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Hi-C analysis: from data generation to integration

visualizing such large genomics datasets. KeywordsChromatin 3D architecture Epigenomics Computational biology High-throughput sequencing Chromosome conformation capture  Mattia Forcato and Francesco Ferrari ... declares that he has no conflict of interest. Mattia Forcato declares that he has no conflict of interest. Francesco Ferrari declares that he has no conflict of interest. Ethical approval This article does

Comprehensive analysis of promoter-proximal RNA polymerase II pausing across mammalian cell types

Background For many genes, RNA polymerase II stably pauses before transitioning to productive elongation. Although polymerase II pausing has been shown to be a mechanism for regulating transcriptional activation, the extent to which it is involved in control of mammalian gene expression and its relationship to chromatin structure remain poorly understood. Results Here, we analyze...

Mirror neuron research: the past and the future

Pier Francesco Ferrari Giacomo Rizzolatti Articles on similar topics can be found in the following collections Receive free email alerts when new articles cite this article - sign up in the box at ... the top right-hand corner of the article or click here - Subject collections Email alerting service rstb.royalsocietypublishing.org Introduction Author for correspondence: Pier Francesco Ferrari e

In Play We Trust. Rapid Facial Mimicry Predicts the Duration of Playful Interactions in Geladas

The primate play-face is homologous to the human facial display accompanying laughter. Through facial mimicry, the play-face evokes in the perceiver a similar positive emotional state. This sensorimotor and emotional sharing can be adaptive, as it allows individuals to fine-tune their own motor sequences accordingly thus increasing cooperation in play. It has been recently...

From action to language: comparative perspectives on primate tool use, gesture and the evolution of human language

The papers in this Special Issue examine tool use and manual gestures in primates as a window on the evolution of the human capacity for language. Neurophysiological research has supported the hypothesis of a close association between some aspects of human action organization and of language representation, in both phonology and semantics. Tool use provides an excellent...

Neuronal Chains for Actions in the Parietal Lobe: A Computational Model

The inferior part of the parietal lobe (IPL) is known to play a very important role in sensorimotor integration. Neurons in this region code goal-related motor acts performed with the mouth, with the hand and with the arm. It has been demonstrated that most IPL motor neurons coding a specific motor act (e.g., grasping) show markedly different activation patterns according to the...

PREDA: an R-package to identify regional variations in genomic data

Summary: Chromosomal patterns of genomic signals represent molecular fingerprints that may reveal how the local structural organization of a genome impacts the functional control mechanisms. Thus, the integrative analysis of multiple sources of genomic data and information deepens the resolution and enhances the interpretation of stand-alone high-throughput data. In this note, we...

Impact of sequencing depth in ChIP-seq experiments

In a chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) experiment, an important consideration in experimental design is the minimum number of sequenced reads required to obtain statistically significant results. We present an extensive evaluation of the impact of sequencing depth on identification of enriched regions for key histone modifications...

Neurons Controlling Voluntary Vocalization in the Macaque Ventral Premotor Cortex

The voluntary control of phonation is a crucial achievement in the evolution of speech. In humans, ventral premotor cortex (PMv) and Broca's area are known to be involved in voluntary phonation. In contrast, no neurophysiological data are available about the role of the oro-facial sector of nonhuman primates PMv in this function. In order to address this issue, we recorded PMv...

Expression Profiling of FSHD-1 and FSHD-2 Cells during Myogenic Differentiation Evidences Common and Distinctive Gene Dysregulation Patterns

Background Determine global gene dysregulation affecting 4q-linked (FSHD-1) and non 4q-linked (FSHD-2) cells during early stages of myogenic differentiation. This approach has been never applied to FSHD pathogenesis. Methodology/Principal Findings By in vitro differentiation of FSHD-1 and FSHD-2 myoblasts and gene chip analysis we derived that gene expression profile is altered...

A-MADMAN: Annotation-based microarray data meta-analysis tool

Background Publicly available datasets of microarray gene expression signals represent an unprecedented opportunity for extracting genomic relevant information and validating biological hypotheses. However, the exploitation of this exceptionally rich mine of information is still hampered by the lack of appropriate computational tools, able to overcome the critical issues raised...

PPARδ is a ligand-dependent negative regulator of vitamin D3-induced monocyte differentiation

A number of reports indicate that peroxisome proliferator-activated receptor (PPAR) δ is involved in the molecular control of monocyte–macrophage differentiation. In this regard, the recent demonstration that PPARδ is a primary response gene of 1α,25-dihydroxyvitamin D3 (VD), i.e. a powerful inducer of such process, allowed us to hypothesize the existence of a cross talk between...

Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation

Genes co-expressed may be under similar promoter-based and/or position-based regulation. Although data on expression, position and function of human genes are available, their true integration still represents a challenge for computational biology, hampering the identification of regulatory mechanisms. We carried out an integrative analysis of genomic position, functional...

Microarray data mining using Bioconductor packages

Background This paper describes the results of a Gene Ontology (GO) term enrichment analysis of chicken microarray data using the Bioconductor packages. By checking the enriched GO terms in three contrasts, MM8-PM8, MM8-MA8, and MM8-MM24, of the provided microarray data during this workshop, this analysis aimed to investigate the host reactions in chickens occurring shortly after...

A computational procedure to identify significant overlap of differentially expressed and genomic imbalanced regions in cancer datasets†

The integration of high-throughput genomic data represents an opportunity for deciphering the interplay between structural and functional organization of genomes and for discovering novel biomarkers. However, the development of integrative approaches to complement gene expression (GE) data with other types of gene information, such as copy number (CN) and chromosomal localization...

Phenotypes and gene expression profiles of Saccharopolyspora erythraea rifampicin-resistant (rif) mutants affected in erythromycin production

Background There is evidence from previous works that bacterial secondary metabolism may be stimulated by genetic manipulation of RNA polymerase (RNAP). In this study we have used rifampicin selection as a strategy to genetically improve the erythromycin producer Saccharopolyspora erythraea. Results Spontaneous rifampicin-resistant (rif) mutants were isolated from the parental...

The Lkb1 metabolic sensor maintains haematopoietic stem cell survival

Fatih Ozsolak Patrice Milos Francesco Ferrari Peter J. Park Orian S. Shirihai David T. Scadden Nabeel Bardeesy In this Article, Figs 1f and 2e appeared incorrectly (the corrected figure parts are shown

Transcriptional profiling in response to terminal drought stress reveals differential responses along the wheat genome

Background Water stress during grain filling has a marked effect on grain yield, leading to a reduced endosperm cell number and thus sink capacity to accumulate dry matter. The bread wheat cultivar Chinese Spring (CS), a Chinese Spring terminal deletion line (CS_5AL-10) and the durum wheat cultivar Creso were subjected to transcriptional profiling after exposure to mild and...

Genomic expression during human myelopoiesis

Background Human myelopoiesis is an exciting biological model for cellular differentiation since it represents a plastic process where multipotent stem cells gradually limit their differentiation potential, generating different precursor cells which finally evolve into distinct terminally differentiated cells. This study aimed at investigating the genomic expression during...