Accès ouvert
2021
article
OpenAlex
Kai Blumberg, Alise Jany Ponsero, Matthew Bomhoff, Elisha M. Wood‐Charlson et autres
Marine microbial ecology requires the systematic comparison of biogeochemical and sequence data to analyze environmental influences on the distribution and variability of microbial communities. With ever-increasing quantities of metagenomic data, there is a growing need to make datasets Findable, Accessible, Interoperable, and …
us
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Accès ouvert
2020
article
OpenAlex
Alise Jany Ponsero, Matthew Bomhoff, Kai Blumberg, Ken Youens‐Clark et autres
In recent years, large-scale oceanic sequencing efforts have provided a deeper understanding of marine microbial communities and their dynamics. These research endeavors require the acquisition of complex and varied datasets through large, interdisciplinary and collaborative efforts. However, no unifying framework currently exists …
us
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Accès ouvert
2020
conference-paper
OpenAlex
Kai Blumberg, Alise Jany Ponsero, Matthew Bomhoff, Pier Luigi Buttigieg et autres
Planet Microbe is a federated resource for the discovery and analysis of marine 'omics datasets that have been reconnected with physical, geological, and geochemical datasets. Planet Microbe incorporates many existing public marine metagenomic projects, as well as reconnecting these datasets with other …
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Accès ouvert
2020
article
OpenAlex
Allen Hubbard, Matthew Bomhoff, Carl J. Schmidt
BACKGROUND: Decreasing costs make RNA sequencing technologies increasingly affordable for biologists. However, many researchers who can now afford sequencing lack access to resources necessary for downstream analysis. This means that even as algorithms to process RNA-Seq data improve, many biologists still struggle …
us
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Accès ouvert
2018
article
OpenAlex
Illyoung Choi, Alise Jany Ponsero, Matthew Bomhoff, Ken Youens‐Clark et autres
Background: Shotgun metagenomics provides powerful insights into microbial community biodiversity and function. Yet, inferences from metagenomic studies are often limited by dataset size and complexity and are restricted by the availability and completeness of existing databases. De novo comparative metagenomics enables the …
us
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Accès ouvert
2018
conference-paper
OpenAlex
Illyoung Choi, Alise Jany Ponsero, Ken Youens‐Clark, Matthew Bomhoff et autres
Big-data analytics platforms, such as Hadoop, are appealing for scientific computation because they are ubiquitous, well-supported, and well-understood. Unfortunately, load-balancing is a common challenge of implementing large-scale scientific computing applications on these platforms. In this paper we present the design and implementation …
us
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Accès ouvert
2017
article
OpenAlex
Jeffrey W. Grover, Matthew Bomhoff, Sean W. Davey, Brian D. Gregory et autres
To make genomic and epigenomic analyses more widely available to the biological research community, we have created LoadExp+, a suite of bioinformatics workflows integrated with the web-based comparative genomics platform, CoGe. LoadExp+ allows users to perform transcriptomic (RNA-seq), epigenomic (bisulfite-seq), chromatin-binding (ChIP-seq), …
us
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Accès ouvert
2017
preprint
OpenAlex
Jeffrey W. Grover, Matthew Bomhoff, Sean W. Davey, Brian D. Gregory et autres
Abstract To make genomic and epigenomic analyses more widely available to the biological research community, we have created LoadExp+, a suite of bioinformatics workflows integrated with the web-based comparative genomics platform, CoGe. LoadExp+ allows users to perform transcriptomic (RNA-seq), epigenomic (bisulfite-seq), chromatin-binding …
us
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Accès ouvert
2016
article
OpenAlex
Blake L. Joyce, Asher K. Haug-Baltzell, Sean W. Davey, Matthew Bomhoff et autres
Summary: Following polyploidy events, genomes undergo massive reduction in gene content through a process known as fractionation. Importantly, the fractionation process is not always random, and a bias as to which homeologous chromosome retains or loses more genes can be observed in …
us
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Accès ouvert
2015
article
OpenAlex
Haibao Tang, Matthew Bomhoff, Evan Briones, Liangsheng Zhang et autres
The identification of conserved syntenic regions enables discovery of predicted locations for orthologous and homeologous genes, even when no such gene is present. This capability means that synteny-based methods are far more effective than sequence similarity-based methods in identifying true-negatives, a necessity …
us, cn
(code pays fourni par la source)
2015
conference-paper
OpenAlex
Ronak Etemadpour, Matthew Bomhoff, Eric H. Lyons, Paul Murray et autres
This paper explores the specialized nature of research-oriented web applications that enable interactions with and the visual analysis of ``Big Data,'' i.e., large, heterogeneous scientific datasets. We introduce a pragmatic methodology for the design and evaluation of scientific workflows in research-oriented web …
us
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Accès ouvert
2014
article
OpenAlex
Megan Phifer‐Rixey, Matthew Bomhoff, Michael W. Nachman
One approach to understanding the genetic basis of speciation is to scan the genomes of recently diverged taxa to identify highly differentiated regions. The house mouse, Mus musculus, provides a useful system for the study of speciation. Three subspecies (M. m. castaneus, …
us
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