Tracy K. Teal | |
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| Alma mater | |
| Known for | Democratizing data science skills |
| Scientific career | |
| Fields | |
| Institutions |
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| Thesis | Studies of the spatial organization of metabolism in Shewanella oneidensis and Pseudomonas aeruginosa biofilms (2007) |
| Doctoral advisor | |
| Website | Github |
Tracy Teal is an American bioinformatician and the executive director of Data Carpentry. [1] She is known for her work in open science and biomedical data science education.
Teal received her Bachelors of Science in Cybernetics from the University of California, Los Angeles in 1997 and later received her Master of Arts in Organismal Biology, Ecology, and Evolution in 1999. [2] There, she worked in the laboratory of Charles Taylor, studying how the evolution of language is impacted by the way people learn it. She then earned her PhD from the California Institute of Technology in Computation and Neural Systems in 2007. [3] She did her thesis work under the laboratories of Dianne Newman and Barbara Wold, studying the metabolic organization of bacterial biofilms.
After graduate school, Teal became a National Science Foundation Postdoctoral Fellow at Michigan State University, where she studied how the ecology of microbial communities in soil can change levels of greenhouse gases by either producing or consuming them. [4]
During her postdoctoral fellowship at Michigan State University, Teal studied how agricultural practices affect soil microbe communities, which in turn affect the stability of greenhouse gas levels. Agriculture has a major impact on the diversity of microbes in soil, and a subset of those microbes produce carbon dioxide and consume methane, both greenhouse gases. She wanted to understand how agricultural land use affects the flux of these two greenhouse gases, so she used metagenomics approaches to track the diversity of microbes collected from soil samples across a range of agricultural land use. [5] She tracked the stability of methane consumption and carbon dioxide emission associated with the different soil samples and found that sites that were no longer used for agriculture had a higher diversity of microbes. In particular, she found that sites with a high diversity of methanotrophs, or bacteria that oxidize methane, have more stable levels of methane consumption, which suggested that managing lands to maintain methanotroph diversity could be a good way of managing levels of this greenhouse gas. To do facilitate this work, Teal developed bioinformatics tools to remove systematic artifacts for more precise metagenomics analyses. [6] [7]
Following her fellowship, Teal became a research associate and later assistant professor at Michigan State University in microbiology and molecular biology. Her lab was part of the BEACON Center for the Study of Evolution in Action, a National Science Foundation research center that brings together biologists, computer scientists, and engineers to study evolution in real time and use findings from the natural world to solve real-world problems—from disaster management to engineering safer cars. [8] As a professor, she developed and led a bioinformatics training program in the Microbiology and Molecular Genetics Department. [9] She has also worked to develop open source bioinformatics software for a range of applications, from RNA-sequencing analysis to establishing best practices for computational workflows for biologists. [10] [11] Teal also continued her research in metagenomics and microbial ecology in agriculture, as well as extending her focus out to study the intestinal microbiome and viral communities in ballast water. [12] [13] [14]
During her tenure at Michigan State University, Teal became an instructor for Software Carpentry, an organization that teaches software development to researchers. She and a team of collaborators developed Data Carpentry based on the Software Carpentries model, developing curricula and leading workshops for researchers to increase data literacy in the age of big data. The workshops are geared towards teaching fundamental concepts, skills, and tools to work more effectively and reproducibly with data in a variety of scientific domains. [15] [16]
The workshops became the basis for the organization Data Carpentry, with Teal serving as its executive director. In 2015, Data Carpentry received a $750,000 grant from the Moore Foundation to grow its core team, develop better infrastructure to train and support new instructors, develop domain-specific training content, and conduct more workshops for researchers. [17] In 2016, Data Carpentry drafted its mission and vision statement to "build communities teaching universal data literacy." Through its network of volunteer instructors, Data Carpentry has since developed lesson plans for a variety of scientific domains, including ecology, genomics, and social science and is in the process of developing materials for astronomy, digital humanities, economics, and more. [18] She has co-authored a number of papers establishing roadmaps to data competencies for the current and next-generation of researchers in environmental research and for researchers in general. [19] [20]
Microbial ecology is the ecology of microorganisms: their relationship with one another and with their environment. It concerns the three major domains of life—Eukaryota, Archaea, and Bacteria—as well as viruses.
Metagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomics, ecogenomics, community genomics or microbiomics.
The Human Microbiome Project (HMP) was a United States National Institutes of Health (NIH) research initiative to improve understanding of the microbiota involved in human health and disease. Launched in 2007, the first phase (HMP1) focused on identifying and characterizing human microbiota. The second phase, known as the Integrative Human Microbiome Project (iHMP) launched in 2014 with the aim of generating resources to characterize the microbiome and elucidating the roles of microbes in health and disease states. The program received $170 million in funding by the NIH Common Fund from 2007 to 2016.
MEGAN is a computer program that allows optimized analysis of large metagenomic datasets.
Microbiota are the range of microorganisms that may be commensal, symbiotic, or pathogenic found in and on all multicellular organisms, including plants. Microbiota include bacteria, archaea, protists, fungi, and viruses, and have been found to be crucial for immunologic, hormonal, and metabolic homeostasis of their host.
