A5107974625- Multiple Myeloma Research and Treatments
- Protein Degradation and Inhibitors
- DNA and Biological Computing
- semigroups and automata theory
- Algorithms and Data Compression
- Pluripotent Stem Cells Research
- Advanced biosensing and bioanalysis techniques
- CRISPR and Genetic Engineering
- RNA Research and Splicing
- Genomics and Chromatin Dynamics
- Gene Regulatory Network Analysis
- Molecular Biology Techniques and Applications
- RNA modifications and cancer
- Cellular Automata and Applications
- RNA Interference and Gene Delivery
- Evolutionary Algorithms and Applications
- Modular Robots and Swarm Intelligence
- Epigenetics and DNA Methylation
- Renal and related cancers
- Cancer therapeutics and mechanisms
- DNA Repair Mechanisms
- Genome Rearrangement Algorithms
- Monoclonal and Polyclonal Antibodies Research
- CAR-T cell therapy research
- Virus-based gene therapy research
European Bioinformatics Institute
2008-2020
Wellcome Trust
2009-2020
Wellcome/MRC Cambridge Stem Cell Institute
2014-2018
University of Cambridge
2014-2018
Universitat Rovira i Virgili
2006-2018
Medical Research Council
2014-2017
University of Genoa
1989
Sapienza University of Rome
1989
Current human pluripotent stem cells lack the transcription factor circuitry that governs ground state of mouse embryonic (ESC). Here, we report short-term expression two components, NANOG and KLF2, is sufficient to ignite other elements network reset state. Inhibition ERK protein kinase C sustains a transgene-independent rewired Reset self-renew continuously without signaling, are phenotypically stable, karyotypically intact. They differentiate in vitro form teratomas vivo. Metabolism...
A BLUEPRINT of immune cell development To determine the epigenetic mechanisms that direct blood cells to develop into many components our system, consortium examined regulation DNA and RNA transcription dissect molecular traits govern differentiation. By inducing responses, Saeed et al. document changes in genome underlie Cheng demonstrate trained monocytes are highly dependent on breakdown sugars presence oxygen, which allows produce energy needed mount an response. Chen examine transcripts...
SummaryTranscriptional heterogeneity within embryonic stem cell (ESC) populations has been suggested as a mechanism by which seemingly homogeneous population can initiate differentiation into an array of different types. Chromatin remodeling proteins have shown to control transcriptional variability in yeast and be important for mammalian ESC lineage commitment. Here we show that the Nucleosome Remodeling Deacetylation (NuRD) complex, is required commitment, modulates both dynamic range set...
DNA replication is temporally and spatially organized in all eukaryotes, yet the molecular control biological function of replication-timing program are unclear. Rif1 required for normal genome-wide regulation timing, but its poorly understood. Here we show that mouse embryonic stem cells, coats late-replicating domains and, with Lamin B1, identifies most genome. an essential determinant timing non-Lamin B1-bound late domains. We further demonstrate defines restricts interactions between...
Chromatin remodeling complexes play essential roles in metazoan development through widespread control of gene expression, but the precise molecular mechanisms by which they do this vivo remain ill defined. Using an inducible system with fine temporal resolution, we show that nucleosome and deacetylation (NuRD) complex controls chromatin architecture protein binding repertoire at regulatory regions during cell state transitions. This is primarily exerted its activity while H3K27 follows...
Sall4 is an essential transcription factor for early mammalian development and frequently overexpressed in cancer. Though it reported to play important role embryonic stem cell self-renewal, whether pluripotency has been disputed. Here we show that dispensable ES pluripotency. enhancer-binding protein prevents precocious activation of the neural gene expression programme cells but not required maintenance regulatory network. While a proportion physically associates with Nucleosome...
Chronic lymphocytic leukemia (CLL) cells are highly dependent on microenvironmental and signals. The lymph node (LN) is the critical site of in vivo CLL proliferation development resistance to both chemotherapy targeted agents. We present a new model that incorporates key aspects LN, which enables investigation context protective niche. describe three-dimensional (3D) vitro culture system using ultra-low attachment plates create spheroids derived from peripheral blood. Starting CLL:T cell...
RNA-seq is a reference technology for determining alternative splicing at genome-wide level. Exon arrays remain widely used the analysis of gene expression, but show poor validation rate with regard to events. Commercial that include probes within exon junctions have been developed in order overcome this problem. We compare performance (Illumina HiSeq) and junction (Affymetrix Human Transcriptome array) transcript Three different breast cancer cell lines were treated CX-4945, drug severely...
In this paper, the descriptional complexity of extended finite splicing systems is studied. These are known to generate exactly class regular languages. Upper and lower bounds shown relating size these systems, defined as total length rules initial language system, their equivalent minimal nondeterministic automata (NFA). addition, an accepting model Using variant one can obtain which more than polynomially succinct NFA or generating system.
Abstract Purpose: Cereblon (CRBN), a substrate receptor of the E3 ubiquitin ligase complex CRL4CRBN, is target small molecules lenalidomide and avadomide. Upon binding drugs, Aiolos Ikaros are recruited to ligase, ubiquitylated, subsequently degraded. In diffuse large B-cell lymphoma (DLBCL) cells, direct transcriptional repressors interferon-stimulated genes (ISG) degradation these substrates results in increased ISG protein levels resulting decreased proliferation apoptosis. Herein, we...
Early data suggested that CC-115, a clinical molecule, already known to inhibit the mammalian target of rapamycin kinase (TORK) and DNA-dependent protein (DNA-PK) may have additional targets beyond TORK DNA-PK. Therefore, we aimed identify such target(s) investigate potential therapeutic applicability. Functional profiling 141 cancer cell lines revealed inhibition suppressor morphogenesis in genitalia 1 (SMG1), key regulator RNA degradation mechanism nonsense-mediated mRNA decay (NMD), as an...
ABSTRACT Neutrophils and monocytes provide a first line of defense against infections as part the innate immune system. Here we report integrated analysis transcriptomic epigenetic landscapes for circulating neutrophils with aim to enable downstream interpretation functional validation key regulatory elements in health disease. We collected RNA-seq data, ChIP-seq six histone modifications DNA methylation by bisulfite sequencing at base pair resolution from up 6 individuals per cell type....
In this paper we investigate H systems with strongly non-preserving splicing that exhibit a new feature, namely delay, and introduce variant of the system lies between non-reflexively evolving splicing. Informally, behaves as follows: (1) each step is exactly in splicing; (2) generated language obtained For both have remarkable jump power finite but arbitrarily large those infinite delay. The first can generate non-context-free languages, whereas second do not get beyond regular limit....
In this paper, we present some results regarding the size complexity of Accepting Networks Evolutionary Processors with Filtered Connections (ANEPFCs). We show that there are universal ANEPFCs 10, by devising a method for simulating 2-Tag Systems. This result significantly improves known upper bound which is 18. also propose new, computationally and descriptionally efficient simulation nondeterministic Turing machines ANEPFCs. More precisely, describe (informally, due to space limitations)...