Vera Pancaldi

Publications

• The antitumoral activity of TLR7 ligands is corrupted by the microenvironment of pancreatic tumors
• Molecular Inverse Comorbidity between Alzheimer's Disease and Lung Cancer: New Insights from Matrix Factorization.
• ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C.
• Comparative analysis of neutrophil and monocyte epigenomes
• Epigenetic and Transcriptional Variability Shape Phenotypic Plasticity.
• Automatic identification of informative regions with epigenomic changes associated to hematopoiesis.
• Preface to the special issue “Complexity in the Oil Industry 2007”
• Biological noise to get a sense of direction: an analogy between chemotaxis and stress response
• Whole-genome fingerprint of the DNA methylome during human B cell differentiation
• Topology of functional networks predicts physical binding of proteins
• Activation of Vitamin D Receptor Pathway Enhances Differentiating Capacity in Acute Myeloid Leukemia with Isocitrate Dehydrogenase Mutations
• Interpreting molecular similarity between patients as a determinant of disease comorbidity relationships
• STAG2 loss-of-function affects short-range genomic contacts and modulates urothelial differentiation in bladder cancer cells
• Low replication stress leads to specific replication timing advances associated to chromatin remodelling in cancer cells
• Supporting Clinical Decision-Making during the SARS-CoV-2 Pandemic through a Global Research Commitment: The TERAVOLT Experience.
• Eomes-Dependent Loss of the Co-activating Receptor CD226 Restrains CD8+ T Cell Anti-tumor Functions and Limits the Efficacy of Cancer Immunotherapy.
• Chromatin network markers of leukemia.
• COVID-19 in patients with thoracic malignancies (TERAVOLT): first results of an international, registry-based, cohort study.
• TERAVOLT: Thoracic Cancers International COVID-19 Collaboration.
• Using GARDEN-NET and ChAseR to explore human haematopoietic 3D chromatin interaction networks.
• Community-wide hackathons to identify central themes in single-cell multi-omics.
• Mitochondrial metabolism supports resistance to IDH mutant inhibitors in acute myeloid leukemia.
• GEM-DeCan: Improved tumor immune microenvironment profiling through novel gene expression and DNA methylation signatures predicts immunotherapy response
• CovMulNet19, Integrating Proteins, Diseases, Drugs, and Symptoms: A Network Medicine Approach to COVID-19.
• Tysserand - Fast and accurate reconstruction of spatial networks from bioimages
• Three-dimensional connectivity and chromatin environment mediate the activation efficiency of mammalian DNA replication origins
• Insights on TAM Formation from a Boolean Model of Macrophage Polarization Based on In Vitro Studies
• Unveiling new disease, pathway, and gene associations via multi-scale neural network
• Tysserand—fast and accurate reconstruction of spatial networks from bioimages
• STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells
• Cytidine deaminase protects pancreatic cancer cells from replicative stress and drives resistance to DNA-targeting drugs
• Chromatin Network Analyses: Towards Structure-Function Relationships in Epigenomics
• An Agent-Based Model of Monocyte Differentiation into Tumour-Associated Macrophages in Chronic Lymphocytic Leukemia
• Hierarchical coarse-graining transform
• Meta-analysis of genome regulation and expression variability across hundreds of environmental and genetic perturbations in fission yeast
• AnGeLi: A Tool for the Analysis of Gene Lists from Fission Yeast
• Higher gene expression variability in the more aggressive subtype of chronic lymphocytic leukemia
• A Boolean gene regulatory model of heterosis and speciation
• A Gene Regulatory Network Simulation of Heterosis
• Stress induces remodelling of yeast interaction and co-expression networks
• In silico characterization and prediction of global protein-mRNA interactions in yeast
• Predicting the Fission Yeast Protein Interaction Network
• Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativity
• Chromatin Regulators as a Guide for Cancer Treatment Choice
• Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer.
• Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells.
• The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery.
• Systematic screen for mutants resistant to TORC1 inhibition in fission yeast reveals genes involved in cellular ageing and growth.
• Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types.
• Low Replicative Stress Triggers Cell-Type Specific Inheritable Advanced Replication Timing
• Wavelet-based upscaling of advection equations
• Permeability up-scaling using Haar Wavelets
• Upscaling of the Saturation Equation
• Activation of Vitamin D Receptor Pathway Enhances Differentiating Capacity in Acute Myeloid Leukemia with Isocitrate Dehydrogenase Mutations
• An Agent-Based Model of monocyte differentiation into Tumour-Associated Macrophages in Chronic Lymphocytic Leukemia
• 3D chromatin connectivity underlies replication origin efficiency in mouse embryonic stem cells
• 3D chromatin interactions involving Drosophila insulators are infrequent but preferential and arise before TADs and transcription
• 3D chromatin interactions involvingDrosophilainsulators are infrequent but preferential and arise before TADs and transcription
• mosna reveals different types of cellular interactions predictive of response to immunotherapies in cancer
• mosnareveals different types of cellular interactions predictive of response to immunotherapies in cancer
• Network models of chromatin structure
• An agent-based model of monocyte differentiation into tumour-associated macrophages in chronic lymphocytic leukemia
• Chromatin network rearrangements in differentiation and cancer reveal connections between evolutionary processes and gene regulation
• Automatic identification of informative regions with epigenomic changes associated to hematopoiesis
• A Boolean Model of the Formation of Tumour Associated Macrophages in anin-vitroModel of Chronic Lymphocytic Leukaemia
• Global chromatin reorganization and regulation of genes of specific evolutionary age in differentiation and cancer
• mosna reveals different types of cellular interactions predictive of response to immunotherapies and survival in cancer
• mosnareveals different types of cellular interactions predictive of response to immunotherapies and survival in cancer
• Global chromatin reorganization and regulation of genes with specific evolutionary ages during differentiation and cancer
• Unveiling epigenetic regulatory elements associated with breast cancer development
• Unraveling the network signatures of oncogenicity in virus-human protein-protein interactions
• multideconv - an integrative pipeline for combining first and second generation cell type deconvolution results
• multideconv- an integrative pipeline for combining first and second generation cell type deconvolution results