List of works - Luca Pinello

A methodology to assess the intrinsic discriminative ability of a distance function and its interplay with clustering algorithms for microarray data analysis.

scientific article

A molecular roadmap for induced multi-lineage trans-differentiation of fibroblasts by chemical combinations

scientific article published on 27 January 2017

A motif-independent metric for DNA sequence specificity.

scientific article

A multi-layer method to study genome-scale positions of nucleosomes

scientific article published on 21 November 2008

Acquired Tissue-Specific Promoter Bivalency Is a Basis for PRC2 Necessity in Adult Cells

scientific article published on 19 May 2016

AmpUMI: Design and analysis of unique molecular identifiers for deep amplicon sequencing

An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level.

scientific article published on October 2013

Analyzing CRISPR genome-editing experiments with CRISPResso

scientific article published on July 2016

Applications of alignment-free methods in epigenomics

scientific article

Assessment of computational methods for the analysis of single-cell ATAC-seq data

scientific article published on 18 November 2019

BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis

scientific article

BRCA1 recruitment to transcriptional pause sites is required for R-loop-driven DNA damage repair

scientific article

CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data

scientific article published on 01 December 2018

CRISPResso2 provides accurate and rapid genome editing sequence analysis

scientific article published on 01 March 2019

Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis

scientific article

Developmental control of polycomb subunit composition by GATA factors mediates a switch to non-canonical functions.

scientific article

Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single-cell resolution using RNA sequencing.

scientific article

Distinct and combinatorial functions of Jmjd2b/Kdm4b and Jmjd2c/Kdm4c in mouse embryonic stem cell identity

scientific article published on 19 December 2013

Editing aberrant splice sites efficiently restores β-globin expression in β-thalassemia

scientific article published on 31 January 2019

Enhancer transcribed RNAs arise from hypomethylated, Tet-occupied genomic regions.

scientific article published on 17 October 2013

Forward genetic screen of human transposase genomic rearrangements

scientific article

Functionally distinct patterns of nucleosome remodeling at enhancers in glucocorticoid-treated acute lymphoblastic leukemia

scientific article published on 02 December 2015

Gene regulatory pattern analysis reveals essential role of core transcriptional factors' activation in triple-negative breast cancer

scientific article

Genome-wide CRISPR-Cas9 Screen Identifies Leukemia-Specific Dependence on a Pre-mRNA Metabolic Pathway Regulated by DCPS.

scientific article published on 8 February 2018

Genome-wide characterization of chromatin binding and nucleosome spacing activity of the nucleosome remodelling ATPase ISWI.

scientific article

GiniClust: detecting rare cell types from single-cell gene expression data with Gini index

scientific article

Haystack: systematic analysis of the variation of epigenetic states and cell-type specific regulatory elements

scientific article published on 17 January 2018

High-fat diet enhances stemness and tumorigenicity of intestinal progenitors

scientific article published on March 2016

Identification of Transcribed Enhancers by Genome-Wide Chromatin Immunoprecipitation Sequencing.

scientific article published in January 2017

Impact of the N-Terminal Domain of STAT3 in STAT3-Dependent Transcriptional Activity

scientific article

Integrated design, execution, and analysis of arrayed and pooled CRISPR genome-editing experiments.

scientific article published on 12 April 2018

Multi-scale chromatin state annotation using a hierarchical hidden Markov model

scientific article published on 7 April 2017

Predicting chromatin organization using histone marks.

scientific article published on 14 August 2015

PrimeDesign software for rapid and simplified design of prime editing guide RNAs

scientific article published on 15 February 2021

STAT5 outcompetes STAT3 to regulate the expression of the oncogenic transcriptional modulator BCL6.

scientific article published on 28 May 2013

Serum-Based Culture Conditions Provoke Gene Expression Variability in Mouse Embryonic Stem Cells as Revealed by Single-Cell Analysis

scientific article published on 19 January 2016

Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM

scientific article published on 23 April 2019

The cohesin-associated protein Wapal is required for proper Polycomb-mediated gene silencing

scientific article published on 15 April 2016

The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells.

