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Article
Open AccessCorrection: PaCBAM: fast and scalable processing of whole exome and targeted sequencing data
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Article
Open AccessGermline determinants of aberrant signaling pathways in cancer
Cancer is a complex disease influenced by a heterogeneous landscape of both germline genetic variants and somatic aberrations. While there is growing evidence suggesting an interplay between germline and somat...
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Article
Open AccessLSD1/PRMT6-targeting gene therapy to attenuate androgen receptor toxic gain-of-function ameliorates spinobulbar muscular atrophy phenotypes in flies and mice
Spinobulbar muscular atrophy (SBMA) is caused by CAG expansions in the androgen receptor gene. Androgen binding to polyQ-expanded androgen receptor triggers SBMA through a combination of toxic gain-of-function...
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Article
Open AccessA slow-cycling/quiescent cells subpopulation is involved in glioma invasiveness
Pediatric and adult high-grade gliomas are the most common primary malignant brain tumors, with poor prognosis due to recurrence and tumor infiltration after therapy. Quiescent cells have been implicated in tu...
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Article
Open AccessCalcium cytotoxicity sensitizes prostate cancer cells to standard-of-care treatments for locally advanced tumors
Therapy resistance is a major roadblock in oncology. Exacerbation of molecular dysfunctions typical of cancer cells have proven effective in twisting oncogenic mechanisms to lethal conditions, thus offering ne...
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Article
Open AccessPlasma tumour DNA as an early indicator of treatment response in metastatic castration-resistant prostate cancer
Plasma tumour DNA (ptDNA) levels on treatment are associated with response in a variety of cancers. However, the role of ptDNA in prostate cancer monitoring remains largely unexplored. Here we characterised on...
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Article
Open AccessIntegrative multiplatform molecular profiling of benign prostatic hyperplasia identifies distinct subtypes
Benign prostatic hyperplasia (BPH), a nonmalignant enlargement of the prostate, is among the most common diseases affecting aging men, but the underlying molecular features remain poorly understood, and therap...
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Article
Open AccessPaCBAM: fast and scalable processing of whole exome and targeted sequencing data
Interrogation of whole exome and targeted sequencing NGS data is rapidly becoming a preferred approach for the exploration of large cohorts in the research setting and importantly in the context of precision m...
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Article
Open AccessThird generation EGFR inhibitor osimertinib combined with pemetrexed or cisplatin exerts long-lasting anti-tumor effect in EGFR-mutated pre-clinical models of NSCLC
The third generation Epidermal Growth Factor Receptor (EGFR) Tyrosine Kinase Inhibitor (TKI) osimertinib has been initially approved for T790M positive Non-Small Cell Lung Cancer (NSCLC) and more recently for ...
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Protocol
Allele-Specific Expression Analysis in Cancer Using Next-Generation Sequencing Data
Allele-specific expression arises when transcriptional activity at the different alleles of a gene differs considerably. Although extensive research has been carried out to detect and characterize this phenome...
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Article
A highly specific SpCas9 variant is identified by in vivo screening in yeast
Evolved SpCas9 variant evoCas9 has improved specificity and retains near wild-type on-target activity.
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Article
Open AccessInherited determinants of early recurrent somatic mutations in prostate cancer
Prostate cancer is a highly heritable molecularly and clinically heterogeneous disease. To discover germline events involved in prostate cancer predisposition, we develop a computational approach to nominate h...
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Article
Open AccessHit and go CAS9 delivered through a lentiviral based self-limiting circuit
In vivo application of the CRISPR-Cas9 technology is still limited by unwanted Cas9 genomic cleavages. Long-term expression of Cas9 increases the number of genomic loci non-specifically cleaved by the nuclease. H...
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Article
Open AccessErratum to: Unraveling the clonal hierarchy of somatic genomic aberrations
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Article
Open AccessDevelopment and validation of a whole-exome sequencing test for simultaneous detection of point mutations, indels and copy-number alterations for precision cancer care
We describe Exome Cancer Test v1.0 (EXaCT-1), the first New York State-Department of Health-approved whole-exome sequencing (WES)-based test for precision cancer care. EXaCT-1 uses HaloPlex (Agilent) target en...
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Article
Open AccessASEQ: fast allele-specific studies from next-generation sequencing data
Single base level information from next-generation sequencing (NGS) allows for the quantitative assessment of biological phenomena such as mosaicism or allele-specific features in healthy and diseased cells. S...
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Article
Open AccessUnraveling the clonal hierarchy of somatic genomic aberrations
Defining the chronology of molecular alterations may identify milestones in carcinogenesis. To unravel the temporal evolution of aberrations from clinical tumors, we developed CLONET, which upon estimation of ...
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Chapter
Modelling Self-assembly in BlenX
The process through which disordered components spontaneously arrange themselves into patterns is called self-assembly. Molecular self-assembly describes the process by which molecules adopt a defined arrangem...
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Chapter
Programming Biology in BlenX
We introduce a programming language called BlenX. It has been specifically designed and implemented to model and simulate biological systems and is strongly inspired to process calculi. We describe all the fea...
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Chapter and Conference Paper
BlenX Static and Dynamic Semantics
We introduce a new programming language called BlenX. It is strongly inspired to process calculi and it is an evolution of Beta-binders. It has been specifically designed and implemented to model and simulate bio...
