Heather H. Creasy
A5072709614- Gut microbiota and health
- Single-cell and spatial transcriptomics
- Reproductive tract infections research
- Economic and Financial Impacts of Cancer
- Clostridium difficile and Clostridium perfringens research
- Bioinformatics and Genomic Networks
- Cell Image Analysis Techniques
- Genomics and Phylogenetic Studies
- Cancer Genomics and Diagnostics
- Advances in Oncology and Radiotherapy
- Academic Publishing and Open Access
- Urinary Tract Infections Management
- Neuroinflammation and Neurodegeneration Mechanisms
- Probiotics and Fermented Foods
- Metabolomics and Mass Spectrometry Studies
- Microbial infections and disease research
- Diet and metabolism studies
- Gene expression and cancer classification
- Scientific Computing and Data Management
- Yersinia bacterium, plague, ectoparasites research
- Reproductive System and Pregnancy
- Data Quality and Management
- Gene Regulatory Network Analysis
- Research Data Management Practices
- Advanced Biosensing Techniques and Applications
National Cancer Institute
2025
University of Maryland, Baltimore
2015-2024
Center for Information Technology
2024
University of Baltimore
2012
Studies of the human microbiome have revealed that even healthy individuals differ remarkably in microbes occupy habitats such as gut, skin and vagina. Much this diversity remains unexplained, although diet, environment, host genetics early microbial exposure all been implicated. Accordingly, to characterize ecology human-associated communities, Human Microbiome Project has analysed largest cohort set distinct, clinically relevant body so far. We found abundance each habitat's signature vary...
A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in health disease. The National Institutes Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting broad range quality-controlled resources data including standardized methods for creating, processing interpreting distinct types high-throughput available scientific community. Here...
Abstract The characterization of baseline microbial and functional diversity in the human microbiome has enabled studies microbiome-related disease, diversity, biogeography, molecular function. National Institutes Health Human Microbiome Project provided one broadest such characterizations so far. Here we introduce a second wave data from study, comprising 1,631 new metagenomes (2,355 total) targeting diverse body sites with multiple time points 265 individuals. We applied updated profiling...
Abstract The NIH Human Microbiome Project (HMP) has been carried out over ten years and two phases to provide resources, methods, discoveries that link interactions between humans their microbiomes health-related outcomes. recently completed second phase, the Integrative Project, comprised studies of dynamic changes in microbiome host under three conditions: pregnancy preterm birth; inflammatory bowel diseases; stressors affect individuals with prediabetes. associated research begins...
News from the Inner Tube of Life A major initiative by U.S. National Institutes Health to sequence 900 genomes microorganisms that live on surfaces and orifices human body has established standardized protocols methods for such large-scale reference sequencing. By combining previously accumulated data with new data, Nelson et al. (p. 994 ) present an initial analysis 178 bacterial genomes. The sampling so far barely scratches surface microbial diversity found humans, but work provides...
Abstract Single-cell transcriptomics can provide quantitative molecular signatures for large, unbiased samples of the diverse cell types in brain 1–3 . With proliferation multi-omics datasets, a major challenge is to validate and integrate results into biological understanding cell-type organization. Here we generated transcriptomes epigenomes from more than 500,000 individual cells mouse primary motor cortex, structure that has an evolutionarily conserved role locomotion. We developed...
ABSTRACT Bacillus megaterium is deep-rooted in the phylogeny, making it an evolutionarily key species and of particular importance understanding genome evolution, dynamics, plasticity bacilli. B. a commercially available, nonpathogenic host for biotechnological production several substances, including vitamin B 12 , penicillin acylase, amylases. Here, we report analysis first complete sequences two important strains, plasmidless strain DSM319 QM B1551, which harbors seven indigenous...
The Institute for Genome Sciences (IGS) has developed a prokaryotic annotation pipeline that is used coding gene/RNA prediction and functional of Bacteria Archaea. fully automated accepts one or many genomic sequences as input produces output in variety standard formats. Functional primarily based on similarity searches motif finding combined with hierarchical rule system. annotations can also be loaded into relational database accessed through visualization tools.
Characterizing cellular diversity at different levels of biological organization and across data modalities is a prerequisite to understanding the function cell types in brain. Classification neurons also essential manipulate controlled ways understand their variation vulnerability brain disorders. The BRAIN Initiative Cell Census Network (BICCN) an integrated network data-generating centers, archives, standards developers, with goal systematic multimodal type profiling characterization....
