A5066897615- Gene expression and cancer classification
- Echinoderm biology and ecology
- RNA and protein synthesis mechanisms
- Genetics, Bioinformatics, and Biomedical Research
- Marine Bivalve and Aquaculture Studies
- Genomics and Phylogenetic Studies
- Cancer-related molecular mechanisms research
- Bioinformatics and Genomic Networks
- Gene Regulatory Network Analysis
- Genetic diversity and population structure
- Aquatic life and conservation
- Molecular Biology Techniques and Applications
- Internet Traffic Analysis and Secure E-voting
- Identification and Quantification in Food
- Neuroinflammation and Neurodegeneration Mechanisms
- Neuroscience and Neural Engineering
- Cardiac electrophysiology and arrhythmias
- Neuroscience and Neuropharmacology Research
- Medical Coding and Health Information
- Microbial Community Ecology and Physiology
- Plant and animal studies
- Network Security and Intrusion Detection
- Ion channel regulation and function
- Algorithms and Data Compression
- PARP inhibition in cancer therapy
University of Puerto Rico System
2007-2025
University of Puerto Rico at Río Piedras
2011-2023
University of Cincinnati
1993
University of Cincinnati Medical Center
1992
<ns3:p>The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. provides implementations of probabilistic k-mer counting data structure, compressible De Bruijn graph representation, partitioning, and digital normalization. implemented in C++ Python, under the BSD license at <ns3:ext-link xmlns:ns4="http://www.w3.org/1999/xlink" ext-link-type="uri"...
Hybrid zones can be valuable tools for studying evolution and identifying genomic regions responsible adaptive divergence underlying phenotypic variation. between subspecies of Heliconius butterflies very narrow are maintained by strong selection acting on color pattern. The comimetic species, H. erato melpomene, have parallel hybrid in which both species undergo a change from one pattern form to another. We use restriction-associated DNA sequencing obtain several thousand genome-wide...
The use of image data to quantify, study and compare variation in the colors patterns organisms requires alignment images establish homology, followed by color-based segmentation images. Here we describe an R package for that has applications quantify color a wide range organisms. patternize is quantifies obtained from data. first defines homology between pattern positions across specimens either through manually placed homologous landmarks or automated registration. Pattern identification...
Abstract Background Among deuterostomes, the regenerative potential is maximally expressed in echinoderms, animals that can quickly replace most injured organs. In particular, sea cucumbers are excellent models for studying organ regeneration since they regenerate their digestive tract after evisceration. However, echinoderms have been sidelined modern studies partially because of lack genome-wide profiling approaches afforded by genomic tools. For last decade, our laboratory has using...
Species delimitation is a major quest in biology and essential for adequate management of the organismal diversity. A challenging example comprises fish species red snappers Western Atlantic. Red have been traditionally recognized as two separate based on morphology: Lutjanus campechanus (northern snapper) L. purpureus (southern snapper). Recent genetic studies using mitochondrial markers, however, failed to delineate these nominal species, leading current lumping northern southern...
Abstract Urodele amphibians are unique among adult vertebrates in their ability to regenerate missing limbs. The process of limb regeneration requires several key tissues including a regeneration‐competent wound epidermis called the epithelium (RE). We used microarray analysis profile gene expression RE axolotl, Mexican salamander. A list 125 genes and expressed sequence tags (ESTs) showed ≥1.5‐fold than covering lateral cuff wound. subset ESTs were further characterized for level changes...
Background: Variations in the states of Gene Regulatory Networks significantly influence disease outcomes and drug development. Boolean serve as a tool to conceptualize understand complex relationships between genes. Threshold computation methods are used for binarization gene expression representation its Network. This study aims provide platform that facilitates exploration impact different threshold on subsequent Networks. Methods: implemented binarizing expression, enabling...
The hoatzin is unique among known avian species because of the fermentative function its enlarged crop. A small-bodied flying foregut fermenter a paradox, and this bird provides an interesting model to examine how diet selection gut microbiota contribute maximizing digestive efficiency. Therefore, we characterized bacterial population in crop six adult hoatzins captured from wild. total 1,235 16S rRNA gene sequences were grouped into 580 phylotypes (67% pooled richness sampled, based on...
Abstract Echinoderms comprise a group of animals with impressive regenerative capabilities. They can replace complex internal organs following injury or autotomy. In holothurians sea cucumbers, cellular processes intestinal regeneration have been extensively studied. The molecular machinery behind this faculty, however, remains to be understood. Here we assembled and annotated de novo transcriptome using RNA-seq data consisting regenerating non-regenerating tissues from the cucumber...
