A5035580767- Genomics and Phylogenetic Studies
- Gut microbiota and health
- Epigenetics and DNA Methylation
- Diet and metabolism studies
- Scientific Computing and Data Management
- Bat Biology and Ecology Studies
- Gene expression and cancer classification
- Microbial Community Ecology and Physiology
- Cancer-related molecular mechanisms research
- Distributed and Parallel Computing Systems
- Species Distribution and Climate Change
- Plant Pathogens and Resistance
- Prostate Cancer Treatment and Research
- Molecular Biology Techniques and Applications
- Genetics, Bioinformatics, and Biomedical Research
- Soybean genetics and cultivation
- Legume Nitrogen Fixing Symbiosis
- Insect symbiosis and bacterial influences
- Bioinformatics and Genomic Networks
- Clostridium difficile and Clostridium perfringens research
- Vector-borne infectious diseases
- Environmental DNA in Biodiversity Studies
- Zoonotic diseases and public health
- Plant Disease Resistance and Genetics
- Machine Learning in Bioinformatics
City University of New York
2015-2023
Hunter College
2015-2023
Cornell University
2016-2023
Weill Cornell Medicine
2019-2022
Park Plaza Hospital
2022
Institute of Biosciences and Bioresources
2022
National Research Council
2022
Institute for Biomedicine
2021
City University of Seattle
2020
Research Foundation of The City University of New York
2019
Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and sudden oak death ramorum. Oömycetes such as these species share kingdom Stramenopila with photosynthetic algae diatoms, presence of many genes probable phototroph origin supports a ancestry stramenopiles. Comparison two species' genomes reveals rapid expansion diversification protein families associated plant infection hydrolases, ABC transporters, toxins, proteinase inhibitors, and, in particular,...
The gut microbiome is a community of host-associated symbiotic microbes that fulfills multiple key roles in host metabolism, immune function, and tissue development. Given the ability to impact fitness, there increasing interest studying wild animals better understand these communities context ecology evolution. Human research protocols are well established, but wildlife still developing field. Currently, no standardized set best practices guiding collection samples from wildlife. Gut...
The Arabidopsis Information Portal (https://www.araport.org) is a new online resource for plant biology research. It houses the thaliana genome sequence and associated annotation. was conceived as framework that allows research community to develop release 'modules' integrate, analyze visualize data may reside at remote sites. current implementation provides an indexed database of core genomic information. These are made available through feature-rich web applications provide search, mining,...
A comprehensive knowledge of the types and ratios microbes that inhabit healthy human gut is necessary before any kind pre-clinical or clinical study can be performed attempts to alter microbiome treat a condition improve therapy outcome. To address this need we present an innovative scalable analysis workflow, reference list abundance profile (GutFeelingKB), novel Fecal Biome Population Report (FecalBiome) with applicability. GutFeelingKB provides 157 organisms (8 phyla, 18 classes, 23...
A steep drop in the cost of next-generation sequencing during recent years has made technology affordable to majority researchers, but downstream bioinformatic analysis still poses a resource bottleneck for smaller laboratories and institutes that do not have access substantial computational resources. Sequencing instruments are typically bundled with only minimal processing storage capacity required data capture runs. Given scale sequence datasets, scientific value cannot be obtained from...
Bat communities in the Neotropics are some of most speciose assemblages mammals on Earth, with regions supporting more than 100 sympatric species diverse feeding ecologies. Because bats small, nocturnal, and volant, it is difficult to directly observe their habits, which has resulted classification into broadly defined dietary guilds (e.g., insectivores, carnivores, frugivores). Apart from these broad guilds, we lack detailed information for many therefore have only a limited understanding...
Root system architecture is important for water acquisition and nutrient all crops. In soybean breeding programs, wild alleles have been used successfully to enhance yield seed composition traits, but never investigated improve root architecture. Therefore, in this study, high-density single-feature polymorphic markers simple sequence repeats were map quantitative trait loci (QTLs) governing an inter-specific mapping population developed from a cross between Glycine max soja.Wild cultivated...
Few quantitative trait loci (QTL) have been mapped for the expression of partial resistance to Phytophthora sojae in soybean and very little is known about molecular mechanisms that contribute this trait. Therefore, objectives study were identify additional QTL conferring P. candidate genes may form defense. on chromosomes 12, 13, 14, 17, 19, each explaining 4 7% phenotypic variation, identified using 186 RILs from a cross partially resistant cultivar ‘Conrad’ susceptible ‘Sloan’ through...
Animals evolved in a microbial world, and their gut symbionts have played role ecological diversification. While many recent studies report patterns of phylosymbiosis between hosts bacteria, fewer examine the potentially adaptive functional contributions these microbes to dietary habits hosts. In this study, we examined predicted metabolic pathways bacteria more than 500 individual bats belonging 60 species compare enrichment functions across with distinct ecologies.We found that microbiome...
Abstract Background High throughput methods, such as high density oligonucleotide microarray measurements of mRNA levels, are popular and critical to genome scale analysis systems biology. However understanding the results these analyses in particular very wide range levels transcriptional changes observed is still a significant challenge. Many researchers use an arbitrary cut off two-fold order identify that may be biologically significant. We have used large-scale experiment involving 72...
