Sabah Ul-Hasan
A5003179870- Metabolomics and Mass Spectrometry Studies
- Genetics, Bioinformatics, and Biomedical Research
- Biomedical Text Mining and Ontologies
- Scientific Computing and Data Management
- Semantic Web and Ontologies
- Cardiac, Anesthesia and Surgical Outcomes
- Plant Pathogenic Bacteria Studies
- Abdominal Surgery and Complications
- Marine Invertebrate Physiology and Ecology
- Bioinformatics and Genomic Networks
- Parasite Biology and Host Interactions
- Plant-Microbe Interactions and Immunity
- Yersinia bacterium, plague, ectoparasites research
- Methane Hydrates and Related Phenomena
- Research Data Management Practices
- Cell Image Analysis Techniques
- Legume Nitrogen Fixing Symbiosis
- Advanced Chemical Sensor Technologies
- Enhanced Recovery After Surgery
- Microbial Community Ecology and Physiology
- Nicotinic Acetylcholine Receptors Study
- Acute Kidney Injury Research
- Gut microbiota and health
- Digital Storytelling and Education
- Wikis in Education and Collaboration
Hologic (United States)
2023-2025
Scripps Research Institute
2019-2023
University of California, Merced
2016-2019
Biota Pharmaceuticals (United States)
2019
University of New Hampshire
2018
Joint Genome Institute
2017
University of Utah
2013
We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the research ecosystem, from scientists and engineers clinicians policy makers. 2 provides new features that will drive next generation of research. These include interactive spatial temporal analysis visualization tools, support for metabolomics shotgun metagenomics analysis, automated provenance tracking ensure reproducible, transparent science.
We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the research ecosystem, from scientists and engineers clinicians policy makers. 2 provides new features that will drive next generation of research. These include interactive spatial temporal analysis visualization tools, support for metabolomics shotgun metagenomics analysis, automated provenance tracking ensure reproducible, transparent science.
Diverse soil-resident bacteria can contribute to plant growth and health, but the molecular mechanisms enabling them effectively colonize their hosts remain poorly understood. We used randomly barcoded transposon mutagenesis sequencing (RB-TnSeq) in Pseudomonas simiae, a model root-colonizing bacterium, establish genome-wide map of bacterial genes required for colonization Arabidopsis thaliana root system. identified 115 (2% all P. simiae genes) with functions that are maximal competitive...
We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the research ecosystem, from scientists and engineers clinicians policy makers. 2 provides new features that will drive next generation of research. These include interactive spatial temporal analysis visualization tools, support for metabolomics shotgun metagenomics analysis, automated provenance tracking ensure reproducible, transparent science.
Wikidata is a community-maintained knowledge base that has been assembled from repositories in the fields of genomics, proteomics, genetic variants, pathways, chemical compounds, and diseases, adheres to FAIR principles findability, accessibility, interoperability reusability. Here we describe breadth depth biomedical contained within Wikidata, discuss open-source tools have built add information synchronize it with source databases. We also demonstrate several use cases for including...
Microbial communities control numerous biogeochemical processes critical for ecosystem function and health. Most analyses of coastal microbial focus on the characterization bacteria present in either sediment or seawater, with fewer studies characterizing both seawater together at a given site, even including information about non-bacterial communities. As result, knowledge ecological patterns biodiversity across domains habitats is limited-despite fact that archaea, bacteria, eukaryotes are...
Venom is a known source of novel antimicrobial natural products. The substantial, increasing number these discoveries have unintentionally culminated in the misconception that venom and venom-producing glands are largely sterile environments. Culture-dependent -independent studies on microbial communities microenvironments reveal presence archaea, algae, bacteria, fungi, protozoa, viruses. Venom-centric microbiome relatively sparse to date with adaptive advantages venom-associated microbes...
Biology has been transformed by the rapid development of computing and concurrent rise data-rich approaches such as -omics or high-resolution imaging. However, there is a persistent computational skills gap in biomedical research workforce. Inherent limitations classroom teaching institutional core support highlight need for accessible ways researchers to explore developments biology. An analysis Scripps Research Genomics Core revealed an increasingly diverse set experiments: share...
Increasing rates of antibiotic-resistant bacterial infection are one the most pressing contemporary global health concerns. The ESKAPE pathogen group represents leading cause these infections, and upregulation efflux pump expression is a significant mechanism resistance in pathogens. This has resulted substantial interest development inhibitors to combat infections; however, no widespread treatments have been developed date. Our study evaluates an often-underappreciated aspect resistance—the...
The Biota Project communicates science to populations historically ignored by the scientific community. is comprised of a team young professionals from myriad backgrounds and locations with interests in promoting accessibility equity. We do this highlighting research conducted scientists underrepresented groups relatable yet underrated intention increasing participation science. centers on definition symbiosis as tool for both educating learning its followers. deliver stories environments...
Wikidata is a massive Knowledge Graph (KG), including more than 100 million data items and nearly 1.5 billion statements, covering wide range of topics such as geography, history, scholarly articles, life science data. The large volume difficult to handle for research purposes; many researchers cannot afford the costs hosting GB While provides public SPARQL endpoint, it can only be used short-running queries. Often, require limited from focusing on particular topic their use case. Subsetting...
Abstract Microbial communities control numerous biogeochemical processes critical for ecosystem function and health, particularly in coastal ecosystems. However, comparatively little is known about microbial community structure regions, such that basic patterns of biodiversity, as species richness composition, are generally understudied. To better understand the global biodiversity ecosystems, we characterized sediment seawater three sites near Puerto Nuevo (Baja California, Mexico) using...
A major aspect of our daily lives is the need to acquire, store and prepare food. Storage preparation can have drastic effects on compositional chemistry foods, but we a limited understanding temporal nature processes such as storage, spoilage, fermentation brewing foods eat. Here, performed analysis chemical changes in during common household preparations using untargeted mass spectrometry novel data approaches. Common treatments home yogurt, tea, spoilage meats ripening tomatoes altered...
Abstract Wikidata is a community-maintained knowledge base that epitomizes the FAIR principles of Findability, Accessibility, Interoperability, and Reusability. Here, we describe breadth depth biomedical contained within Wikidata, assembled from primary repositories on genomics, proteomics, genetic variants, pathways, chemical compounds, diseases. We built collection open-source tools simplify addition synchronization with source databases. furthermore demonstrate several use cases how...
Knowledge Graphs (KGs) such as Wikidata act a hub of information from multiple domains and disciplines, is crowdsourced by stakeholders. The vast amount available makes it difficult for researchers to manage the entire KG, which also continually being edited. It necessary develop tools that extract subsets interest. These will help reduce costs time, making data interest more accessible. In last two BioHackathons (BH20, BH21), we have created prototypes easily applicable Wikidata, well...