A5036597784- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Protist diversity and phylogeny
- Advanced biosensing and bioanalysis techniques
- Laser Material Processing Techniques
- Scientific Computing and Data Management
- Polar Research and Ecology
- Bacteriophages and microbial interactions
- Methane Hydrates and Related Phenomena
- Microbial Fuel Cells and Bioremediation
- Advanced Surface Polishing Techniques
- Genetics, Bioinformatics, and Biomedical Research
- Electrochemical Analysis and Applications
- Cloud Computing and Resource Management
- Global Energy and Sustainability Research
- Algorithms and Data Compression
- Advanced machining processes and optimization
- 3D Shape Modeling and Analysis
- Parallel Computing and Optimization Techniques
- Geographies of human-animal interactions
- Gene expression and cancer classification
- Environmental Impact and Sustainability
- Computer Graphics and Visualization Techniques
- Geochemistry and Elemental Analysis
Basque Center for Applied Mathematics
2021-2023
Joint Genome Institute
2015-2020
Tyndall Centre
2017
University of Akron
2012-2013
Dartmouth College
2013
Creare (United States)
2007-2012
Northern Kentucky University
2010-2011
University of Manchester
2010
Montana State University
2010
Princeton University
2002
The Critical Assessment of Metagenome Interpretation (CAMI) community initiative presents results from its first challenge, a rigorous benchmarking software for metagenome assembly, binning and taxonomic profiling. Methods profiling are key to interpreting data, but lack consensus about complicates performance assessment. challenge has engaged the global developer benchmark their programs on highly complex realistic data sets, generated ∼700 newly sequenced microorganisms ∼600 novel viruses...
Software is now both central and essential to modern biology, yet lack of availability, difficult installations, complex user interfaces make software hard obtain use. Containerisation, as exemplified by the Docker platform, has potential solve problems associated with sharing software. We propose bioboxes: containers standardised bioinformatics interchangeable.
Every protein has a biosynthetic cost to the cell based on synthesis of its constituent amino acids. In order optimise growth and reproduction, natural selection is expected, where possible, favour use proteins whose constituents are cheaper produce, as reduced may confer fitness advantage organism. Quantifying acid biosynthesis presents challenges, since energetic requirements change across different cellular environmental conditions. We developed systems biology approach estimate...
Abstract In metagenome analysis, computational methods for assembly, taxonomic profiling and binning are key components facilitating downstream biological data interpretation. However, a lack of consensus about benchmarking datasets evaluation metrics complicates proper performance assessment. The Critical Assessment Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on unprecedented complexity realism. Benchmark metagenomes were...
The banded iron formations (BIF) of Brazil are composed silica and Fe(III) oxide lamina, largely covered by a rock cap BIF fragments in goethite matrix (canga). Despite both canga being highly resistant to erosion poorly soluble, >3,000 ore caves (IOCs) have formed at their interface. reducing microorganisms (FeRM) can reduce the oxides present canga, which could account for observed speleogenesis. Here, we show that IOCs contain variety microbial taxa with member species capable...
Despite the importance of karst aquifers as a source drinking water, little is known about role microorganisms in maintaining quality this water. One limitations exploring microbiology these environments access, which usually limited to wells and surface springs. In study, we compared Madison aquifer sampled via potentiometric lakes Wind Cave with sampling spring. Our data indicated that only Streeter Well (STR), drilled into same hydrogeologic domain Lakes (WCL), allowed access water low...
Abstract Cloud computing platforms have been continuously evolving. Features such as the Elastic Fabric Adapter (EFA) in Amazon Web Services (AWS) platform brought yet another revolution High Performance Computing (HPC) world, further accelerating convergence of HPC and cloud computing. Other public clouds also support similar features fueling this change. In paper, we show how why performance a large-scale computational fluid dynamics (CFD) application on AWS competes very closely with one...