A personalized approach based on a patient's or pathogen’s unique genomic sequence is the foundation of precision medicine. Genomic findings must be robust and reproducible, experimental data capture should adhere to findable, accessible, interoperable, reusable (FAIR) guiding principles. Moreover, effective medicine requires standardized reporting that extends beyond wet-lab procedures computational methods. The BioCompute framework (https://w3id.org/biocompute/1.3.0) enables provenance,...
Carnivores are currently colonizing cities where they were previously absent. These urban environments novel ecosystems characterized by habitat degradation and fragmentation, availability of human food, different prey assemblages than surrounding areas. Coyotes (Canis latrans) established a breeding population in New York City (NYC) over the last few decades, but their ecology within NYC is poorly understood. In this study, we used non-invasive scat sampling DNA metabarcoding to profile...
Current methods used for annotating metagenomics shotgun sequencing (MGS) data rely on a computationally intensive and low-stringency approach of mapping each read to generic database proteins or reference microbial genomes.We developed MGS-Fast, an analysis whole-genome metagenomic utilizing Bowtie2 DNA-DNA alignment reads that is alternative using the integrated catalog genes well-annotated compiled from human microbiome data. This method rapid provides high-stringency matches (>90% DNA...
Understanding the taxonomic composition of a sample, whether from patient, food or environment, is important to several types studies including pathogen diagnostics, epidemiological studies, biodiversity analysis and quality regulation. With decreasing costs sequencing, metagenomic data quickly becoming preferred typed for such analysis.Rapidly defining (both profile relative frequency) in sequence dataset challenging because task mapping millions reads study non-redundant nucleotide...
Abstract Processing of next-generation sequencing (NGS) data requires significant technical skills, involving installation, configuration, and execution bioinformatics pipelines, in addition to specialized postanalysis visualization mining software. In order address some these challenges, developers have leveraged virtualization containers toward seamless deployment preconfigured software pipelines on any computational platform. We present an approach for abstracting the complex operations...
Next-generation sequencing (NGS) technologies have resulted in petabytes of scattered data, decentralized archives, databases and sometimes isolated hard-disks which are inaccessible for browsing analysis. It is expected that curated secondary will help organize some this Big Data thereby allowing users better navigate, search compute on it. To address the above challenge, we implemented a NGS biocuration workflow analyzing short read sequences associated metadata from cancer patients to...
We performed an extensive mutational analysis of the canonical mouse odorant receptor (OR) M71 to determine properties ORs that inhibit plasma membrane trafficking in heterologous expression systems. employed use M71::GFP fusion protein directly assess localization and functionality cells vitro or olfactory sensory neurons (OSNs) vivo. OSN show only small differences activity compared untagged M71. However, could not traffic even presence proposed accessory proteins RTP1S mβ2AR. To ask if...
<ns4:p>RNA-Seq is increasingly being used to measure human RNA expression on a genome-wide scale. Expression profiles can be interrogated identify and functionally characterize treatment-responsive genes. Ultimately, such controlled studies promise reveal insights into molecular mechanisms of treatment effects, biomarkers, realize personalized medicine. RNA-Seq Reports (RSEQREP) new open-source cloud-enabled framework that allows users execute start-to-end gene-level analysis preconfigured...
Given the abundance of genome sequencing and omics data, an opprtunity challenge in bioinformatics relates to data mining visualization. The majority current visualizations are implemented either as multi-tier web server applications that require significant maintenance effort, or client software presumes technical expertise for installation. Here we present Visual Omics Explorer (VOE), a cross-platform visualization portal is using only HTML Javascript code. VOE standalone can be loaded...
High mortality rates of prostate cancer (PCa) are associated with metastatic castration-resistant (CRPC) due to the maintenance androgen receptor (AR) signaling despite deprivation therapies (ADTs). The 8q24 chromosomal locus is a region very high PCa susceptibility that carries genetic variants risk incidence. This also frequent amplifications PVT1 gene, non-protein coding gene encodes cluster microRNAs including, microRNA-1205 (miR-1205), which largely understudied. Herein, we demonstrate...
Suitable habitat fragment size, isolation, and distance from a source are important variables influencing community composition of plants animals, but the role these environmental factors in determining variation host-associated microbial communities is poorly known. In parasite-associated communities, it hypothesized that evolution ecology an arthropod parasite will influence its microbiome more than broader factors, this hypothesis has not been extensively tested. To examine environment on...
Fragments of mitochondrial DNA (mtDNA) transferred to the nuclear genome are called DNAs (NUMTs). We report here a comparison NUMT content between genomes from two species same genus. Analysis Phytophthora sojae and P. ramorum revealed large differences in genomes: 16.27 × 10 −3 2.28 % each genome, respectively. Substantial also exist sizes NUMTs found with ranges 20 405 bp for 19 137 ramorum. Furthermore, sojae, fragments genes rns, rnl, cox1, nad (various subunits) most frequently, whereas...