness in two Italian cattle breeds.

scientific article published on 9 February 2016

Type I DNA Topoisomerases

scientific article published on 10 January 2017

UV-vis spectra of the anticancer camptothecin family drugs in aqueous solution: specific spectroscopic signatures unraveled by a combined computational and experimental study

scientific article

Valproic acid induces neuroendocrine differentiation and UGT2B7 up-regulation in human prostate carcinoma cell line

scientific article published on 19 March 2007

Was the Cinta Senese Pig Already a Luxury Food in the Late Middle Ages? Ancient DNA and Archaeozoological Evidence from Central Italy

scientific article published on 11 January 2020

Whole-exome sequencing and targeted gene sequencing provide insights into the role of PALB2 as a male breast cancer susceptibility gene.

scientific article published on 20 September 2016

X-ray absorption study of the solvation structure of Cu2+ in methanol and dimethyl sulfoxide.

scientific article published in August 2012

List of works by Giovanni Chillemi

A coupled molecular dynamics and XANES data analysis investigation of aqueous cadmium(II).

A gene expression atlas for different kinds of stress in the mouse brain

A molecular dynamics simulation study decodes the early stage of the disassembly process abolishing the human SAMHD1 function

A single mutation in the 729 residue modulates human DNA topoisomerase IB DNA binding and drug resistance.

A specific transcriptional response of yeast cells to camptothecin dependent on the Swi4 and Mbp1 factors

A tool for sheep product quality: custom microarrays from public databases.

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 mutant

Analysis of co-receptor usage of circulating viral and proviral HIV genome quasispecies by ultra-deep pyrosequencing in patients who are candidates for CCR5 antagonist treatment.

Anti-Inflammatory Potential of Cow, Donkey and Goat Milk Extracellular Vesicles as Revealed by Metabolomic Profile

Antisense transcripts enhanced by camptothecin at divergent CpG-island promoters associated with bursts of topoisomerase I-DNA cleavage complex and R-loop formation

Archived HIV-1 minority variants detected by ultra-deep pyrosequencing in provirus may be fully replication competent

Assembly and characterization of pandemic influenza A H1N1 genome in nasopharyngeal swabs using high-throughput pyrosequencing.

Assignment of UV-vis spectrum of (3,3')-diindolylmethane, a Leishmania donovani topoisomerase IB inhibitor and a candidate DNA minor groove binder.

Biallelic Mutations in TBCD, Encoding the Tubulin Folding Cofactor D, Perturb Microtubule Dynamics and Cause Early-Onset Encephalopathy

Binding of an Indenoisoquinoline to the topoisomerase-DNA complex induces reduction of linker mobility and strengthening of protein-DNA interaction

Carbon monoxide binding to the heme group at the dimeric interface modulates structure and copper accessibility in the Cu,Zn superoxide dismutase from Haemophilus ducreyi: in silico and in vitro evidences

Clinical and functional characterization of a novel RASopathy-causing SHOC2 mutation associated with prenatal-onset hypertrophic cardiomyopathy

CoVaCS: a consensus variant calling system

Coding-Gene Coevolution Analysis of Rotavirus Proteins: A Bioinformatics and Statistical Approach

Computational Evidence for a Variable First Shell Coordination of the Cadmium(II) Ion in Aqueous Solution

Conformational Dynamics of Lysine Methyltransferase Smyd2. Insights into the Different Substrate Crevice Characteristics of Smyd2 and Smyd3.

DROPA: DRIP-seq optimized peak annotator ⬇️

Deciphering the structural properties that confer stability to a DNA nanocage.

Detection of Second Hydration Shells in Ionic Solutions by XANES: Computed Spectra for Ni2+in Water Based on Molecular Dynamics

Development and validation of an integrated computational approach for the study of ionic species in solution by means of effective two-body potentials. The case of Zn2+, Ni2+, and Co2+ in aqueous solutions.

Dynamic Investigation of Protein Metal Active Sites: Interplay of XANES and Molecular Dynamics Simulations

Dynamic changes in gene expression profiles of 22q11 and related orthologous genes during mouse development

Dynamic multiple-scattering treatment of X-ray absorption: Parameterization of a new molecular dynamics force field for myoglobin

Effect of the Zn2+and Hg2+Ions on the Structure of Liquid Water

Effects of dutasteride on the expression of genes related to androgen metabolism and related pathway in human prostate cancer cell lines.

Effects of the pathological Q212P mutation on human prion protein non-octarepeat copper-binding site

Elite Food Between the Late Middle Ages and Renaissance: Some Case Studies from Latium

Equilibrium between 5- and 6-Fold Coordination in the First Hydration Shell of Cu(II).

Erybraedin C, a natural compound from the plant Bituminaria bituminosa, inhibits both the cleavage and religation activities of human topoisomerase I.

Evidence for sevenfold coordination in the first solvation shell of Hg(II) aqua ion.

