A5090923781- RNA Research and Splicing
- Genomics and Chromatin Dynamics
- Genomics and Phylogenetic Studies
- Epigenetics and DNA Methylation
- Cancer-related molecular mechanisms research
- RNA and protein synthesis mechanisms
- CRISPR and Genetic Engineering
- RNA Interference and Gene Delivery
- Virus-based gene therapy research
- Animal Genetics and Reproduction
- Cancer Genomics and Diagnostics
- Immune Cell Function and Interaction
- Gene expression and cancer classification
- MicroRNA in disease regulation
- Genomic variations and chromosomal abnormalities
- Acute Myeloid Leukemia Research
- CAR-T cell therapy research
- Birth, Development, and Health
- RNA modifications and cancer
- Asthma and respiratory diseases
- interferon and immune responses
- Hedgehog Signaling Pathway Studies
- IL-33, ST2, and ILC Pathways
- T-cell and B-cell Immunology
- Genetic factors in colorectal cancer
Istituto di Ricovero e Cura a Carattere Scientifico San Raffaele
2017-2022
Istituti di Ricovero e Cura a Carattere Scientifico
2017-2022
Community Catalyst
2020
Vita-Salute San Raffaele University
2012-2019
Harvard University
2018-2019
Dana-Farber Cancer Institute
2018-2019
Boehringer Ingelheim (Germany)
2015-2018
Target (Germany)
2017-2018
University College London
2009-2015
IRCCS Ospedale San Raffaele
2002-2015
The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into most comprehensive library Perl modules available for managing manipulating life-science information. provides easy-to-use, stable, consistent programming interface bioinformatics application programmers. have been successfully repeatedly used to reduce otherwise complex tasks only a few lines code. object model proven be...
The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is comprehensive source stable automatic annotation human genome sequence, with confirmed gene predictions that have been integrated external data sources, and available as either an interactive web site or flat files. also open software engineering develop portable system able handle very genomes associated requirements from sequence...
The compact genome of Fugu rubripes has been sequenced to over 95% coverage, and more than 80% the assembly is in multigene-sized scaffolds. In this 365-megabase vertebrate genome, repetitive DNA accounts for less one-sixth sequence, gene loci occupy about one-third genome. As with human are not evenly distributed, but clustered into sparse dense regions. Some “giant” genes were observed that had average coding sequence sizes spread genomic lengths significantly larger those their orthologs....
Metachromatic leukodystrophy (MLD) is an inherited lysosomal storage disease caused by arylsulfatase A (ARSA) deficiency. Patients with MLD exhibit progressive motor and cognitive impairment die within a few years of symptom onset. We used lentiviral vector to transfer functional ARSA gene into hematopoietic stem cells (HSCs) from three presymptomatic patients who showed genetic, biochemical, neurophysiological evidence late infantile MLD. After reinfusion the gene-corrected HSCs, extensive...
The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide unified interface biomedical databases that are distributed worldwide. portal provides access numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the independently administered funded their host data federation...
Evolution is typically thought to proceed through divergence of genes, proteins and ultimately phenotypes. However, similar traits might also evolve convergently in unrelated taxa owing selection pressures. Adaptive phenotypic convergence widespread nature, recent results from several genes have suggested that this phenomenon powerful enough drive recurrent evolution at the sequence level. Where homoplasious substitutions do occur these long been considered result neutral processes. studies...
Recent multi-dimensional approaches to the study of complex disease have revealed powerful insights into how genetic and epigenetic factors may underlie their aetiopathogenesis. We examined genotype-epigenotype interactions in context Type 2 Diabetes (T2D), focussing on known regions genomic susceptibility. assayed DNA methylation 60 females, stratified according susceptibility haplotype using previously identified association loci. CpG was assessed methylated immunoprecipitation a targeted...
Germline CDH1 point or small frameshift mutations can be identified in 30–50% of hereditary diffuse gastric cancer (HDGC) families. We hypothesized that genomic rearrangements would found HDGC and 160 families with either two cancers first-degree relatives at least one (DGC) diagnosed before age 50, three more DGC close any age. Sixty-seven carried germline mutations. screened DNA from the 93 mutation negative probands for large by Multiplex Ligation-Dependent Probe Amplification. Potential...
