A5035667949- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- RNA modifications and cancer
- Genomics and Phylogenetic Studies
- Cancer Genomics and Diagnostics
- Gene expression and cancer classification
- Genomics and Chromatin Dynamics
- Bioinformatics and Genomic Networks
- Molecular Biology Techniques and Applications
- Machine Learning in Bioinformatics
- Advanced Proteomics Techniques and Applications
- Immunotherapy and Immune Responses
- vaccines and immunoinformatics approaches
- Genomics and Rare Diseases
- Glycosylation and Glycoproteins Research
- Epigenetics and DNA Methylation
- Genetic factors in colorectal cancer
- BRCA gene mutations in cancer
- Evolution and Genetic Dynamics
- Cell Adhesion Molecules Research
- Bacteriophages and microbial interactions
- Ubiquitin and proteasome pathways
- Cancer-related molecular mechanisms research
- Bacterial Genetics and Biotechnology
- DNA Repair Mechanisms
Universidade Federal do Rio Grande do Norte
2016-2025
GTx (United States)
2025
Sichuan University
2020-2022
West China Hospital of Sichuan University
2022
Instituto Federal do Rio Grande do Norte
2013-2021
Instituto do Cérebro de Brasília
2016-2020
PharmacoGenetics (China)
2020
Allen Institute for Brain Science
2018
Instituto Paulo Gontijo
1992-2013
Hospital Alemão Oswaldo Cruz
2007-2013
The human genome sequence defines our inherent biological potential; the realization of biology encoded therein requires knowledge function each gene. Currently, in this area is still limited. Several lines investigation have been used to elucidate structure and genes genome. Even so, gene prediction remains a difficult task, as varieties transcripts may vary great extent. We thus performed an exhaustive integrative characterization 41,118 full-length cDNAs that capture complete functional...
A gene's expression pattern provides clues to its role in normal physiology and disease. To provide quantitative levels on a genome-wide scale, the Cancer Genome Anatomy Project (CGAP) uses serial analysis of gene (SAGE). Over 5 million transcript tags from more than 100 human cell types have been assembled. enhance utility this data, CGAP SAGE project created Genie, web site for presentation data (http://cgap.nci.nih.gov/SAGE). Genie an automatic link between names levels, accounting...
We discuss two tests of the hypothesis that first genes were assembled from exons. The exon shuffling in progenote predicts intron phases will be correlated so exons an integer number codons and with compact regions polypeptide chain. These predictions have been tested on ancient conserved proteins (proteins without introns prokaryotes but eukaryotes) hold high statistical significance. conclude are features 15-, 22-, or 30-amino acid residues long, as was predicted by “The Exon Theory Genes.”
Alternative splicing is a very frequent phenomenon in the human transcriptome. There are four major types of alternative splicing: exon skipping, 3′ splice site, 5′ and intron retention. Here we present large-scale analysis retention set 21,106 known genes. We observed that 14.8% these genes showed evidence at least one event. Most events located within untranslated regions (UTRs) transcripts. For those retained introns interrupting coding region, GC content, codon usage, frequency stop...
Theoretical considerations predict that amplification of expressed gene transcripts by reverse transcription–PCR using arbitrarily chosen primers will result in the preferential central portion transcript. Systematic, high-throughput sequencing such products would an sequence tag (EST) database consisting central, generally coding regions genes. Such a add significant value to existing public EST databases, which consist mostly sequences derived from extremities cDNAs, and facilitate...
The era of whole-genome sequencing has revealed that gene copy-number changes caused by duplication and deletion events have important evolutionary, functional, phenotypic consequences. Recent studies therefore focused on revealing the extent variation in within natural populations humans other species. These found a large number variants (CNVs) humans, many which been shown to clinical or evolutionary importance. For most part, these failed detect an class polymorphism: duplications...
We present evidence that a well defined subset of intron positions shows non-random distribution in ancient genes. analyze database conserved regions drawn from GenBank 101 to retest two predictions the theory first genes were constructed by exon shuffling. These are there should be an excess symmetric exons (and sets exons) flanked introns same phase (positions within codon) and proteins correlate with boundaries compact protein modules. Both these supported data, considerable statistical...
Open reading frame expressed sequences tags (ORESTES) differ from conventional ESTs by providing sequence data the central protein coding portion of transcripts. We generated a total 696,745 ORESTES 24 human tissues and used subset that correspond to set 15,095 full-length mRNAs as means assessing efficiency strategy its potential contribution definition transcriptome. estimate sampled over 80% all highly moderately expressed, between 40% 50% rarely genes. In our most thoroughly sequenced...
Cell surface proteins are excellent targets for diagnostic and therapeutic interventions. By using bioinformatics tools, we generated a catalog of 3,702 transmembrane located at the human cells (human cell surfaceome). We explored genetic diversity surfaceome different levels, including distribution polymorphisms, conservation among eukaryotic species, patterns gene expression. integrating expression information from variety sources, were able to identify genes with restricted in normal...
We have identified new genomic alterations in the breast cancer cell line HCC1954, using high-throughput transcriptome sequencing. With 120 Mb of cDNA sequences, we were able to identify rearrangement events leading fusions or truncations genes including MRE11 and NSD1, already implicated oncogenesis, 7 rearrangements involving other additional genes. This approach demonstrates that sequencing is an effective strategy for characterization cancers.
