Yamila N. Torres Cleuren

Yamila N. Torres Cleuren
University of Bergen | UiB · Department of Clinical Medicine

PhD

About

23
Publications
4,223
Reads
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869
Citations
Citations since 2017
18 Research Items
847 Citations
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2017201820192020202120222023050100150200250300
2017201820192020202120222023050100150200250300
Introduction
Skills and Expertise
Additional affiliations
October 2020 - present
Haukeland University Hospital
Position
  • Research Adviser
August 2016 - September 2020
University of Bergen
Position
  • PostDoc Position
January 2016 - July 2016
University of California, Santa Barbara
Position
  • PostDoc Position

Publications

Publications (23)
Article
Full-text available
Innovations in metazoan development arise from evolutionary modification of gene regulatory networks (GRNs). We report widespread cryptic variation in the requirement for two key regulatory inputs, SKN-1/Nrf2 and MOM-2/Wnt, into the C. elegans endoderm GRN. While some natural isolates show a nearly absolute requirement for these two regulators, in...
Article
Full-text available
Translation initiation is often attributed as the rate-determining step of eukaryotic protein synthesis and key to gene expression control. Despite this centrality, the series of steps involved in this process is poorly understood. Here, we capture the transcriptome-wide occupancy of ribosomes across all stages of translation initiation, enabling u...
Article
Significance It has become apparent in recent years that the DNA code is not the sole basis for biological inheritance. Epigenetic tags including DNA methylation, histone modifications, and regulatory RNAs can be transmitted across generations. However, the impact of heritable epigenetic factors on embryonic development is not well understood. We f...
Article
Full-text available
Background With the rapid growth in the use of high-throughput methods for characterizing translation and the continued expansion of multi-omics, there is a need for back-end functions and streamlined tools for processing, analyzing, and characterizing data produced by these assays. Results Here, we introduce ORFik, a user-friendly R/Bioconductor...
Article
Full-text available
Polyadenylation at the 3'-end is a major regulator of messenger RNA and its length is known to affect nuclear export, stability, and translation, among others. Only recently have strategies emerged that allow for genome-wide poly(A) length assessment. These methods identify genes connected to poly(A) tail measurements indirectly by short-read align...
Preprint
Full-text available
The heteroplasmic state of eukaryotic cells allows for cryptic accumulation of defective mitochondrial genomes (mtDNA). Purifying selection mechanisms operate to remove such dysfunctional mtDNAs. We found that pro-apoptotic regulators, including the CED-3 and CSP-1 caspases, the BH3-only protein CED-13, and PCD corpse engulfment factors, are requir...
Article
Full-text available
The design of optimal guide RNA (gRNA) sequences for CRISPR systems is challenged by the need to achieve highly efficient editing at the desired location (on‐target editing) with minimal editing at unintended locations (off‐target editing). Although laboratory validation should ideally be used to detect off‐target activity, computational prediction...
Preprint
Full-text available
Background: With the rapid growth in the use of high-throughput methods for characterizing translation and the continued expansion of multi-omics, there is a need for back-end functions and streamlined tools for processing, analyzing, and characterizing data produced by these assays. Results: Here, we introduce ORFik, a user-friendly R/Bioconductor...
Article
Full-text available
Developmental gene regulatory networks (GRNs) underpin metazoan embryogenesis and have undergone substantial modification to generate the tremendous variety of animal forms present on Earth today. The nematode Caenorhabditis elegans has been a central model for advancing many important discoveries in fundamental mechanistic biology and, more recent...
Article
Full-text available
Background: In phylogenetically diverse organisms, the 5' ends of a subset of mRNAs are trans-spliced with a spliced leader (SL) RNA. The functions of SL trans-splicing, however, remain largely enigmatic. Results: We quantified translation genome-wide in the marine chordate, Oikopleura dioica, under inhibition of mTOR, a central growth regulator...
Preprint
Full-text available
Gene regulatory networks (GRNs) that direct animal embryogenesis must respond to varying environmental and physiological conditions to ensure robust construction of organ systems. While GRNs are evolutionarily modified by natural genomic variation, the roles of epigenetic processes in shaping plasticity of GRN architecture are not well-understood....
Preprint
Full-text available
Translation initiation is often attributed as the rate determining step of eukaryotic protein synthesis and key to gene expression control. Despite this centrality the series of steps involved in this process are poorly understood. Here we capture the transcriptome-wide occupancy of ribosomes across all stages of translation initiation, enabling us...
Article
Full-text available
The CRISPR-Cas system is a powerful genome editing tool that functions in a diverse array of organisms and cell types. The technology was initially developed to induce targeted mutations in DNA, but CRISPR-Cas has now been adapted to target nucleic acids for a range of purposes. CHOPCHOP is a web tool for identifying CRISPR-Cas single guide RNA (sg...
Preprint
Full-text available
Innovations in metazoan development arise from evolutionary modifications of gene regulatory networks (GRNs). We report large cryptic variation in the requirement for two key inputs, SKN-1/Nrf2 and MOM-2/Wnt, into the C. elegans endoderm-determining GRN. Some natural variants show a nearly absolute requirement for SKN-1 and MOM-2, while in others,...
Preprint
Full-text available
Polyadenylation at the 3’-end is a major regulator of messenger RNA and its length is known to affect nuclear export, stability and translation, among others. Only recently, strategies have emerged that allow for genome-wide poly(A) length assessment. These methods identify genes connected to poly(A) tail measurements indirectly by short-read align...
Preprint
Full-text available
In phylogenetically diverse organisms, the 5' ends of a subset of mRNAs are trans-spliced with a spliced leader (SL) RNA. The functions of SL trans-splicing, however, remain largely enigmatic. Here, we quantified translation genome-wide in the marine chordate, Oikopleura dioica, under inhibition of mTOR, a central growth regulator. Translation of t...
Poster
Genome-wide association studies (GWAS) and quantitative trait loci (QTL) mapping have been successful in identifying genetic variants associated with complex traits in both humans and model organisms. However, in complex diseases or traits where multiple loci contribute, those that show small effects individually may be missed by these methods due...
Article
Full-text available
Although the arrangement of internal organs in most metazoans is profoundly left–right (L/R) asymmetric with a predominant handedness, rare individuals show full (mirror-symmetric) or partial (heterotaxy) reversals. While the nematode Caenorhabditis elegans is known for its highly determinate development, including stereotyped L/R organ handedness,...
Article
Although the arrangement of internal organs in most metazoans is profoundly left–right (L/R) asymmetric with a predominant handedness, rare individuals show full (mirror-symmetric) or partial (heterotaxy) reversals. While the nematode Caenorhabditis elegans is known for its highly determinate development, including stereotyped L/R organ handedness,...
Article
Full-text available
Heterozygous loss of function mutations in the type II bone morphogenetic protein receptor (BMPR-II), a member of the transforming growth factor (TGF-β) receptor family, underlie the majority of familial cases of pulmonary arterial hypertension (PAH). The TGF-β1 pathway is activated in PAH and inhibitors of TGF-β1 signaling prevent the development...
Article
Full-text available
Actin is a globular protein found in all eukaryotic cells. Depending on its location, it can form different structures and perform various functions. Actin monomers (G-actin) come together to form filaments (F-actin); it is found abundantly in the form of microfilaments and thin filaments in cells. With the help of different actin-binding proteins...

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