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Article
Open AccessAuthor Correction: Pathway level subty** identifies a slow-cycling biological phenotype associated with poor clinical outcomes in colorectal cancer
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Article
Open AccessPathway level subty** identifies a slow-cycling biological phenotype associated with poor clinical outcomes in colorectal cancer
Molecular stratification using gene-level transcriptional data has identified subtypes with distinctive genotypic and phenotypic traits, as exemplified by the consensus molecular subtypes (CMS) in colorectal c...
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Article
Open AccessMulti-label transcriptional classification of colorectal cancer reflects tumor cell population heterogeneity
Transcriptional classification has been used to stratify colorectal cancer (CRC) into molecular subtypes with distinct biological and clinical features. However, it is not clear whether such subtypes represent...
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Article
Open AccessColorectal cancer patient-derived organoids and cell lines harboring ATRX and/or DAXX mutations lack Alternative Lengthening of Telomeres (ALT)
Telomere maintenance is necessary to maintain cancer cell unlimited viability. However, the mechanisms maintaining telomere length in colorectal cancer (CRC) have not been extensively investigated. Telomere ma...
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Article
Towards precision oncology with patient-derived xenografts
Under the selective pressure of therapy, tumours dynamically evolve multiple adaptive mechanisms that make static interrogation of genomic alterations insufficient to guide treatment decisions. Clinical resear...
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Article
Chromatin Velocity reveals epigenetic dynamics by single-cell profiling of heterochromatin and euchromatin
Recent efforts have succeeded in surveying open chromatin at the single-cell level, but high-throughput, single-cell assessment of heterochromatin and its underlying genomic determinants remains challenging. W...
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Article
Open AccessPhyliCS: a Python library to explore scCNA data and quantify spatial tumor heterogeneity
Tumors are composed by a number of cancer cell subpopulations (subclones), characterized by a distinguishable set of mutations. This phenomenon, known as intra-tumor heterogeneity (ITH), may be studied using C...
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Protocol
eQTL Map** Using Transcription Factor Affinity
In the last decades, thousands of common genetic variants have been associated with human diseases by genome-wide association studies (GWAS). However, the functional interpretation of GWAS hits is usually nont...
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Article
A functional strategy to characterize expression Quantitative Trait Loci
The study of genetic variation has been revolutionized by the advent of high-throughput technologies able to determine the complete genomic sequence of thousands of individuals. Understanding the functional re...
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Article
Open AccessDysregulation of Blimp1 transcriptional repressor unleashes p130Cas/ErbB2 breast cancer invasion
ErbB2 overexpression is detected in approximately 20% of breast cancers and is correlated with poor survival. It was previously shown that the adaptor protein p130Cas/BCAR1 is a crucial mediator of ErbB2 trans...
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Article
Open AccessRoar: detecting alternative polyadenylation with standard mRNA sequencing libraries
Post-transcriptional regulation is a complex mechanism that plays a central role in defining multiple cellular identities starting from a common genome. Modifications in the length of 3’UTRs have been found to...
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Chapter
Modelling Ammonium Transporters in Arbuscular Mycorrhiza Symbiosis
The Stochastic Calculus of Wrapped Compartments (SCWC) is a recently proposed variant of the Stochastic Calculus of Loo** Sequences (SCLS), a language for the representation and simulation of biological syst...
