A5083018192- Genomics and Phylogenetic Studies
- Algorithms and Data Compression
- Machine Learning in Bioinformatics
- RNA and protein synthesis mechanisms
- Fractal and DNA sequence analysis
- Historical and Archaeological Studies
- Vector-borne infectious diseases
- Legume Nitrogen Fixing Symbiosis
- Mosquito-borne diseases and control
- Genetics, Bioinformatics, and Biomedical Research
- Toxin Mechanisms and Immunotoxins
- Genomic variations and chromosomal abnormalities
- RNA modifications and cancer
- Vector-Borne Animal Diseases
- Coding theory and cryptography
- Genome Rearrangement Algorithms
- DNA and Biological Computing
- Viral Infectious Diseases and Gene Expression in Insects
- graph theory and CDMA systems
- Advanced Proteomics Techniques and Applications
- Plant Pathogenic Bacteria Studies
- Gene expression and cancer classification
- Insect and Pesticide Research
- RNA Research and Splicing
- Software Testing and Debugging Techniques
Universidade Federal de Mato Grosso do Sul
2012-2024
Barro Colorado Island
2022
Universidade de São Paulo
2001-2005
Universidade Cidade de São Paulo
2001
Abstract Background Citrus canker is a disease that has severe economic impact on the citrus industry worldwide. There are three types of canker, called A, B, and C. The have different phenotypes affect species. causative agent for type A Xanthomonas citri subsp. , whose genome sequence was made available in 2002. fuscans aurantifolii strain B causes C Results We sequenced genomes strains to draft status. compared their genomic content X. other genomes, with special emphasis III secreted...
The sequencing of the complete genome Anaplasma marginale has enabled identification several genes that encode membrane proteins, thereby increasing chances identifying candidate immunogens. Little is known regarding genetic variability proteins in A. isolates. aim present study was to determine degree conservation predicted amino acid sequences OMP1, OMP4, OMP5, OMP7, OMP8, OMP10, OMP14, OMP15, SODb, OPAG1, OPAG3, VirB3, VirB9-1, PepA, EF-Tu and AM854 a Brazilian isolate compared other...
Abstract In computational biology, mapping a sequence s onto graph G poses significant challenge. One possible approach to tackling this problem is find walk p in that spells most similar . This challenge formally known as the Graph Sequence Mapping Problem ( GSMP ). paper, we delve into an alternative formulation De Bruijn BSMP Both problems have three variants: changes only sequence, graph, and both graph. We concentrate on addressing variant involving literature, when does not allow...
Abstract In computational biology, mapping a sequence s onto graph G is significant challenge. One possible approach to addressing this problem identify walk p in that spells which most similar . This known as the Graph Sequence Mapping Problem ( GSMP ). paper, we study an alternative formulation, namely De Bruijn BSMP ), can be stated follows: given and k (where ≥ 2), find according distance metric. We present both exact algorithms approximate heuristics for solving problem, using edit...
Given two sets of sequences A and B, the Substring Specific problem is to find all minimum substrings in having distance at least k for each subsequence B. This work addresses three new implementations Maaß algorithm when Hamming considered: a naive cubic-time quadratic-time algorithms. We run tests compare running time these another recently described implementation that uses edit distance. In addition, we conducted preliminary testing on large Tara Ocean database, looking efficient...
Abstract Given the increasing number of available genomic sequences, one now faces task identifying their protein coding regions. The gene prediction problem can be addressed in several ways, and most promising methods makes use information derived from comparison homologous sequences. In this work, we develop a new comparative-based program, called Exon_Finder2 . This tool is based on type alignment propose, syntenic global alignment, that deal satisfactorily with sequences share regions...
Introduction One of manually infeasible tasks from Molecular Biology is to find the genes encoded in one or more eukaryotic DNA sequences interest. Within context Computational Biology, this problem known as gene prediction and can be stated as: given a sequence, limits exons that compose all its genes. The task modelled combinatorial optimization problem, namely, Spliced Alignment Problem, proposed solved by Gelfand et al. [4]. In sequence transcript objective whose concatenation best fit...
Summary Given the increasing number of available genomic sequences, one now faces task identifying their functional parts, like protein coding regions. The gene prediction problem can be addressed in several ways. One most promising methods makes use similarity information between DNA and previously annotated sequences (proteins, cDNAs ESTs). Recently, given huge amount newly sequenced genomes, new similarity-based are being successfully applied prediction. so-called comparative-based lie...
Reconstruct and quantify the RNA molecules in a cell at given moment is an important problem molecular biology that allows one to know which genes are being expressed intensity level. Such known as transcriptome reconstruction quantification (TRQP). Although several approaches were already designed for TRQP, none of them model it combinatorial optimisation over strings. In order narrow this gap, we present here new called maximum similarity partitioning (MSPP) models TRQP. addition, prove...
O Problema da Seleção de Segmentos Específicos recebe como entrada duas ou mais sequências DNA e devolve saída o menor segmento uma das que possui pelo menos k diferenças com relação a todos os segmentos outras sequências. Esse problema é recorrente na Biologia, sua solução pode ser utilizada, por exemplo, no desenho primers específicos, permite, usando técnica PCR, amplificação exata regiões específicas em laboratório. Dada importância dessas detecção diagnóstico doenças infecciosas, nós...
An important problem in Computational Biology is to determine genetic markers, substrings of a set sequences that do not occur on other sets. Applications for this include finding small specific regions primer design and find organisms or metagenomes. Genetic markers can be addressed by the Specific Substring Problem - SSP which consists all minimal given with at least k differences among another sequence set. Since spend quadratic time when Hamming distance considered we have, general,...