Inês de Santiago

Smoking-associated gene expression alterations in nasal epithelium reveal immune impairment linked to lung cancer risk

Maria Stella de Biase, Florian Massip, Tzu‐Ting Wei, Federico M. Giorgi et autres

BACKGROUND: Lung cancer is the leading cause of cancer-related death in the world. In contrast to many other cancers, a direct connection to modifiable lifestyle risk in the form of tobacco smoke has long been established. More than 50% of all smoking-related …

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Data-Driven Medicine in the Diagnosis and Treatment of Infertility

Inês de Santiago, Łukasz Polański

Infertility, although not a life-threatening condition, affects around 15% of couples trying for a pregnancy. The increasing availability of large datasets from various sources, together with advances in machine learning (ML) and artificial intelligence (AI), are enabling a transformational change in infertility …

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Clonal somatic copy number altered driver events inform drug sensitivity in high-grade serous ovarian cancer

Filipe Correia Martins, Dominique‐Laurent Couturier, Inês de Santiago, Carolin M. Sauer et autres

Chromosomal instability is a major challenge to patient stratification and targeted drug development for high-grade serous ovarian carcinoma (HGSOC). Here we show that somatic copy number alterations (SCNAs) in frequently amplified HGSOC cancer genes significantly correlate with gene expression and methylation status. …

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Smoking-dependent expression alterations in nasal epithelium reveal immune impairment linked to germline variation and lung cancer risk

Maria Stella de Biase, Florian Massip, Tzu‐Ting Wei, Federico M. Giorgi et autres

Abstract Lung cancer is the leading cause of cancer-related death in the world. In contrast to many other cancers, a direct connection to modifiable lifestyle risk in the form of tobacco smoke has long been established. More than 50% of all smoking-related …

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The landscape of high-affinity human antibodies against intratumoral antigens

Goran Rakočević, Irina Glotova, Inês de Santiago, Berke Ç. Toptaş et autres

Abstract High expression of immunoglobulin transcripts is often detected in human tumours and correlates with favourable clinical outcomes across different cancer types. However, the antigens recognized by such immunoglobulins (Ig) and their biological significance remain largely unknown. We computationally inferred the paired …

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Big Data and Artificial Intelligence (AI) are Poised to Transform Infertility Healthcare

Inês de Santiago, Łukasz Polański

Advances in machine learning (ML) and artificial intelligence (AI) are transforming the way we treat patients in ways not even imagined a few years ago. Cancer research is at the forefront of this movement. Infertility, though not a life-threatening condition, affects around …

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Analysis of ChIP-seq Data in R/Bioconductor

Inês de Santiago, Thomas Carroll

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Immuno-phenotypes of Pancreatic Ductal Adenocarcinoma: Metaanalysis of transcriptional subtypes

Inês de Santiago, Christopher Yau, Mark R. Middleton, Michael L. Dustin et autres

Abstract Pancreatic ductal adenocarcinoma (PDAC) is the most common malignancy of the pancreas and has one of the highest mortality rates of any cancer type with a 5-year survival rate of < 5% and median overall survival of typically six months from …

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RNA polymerase II primes Polycomb‐repressed developmental genes throughout terminal neuronal differentiation

Carmelo Ferrai, Elena Torlai Triglia, Jessica R. Risner-Janiczek, Tiago Rito et autres

Polycomb repression in mouse embryonic stem cells (ESCs) is tightly associated with promoter co-occupancy of RNA polymerase II (RNAPII) which is thought to prime genes for activation during early development. However, it is unknown whether RNAPII poising is a general feature of …

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Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells

Mariano Barbieri, Sheila Q. Xie, Elena Torlai Triglia, Andrea M. Chiariello et autres

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Complex multi-enhancer contacts captured by genome architecture mapping

Robert A. Beagrie, Antonio Scialdone, Markus Schueler, Dorothee Kraemer et autres

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Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells

Mariano Barbieri, Sheila Q. Xie, Elena Torlai Triglia, Inês de Santiago et autres

Abstract Gene expression states influence the three-dimensional conformation of the genome through poorly understood mechanisms. Here, we investigate the conformation of the murine HoxB locus, a gene-dense genomic region containing closely spaced genes with distinct activation states in mouse embryonic stem (ES) …

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