Gonzalo Riadi

Gonzalo Riadi
Universidad de Talca · Center for Bioinformatics Simulation and Modeling (CBSM)

About

55
Publications
4,372
Reads
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384
Citations
Citations since 2016
38 Research Items
269 Citations
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201620172018201920202021202201020304050
201620172018201920202021202201020304050
201620172018201920202021202201020304050

Publications

Publications (55)
Article
Full-text available
Lymphatic vasculature is a network of capillaries and vessels capable of draining extracellular fluid back to blood circulation and to facilitate immune cell migration. Although the role of the lymphatic vasculature as coordinator of fluid homeostasis has been extensively studied, the consequences of abnormal lymphatic vasculature function and impa...
Article
Full-text available
Is it possible to learn and create a first Hidden Markov Model (HMM) without programming skills or understanding the algorithms in detail? In this concise tutorial, we present the HMM through the 2 general questions it was initially developed to answer and describe its elements. The HMM elements include variables, hidden and observed parameters, th...
Article
Full-text available
PGC1α is a transcriptional coactivator in peripheral tissues, but its function in the brain remains poorly understood. Various brain-specific Pgc1 α isoforms have been reported in mice and humans, including two fusion transcripts (FTs) with non-coding repetitive sequences, but their function is unknown. The FTs initiate at a simple sequence repeat...
Article
Full-text available
Transposable Elements (TEs) are ubiquitous genetic elements with the ability to move within a genome. TEs contribute to a large fraction of the repetitive elements of a genome, and because of their nature, they are not routinely analyzed in RNA-Seq gene expression studies. Amyotrophic Lateral Sclerosis (ALS) is a lethal neurodegenerative disease, a...
Article
The first step in any genome research after obtaining the read data is to perform a due quality control of the sequenced reads. In a de novo genome assembly project, the second step is to estimate two important features, the genome size and ‘best k -mer’, to start the assembly tests with different de novo assembly software and its parameters. Howev...
Article
Full-text available
During early development, embryos secrete extracellular vesicles (EVs) that participate in embryo-maternal communication. Among other molecules, EVs carry microRNAs (miRNAs) that interfere with gene expression in target cells; miRNAs participate in embryo-maternal communication. Embryo selection based on secreted miRNAs may have an impact on bovine...
Article
Equine endometrial and adipose mesenchymal stem cells (eMSCs and aMSCs, respectively) were isolated from the same donors of thoroughbred mares. The cells displayed characteristic features of MSCs, including trilineage mesodermal and also neurogenic differentiation. We evaluated the influence of cellular origin on their transcriptome profile. Cellul...
Preprint
Full-text available
The peroxisome proliferator-activated receptor gamma co-activator 1 alpha (PGC1α) is known as a transcriptional co-activator in peripheral tissues but its function in the brain remains poorly understood. Various brain-specific Pgc1α isoforms have been reported in mice and humans, including transcripts derived from a novel promoter about ∼580 Kb ups...
Article
Phylogenetic analysis can be a powerful tool for generating hypotheses regarding the evolution of physiological processes. Here, we provide an updated view of the evolution of the main cation channels in plant electrical signalling: the Shaker family of voltage-gated potassium channels and the two-pore cation (K⁺) channel (TPC1) family. Strikingly,...
Article
Full-text available
The impact of mitochondrial dysfunction in epigenetics is emerging, but our understanding of this relationship and its effect on gene expression remains incomplete. We previously showed that acute mitochondrial DNA (mtDNA) loss leads to histone hypoacetylation. It remains to be defined if these changes are maintained when mitochondrial dysfunction...
Preprint
Full-text available
The impact of mitochondria in epigenetics is emerging but our understanding of this relationship and its impact on gene expression remain incomplete. We previously showed that acute mitochondrial DNA (mtDNA) loss leads to histone hypoacetylation. It remains to be defined if these changes are maintained when mitochondrial dysfunction is chronic and,...
Article
Full-text available
Motivation: In recent years, Transposable Elements (TEs) have been related to gene regulation. However, estimating the origin of expression of TEs through RNA-seq is complicated by multimapping reads coming from their repetitive sequences. Current approaches that address multimapping reads are focused in expression quantification and not in findin...
Article
Full-text available
The potassium channel AKT2 plays important roles in phloem loading and unloading. It can operate as inward-rectifying channel that allows H+-ATPase-energized K+ uptake. Moreover, through reversible post-translational modifications it can also function as an open, K+-selective channel, which taps a ‘potassium battery’, providing additional energy fo...
Article