Castor bean is an important oil-producing plant in the Euphorbiaceae family. Its high-quality oil contains up to 90% of unusual fatty acid ricinoleate, which has many industrial and medical applications. seeds also contain ricin, a highly toxic Type 2 ribosome-inactivating protein, gained relevance recent years due biosafety concerns. In order gain knowledge on global genetic diversity castor ultimately help development breeding forensic tools, we carried out extensive chloroplast sequence...
Abstract Single cell transcriptomics has transformed the characterization of brain identity by providing quantitative molecular signatures for large, unbiased samples populations. With proliferation taxonomies based on individual datasets, a major challenge is to integrate and validate results toward defining biologically meaningful types. We used battery single-cell transcriptome epigenome measurements generated BRAIN Initiative Cell Census Network (BICCN) comprehensively assess types in...
ABSTRACT It is not currently possible to predict the probability of whether a woman with chlamydial genital infection will develop pelvic inflammatory disease (PID). To determine if specific biomarkers may be associated distinct pathotypes, we utilized two Chlamydia muridarum variants ( C. Var001 [CmVar001] and CmVar004) that differ in their abilities elicit upper tract pathology mouse model. CmVar004 has lower growth rate vitro induces only 20% C57BL/6 oviducts versus 83.3%...
Scalable technologies to sequence the transcriptomes and epigenomes of single cells are transforming our understanding cell types states. The Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative Cell Census Network (BICCN) is applying these at unprecedented scale map in mammalian brain. In an effort increase data FAIRness (Findable, Accessible, Interoperable, Reusable), NIH has established repositories make generated by BICCN related BRAIN projects accessible...
Abstract The NCI Cancer Research Data Commons (CRDC) is a collection of data commons, analysis platforms, and tools that make existing cancer more findable accessible by the research community. In practice, two biggest hurdles to finding using for discovery are wide variety models ontologies used describe data, dispersed storage data. Here, we outline core CRDC services aggregate descriptive information from multiple studies findability via single interface provide access method spans...
Cancer research data is generated and managed in silos. Data repositories frequently use different models vocabularies to describe their holdings, many specialize certain types, necessitating that from a large integrative project be spread across several repositories. For researchers who want reuse existing cancer data, just navigating this ecosystem of repositories, formats can overwhelming. The Aggregator (CDA) new free National Institute (NCI) service aims increase the discoverability...
Chlamydia pecorum is an obligate intracellular bacterial pathogen that causes diverse disease in a wide variety of economically important mammals. We report the finished complete genome sequence C. E58, type strain for species.
ABSTRACT We report the generation of a multimodal cell census and atlas mammalian primary motor cortex (MOp or M1) as initial product BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved morphological electrophysiological properties, cellular resolution input-output mapping, integrated through cross-modal computational analysis. Together, our results advance...
The Common Fund Data Ecosystem (CFDE) has created a flexible system of data federation that enables researchers to discover datasets from across the US National Institutes Health without requiring owners move, reformat, or rehost those data. This is centered on catalog integrates detailed descriptions biomedical individual Programs' Coordination Centers (DCCs) into uniform metadata model can then be indexed and searched centralized portal. Crosscut Metadata Model (C2M2) supports wide variety...
Chlamydia psittaci is a highly prevalent avian pathogen and the cause of potentially lethal zoonosis, causing life-threatening pneumonia in humans. We report genome sequences C. 6BC, prototype strain species, Cal10, widely used laboratory strain.
The Human Microbiome Project (HMP) explored microbial communities of the human body in both healthy and disease states. Two phases HMP (HMP iHMP) together generated >48TB data (public controlled access) from multiple, varied omics studies microbiome associated hosts. Data Coordination Center (HMPDACC) was established to provide a portal access resources produced by HMP. HMPDACC provides unified repository, multi-faceted search functionality, analysis pipelines standardized protocols...
Many datasets are being produced by consortia that seek to characterize healthy and disease tissues at single-cell resolution. While biospecimen experimental information is often captured, detailed metadata standards related data matrices analysis workflows currently lacking. To address this, we develop the matrix (MAMS) serve as a resource for centers, repositories, tool developers. We define fields parameters commonly utilized in analytical developed rmams package extract MAMS from...
Inactivation of Ataxia-telangiectasia mutated (ATM) gene results in an increased risk to develop cancer. We show that ATM deficiency diffuse large B-cell lymphoma (DLBCL) significantly induce mitochondrial deacetylase sirtuin-3 (SIRT3) activity, disrupted structure, decreased respiration, and compromised TCA flux compared with DLBCL cells expressing wild type (WT)-ATM. This corresponded enrichment glutamate receptor glutamine pathways deficient background WT-ATM cells. ATM-/- have apoptosis...