List of works - Francesca Chiaromonte

A genome-wide analysis of common fragile sites: what features determine chromosomal instability in the human genome?

scientific article

A genome-wide view of mutation rate co-variation using multivariate analyses ⬇️

scientific article published on March 22, 2011

A macaque's-eye view of human insertions and deletions: differences in mechanisms

scientific article

A matter of life or death: how microsatellites emerge in and vanish from the human genome

scientific article published on 12 October 2011

Age-related accumulation of de novo mitochondrial mutations in mammalian oocytes and somatic tissues

scientific article published on 15 July 2020

An attraction-repulsion point process model for respiratory syncytial virus infections

scientific article published on 6 February 2015

Child Weight Gain Trajectories Linked To Oral Microbiota Composition

scientific article published in Scientific Reports

Complete Khoisan and Bantu genomes from southern Africa

scientific article

Corrigendum: A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome?

scientific article published on October 2016

Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution

scientific article

Dimension reduction strategies for analyzing global gene expression data with a response

scientific article

Distinct Mutational Behaviors Differentiate Short Tandem Repeats from Microsatellites in the Human Genome ⬇️

scientific article published on January 1, 2013

Distinguishing regulatory DNA from neutral sites

scientific article published on January 2003

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration

scientific article

ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements

scientific article

Error correction and statistical analyses for intra-host comparisons of feline immunodeficiency virus diversity from high-throughput sequencing data

scientific article

Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression

scientific article

Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences

scientific article

Evidence for sharp increase in the economic damages of extreme natural disasters

scientific article published on 07 October 2019

Experimental validation of predicted mammalian erythroid cis-regulatory modules

scientific article

Exploratory Spatial Analysis of in vitro Respiratory Syncytial Virus Co-infections ⬇️

scientific article published on December 22, 2010

Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data

scientific article

Functional data analysis for computational biology

scientific article published on 01 September 2019

Gene Length and Proximity to Neighbors Affect Genome-Wide Expression Levels ⬇️

scientific article published on November 12, 2003

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

scientific article

Genomic environment predicts expression patterns on the human inactive X chromosome

scientific article

Genomic landscape of human, bat, and ex vivo DNA transposon integrations

scientific article

High satellite repeat turnover in great apes studied with short- and long-read technologies

scientific article published on 02 July 2019

Human L1 Transposition Dynamics Unraveled with Functional Data Analysis

scientific article published on 28 July 2020

Human-macaque comparisons illuminate variation in neutral substitution rates

scientific article published on 30 April 2008

IWTomics: testing high-resolution sequence-based "Omics" data at multiple locations and scales.

scientific article published on 20 February 2018

Initial sequencing and comparative analysis of the mouse genome

scientific article

Insertions and deletions are male biased too: a whole-genome analysis in rodents

scientific article published on April 2004

Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis

scientific article (publication date: June 2016)

Knowledge and social relatedness shape research portfolio diversification

scientific article published on 28 August 2020

Learning the properties of adaptive regions with functional data analysis

scientific article published on 27 August 2020

Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate

scientific article published on 06 November 2018

Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA.

scientific article published on 13 October 2014

Multivariate statistical analyses demonstrate unique host immune responses to single and dual lentiviral infection

scientific article

On the bias of H-scores for comparing biclusters, and how to correct it

scientific article published on 27 January 2020

Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes

scientific article published on April 2004

Primary sequence and epigenetic determinants of in vivo occupancy of genomic DNA by GATA1.

scientific article

Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis

scientific article

Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat

scientific article published on April 2004

Reply to Geiger and Stomper: On capital intensity and observed increases in the economic damages of extreme natural disasters

scientific article published on 10 March 2020

Rescuing Alu: Recovery of New Inserts Shows LINE-1 Preserves Alu Activity through A-Tail Expansion ⬇️

scientific article published on August 9, 2012

Ride the wavelet: A multiscale analysis of genomic contexts flanking small insertions and deletions

scientific article published on 05 June 2009

Segmenting the human genome based on states of neutral genetic divergence ⬇️

scientific article published on August 19, 2013

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

scientific article

Strong and weak male mutation bias at different sites in the primate genomes: insights from the human-chimpanzee comparison

scientific article published on 9 November 2005

Structured Ordinary Least Squares: A Sufficient Dimension Reduction approach for regressions with partitioned predictors and heterogeneous units

scientific article

Support vector machines categorize the scaling of human grip configurations

scientific article published in November 2007

The genome-wide determinants of human and chimpanzee microsatellite evolution

scientific article

Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif.