One of the primary goals of applied proteomics is the development of new computational methods for modeling the properties of the proteins from the primary structure. In this work, we used the concept of semi-supervised learning, which is relatively new machine learning philosophy that combines labeled and unlabeled instances simultaneously, to per...
Conference Paper
Chargaff’s second parity rule holds that for each of the two DNA strands in a genome, the %A is similar to %T and %G is similar to %C. Although the validity of the second rule is still in debate and the biological cause is unknown, a generalized form of the second parity rule has already been proposed. The generalization states that the frequency o...
Conference Paper
Hidden Markov Modeling (HMM) is a statistical technique to represent and predict a sequence of hidden features in a sequence of observed data. For example, a HMM could distinguish words in a stream of sounds. This technique can be very useful in Bioinformatic Sequence Analysis as public databases count with an ever growing number of sequences of nu...
Conference Paper
Eukaryotic transposons are DNA sequences able to move inside a genome. They are characterized by a sequence that encodes a transposase protein of ~300 aminoacids and flanking it, short terminal inverted repeats of ~30bp. Active DNA transposons are very difficult to predict computationally because: 1. Due to their activity, there are many copies, or...
Article
Mitochondria are well-recognized for their role in ATP and reactive oxygen species generation, in addition to producing intermediate metabolites through the TCA (tricarboxylic acid) cycle. We recently showed in an acute model of mitochondrial DNA (mtDNA) depletion that electron flow sustains a functional oxidative TCA cycle, which in turn is necess...
Article
Full-text available
Repetitive elements (REs) comprise 40–60% of the mammalian genome and have been shown to epigenetically influence the expression of genes through the formation of fusion transcript (FTs). We previously showed that an intracisternal A particle forms an FT with the agouti gene in mice, causing obesity/type 2 diabetes. To determine the frequency of FT...
Data
Primer sequences for fusion validation and expression comparison. Forward (F) and reverse (R) primers were designed to amplify the RE and exon present in each FT. In some cases the same exon was amplified with a primer from an adjacent exon in order to compare the level of the FT with that of the non-fusion isoform (control locus, con). (XLSX)
Data
Schematic representation of analytical workflow using TopHat-Fusion. TopHat-Fusion was used to identify FTs. Reads were allowed to be mapped to one unique genomic locus on the reference genome to increase specificity of findings. The stringent criteria adopted to determine whether a transcript was expressed as a fusion are depicted in the figure. (...
Data
Regulation of fusion transcript expression differs from the non-fusion counterpart during development. Pattern of expression of fusion or non-fusion isoforms as a function of neocortex development. Bars represent average read counts ± SE from 2 samples (1 data set from males and other data set from female mice); thus statistical significance could...
Data
Epigenetic marks associated with promoters are identified on the SSR present in the newly identified Atp2b1 fusion. ChIP-seq was performed using different histone marks and RNA polymerase II (for more details see reference 19). The different histone marks analyzed are shown on the first 3 tracks; Pol II peak is also included (green) as are the RNA-...
Data
Conservation of the SSR present in the Atp2b1 fusion. RepeatMasker track indicate in grey the SSR involved in this fusion. Below the nucleotide sequence of the repeat in various organisms is shown. The chromosomal coordinates for the SSR is shown above the figure. (PDF)
Data
Full list of the 438 genes that express 813 FTs as identified by the TopHat-Fusion analysis. Gene name, fusion type, chromosomal coordinates, direction of the fusion and read count in saline- or cocaine-treated samples are shown. The type of repeat, the family and class of the RE as well as the strand of the elements involved in the fusion are also...
Data
Conservation of the SINE and SSR present in the Pgc1α fusion in different species. RepeatMasker track indicate in grey the SINE (upper panel) and the SSR (lower panel) involved in this fusion. The nucleotide sequence of the repeat in various organisms is shown below the RepeatMasker track; the genomic coordinates of each individual repeat are shown...
Data
Expected versus observed frequency of repeats in each fusion transcript. The list of 813 FTs (from S1 Table) was used to calculate the observed frequency of repeats per RE class relative to the expected frequency considering the genomic annotation of the repeats. Depicted on the table are the RE class, the number (#) of events observed involved REs...
Data
Full list of candidate genes to express FTs as per the hard clipping analysis. Only gene name is shown. In bold are the genes also identified by the TopHat-Fusion pipeline as FT-expressing genes. (XLSX)
Data
FTs are expressed in the NAc. Reverse-transcription PCR was performed to determine expression of FTs in RNA samples from the NAc of animals exposed to saline or cocaine. Arhgef10 fusion A (lane 1) and fusion B (lane 2) are depicted as representative of the fusion events validated. Gel has been cropped to remove irrelevant data; DNA marker was prese...
