Uciel Pablo Chorostecki

Uciel Pablo Chorostecki
Barcelona Supercomputing Center · Department of Life Sciences

PhD Biological Sciences. MSc in Computer Science
Postdoctoral research at Barcelona SuperComputing Center

About

21
Publications
2,979
Reads
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516
Citations
Citations since 2016
16 Research Items
421 Citations
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2016201720182019202020212022020406080100
2016201720182019202020212022020406080100
Introduction
Established Researcher at Barcelona Supercomputing Center Interested in the evolution of lncRNAs. My research is focused on the study of lncRNAs structures from different species.
Additional affiliations
April 2019 - present
Barcelona Supercomputing Center
Position
  • PostDoc Position
May 2017 - March 2019
Centre for Genomic Regulation
Position
  • PostDoc Position
April 2016 - March 2017
Instituto de Biología Molecular y Celular de Rosario
Position
  • PostDoc Position
Education
May 2003 - May 2011
Rosario National University
Field of study
  • Computer Sciences

Publications

Publications (21)
Article
Full-text available
Motivation: In contrast to messenger RNAs, the function of the wide range of existing long noncoding RNAs (lncRNAs) largely depends on their structure, which determines interactions with partner molecules. Thus, the determination or prediction of the secondary structure of lncRNAs is critical to uncover their function. Classical approaches for pre...
Article
Full-text available
PhylomeDB is a unique knowledge base providing public access to minable and browsable catalogues of pre-computed genome-wide collections of annotated sequences, alignments and phylogenies (i.e. phylomes) of homologous genes, as well as to their corresponding phylogeny-based orthology and paralogy relationships. In addition, PhylomeDB trees and alig...
Article
Full-text available
Long non-coding RNAs (lncRNAs) can perform a variety of key cellular functions by interacting with proteins and other RNAs. Recent studies have shown that the functions of lncRNAS are largely mediated by their structures. However, our structural knowledge for most lncRNAS is limited to sequence-based computational predictions. Non-coding RNA activa...
Chapter
RNA molecules play important roles in almost every cellular process, and their functions are mediated by their sequence and structure. Determining the secondary structure of RNAs is central to understanding RNA function and evolution. RNA structure probing techniques coupled to high-throughput sequencing allow determining structural features of RNA...
Preprint
Full-text available
Long non-coding RNAs (lncRNAs) can perform a variety of key cellular functions by interacting with proteins and other RNAs. Recent studies have shown that the function of lncRNAS are largely mediated by their structures. However, our structural knowledge for most lncRNAS is limited to sequence-based computational predictions. Non-coding RNA activat...
Article
Full-text available
MicroRNAs (miRNAs) are endogenous small RNAs of ∼21 nt that regulate multiple biological pathways in multicellular organisms. They derive from longer transcripts that harbor an imperfect stem-loop structure. In plants, the ribonuclease type III DICER-LIKE1 assisted by accessory proteins cleaves the precursor to release the mature miRNA. Numerous st...
Article
Full-text available
Inferring homology relationships across genes in different species is a central task in comparative genomics. Therefore, a large number of resources and methods have been developed over the years. Some public databases include phylogenetic trees of homologous gene families which can be used to further differentiate homology relationships into ortho...
Article
Long non-coding RNAs (lncRNAs) are a heterogeneous class of genes that do not code for proteins. Since lncRNAs (or a fraction thereof) are expected to be functional, many efforts have been dedicated to catalog lncRNAs in numerous organisms, but our knowledge of lncRNAs in non vertebrate species remains very limited. Here, we annotated lncRNAs using...
Article
Full-text available
Many evolutionarily conserved microRNAs (miRNAs) in plants regulate transcription factors with key functions in development. Hence, mutations in the core components of the miRNA biogenesis machinery cause strong growth defects. An essential aspect of miRNA biogenesis is the precise excision of the small RNA from its precursor. In plants, miRNA prec...
Preprint
Full-text available
Long non-coding RNAs (lncRNAs) are a heterogeneous class of genes that do not code for proteins. Since lncRNAs (or a fraction thereof) are expected to be functional, many efforts have been dedicated to catalog lncRNAs in numerous organisms, but our knowledge of lncRNAs in non vertebrate species remains very limited. Here, we annotated lncRNAs using...
Preprint
Full-text available
Many evolutionarily conserved microRNAs (miRNAs) in plants regulate transcription factors with key functions in development. Hence, mutations in the core components of the miRNA biogenesis machinery cause strong growth defects. An essential aspect of miRNA biogenesis is the precise excision of the small RNA from its precursor. In plants, miRNA prec...
Article
Full-text available
The characteristic leaf shapes we see in all plants are in good part outcome of the combined action of several transcription factor networks that translate into cell division activity during the early development of the organ. We show here that wild-type leaves have distinct transcriptomic profiles in center and marginal regions. Certain transcript...
Article
Full-text available
MicroRNAs (miRNAs) are endogenous small RNAs that recognize target sequences by base complementarity and play a role in the regulation of target gene expression. They are processed from longer precursor molecules that harbor a fold-back structure. Plant miRNA precursors are quite variable in size and shape, and are recognized by the processing mach...
Preprint
MicroRNAs (miRNAs) are endogenous small RNAs that recognize target sequences by base complementarity. They are processed from longer precursors that harbor a fold-back structure. Plant miRNA precursors are quite variable in size and shape, and are recognized by the processing machinery in different ways. However, ancient miRNAs and their binding si...
Article
Full-text available
MicroRNAs (miRNAs) are major regulators of gene expression in plants and animals. They recognize their target mRNAs by sequence complementarity and guide them to cleavage or translational arrest. So far, the prediction of plant miRNA-target pairs generally relies on the use of empirical parameters deduced from known miRNA-target interactions. We de...
Article
Full-text available
MicroRNAs (miRNAs) derive from longer precursors with fold-back structures. While animal miRNA precursors have homogenous structures, plant precursors comprise a collection of fold-backs with variable size and shape. Here, we design an approach to systematically analyze miRNA processing intermediates and characterize the biogenesis of most of the e...
Article
Full-text available
MicroRNAs (miRNAs) are major regulators of gene expression in multicellular organisms. They recognize their targets by sequence complementarity and guide them to cleavage or translational arrest. It is generally accepted that plant miRNAs have extensive complementarity to their targets and their prediction usually relies on the use of empirical par...
Article
MicroRNAs (miRNAs) are widespread posttranscriptional regulators of gene expression. They are processed from longer primary transcripts that contain foldback structures (reviewed in). In animals, a complex formed by Drosha and DGCR8/Pasha recognizes the transition between the single-stranded RNA sequences and the stem loop to produce the first clea...

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