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Kristen Beck

Kristen Beck
IBM · Computer Science, Almaden

Doctor of Philosophy Biochemistry and Molecular Biology

About

40
Publications
4,836
Reads
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259
Citations
Additional affiliations
July 2015 - January 2016
IBM
Position
  • PostDoc Position
July 2015 - May 2016
IBM
Position
  • PostDoc Position

Publications

Publications (40)
Article
Full-text available
Epitopes are short amino acid sequences that define the antigen signature to which an antibody or T cell receptor binds. In light of the current pandemic, epitope analysis and prediction are paramount to improving serological testing and developing vaccines. In this paper, known epitope sequences from SARS-CoV, SARS-CoV-2, and other Coronaviridae w...
Preprint
Full-text available
The increasing knowledge of microbial ecology in food products relating to quality and safety as well as the established usefulness of machine learning algorithms for anomaly detection in multiple scenarios suggests that the application of microbiome data in food production systems for anomaly detection is an important next step toward bettering ou...
Preprint
Monitoring wastewater samples at building-level resolution screens large populations for SARS-CoV-2, prioritizing testing and isolation efforts. Here we perform untargeted metatranscriptomics on virally-enriched wastewater samples from 10 locations on the UC San Diego campus, demonstrating that resulting bacterial taxonomic and functional profiles...
Preprint
Epitopes are short amino acid sequences that define the antigen signature to which an antibody binds. In light of the current pandemic, epitope analysis and prediction is paramount to improving serological testing and developing vaccines. In this paper, we leverage known epitope sequences from SARS-CoV, SARS-CoV-2 and other Coronaviridae and use th...
Article
Full-text available
SARS-CoV-2 genomic sequencing efforts have scaled dramatically to address the current global pandemic and aid public health. However, autonomous genome annotation of SARS-CoV-2 genes, proteins, and domains is not readily accomplished by existing methods and results in missing or incorrect sequences. To overcome this limitation, we developed a novel...
Article
Full-text available
In this work, we hypothesized that shifts in the food microbiome can be used as an indicator of unexpected contaminants or environmental changes. To test this hypothesis, we sequenced the total RNA of 31 high protein powder (HPP) samples of poultry meal pet food ingredients. We developed a microbiome analysis pipeline employing a key eukaryotic mat...
Article
The number of publicly available microbiome samples is continually growing. As dataset size increases, bottlenecks arise in standard analytical pipelines. Faith’s phylogenetic diversity is a highly utilized phylogenetic alpha diversity metric that has thus far failed to effectively scale to trees with millions of vertices. Stacked Faith's Phylogene...
Article
Full-text available
Untargeted sequencing of nucleic acids present in food can inform the detection of food safety and origin, as well as product tampering and mislabeling issues. The application of such technologies to food analysis may reveal valuable insights that are simply unobtainable by targeted testing, leading to the efforts of applying such technologies in t...
Article
Full-text available
Background SARS-CoV-2 is an RNA virus responsible for the coronavirus disease 2019 (COVID-19) pandemic. Viruses exist in complex microbial environments, and recent studies have revealed both synergistic and antagonistic effects of specific bacterial taxa on viral prevalence and infectivity. We set out to test whether specific bacterial communities...
Preprint
Full-text available
Microbes produce an array of secondary metabolites that perform diverse functions from communication to defense. These metabolites have been used to benefit human health and sustainability. In their analysis of the Genomes from Earth's Microbiomes (GEM) catalog, Nayfach and co-authors observed that, whereas genes coding for certain classes of secon...
Preprint
SARS-CoV-2 genomic sequencing efforts have scaled dramatically to address the current global pandemic and aid public health. In this work, we analyzed a corpus of 66,000 SARS-CoV-2 genome sequences. We developed a novel semi-supervised pipeline for automated gene, protein, and functional domain annotation of SARS-CoV-2 genomes that differentiates i...
Article
Full-text available
Rapid tests for active SARS-CoV-2 infections rely on reverse transcription polymerase chain reaction (RT-PCR). RT-PCR uses reverse transcription of RNA into complementary DNA (cDNA) and amplification of specific DNA (primer and probe) targets using polymerase chain reaction (PCR). The technology makes rapid and specific identification of the virus...
Article
Full-text available
Standard workflows for analyzing microbiomes often include the creation and curation of phylogenetic trees. Here we present EMPress, an interactive web tool for visualizing trees in the context of microbiome, metabolome, and other community data scalable to trees with well over 500,000 nodes. EMPress provides novel functionality—including ordinatio...
Article
Full-text available
Microbiome samples are inherently defined by the environment in which they are found. Therefore, data that provide context and enable interpretation of measurements produced from biological samples, often referred to as metadata, are critical. Important contributions have been made in the development of community-driven metadata standards; however,...
Preprint
Full-text available
Rapid tests for active SARS-CoV-2 infections rely on reverse transcription polymerase chain reaction (RT-PCR). RT-PCR uses reverse transcription of RNA into complementary DNA (cDNA) and amplification of specific DNA (primer and probe) targets using polymerase chain reaction (PCR). The technology makes rapid and specific identification of the virus...
Preprint
Full-text available
Synergistic effects of bacteria on viral stability and transmission are widely documented but remain unclear in the context of SARS-CoV-2. We collected 972 samples from hospitalized patients with coronavirus disease 2019 (COVID-19), their health care providers, and hospital surfaces before, during, and after admission. We screened for SARS-CoV-2 us...
Preprint
Full-text available
Standard workflows for analyzing microbiomes often include the creation and curation of phylogenetic trees. Here we present EMPress, an interactive tool for visualizing trees in the context of microbiome, metabolome, etc. community data scalable beyond modern large datasets like the Earth Microbiome Project. EMPress provides novel functionality—inc...