scientific article published on 19 December 2016

The role of Cdx2 as a lineage specific transcriptional repressor for pluripotent network during the first developmental cell lineage segregation

scientific article published on 7 December 2017

Transcription factor competition at the γ-globin promoters controls hemoglobin switching

scientific article published on 01 March 2021

Variant-aware saturating mutagenesis using multiple Cas9 nucleases identifies regulatory elements at trait-associated loci.

scientific article

List of works by Luca Pinello

A methodology to assess the intrinsic discriminative ability of a distance function and its interplay with clustering algorithms for microarray data analysis.

A molecular roadmap for induced multi-lineage trans-differentiation of fibroblasts by chemical combinations

A motif-independent metric for DNA sequence specificity.

A multi-layer method to study genome-scale positions of nucleosomes

Acquired Tissue-Specific Promoter Bivalency Is a Basis for PRC2 Necessity in Adult Cells

AmpUMI: Design and analysis of unique molecular identifiers for deep amplicon sequencing

An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level.

Analyzing CRISPR genome-editing experiments with CRISPResso

Applications of alignment-free methods in epigenomics

Assessment of computational methods for the analysis of single-cell ATAC-seq data

BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis

BRCA1 recruitment to transcriptional pause sites is required for R-loop-driven DNA damage repair

CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data

CRISPResso2 provides accurate and rapid genome editing sequence analysis

Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis

Developmental control of polycomb subunit composition by GATA factors mediates a switch to non-canonical functions.

Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single-cell resolution using RNA sequencing.

Distinct and combinatorial functions of Jmjd2b/Kdm4b and Jmjd2c/Kdm4c in mouse embryonic stem cell identity

Editing aberrant splice sites efficiently restores β-globin expression in β-thalassemia

Enhancer transcribed RNAs arise from hypomethylated, Tet-occupied genomic regions.

Forward genetic screen of human transposase genomic rearrangements

Functionally distinct patterns of nucleosome remodeling at enhancers in glucocorticoid-treated acute lymphoblastic leukemia

Gene regulatory pattern analysis reveals essential role of core transcriptional factors' activation in triple-negative breast cancer

Genome-wide CRISPR-Cas9 Screen Identifies Leukemia-Specific Dependence on a Pre-mRNA Metabolic Pathway Regulated by DCPS.

Genome-wide characterization of chromatin binding and nucleosome spacing activity of the nucleosome remodelling ATPase ISWI.

GiniClust: detecting rare cell types from single-cell gene expression data with Gini index

Haystack: systematic analysis of the variation of epigenetic states and cell-type specific regulatory elements

High-fat diet enhances stemness and tumorigenicity of intestinal progenitors

Identification of Transcribed Enhancers by Genome-Wide Chromatin Immunoprecipitation Sequencing.

Impact of the N-Terminal Domain of STAT3 in STAT3-Dependent Transcriptional Activity

Integrated design, execution, and analysis of arrayed and pooled CRISPR genome-editing experiments.

Multi-scale chromatin state annotation using a hierarchical hidden Markov model

Predicting chromatin organization using histone marks.

PrimeDesign software for rapid and simplified design of prime editing guide RNAs

STAT5 outcompetes STAT3 to regulate the expression of the oncogenic transcriptional modulator BCL6.

Serum-Based Culture Conditions Provoke Gene Expression Variability in Mouse Embryonic Stem Cells as Revealed by Single-Cell Analysis

Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM

The cohesin-associated protein Wapal is required for proper Polycomb-mediated gene silencing

The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells.

The role of Cdx2 as a lineage specific transcriptional repressor for pluripotent network during the first developmental cell lineage segregation

Transcription factor competition at the γ-globin promoters controls hemoglobin switching

Variant-aware saturating mutagenesis using multiple Cas9 nucleases identifies regulatory elements at trait-associated loci.