Data
Some genes expressing FTs are expressed in several tissues while others are expressed in a tissue-specific manner. Read counts were compared between FTs and non-fusion isoforms in different areas of the brain including the amigdala (AMY), hippocampus (HIP), NAc, prefrontal cortex (PFC) and the ventral tegmental area (VTA) as well as in different ti...
Data
Architecture and types of FTs detected in the NAc. Representation of the fusion events predicted in 24 additional randomly selected genes out of the 813 events detected. The canonical start codon (ATG) is shown based on gene annotation; directionally of transcription is indicated with red arrow above and below the panels based on UCSC gene annotati...
Article
Full-text available
Background: The clawed African frog Xenopus laevis has been one of the main vertebrate models for studies in developmental biology. However, for genetic studies, Xenopus tropicalis has been the experimental model of choice because it shorter life cycle and due to a more tractable genome that does not result from genome duplication as in the case o...
Article
Amelogenesis imperfecta (AI) is a group of clinically and genetically heterogeneous inherited conditions, causing alterations in the structure of enamel and chemical composition of enamel matrix during development. The objective of this study was to compare the clinical, radiographic, histological and immunohistochemical phenotypes of subjects affe...
Article
Full-text available
Two-pore domain potassium (K2P) channels are membrane proteins widely identified in mammals, plants, and other organisms. A functional channel is a dimer with each subunit comprising two pore-forming loops and four transmembrane domains. The genome of the model plant Arabidopsis thaliana harbors five genes coding for K2P channels. Homologs of Arabi...
Article
The structures of proteins in Protein Data Bank (PDB) contain a lot of information that can be revealed through the use of tools to facilitate their organization and analysis. The increase in available structural data of nonphosphorylated and phosphorylated CDK2cyclin A (npCDK2cycA and pCDK2cycA) complexes has enabled a more realistic description o...
Article
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Acidithiobacillus caldus is a sulfur oxidizing extreme acidophile and the only known mesothermophile within the Acidithiobacillales. As such, it is one of the preferred microbes for mineral bioprocessing at moderately high temperatures. In this study, we explore the genomic diversity of A. caldus strains using a combination of bioinformatic and exp...
Article
Full-text available
Transposases (Tnps) are enzymes that participate in the movement of insertion sequences (ISs) within and between genomes. Genes that encode Tnps are amongst the most abundant and widely distributed genes in nature. However, they are difficult to predict bioinformatically and given the increasing availability of prokaryotic genomes and metagenomes,...
Data
The Supplementary Materials include the following files: Excel file showing each IS amily HMM profile ROC curve, sensitivity and selectivity. Acaryochloris marina MBIC11017 uid58167 TnpPred annotation in genbank format (.gbk). Stenotrophomonas maltophilia K279a TnpPred annotation in genbank format (.gbk). Acaryochloris marina MBIC11017 uid58167 ful...
Article
Full-text available
The high diversity of HLA binding preferences has been driven by the sequence diversity of short segments of relevant pathogenic proteins presented by HLA molecules to the immune system. To identify possible commonalities in HLA binding preferences, we quantify these using a novel measure termed "targeting efficiency," which captures the correlatio...
Data
##Genome-Assembly-Data-START## Assembly Method :: Phred/Phrap v. 0.020425.c Genome Coverage :: 9X Sequencing Technology :: ABI3730 ##Genome-Assembly-Data-END##
Article
Full-text available
The p53 tumor suppressor gene (TP53; OMIM: 191170) plays an important role in tumorigenesis in lung epithelial cells. TP53 encodes a sequence-specific DNA-binding protein that regulates transcription of several genes in response to DNA damage promoting cell cycle arrest, DNA repair or apoptosis. A mutation does not necessarily alter the protein fun...
Article
MD simulations of a pentasaccharide having D-glucopyranoside residues connected by (1→4)-β glycosidic linkages, as a model of cellulose solvated in water, were carried out comparing the solvation of the hydroxyl group at C2 of the central ring of the pentamer and that of a single glucopyranose ring. MD simulations of 10 nsec were carried under NPT...
Article
Rotavirus NSP2 is an abundant non-structural RNA-binding protein essential for forming the viral factories that support replication of the double-stranded RNA genome. NSP2 exists as stable doughnut-shaped octamers within the infected cell, representing the tail-to-tail interaction of two tetramers. Extending diagonally across the surface of each oc...
Article
Full-text available
Analysis of over 300,000 annotated genes in 105 bacterial and archaeal genomes reveals an unexpectedly high frequency of large (>300 nucleotides) alternate open reading frames (ORFs). Especially notable is the very high frequency of alternate ORFs in frames +3 and -1 (where the annotated gene is defined as frame +1). The occurrence of alternate ORF...

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