Author details

Full Name

Francesco Ferrari

Affiliation

ORCID

Career Start Year

2002

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
36702890	Author Correction: Tissue fluidification promotes a cGAS-STING cytosolic DNA response in invasive breast cancer.		2023
36581770	Tissue fluidification promotes a cGAS-STING cytosolic DNA response in invasive breast cancer.		2023
34415532	Visualizing and Annotating Hi-C Data.	Methods in Molecular Biology	2022
34197622	Leveraging three-dimensional chromatin architecture for effective reconstruction of enhancer-target gene regulatory interactions.	Nucleic Acids Research	2021
34233445	Single-cell profiling reveals the dynamics of cytomegalovirus-specific T cells in haploidentical hematopoietic stem cell transplantation.	Haematologica	2021
33963009	Oncolytic adenovirus and gene therapy with EphA2-BiTE for the treatment of pediatric high-grade gliomas.	Journal for ImmunoTherapy of Cancer	2021
33941587	T Cells Expressing Receptor Recombination/Revision Machinery Are Detected in the Tumor Microenvironment and Expanded in Genomically Over-unstable Models.	Cancer Immunology Research	2021
33060580	DOT1L-mediated murine neuronal differentiation associates with H3K79me2 accumulation and preserves SOX2-enhancer accessibility.	Nature Communications	2020
31999646	Dysfunctional polycomb transcriptional repression contributes to lamin A/C-dependent muscular dystrophy.	J Clin Invest	2020
32163370	ATR expands embryonic stem cell fate potential in response to replication stress.	eLife	2020
32471461	Differentiation and localization of interneurons in the developing spinal cord depends on DOT1L expression.	Molecular Brain	2020
33293552	SAMMY-seq reveals early alteration of heterochromatin and deregulation of bivalent genes in Hutchinson-Gilford Progeria Syndrome.	Nature Communications	2020
31316726	Computational Biology Solutions to Identify Enhancers-target Gene Pairs.	Computational and Structural Biotechnology Journal	2019
31697323	HiCBricks: building blocks for efficient handling of large Hi-C datasets.		2019
31740485	CXCR3 Identifies Human Naive CD8<sup>+</sup> T Cells with Enhanced Effector Differentiation Potential.	J Immunol	2019
31767860	Global chromatin conformation differences in the Drosophila dosage compensated chromosome X.	Nature Communications	2019
31869378	The acute myeloid leukemia associated AML1-ETO fusion protein alters the transcriptome and cellular progression in a single-oncogene expressing in vitro induced pluripotent stem cell based granulocyte differentiation model.	PLoS ONE	2019
30570701	Hi-C analysis: from data generation to integration.	Biophysical Reviews	2019
30154266	High-dimensional single cell analysis identifies stem-like cytotoxic CD8 T cells infiltrating human tumors.	Journal of Experimental Medicine	2018
28460063	WoPPER: Web server for Position Related data analysis of gene Expression in Prokaryotes.	Nucleic Acids Research	2017
28604721	Comparison of computational methods for Hi-C data analysis.	Nature Methods	2017
26675720	Corrigendum: Failure to replicate the STAP cell phenomenon.	Nature	2016
27259512	Comprehensive analysis of promoter-proximal RNA polymerase II pausing across mammalian cell types.	Genome Biol	2016
26675727	Corrigendum: Hallmarks of pluripotency.	Nature	2016
26501951	A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs.	Nat Biotechnol	2015
25574027	Htt CAG repeat expansion confers pleiotropic gains of mutant huntingtin function in chromatin regulation.	Hum Mol Genet	2015
26659182	The histone chaperone CAF-1 safeguards somatic cell identity.	Nature	2015
26399835	Failure to replicate the STAP cell phenomenon.	Nature	2015
26399828	Hallmarks of pluripotency.	Nature	2015
25164756	Comparative analysis of metazoan chromatin organization.	Nature	2014
24241209	Rearranging the chromatin for pluripotency.	Cell Cycle	2014
24500429	Transcriptional control of a whole chromosome: emerging models for dosage compensation.	Nat Struct Mol Biol	2014
24598259	Impact of sequencing depth in ChIP-seq experiments.	Nucleic Acids Res	2014
23665121	Genome-wide chromatin interactions of the Nanog locus in pluripotency, differentiation, and reprogramming.	Cell Stem Cell	2013
24183666	"Jump start and gain" model for dosage compensation in Drosophila based on direct sequencing of nascent transcripts.	Cell Rep	2013
23321669	KDM2B promotes pancreatic cancer via Polycomb-dependent and -independent transcriptional programs.	J Clin Invest	2013
23599463	Comment on "Drosophila dosage compensation involves enhanced Pol II recruitment to male X-linked promoters".	Science	2013
22885124	Valproic acid triggers erythro/megakaryocyte lineage decision through induction of GFI1B and MLLT3 expression.	Experimental Hematology	2012
22807198	Transcriptional profiles underlying vulnerability and resilience in rats exposed to an acute unavoidable stress.	Journal of Neuroscience Research	2012
22387999	Ascorbic acid prevents loss of Dlk1-Dio3 imprinting and facilitates generation of all-iPS cell mice from terminally differentiated B cells.	Nat Genet	2012
21695143	Expression profiling of FSHD-1 and FSHD-2 cells during myogenic differentiation evidences common and distinctive gene dysregulation patterns.	PLoS One	2011
21890453	The reconstruction of transcriptional networks reveals critical genes with implications for clinical outcome of multiple myeloma.	Clinical Cancer Research	2011
21742634	PREDA: an R-package to identify regional variations in genomic data.		2011
19908392	Critical analysis of transcriptional and post-transcriptional regulatory networks in multiple myeloma.	Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing	2010
21124451	The Lkb1 metabolic sensor maintains haematopoietic stem cell survival.	Nature	2010
20947517	Integrative genomics analyses reveal molecularly distinct subgroups of B-cell chronic lymphocytic leukemia patients with 13q14 deletion.	Clinical Cancer Research	2010
21364636	Integrated analysis of microRNA and mRNA expression profiles in physiological myelopoiesis: role of hsa-mir-299-5p in CD34+ progenitor cells commitment.	Cell Death and Disease	2010
20603000	A MicroRNA targeting dicer for metastasis control.	Cell	2010
19056929	PPARdelta is a ligand-dependent negative regulator of vitamin D3-induced monocyte differentiation.	Carcinogenesis	2009
19552804	Transcriptional profiling in response to terminal drought stress reveals differential responses along the wheat genome.	BMC Genomics	2009