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Thurlow KE, Lovering RC, De Miranda Pinheiro S. Student biocuration projects as a learning environment. F1000Res 2022; 10:1023. [PMID: 35211294 PMCID: PMC8831850 DOI: 10.12688/f1000research.72808.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/06/2022] [Indexed: 11/20/2022] Open
Abstract
Background: Bioinformatics is becoming an essential tool for the majority of biological and biomedical researchers. Although bioinformatics data is exploited by academic and industrial researchers, limited focus is on teaching this area to undergraduates, postgraduates and senior scientists. Many scientists are developing their own expertise without formal training and often without appreciating the source of the data they are reliant upon. Some universities do provide courses on a variety of bioinformatics resources and tools, a few also provide biocuration projects, during which students submit data to annotation resources. Methods: To assess the usefulness and enjoyability of annotation projects a survey was sent to University College London (UCL) students who have undertaken Gene Ontology biocuration projects. Results: Analysis of survey responses suggest that these projects provide students with an opportunity not only to learn about bioinformatics resources but also to improve their literature analysis, presentation and writing skills. Conclusion: Biocuration student projects provide valuable annotations as well as enabling students to develop a variety of skills relevant to their future careers. It is also hoped that, as future scientists, these students will critically assess their own manuscripts and ensure that these are written with the biocurators of the future in mind.
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Affiliation(s)
- Katherine E. Thurlow
- Functional Gene Annotation, Preclinical and Fundamental Science, Institute of Cardiovascular Science, University College London (UCL), London, WC1E 6JF, UK
| | - Ruth C. Lovering
- Functional Gene Annotation, Preclinical and Fundamental Science, Institute of Cardiovascular Science, University College London (UCL), London, WC1E 6JF, UK
| | - Sandra De Miranda Pinheiro
- Functional Gene Annotation, Preclinical and Fundamental Science, Institute of Cardiovascular Science, University College London (UCL), London, WC1E 6JF, UK
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Reynolds KA, Rosa-Molinar E, Ward RE, Zhang H, Urbanowicz BR, Settles AM. Accelerating biological insight for understudied genes. Integr Comp Biol 2021; 61:2233-2243. [PMID: 33970251 DOI: 10.1093/icb/icab029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The rapid expansion of genome sequence data is increasing the discovery of protein-coding genes across all domains of life. Annotating these genes with reliable functional information is necessary to understand evolution, to define the full biochemical space accessed by nature, and to identify target genes for biotechnology improvements. The vast majority of proteins are annotated based on sequence conservation with no specific biological, biochemical, genetic, or cellular function identified. Recent technical advances throughout the biological sciences enable experimental research on these understudied protein-coding genes in a broader collection of species. However, scientists have incentives and biases to continue focusing on well documented genes within their preferred model organism. This perspective suggests a research model that seeks to break historic silos of research bias by enabling interdisciplinary teams to accelerate biological functional annotation. We propose an initiative to develop coordinated projects of collaborating evolutionary biologists, cell biologists, geneticists, and biochemists that will focus on subsets of target genes in multiple model organisms. Concurrent analysis in multiple organisms takes advantage of evolutionary divergence and selection, which causes individual species to be better suited as experimental models for specific genes. Most importantly, multisystem approaches would encourage transdisciplinary critical thinking and hypothesis testing that is inherently slow in current biological research.