Evidence of distinct gene functional patterns in GC-poor and GC-rich isochores in Bos taurus

Evidence of the crucial role of the linker domain on the catalytic activity of human topoisomerase I by experimental and simulative characterization of the Lys681Ala mutant.

Expanding the molecular diversity and phenotypic spectrum of glycerol 3-phosphate dehydrogenase 1 deficiency.

Experimental evidence for a variable first coordination shell of the cadmium(II) ion in aqueous, dimethyl sulfoxide, and N,N'-dimethylpropyleneurea solution

Gallop Racing Shifts Mature mRNA towards Introns: Does Exercise-Induced Stress Enhance Genome Plasticity?

Genome assembly and transcriptome resource for river buffalo, Bubalus bubalis (2n = 50).

Genome-Wide DNA Methylation and Gene Expression Profiles in Cows Subjected to Different Stress Level as Assessed by Cortisol in Milk

Global transcription regulation by DNA topoisomerase I in exponentially growing Saccharomyces cerevisiae cells: activation of telomere-proximal genes by TOP1 deletion

HECT-Type E3 Ubiquitin Ligases in Cancer

Hif1α down-regulation is associated with transposition of great arteries in mice treated with a retinoic acid antagonist

Hydrogen and Higher Shell Contributions in Zn2+, Ni2+, and Co2+Aqueous Solutions: An X-ray Absorption Fine Structure and Molecular Dynamics Study

Identification of a short region on chromosome 6 affecting direct calving ease in Piedmontese cattle breed

Importance of V3 Loop Flexibility and Net Charge in the Context of Co-Receptor Recognition. A Molecular Dynamics Study on HIV gp120

Integrated experimental and theoretical approach for the structural characterization of Hg2+ aqueous solutions

Massive NGS data analysis reveals hundreds of potential novel gene fusions in human cell lines

Massive screening of copy number population-scale variation in Bos taurus genome

Massively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte sub-populations

Microarray gene expression profiling of neural tissues in bovine spastic paresis

Microarrays and high-throughput transcriptomic analysis in species with incomplete availability of genomic sequences.

Microcephaly, intractable seizures and developmental delay caused by biallelic variants in TBCD: further delineation of a new chaperone-mediated tubulinopathy.

Modeling conformational transitions in kinases by molecular dynamics simulations: achievements, difficulties, and open challenges

Molecular Characterization of the First Ebola Virus Isolated in Italy, from a Health Care Worker Repatriated from Sierra Leone

Molecular Signature of the Ebola Virus Associated with the Fishermen Community Outbreak in Aberdeen, Sierra Leone, in February 2015

Molecular dynamics recipes for genome research.

Multiple Recombination Events and Strong Purifying Selection at the Origin of SARS-CoV-2 Spike Glycoprotein Increased Correlated Dynamic Movements

Muscle transcriptome analysis identifies genes involved in ciliogenesis and the molecular cascade associated with intramuscular fat content in Large White heavy pigs

New hints on the Ph-driven tautomeric equilibria of the topotecan anticancer drug in aqueous solutions from an integrated spectroscopic and quantum-mechanical approach

Novel and known genetic variants for male breast cancer risk at 8q24.21, 9p21.3, 11q13.3 and 14q24.1: results from a multicenter study in Italy

On the Solvation of the Zn2+Ion in Methanol: A Combined Quantum Mechanics, Molecular Dynamics, and EXAFS Approach

PeachVar-DB: a curated collection of genetic variations for the interactive analysis of peach genome data

Protein concerted motions in the DNA-human topoisomerase I complex.

Quantitative analysis of XANES spectra of disordered systems based on molecular dynamics

RNA-Sequencing for profiling goat milk transcriptome in colostrum and mature milk

Revised Ionic Radii of Lanthanoid(III) Ions in Aqueous Solution

Role of the keratin 1 and keratin 10 tails in the pathogenesis of ichthyosis hystrix of Curth Macklin.

Role of the linker domain and the 203-214 N-terminal residues in the human topoisomerase I DNA complex dynamics.

SHOC2 subcellular shuttling requires the KEKE motif-rich region and N-terminal leucine-rich repeat domain and impacts on ERK signalling

Signatures of selection in five Italian cattle breeds detected by a 54K SNP panel.

Simulations of DNA topoisomerase 1B bound to supercoiled DNA reveal changes in the flexibility pattern of the enzyme and a secondary protein-DNA binding site

Simulative Analysis of a Truncated Octahedral DNA Nanocage Family Indicates the Single-Stranded Thymidine Linkers as the Major Player for the Conformational Variability

Single mutation in the linker domain confers protein flexibility and camptothecin resistance to human topoisomerase I.

Skeletal muscle transcriptional profiles in two Italian beef breeds, Chianina and Maremmana, reveal breed specific variation

Smyd2 conformational changes in response to p53 binding: role of the C-terminal domain.

Smyd3 open & closed lock mechanism for substrate recruitment: The hinge motion of C-terminal domain inferred from μ-second molecular dynamics simulations