Microbial adaptation to environmental conditions is a complex process, including acquisition of positive traits through horizontal gene transfer or the modification existing genes duplication and/or mutation. In this study, we examined Pseudomonas fluorescens isolate (R124) from nutrient-limited mineral environment silica cave in comparison with P. isolates surface soil and rhizosphere. Examination metal homeostasis pathways demonstrated high degree conservation, suggesting that such systems...
On this Phase I SBIR project, Creare’s overall objective was to develop and transition a technology that will increase cutting tool life reduce production costs of machining ceramic matrix composite (CMC) materials. We successfully demonstrated the feasibility CMC materials using Laser-Assisted Machining (LAM) approach, which utilizes laser preheat thin layer material prior its removal conventional machine tools. In particular, we forces were reduced by as much 40% compared processes. This...
The assembly of next-generation short-read sequencing data can result in a fragmented non-contiguous set genomic sequences. Therefore common step genome project is to join neighbouring sequence regions together and fill gaps. This scaffolding non-trivial requires manually editing large blocks nucleotide sequence. Joining these sequences also hides the source each region final Taken considerations may make reproducing or an existing scaffold difficult. software outlined here, "Scaffolder,"...
Every protein has a biosynthetic cost to the cell based on synthesis of its constituent amino acids.In order optimise growth and reproduction, natural selection is expected, where possible, favour use proteins whose constituents are cheaper produce, as reduced may confer fitness advantage organism.Quantifying acid biosynthesis presents challenges, since energetic requirements change across different cellular environmental conditions.We developed systems biology approach estimate genome-scale...
Cyanobacteria are found in most illuminated environments and key players global carbon nitrogen cycling. Although significant efforts have been made to advance our understanding of this important phylum, still little is known about how members the cyanobacteria affect respond changes complex biological systems. This lack knowledge part due dependence on pure cultures when determining metabolism function a microorganism. In work presented here we took advantage Culture Collection...
At Creare, we are developing a laser-assisted, pre-finishing system that enables the single-point diamond turning of super-hard ceramics into hemispheres, ogives, and other shapes ready for final optical finishing. Currently, ceramic materials cannot be affordably processed due to low material removal rates high amount sub-surface damage associated with current processes. Our innovation uses low-power, far-infrared laser heat, but not ablate, thin layer prior its removal. By heating...
The addition of advanced sensors, targeting systems and electronic countermeasures to military vehicles has created a strategic need for additional electric power. By incorporating thermoelectric (TE) waste heat recovery system convert available exhaust electricity, increased power needs can be met without reducing the energy efficiency vehicle. This approach allows existing upgraded requiring complete re-design engine powertrain support integration sensors that keep performance at state art...
The increasing accessibility and reduced costs of sequencing has made genome analysis accessible to more researchers. Yet there remains a steep learning curve in the subsequent computational steps required process raw reads into database-deposited sequence. Here we describe “Genomer,” tool simplify manual tasks finishing uploading sequence database. Genomer can format scaffold common files for submission GenBank. This software also simplifies updating by allowing human-readable YAML file be...
We describe a technique to build soft-walled colon phantom that provides realistic lumen anatomy in computed tomography (CT) images. The begins with the geometry of human measured during CT colonography (CTC). three-dimensional air-filled colonic is segmented and then replicated using stereolithography (SLA). rigid SLA model includes large-scale features (e.g., haustral folds tenia coli bands) down small-scale small pedunculated polyp). Since represents internal volume, highly-pliable...
ABSTRACT Cyanobacteria are found in most illuminated environments and key players global carbon nitrogen cycling. Although significant efforts have been made to advance our understanding of this important phylum, still little is known about how members the cyanobacteria affect respond changes complex biological systems. This lack knowledge part due dependence on pure cultures when determining metabolism function a microorganism. In work presented here we took advantage Culture Collection...
Abstract Background: Assembly of short-read sequencing data can result in a fragmented non-contiguous series genomic sequences. Therefore common step genome project is to join neighboring sequence regions together and fill gaps the assembly using additional This scaffolding step, however, non-trivial requires manually editing large blocks nucleotide sequence. Joining these sequences also hides source each region final Taken together, considerations may make reproducing or an existing build...