PRGdb is a web accessible open-source (http://www.prgdb.org) database that represents the first bioinformatic resource providing comprehensive overview of resistance genes (R-genes) in plants. holds more than 16 000 known and putative R-genes belonging to 192 plant species challenged by 115 different pathogens linked with useful biological information. The complete includes set 73 manually curated reference R-genes, 6308 collected from NCBI 10463 computationally predicted R-genes. Thanks...
Recent epidemiological reports of associations between socioeconomic status and epigenetic markers that predict vulnerability to diseases are bringing light substantial biological effects social inequalities. Here, we start the discussion moral consequences these findings. We firstly highlight their explanatory importance in context research program on Developmental Origins Health Disease (DOHaD) determinants health. In second section, review some theories health Rather than a complete...
Spatiotemporal control of gene expression is central to animal development. Core promoters represent a previously unanticipated regulatory level by interacting with cis -regulatory elements and transcription initiation in different physiological developmental contexts. Here, we provide first comprehensive description the core promoter repertoire its dynamic use during development vertebrate embryo. By using cap analysis (CAGE), mapped events at single nucleotide resolution across 12 stages...
Abstract Gene functionality is closely connected to its expression specificity across tissues and cell types. RNA-Seq a powerful quantitative tool explore genome wide expression. The aim of this study provide comprehensive dataset the same 13 for mouse rat, two most relevant species biomedical research. provides transcriptome from three male C57BL6 mice Han Wistar rats. We also describe our bioinformatics pipeline process technically validate data. Principal component analysis shows that...
Recruitment and activation of thermogenic adipocytes have received increasing attention as a strategy to improve systemic metabolic control. The analysis brown brite is complicated by the complexity adipose tissue biopsies. Here, we provide an in-depth pure brown, brite, white adipocyte transcriptomes. By combining mouse human transcriptome data, identify gene signature that can classify in mice men. Using machine-learning-based cell deconvolution approach, develop algorithm proficient...
Aberrant DNA methylation (DNAm) was first linked to cancer over 25 yr ago. Since then, many studies have associated hypermethylation of tumor suppressor genes and hypomethylation oncogenes the tumorigenic process. However, most these been limited analysis promoters CpG islands (CGIs). Recently, new technologies for whole-genome DNAm (methylome) developed, enabling unbiased methylomes. By using MeDIP-seq, we report a sequencing-based comparative methylome malignant peripheral nerve sheath...
The transition from quiescence to proliferation is a key regulatory step that can be induced by serum stimulation in cultured fibroblasts. transcription factor Myc directly mitogens and drives secondary gene expression program remains largely unknown. Using mRNA profiling, we identify close 300 Myc-dependent response (MDSR) genes, which are manner mouse Mapping of genomic Myc-binding sites ChIP-seq technology revealed most MDSR genes were targeted Myc, but represented minor fraction (5.5%)...
The International Knockout Mouse Consortium (IKMC) aims to mutate all protein-coding genes in the mouse using a combination of gene targeting and trapping embryonic stem (ES) cells make generated resources readily available research community. IKMC database web portal ( www.knockoutmouse.org ) serves as central public site for data facilitates coordination prioritization work within consortium. Researchers can access up-to-date information on knockout vectors, ES mice specific genes, follow...
We describe a previously unreported syndrome characterized by secondary (post-natal) microcephaly with fronto-temporal lobe hypoplasia, multiple pituitary hormone deficiency, seizures, severe visual impairment and abnormalities of the kidneys urinary tract in highly consanguineous family six affected children. Homozygosity mapping exome sequencing revealed novel homozygous frameshift mutation basic helix-loop-helix transcription factor gene ARNT2 (c.1373_1374dupTC) individuals. This results...
<h3>Background</h3> Mutations in microtubule-regulating genes are associated with disorders of neuronal migration and microcephaly. Regulation centriole length has been shown to underlie the pathogenesis certain ciliopathy phenotypes. Using a next-generation sequencing approach, we identified mutations novel centriolar disease gene kindred an embryonic lethal phenotype patient primary <h3>Methods results</h3> Whole exome data from non-consanguineous Caucasian exhibiting mid-gestation...
Breast cancer is the most common malignancy in women worldwide. Among breast subtypes, triple-negative (TNBC) aggressive and difficult to treat. One of master regulators TNBC progression architectural transcription factor HMGA1. This study aimed further explore HMGA1 molecular network identify mechanisms involved progression.RNA from MDA-MB-231 cell line, silenced for expression, was sequenced and, with a bioinformatic analysis, partners could cooperate regulating downstream gene networks...