Article
The rapid growth in biological sequence data is revolutionizing our understanding of genotypic diversity and challenging conventional approaches to informatics. Due to the increasing available genomic data, traditional bioinformatic tools require substantial computational time and the creation of ever-larger indices each time a researcher seeks to...
Preprint
Full-text available
Untargeted sequencing of nucleic acids present in food can inform the detection of food safety and origin, as well as product tampering and mislabeling issues. The application of such technologies to food analysis could reveal valuable insights that are simply unobtainable by targeted testing, leading to the efforts of applying such technologies in...
Presentation
Full-text available
Video Presentation of the capabilities and current research supported by IBM Functional Genomics Platform which was released as part of IBM's COVID-19 response. https://www.ibm.com/impact/covid-19/
Preprint
Full-text available
In this work, we hypothesized that shifts in the food microbiome can be used as an indicator of unexpected contaminants or environmental changes. To test this hypothesis, we sequenced total RNA of 31 high protein powder (HPP) samples of poultry meal pet food ingredients. We developed a microbiome analysis pipeline employing a key eukaryotic matrix...
Preprint
Full-text available
The rapid growth in biological sequence data is revolutionizing our understanding of genotypic diversity and challenging conventional approaches to informatics. With the increasing availability of genomic data, traditional bioinformatic tools require substantial computational time and the creation of ever-larger indices each time a researcher seeks...
Article
Full-text available
Here we propose that using shotgun sequencing to examine food leads to accurate authentication of ingredients and detection of contaminants. To demonstrate this, we developed a bioinformatic pipeline, FASER (Food Authentication from SEquencing Reads), designed to resolve the relative composition of mixtures of eukaryotic species using RNA or DNA se...
Article
Full-text available
Traditional taxonomy in biology assumes that life is organized in a simple tree. Attempts to classify microorganisms in this way in the genomics era led microbiologists to look for finite sets of 'core' genes that uniquely group taxa as clades in the tree. However, the diversity revealed by large-scale whole genome sequencing is calling into questi...
Article
Full-text available
Ontologies are built in various domains such as biology, chemistry, and business. Ontologies as knowledge bases have great potential to serve as providers of context for analytics not only to yield more relevant results but also to provide meaning in explaining results. Simply put, analysis without context ignores the underlying meaning in data. In...
Conference Paper
Full-text available
ABSTRACT Ontologies are built in various domains such as biology, chemistry, and business. Ontologies as knowledge bases have great potential to serve as providers of context for analytics not only to yield more relevant results but also to provide meaning in explaining results. Simply put, analysis without context ignores the underlying meaning in...
Article
Full-text available
The diversity revealed by large scale genomics in microbiology is calling into question long held beliefs about genome stability, evolutionary rate, even the definition of a species. MacArthur and Wilson's theory of insular biogeography provides an explanation for the diversity of macroscopic animal and plant species as a consequence of the associa...
Poster
Full-text available
The placenta is a functionally complex temporary organ of fetal origin, which among many roles serves as an immunological barrier, protecting the developing fetus from the maternal immune system. Due to its central role in fetal development and maintenance of pregnancy, placental pathology is implicated in several disorders and long-term health eff...
Article
Full-text available
The techniques of microbe community genome sequencing as applied to environmental samples - metagenomics - offer powerful insight into microbial community structure and ecology that can affect food safety decisions for public health security. In this paper, the design and characteristics of a new informatics service, the Metagenomics Computation an...
Article
Milk has been well established as the optimal nutrition source for infants, yet there is still much to be understood about its molecular composition. Therefore, our objective was to develop and compare comprehensive milk proteomes for human and rhesus macaques to highlight differences in neonatal nutrition. We developed a milk proteomics technique...
Article
The distribution of omega-6 and omega-3 polyunsaturated fatty acid (PUFA) intake in Western diets is disproportionate, containing an overabundance of the omega-6 PUFA, linoleic acid (LA; C18:2). Increased enrichment with LA has been shown to contribute to the enhancement of tumorigenesis in several cancer models. Previous work has indicated that ph...
Article
The omega-6 polyunsaturated fatty acid, linoleic acid (LA), is prevalent in Western diets and is known to enhance the tumorigenesis of mammary cancer models; with previous work demonstrating an upregulation of phosphatidylinositol-3-kinase (PI3K) signaling may play a key role. In this study, a mechanism for LA's upregulation of cancer cell growth i...

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Projects

Projects (2)
Project
The IBM Functional Genomics Platform accelerates the study microbial life at scale by delivering high quality data of an unmatched magnitude. It contains over 300M bacterial and viral sequences describing the genotype of microbes as well as all of the biological activity (phenotype) they produce— genes, proteins, domains, and metabolic pathways. This cloud-based platform is structured in a unique manner such that users can traverse these biological entities seamlessly and in a performant manner. Together, this rich big data repository and underlying architecture removes substantial hard work speeding up the discovery of disease mechanisms to address global public health challenges.
Project
Determine hazards that are transmitted via the food supply chain that begins at the farm and ends in consumption. The focus is to establish genomic techniques that enable culture independent methods via metaRNAseq to find pathogenic bacteria.