A5053862694- Bioinformatics and Genomic Networks
- SARS-CoV-2 and COVID-19 Research
- Machine Learning in Bioinformatics
- Gene expression and cancer classification
- Prenatal Screening and Diagnostics
- Epigenetics and DNA Methylation
- Genetics, Bioinformatics, and Biomedical Research
- interferon and immune responses
- Genomics and Phylogenetic Studies
- Environmental Toxicology and Ecotoxicology
- Artificial Intelligence in Healthcare
- Computational Drug Discovery Methods
- Gut microbiota and health
- RNA and protein synthesis mechanisms
- Machine Learning in Healthcare
- Fetal and Pediatric Neurological Disorders
- Marine Bivalve and Aquaculture Studies
- Pediatric health and respiratory diseases
- Viral gastroenteritis research and epidemiology
- Genomic variations and chromosomal abnormalities
- CRISPR and Genetic Engineering
- Animal Virus Infections Studies
- Chronic Obstructive Pulmonary Disease (COPD) Research
- Aquatic Invertebrate Ecology and Behavior
- Genomics and Rare Diseases
Weill Cornell Medicine
2017-2024
University of Miami
2020-2024
Cornell University
2017-2024
MIND Research Institute
2017-2024
Florida International University
2015-2023
American Orchid Society
2022-2023
Baylor College of Medicine
2022
Center for Neuro-Oncology
2017-2021
Universidade da Coruña
2010-2015
The Royal Free Hospital
2015
Abstract Expansions of tandem repeats (TRs) cause approximately 60 monogenic diseases. We expect that the discovery additional pathogenic repeat expansions will narrow diagnostic gap in many A growing number TR are being identified, and interpreting them is a challenge. present RExPRT (Repeat EXpansion Pathogenicity pRediction Tool), machine learning tool for distinguishing from benign expansions. Our results demonstrate an ensemble approach classifies TRs with average precision 93% recall...
The novel betacoronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused a worldwide pandemic (COVID-19) after emerging in Wuhan, China. Here we analyzed public host and viral RNA sequencing data to better understand how SARS-CoV-2 interacts with human cells. We identified genes, isoforms transposable element families that are specifically altered SARS-CoV-2-infected Well-known immunoregulatory genes including CSF2, IL32, IL-6 SERPINA3 were differentially expressed,...
Okadaic Acid (OA) constitutes the main active principle in Diarrhetic Shellfish Poisoning (DSP) toxins produced during Harmful Algal Blooms (HABs), representing a serious threat for human consumers of edible shellfish. Furthermore, OA conveys critical deleterious effects marine organisms due to its genotoxic potential. Many efforts have been dedicated biomonitoring last three decades. However, it is only now with current availability detailed molecular information on DNA organization and...
Next-generation sequencing has implicated some risk variants for human spina bifida (SB), but the genome-wide contribution of structural variation to this complex genetic disorder remains largely unknown. We examined copy-number variant (CNV) participation in architecture underlying SB risk.A high-confidence ensemble approach genome sequences (GS) was benchmarked and employed systematic detection common rare CNVs two separate ancestry-matched case-control cohorts.SB cases were enriched with...
Fast cancer diagnosis represents a real necessity in applied medicine due to the importance of this disease. Thus, theoretical models can help as prediction tools. Graph theory representation is one option because it permits us numerically describe any system such protein macromolecules by transforming properties into molecular graph topological indices. This study proposes new classification model for proteins linked with human colon using spiral indices amino acid sequences. The best...
The lung microbiome impacts on function, making any smoking-induced changes in the potentially significant. complex co-occurrence and co-avoidance patterns between bacterial taxa lower respiratory tract (LRT) were explored for a cohort of active (AS), former (FS) never (NS) smokers. Bronchoalveolar lavages (BALs) collected from 55 volunteer subjects (9 NS, 24 FS 22 AS). LRT composition was assessed using 16S rRNA amplicon sequencing. Identification differentially abundant patterns,...
Single nucleotide polymorphisms (SNPs) can be used as inputs in disease computational studies such pattern searching and classification models. Schizophrenia is an example of a complex with important social impact. The multiple causes this create the need new genetic or proteomic patterns that diagnose patients using biological information. This work presents study machine learning models only single at HTR2A DRD3 genes from Galician (Northwest Spain) schizophrenic patients. These establish...