scientific article published on 25 September 2008

What Is a Microsatellite: A Computational and Experimental Definition Based upon Repeat Mutational Behavior at A/T and GT/AC Repeats ⬇️

scientific article published on July 28, 2010

Windshield splatter analysis with the Galaxy metagenomic pipeline

scientific article published on 09 October 2009

List of works by Francesca Chiaromonte

A genome-wide analysis of common fragile sites: what features determine chromosomal instability in the human genome?

A genome-wide view of mutation rate co-variation using multivariate analyses ⬇️

A macaque's-eye view of human insertions and deletions: differences in mechanisms

A matter of life or death: how microsatellites emerge in and vanish from the human genome

Age-related accumulation of de novo mitochondrial mutations in mammalian oocytes and somatic tissues

An attraction-repulsion point process model for respiratory syncytial virus infections

Child Weight Gain Trajectories Linked To Oral Microbiota Composition

Complete Khoisan and Bantu genomes from southern Africa

Corrigendum: A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome?

Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution

Dimension reduction strategies for analyzing global gene expression data with a response

Distinct Mutational Behaviors Differentiate Short Tandem Repeats from Microsatellites in the Human Genome ⬇️

Distinguishing regulatory DNA from neutral sites

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration

ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements

Error correction and statistical analyses for intra-host comparisons of feline immunodeficiency virus diversity from high-throughput sequencing data

Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression

Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences

Evidence for sharp increase in the economic damages of extreme natural disasters

Experimental validation of predicted mammalian erythroid cis-regulatory modules

Exploratory Spatial Analysis of in vitro Respiratory Syncytial Virus Co-infections ⬇️

Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data

Functional data analysis for computational biology

Gene Length and Proximity to Neighbors Affect Genome-Wide Expression Levels ⬇️

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

Genomic environment predicts expression patterns on the human inactive X chromosome

Genomic landscape of human, bat, and ex vivo DNA transposon integrations

High satellite repeat turnover in great apes studied with short- and long-read technologies

Human L1 Transposition Dynamics Unraveled with Functional Data Analysis

Human-macaque comparisons illuminate variation in neutral substitution rates

IWTomics: testing high-resolution sequence-based "Omics" data at multiple locations and scales.

Initial sequencing and comparative analysis of the mouse genome

Insertions and deletions are male biased too: a whole-genome analysis in rodents

Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis

Knowledge and social relatedness shape research portfolio diversification

Learning the properties of adaptive regions with functional data analysis

Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate

Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA.

Multivariate statistical analyses demonstrate unique host immune responses to single and dual lentiviral infection

On the bias of H-scores for comparing biclusters, and how to correct it

Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes

Primary sequence and epigenetic determinants of in vivo occupancy of genomic DNA by GATA1.

Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis

Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat

Reply to Geiger and Stomper: On capital intensity and observed increases in the economic damages of extreme natural disasters

Rescuing Alu: Recovery of New Inserts Shows LINE-1 Preserves Alu Activity through A-Tail Expansion ⬇️

Ride the wavelet: A multiscale analysis of genomic contexts flanking small insertions and deletions

Segmenting the human genome based on states of neutral genetic divergence ⬇️

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

Strong and weak male mutation bias at different sites in the primate genomes: insights from the human-chimpanzee comparison

Structured Ordinary Least Squares: A Sufficient Dimension Reduction approach for regressions with partitioned predictors and heterogeneous units

Support vector machines categorize the scaling of human grip configurations

The genome-wide determinants of human and chimpanzee microsatellite evolution

Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif.

What Is a Microsatellite: A Computational and Experimental Definition Based upon Repeat Mutational Behavior at A/T and GT/AC Repeats ⬇️

Windshield splatter analysis with the Galaxy metagenomic pipeline