We analyze the three-dimensional structure of proteins by a computer program that finds regions sequence contain module boundaries, defining as segment polypeptide chain bounded in space specific given distance. The defines set “linker regions” have property if an intron were to be placed into each linker region, protein would dissected modules all less than specified diameter. test 32 proteins, ancient origin, and corresponding 570 positions, ask there is statistically significant excess...
The coding sequence at the boundaries of exons flanking nuclear introns shows some degree conservation. To extent that such sequences might be recognized by splicing machinery, this conservation may a derived result evolution for efficient splicing. Alternatively, conserved remnants proto-splice sites, which have existed early in eukaryotic genes and served as targets insertion introns, has been proposed introns-late theory. distribution intron phases, position within codon, is biased with...
Abstract Background To identify potential tumor suppressor genes, genome-wide data from exome and transcriptome sequencing were combined to search for genes with loss of heterozygosity allele-specific expression. The analysis was conducted on the breast cancer cell line HCC1954, a lymphoblast same individual, HCC1954BL. Results By comparing sequences two lines, we identified events at 403 in HCC1954 one gene combination sequence also revealed 86 50 allele specific expression HCC1954BL, which...
Oxidative stress generated during inflammation is associated with a wide range of pathologies. Resveratrol (RESV) displays anti-inflammatory and antioxidant activities, being candidate for the development adjuvant therapies several inflammatory diseases. Despite this potential, cellular responses induced by RESV are not well known. In work, transcriptomic analysis was performed following lipopolysaccharide (LPS) stimulation monocyte cultures in presence RESV. Induction an response observed...
// Vandeclecio Lira da Silva 1, 2, 3, * , André Faustino Fonseca Marbella 1 Thayna Emilia Ana Carolina Coelho 3 José Eduardo Kroll 4 Jorge Estefano Santana de Souza 5 Beatriz Stransky 6 Gustavo Antonio 1,3 and Sandro Instituto do Cérebro, UFRN, Natal, Brazil 2 Ph.D. Program in Bioinformatics, Bioinformatics Multidisciplinary Environment (BioME), Digital Metropolis Institute, Bioinformática e Biotecnologia, Metrópole Digital, Departmento Engenharia Biomédica, These authors have contributed...
Methods based around statistics and linear algebra have been increasingly used in attempts to address emerging questions microarray literature. Microarray technology is a long-used tool the global analysis of gene expression, allowing for simultaneous investigation hundreds or thousands genes sample. It characterized by low sample size large feature number created non-square matrix, incomplete rank, that can generate countless more solution classifiers. To avoid problem 'curse...
Since most of the examples "exon shuffling" are between vertebrate genes, view is often expressed that exon shuffling limited to evolutionarily recent lineage vertebrates. Although in plants has been inferred from analysis intron phases plant genes [Long, M., Rosenberg, C. & Gilbert, W. (1995) Proc. Natl. Acad. Sci. USA 92, 12495-12499] and comparison two functionally unknown sunflower [Domon, Steinmetz, A. (1994) Mol. Gen. Genet. 244, 312-317], clear cases remain be uncovered. Here, we...
Tissue degradation and invasion are hallmarks of the metastatic phenotype. While several extracellular matrix components can be digested by proteases, interstitial collagen is selectively initiated collagenase. It obvious that inhibitors collagenase activity would extremely useful in preventing tissue destruction tumor cell thus prove invaluable therapeutic agents. We describe here possible development such through use principle complementary hydropathy. A peptide was deduced from nucleotide...
A significant number of genes in mammalian genomes are being found to have natural antisense transcripts (NATs). These sense-antisense (S-AS) pairs believed be involved several cellular phenomena.Here, we generated a catalog S-AS occurring the human and mouse by analyzing different sources expressed sequences available public domain plus 122 massively parallel signature sequencing (MPSS) libraries from variety tissues. Using this dataset almost 20,000 both investigated, computational...
Here we report the new features and improvements in our latest release of H-Invitational Database (H-InvDB; http://www.h-invitational.jp/ ), a comprehensive annotation resource for human genes transcripts. H-InvDB, originally developed as an integrated database transcriptome based on extensive large sets full-length cDNA (FLcDNA) clones, now provides 120 558 mRNAs extracted from International Nucleotide Sequence Databases (INSD), addition to 54 978 FLcDNAs, H-InvDB_4.6. We mapped those...
Abstract Gross chromosomal rearrangements (GCRs) play an important role in human diseases, including cancer. The identity of all Genome Instability Suppressing (GIS) genes is not currently known. Here multiple Saccharomyces cerevisiae GCR assays and query mutations were crossed into arrays mutants to identify progeny with increased rates. One hundred eighty two GIS identified that suppressed formation. Another 438 cooperatively acting genes, but the genome instability caused by individual...
The Pirarucu (Arapaima gigas) is one of the world's largest freshwater fishes and member superorder Osteoglossomorpha (bonytongues), oldest lineages ray-finned fishes. This species an obligate air-breather found in basin Amazon River with attractive potential for aquaculture. Its phylogenetic position among bony makes a relevant subject evolutionary studies early teleost diversification. Here, we present, first time, draft genome version A. gigas genome, providing useful information further...
Studies on the peopling of South America have been limited by paucity sequence data from Native Americans, especially east part Amazon region. Here, we investigate whole exome variation 58 American individuals (eight different populations) region and draw insights into America. By using generated here together with public domain, confirmed a strong genetic distinction between Andean Amazonian populations. Furthermore, weak Australasian signal was found in two populations sequenced here:...