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Affiliation(s)
- Kimberly A Reynolds
- The Green Center for Systems Biology and the Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Eduardo Rosa-Molinar
- Department of Pharmacology & Toxicology, The University of Kansas, Lawrence, KS 66047, USA
| | - Robert E Ward
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Hongbin Zhang
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Breeanna R Urbanowicz
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - A Mark Settles
- Bioengineering Branch, NASA Ames Research Center, Moffett Field, CA USA
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Liu Y, Ding D, Liu H, Sun X. The accessible chromatin landscape during conversion of human embryonic stem cells to trophoblast by bone morphogenetic protein 4. Biol Reprod 2018; 96:1267-1278. [PMID: 28430877 DOI: 10.1093/biolre/iox028] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 04/14/2017] [Indexed: 12/12/2022] Open
Abstract
Human embryonic stem cells (hESCs) exposed to the growth factor bone morphogenetic protein 4 (BMP4) in the absence of FGF2 have been used as a model to study the development of placental development. However, little is known about the cis-regulatory mechanisms underlying this important process. In this study, we used the public available chromatin accessibility data of hESC H1 cells and BMP4-induced trophoblast (TB) cell lines to identify DNase I hypersensitive sites (DHSs) in the two cell lines, as well as the transcription factor (TF) binding sites within the DHSs. By comparing read profiles in H1 and TB, we identified 17 472 TB-specific DHSs. The TB-specific DHSs are enriched in terms of "blood vessel" and "trophectoderm," consisting of TF motifs family: Leucine Zipper, Helix-Loop-Helix, GATA, and ETS. To validate differential expression of the TFs binding to these motifs, we analyzed public available RNA-seq and microarray data in the same context. Finally, by integrating the protein-protein interaction data, we constructed a TF network for placenta development and identified top 20 key TFs through centrality analysis in the network. Our results indicate BMP4-induced TB system provided an invaluable model for the study of TB development and highlighted novel candidate genes in placenta development in human.
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Affiliation(s)
- Yajun Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, P.R. China
| | - Dewu Ding
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, P.R. China.,Department of Mathematics and Computer Science, Chizhou College, Chizhou, P.R. China
| | - Hongde Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, P.R. China
| | - Xiao Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, P.R. China
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Mlecnik B, Galon J, Bindea G. Comprehensive functional analysis of large lists of genes and proteins. J Proteomics 2018; 171:2-10. [DOI: 10.1016/j.jprot.2017.03.016] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/13/2017] [Accepted: 03/19/2017] [Indexed: 01/16/2023]
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Abstract
The Gene Ontology Consortium (GOC) produces a wealth of resources widely used throughout the scientific community. In this chapter, we discuss the different ways in which researchers can access the resources of the GOC. We here share details about the mechanics of obtaining GO annotations, both by manually browsing, querying, and downloading data from the GO website, as well as computationally accessing the resources from the command line, including the ability to restrict the data being retrieved to subsets with only certain attributes.
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Abstract
The Gene Ontology (GO) project is the largest resource for cataloguing gene function. The combination of solid conceptual underpinnings and a practical set of features have made the GO a widely adopted resource in the research community and an essential resource for data analysis. In this chapter, we provide a concise primer for all users of the GO. We briefly introduce the structure of the ontology and explain how to interpret annotations associated with the GO.
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Affiliation(s)
- Pascale Gaudet
- CALIPHO group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 Michel-Servet, 1211, Geneva, Switzerland. .,Department of Human Protein Sciences, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
| | - Nives Škunca
- Department of Computer Science, ETH Zurich, Universitätstrasse 19, 8092, Zurich, Switzerland.,SIB Swiss Institute of Bioinformatics, Universitätstr. 19, 8092, Zurich, Switzerland.,University College London, Gower St, London, WC1E 6BT, UK
| | - James C Hu
- Department of Biochemistry and Biophysics, Texas A&M University and Texas AgriLife Research, College Station, TX, USA
| | - Christophe Dessimoz
- Department of Genetics, Evolution & Environment, University College London, Gower St, London, WC1E 6BT, UK.,Swiss Institute of Bioinformatics, Biophore, 1015, Lausanne, Switzerland.,Department of Ecology and Evolution, University of Lausanne, Street Biophore, 1015, Lausanne, Switzerland.,Center of Integrative Genomics, University of Lausanne, Biophore, 1015, Lausanne, Switzerland.,Department of Computer Science, University College London, Gower St, Lausanne, WC1E 6BT, UK
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Abstract
The overarching goal of the Gene Ontology (GO) Consortium is to provide researchers in biology and biomedicine with all current functional information concerning genes and the cellular context under which these occur. When the GO was started in the 1990s surprisingly little attention had been given to how functional information about genes was to be uniformly captured, structured in a computable form, and made accessible to biologists. Because knowledge of gene, protein, ncRNA, and molecular complex roles is continuously accumulating and changing, the GO needed to be a dynamic resource, accurately tracking ongoing research results over time. Here I describe the progress that has been made over the years towards this goal, and the work that still remains to be done, to make of the Gene Ontology (GO) Consortium realize its goal of offering the most comprehensive and up-to-date resource for information on gene function.
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Affiliation(s)
- Suzanna E Lewis
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
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