Hugo A. Guillen-Ramirez

• PhD in Computer Science
• Advanced postdoc at University of Bern

CRISPR-Cas9 deletion (CRISPR-del) is the leading approach for eliminating DNA from mammalian cells and underpins a variety of genome-editing applications. Target DNA, defined by a pair of double-strand breaks (DSBs), is removed during nonhomologous end-joining (NHEJ). However, the low efficiency of CRISPR-del results in laborious experiments and fa...

Abstract The increasing interest in bioactive peptides with therapeutic potentials has been reflected in a large variety of biological databases published over the last years. However, the knowledge discovery process from these heterogeneous data sources is a nontrivial task, becoming the essence of our research endeavor. Therefore, we devise a uni...

Riboswitches are non-coding RNAs that regulate gene expression by altering the structural conformation of mRNA transcripts. Their regulation mechanism might be exploited for interesting biomedical applications such as drug targets and biosensors. A major challenge consists in accurately identifying metabolite-binding RNA switches which are structur...

We describe a method for inverting spectroscopic data of the absorption and extinction properties of colloidal samples of resonant particles. We show that, with some prior knowledge, the genetic algorithm employed is able to estimate the probability density function of particle sizes. Since the data are sensitive to the shape and material of the pa...

Background Noise in the operating room has been shown to distract the surgical team and to be associated with postoperative complications. It is, however, unclear whether complications after noisy operations are the result of objective or subjective surgical difficulty or the consequence of distraction of the operating room team by noise. Methods...

Infections following surgery drive patient morbidity and mortality, making early detection essential. Traditional predictive models utilize preoperative patient characteristics and features of the surgical procedure. This study enhances these baseline determinants by incorporating postoperative responses. We have designed and tested a procedure-agn...

Background: Although the impact of surgery- and patient-dependent factors on surgical-site infections (SSIs) have been studied extensively, their influence on the microbial composition of SSI remains unexplored. The aim of this study was to identify patient-dependent predictors of the microbial composition of SSIs across different types of surgery...

A key attribute of some long noncoding RNAs (lncRNAs) is their ability to regulate expression of neighbouring genes in cis. However, such ‘cis-lncRNAs’ are presently defined using ad hoc criteria that, we show, are prone to false-positive predictions. The resulting lack of cis-lncRNA catalogues hinders our understanding of their extent, characteris...

Background and state of research: The Swiss Personalized Health Network (SPHN) is a Swiss national initiative. It contributes to the development of coordinated data infrastructures to make health-relevant data interoperable for research. SPHN developed a framework based on a semantic layer of information and graph technologies for exchange. The SPH...

Long noncoding RNAs (lncRNAs) are linked to cancer via pathogenic changes in their expression levels. Yet, it remains unclear whether lncRNAs can also impact tumour cell fitness via function-altering somatic “driver” mutations. To search for such driver-lncRNAs, we here perform a genome-wide analysis of fitness-altering single nucleotide variants (...

Long noncoding RNAs (lncRNAs) can positively and negatively regulate expression of target genes encoded in cis. However, the extent, characteristics and mechanisms of such cis-regulatory lncRNAs (cis-lncRNAs) remain obscure. Until now, they have been defined using inconsistent, ad hoc criteria that can result in false-positive predictions. Here, we...

Long noncoding RNAs (lncRNAs) are widely dysregulated in cancer, yet their functional roles in cancer hallmarks remain unclear. We employ pooled CRISPR deletion to perturb 831 lncRNAs detected in KRAS-mutant non-small cell lung cancer (NSCLC) and measure their contribution to proliferation, chemoresistance, and migration across two cell backgrounds...

Long noncoding RNAs (lncRNAs) can act as tumour suppressor or oncogenes to contrast/promote tumour cell proliferation via RNA-dependent mechanisms. Recently, genome sequencing has identified elevated densities of tumour somatic single nucleotide variants (SNVs) in lncRNA genes. However, this has been attributed to phenotypically-neutral “passenger”...

Tumour DNA contains thousands of single nucleotide variants (SNVs) in non-protein-coding regions, yet it remains unclear which are driver mutations that promote cell fitness. Amongst the most highly mutated non-coding elements are long noncoding RNAs (lncRNAs), which can promote cancer and may be targeted therapeutically. We here searched for evide...

Long noncoding RNAs (lncRNAs) are widely dysregulated in cancer, yet their functional roles in cellular disease hallmarks remain unclear. Here we employ pooled CRISPR deletion to perturb all 831 lncRNAs in KRAS-mutant non-small cell lung cancer (NSCLC), and measure their contribution to proliferation, chemoresistance and migration across two cell b...

MOTIVATION: Bioactive peptides have gained great attention in the academy and pharmaceutical industry since they play an important role in human health. However, the increasing number of bioactive peptide databases is causing the problem of data redundancy and duplicated efforts. Even worse is the fact that the available data is non-standardized an...

Los algoritmos de aprendizaje automático supervisado están limitados tanto por el etiquetado de las instancias a aprender, como del conocimiento del dominio de los problemas a resolver. Extraer dicho conocimiento sin intervención humana es una tarea compleja que pudiera realizarse utilizando algoritmos de aprendizaje por refuerzo, entre los que se...

This is a brief introduction to the refractivesqlite package (https://github.com/HugoGuillen/refractiveindex.info-sqlite) developed by Hugo Guillén (https://github.com/HugoGuillen). This package is a wrapper in Python 3 for the database of optical constants refractiveindex.info (http://refractiveindex.info/) developed by Mikhail Polyanskiy (https:/...

Se muestran algunos recursos en línea para ayudar a aumentar la detectabilidad (discoverability) del trabajo de investigación.

The development of new technologies for the design of DNA microarrays has boosted the generation of large volumes of biological data, which requires the development of efficient computational methods for their analysis and annotation. Among these methods, biclusters generation algorithms attempt to identify coherent associations of genes and experi...