Repair and regeneration are key processes for tissue maintenance, their disruption may lead to disease states. Little is known about the molecular mechanisms that underline repair of digestive tract. The sea cucumber Holothuria glaberrima represents an excellent model dissect characterize events during intestinal regeneration. To study gene expression profile, cDNA libraries were constructed from normal, 3-day, 7-day regenerating intestines H. glaberrima. Clones randomly sequenced queried...
// Ingrid S. Forestier-Román 1, 2 , Andrés López-Rivas 2, 3 María M. Sánchez-Vázquez Krizia Rohena-Rivera Gretchen Nieves-Burgos Humberto Ortiz-Zuazaga 4 Carlos A. Torres-Ramos 5 and Magaly Martínez-Ferrer 6 1 Department of Biochemistry, School Medicine, University Puerto Rico, San Juan, USA Rico Comprehensive Cancer Center, Division Biology, at Rio Piedras, Computer Sciences, Physiology, Pharmaceutical Pharmacy, Correspondence to: Martínez-Ferrer, email: magaly.martinez1@upr.edu Keywords:...
Wnt signaling has been shown to play multiple roles in regenerative processes, one of the most widely studied which is regeneration intestinal luminal epithelia. Most studies this area have focused on self-renewal stem cells; however, may also more dynamic functions, such as facilitating organogenesis. To explore possibility, we employed sea cucumber Holothuria glaberrima that can regenerate a full intestine over course 21 days after evisceration. We collected RNA-seq data from various...
The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. provides implementations of probabilistic k-mer counting data structure, compressible De Bruijn graph representation, partitioning, and digital normalization. implemented in C++ Python, under the BSD license at http://github.com/ged-lab/khmer/.
Abstract The euryhaline marine yeast Debaromyces hansenii is a model system for the study of processes related to osmoadaptation. In this study, microarray‐based gene expression analyses entire genome D. was used its response osmotic stress. Differential expression, compared control, examined at three time points (0.5, 3 and 6 h) after exposure cultures high salt concentration. Among 1.72% genes showing statistically significant differences in only 65 displayed least three‐fold increases...
We previously proposed that DNA recombination/repair processes play a role in memory formation. Here, we examined the possible of fen-1 gene, encoding flap structure-specific endonuclease, consolidation conditioned taste aversion (CTA). Quantitative real-time PCR showed amygdalar mRNA induction was associated to central processing illness experience related CTA and itself, but not resulting from presentation novel flavor. also increased expression Fen-1 protein amygdala, insular cortex. In...
An increasing body of evidence suggests that mechanisms related to the introduction and repair DNA double strand breaks (DSBs) may be associated with long-term memory (LTM) processes. Previous studies from our group suggested factors known function in recombination/repair machineries, such as ligases, polymerases, endonucleases, play a role LTM. Here we report data using C57BL/6 mice showing V(D)J recombination-activating gene 1 ( RAG1 ), which encodes factor introduces DSBs immunoglobulin...
ABSTRACT Hybrid zones can be valuable tools for studying evolution and identifying genomic regions responsible adaptive divergence underlying phenotypic variation. between subspecies of Heliconius butterflies very narrow are maintained by strong selection acting on colour pattern. The co-mimetic species H. erato melpomene have parallel hybrid where both undergo a change from one pattern form to another. We use restriction associated DNA sequencing obtain several thousand genome wide sequence...
Representation of Hispanics, and in particular Hispanic women, is notoriously low computer science programs higher education the tech industry. The engagement undergraduate students research, often early their path towards degree completion, has been championed as one principal reforms necessary to increase number capable professionals Science, Technology, Engineering, Mathematics (STEM). benefits attributed research experiences have reported disproportionately benefit individuals from...
Purpose: This paper describes SalHUD, a prototype web-based application for visualizing health data from Puerto Rico. Our initial focus was to provide interactive maps displaying years of potential life lost (YPLL). Methods: The public-use mortality file year 2008 downloaded the Rico Institute Statistics website. Data processed with R, Python and EpiInfo calculate leading causes death on each 78 municipalities in island. Death records were classified according ICD-10 codes. YPLL municipality...
In terms of IP networks, anomalies are unusual and significant changes in a network’s traffic level. At the present, researchers work to find methods that help detect efficiently. this report, we explore two for detection. First, see how subspace method can be used following different types flows: byte counts, packets counts IP-flow counts. Next, Benford’s law is inter-arrival SYN flow packets. Then, make an implementation which separates identify numbers generated most network. Another was...