DNA damage response (DDR) genes orchestrating the network of repair, cell cycle control, are essential for rapid proliferation neural progenitor cells. To date, potential association between specific DDR and risk human tube defects (NTDs) has not been investigated. Using whole-genome sequencing targeted sequencing, we identified significant enrichment rare deleterious RAD9B variants in spina bifida cases compared to controls (8/409 vs. 0/298; p = .0241). Among eight variants, two frameshift...
Abstract The human sperm is one of the smallest cells in body, but also most important, as it serves entire paternal genetic contribution to a child. Investigating RNA and mutations especially relevant for diseases such autism spectrum disorders (ASD), which have been correlated with advanced age. Historically, studies focused on assessment bulk sperm, wherein millions individual are present only high-frequency variants can be detected. Using 10× Chromium single-cell sequencing technology,...
Significance Genetic investigations of most structural birth defects, including spina bifida (SB), congenital heart disease, and craniofacial anomalies, have been underpowered for genome-wide association studies because their rarity, genetic heterogeneity, incomplete penetrance, environmental influences. Our systems biology strategy to investigate SB predisposition controls population stratification avoids much the bias inherent in candidate gene searches that are pervasive field. We examine...
Background. Harmful Algal Blooms (HABs) responsible for Diarrhetic Shellfish Poisoning (DSP) represent a major threat human consumers of shellfish. The biotoxin Okadaic Acid (OA), well-known phosphatase inhibitor and tumor promoter, is the primary cause acute DSP intoxications. Although several studies have described molecular effects high OA concentrations on sentinel organisms (e.g., bivalve molluscs), effect prolonged exposures to low (sublethal) still unknown. In order fill this gap,...
Data mining, a part of the Knowledge Discovery in Databases process (KDD), is extracting patterns from large data sets by combining methods statistics and artificial intelligence with database management. Analyses epigenetic have evolved towards genome-wide high-throughput approaches, thus generating great amounts for which mining essential. Part these may contain information are mitotically and/or meiotically heritable determining gene expression cellular differentiation, as well fate....
The notion of centrality is used to identify "important" nodes in social networks. Importance not well-defined, and many different notions exist the literature. challenge defining meaningful ways when network edges can be positively or negatively weighted has been adequately addressed Existing algorithms also have a second shortcoming, i.e., list most central are often clustered specific region well represented across network.We address both by proposing Ablatio Triadum (ATria), an iterative...
Abstract Tandem repeats (TRs) are polymorphic sequences of DNA that composed repeating units motifs, whose lengths can vary depending on the type TR. Expansions TRs responsible for approximately 50 monogenic diseases, compared to over 4,300 disease causing genes disrupted by single nucleotide variants and small indels. It appears thus reasonable expect discovery additional pathogenic repeat expansions, which has potential significantly narrowing current diagnostic gap in many diseases....
In recent years, in the post genomic era, more and data is being generated by biological high throughput technologies, such as proteomics transcriptomics. This omics can be very useful, but real challenge to analyze all this data, a whole, after integrating it. Biomedical integration enables making queries different, heterogeneous distributed biomedical sources. Data solutions useful not only context of drug design, also information retrieval, clinical diagnosis, system biology, etc. review,...
Abstract Tissue‐specific differentially methylated regions (tDMRs) are of the genome with methylation patterns that modulate gene expression in those tissue types. The detection tDMRs forensic evidence can permit identification body fluids at trace levels. In this report, we have performed a bioinformatic analysis an existing array dataset to determine if new could be identified for use fluid from evidence. Once these sites were identified, primers designed and bisulfite modification was...
ANNs are one of the most successful learning systems. For this reason, many techniques have been published that allow obtaining feed-forward networks. However, few works describe for developing recurrent This work uses a genetic algorithm automatic ANN development. system has applied to solve well-known problem: classification EEG signals from epileptic patients. Results show high performance system, and its ability develop simple networks, with low number neurons connections.
In recent years, in the post genomic era, more and data is being generated by biological high throughput technologies, such as proteomics transcriptomics. This omics can be very useful, but real challenge to analyze all this data, a whole, after integrating it. Biomedical integration enables making queries different, heterogeneous distributed biomedical sources. Data solutions useful not only context of drug design, also information retrieval, clinical diagnosis, system biology, etc. review,...