CAMERA, or the Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis, is an online cloud computing service that provides hosted software tools and a high-performance computing infrastructure for the analysis of metagenomic data. The project was announced in January 2006, becoming Calit2's flagship project.
The Earth Microbiome Project (EMP) is an initiative founded by Janet Jansson, Jack Gilbert and Rob Knight in 2010 to collect natural samples and to analyze the microbial community around the globe.
Biological dark matter is an informal term for unclassified or poorly understood genetic material. This genetic material may refer to genetic material produced by unclassified microorganisms. By extension, biological dark matter may also refer to the un-isolated microorganism whose existence can only be inferred from the genetic material that they produce. Some of the genetic material may not fall under the three existing domains of life: Bacteria, Archaea and Eukaryota; thus, it has been suggested that a possible fourth domain of life may yet be discovered, although other explanations are also probable. Alternatively, the genetic material may refer to non-coding DNA and non-coding RNA produced by known organisms.
In metagenomics, binning is the process of grouping reads or contigs and assigning them to individual genome. Binning methods can be based on either compositional features or alignment (similarity), or both.
Viral metagenomics is the study of viral genetic material obtained from environmental DNA samples or clinical DNA samples obtained from a host or natural reservoir. Metagenomic methods can be applied to study viruses in any system and has been used to describe various viruses associated with cancerous tumors, extreme environments, terrestrial ecosystems, and the blood and feces of humans. The term virome is also used to refer to viruses investigated by metagenomic sequencing of viral nucleic acids and is frequently used to describe environmental shotgun metagenomes. Viral metagenomics is a culture independent methodology that provides insights on viral diversity, abundance, and functional potential of viruses within the environment. Viruses lack a universal phylogenetic marker making metagenomics the only way to assess the genetic diversity of viruses in an environmental sample. With the advancements of techniques that can exploit next-generation sequencing, viruses can now be studied outside of culturable virus-host pairs. This approach has created improvements in molecular epidemiology and accelerated the discovery of novel viruses.
Mark J. Pallen is a Research Leader at the Quadram Institute and Professor of Microbial Genomics at the University of East Anglia. In recent years, he has been at the forefront of efforts to apply next-generation sequencing to problems in microbiology and ancient DNA research.
Metatranscriptomics is the set of techniques used to study gene expression of microbes within natural environments, i.e., the metatranscriptome.
Virome refers to the assemblage of viruses that is often investigated and described by metagenomic sequencing of viral nucleic acids that are found associated with a particular ecosystem, organism or holobiont. The word is frequently used to describe environmental viral shotgun metagenomes. Viruses, including bacteriophages, are found in all environments, and studies of the virome have provided insights into nutrient cycling, development of immunity, and a major source of genes through lysogenic conversion.
Alison Murray is an American microbial ecologist and Antarctic researcher, best known for studying the diversity, ecology and biogeography of Antarctic marine plankton dynamics of the plankton over the annual cycle; and her work demonstrating the existence of microbial life within an ice-sealed Antarctic lake. She studies how microorganisms persist and function in extremely cold and harsh environments, including those that lack oxygen and biological sources of energy.
Mary Ann Moran is a distinguished research professor of marine sciences at the University of Georgia in Athens. She studies the role of bacteria in Earth's marine nutrient cycles, and is a leader in the fields of marine sciences and biogeochemistry. Her work is focused on how microbes interact with dissolved organic matter and the impact of microbial diversity on the global carbon and sulfur cycles. By defining the roles of diverse bacteria in the carbon and sulfur cycles, she connects the biogeochemical and organismal approaches in marine science.
Nikos Kyrpides is a Greek-American bioscientist who has worked on the origins of life, information processing, bioinformatics, microbiology, metagenomics and microbiome data science. He is a senior staff scientist at the Berkeley National Laboratory, head of the Prokaryote Super Program and leads the Microbiome Data Science program at the US Department of Energy Joint Genome Institute.
Emily P. Balskus is an American chemical biologist, enzymologist, microbiologist, and biochemist born in Cincinnati, Ohio in 1980. She has been on the faculty of the Chemistry and Chemical Biology department of Harvard University since 2011 and is currently the Morris Kahn Professor. She has published more than 80 peer-reviewed papers and three book chapters. Since 2012 she has been invited to give over 170 lectures, has held positions on various editorial boards, and served as a reviewer for ACS and Nature journals among others. Balskus also currently serves as a consultant for Novartis, Kintai Therapeutics, and Merck & Co.
Kristen M. DeAngelis is a professor in the department of Microbiology at the University of Massachusetts where she studies soil microbes in relation to climate change.
A. Murat Eren (Meren) is computer scientist known for his work on microbial ecology and developing novel, open-source, computational tools for analysis of large data sets.
Ashley L. Shade is the Director of Research at the Institute of Ecology and the Environment within Le Centre National de la Recherche Scientifique. Shade is an associate professor at Michigan State University in the Department of Microbiology and Molecular Genetics and Department of Plant, Soil and Microbial Sciences. She is best known for her work in microbial ecology and plant-microbe interactions.
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