1
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Saleem S, Dhuey E, White L, Waese J, Perlman M. Analyzing referencing patterns in grey literature produced by influential global management consulting firms and international organizations. PLoS One 2023; 18:e0279723. [PMID: 36854017 PMCID: PMC9974120 DOI: 10.1371/journal.pone.0279723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 12/13/2022] [Indexed: 03/02/2023] Open
Abstract
Given the growing influence of non-academic organizations in the policy sphere, it is important to investigate the evidence both produced by and relied on by these organizations. Using citation analysis, a methodology primarily used in academic literature, we investigated the evidence base supporting the grey literature published by leading global management consulting firms (GMCFs) and international organizations (IOs). With the topic of the skills needed for the future of work as a case study, we collected 234 reports published by influential GMCFs and IOs over twenty years. By extracting references from the bibliographies of these reports we: 1) analyzed referencing patterns by measuring citation counts, institutional self-referencing and utilization of scholarly sources; 2) compared reference patterns across GMCFs and IOs; and 3) described the most influential sources. Overall, both GMCFs and IOs showed increasing reliance on grey literature, demonstrated high levels of self-referencing, and had considerable variation in the number of sources referred to. Across type of publishing organization, we found that IOs had better referencing practices than GMCFs. Our findings call into question the evidence-base behind the reports published by these policy actors. We emphasize the need to rely on strong academic literature to inform policy decisions around the future of work.
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Affiliation(s)
- Sumayya Saleem
- Ontario Institute for Studies in Education, Applied Psychology and Human Development, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
| | - Elizabeth Dhuey
- Department of Management, University of Toronto, Toronto, Ontario, Canada
| | - Linda White
- Department of Political Science, University of Toronto, Toronto, Ontario, Canada
| | - Jamie Waese
- BAM! Global Industries, Toronto, Ontario, Canada
| | - Michal Perlman
- Ontario Institute for Studies in Education, Applied Psychology and Human Development, University of Toronto, Toronto, Ontario, Canada
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2
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Fahlgren N, Kapoor M, Yordanova G, Papatheodorou I, Waese J, Cole B, Harrison P, Ware D, Tickle T, Paten B, Burdett T, Elsik CG, Tuggle CK, Provart NJ. Toward a data infrastructure for the Plant Cell Atlas. Plant Physiol 2023; 191:35-46. [PMID: 36200899 PMCID: PMC9806565 DOI: 10.1093/plphys/kiac468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/18/2022] [Indexed: 06/16/2023]
Abstract
We review how a data infrastructure for the Plant Cell Atlas might be built using existing infrastructure and platforms. The Human Cell Atlas has developed an extensive infrastructure for human and mouse single cell data, while the European Bioinformatics Institute has developed a Single Cell Expression Atlas, that currently houses several plant data sets. We discuss issues related to appropriate ontologies for describing a plant single cell experiment. We imagine how such an infrastructure will enable biologists and data scientists to glean new insights into plant biology in the coming decades, as long as such data are made accessible to the community in an open manner.
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Affiliation(s)
- Noah Fahlgren
- Donald Danforth Plant Science Center, Saint Louis, Missouri 63132, USA
| | - Muskan Kapoor
- Bioinformatics and Computational Biology Program, Department of Animal Science, Iowa State University, Ames, Iowa 50011, USA
| | | | | | - Jamie Waese
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Benjamin Cole
- DOE-Joint Genome Institute, Lawrence Berkeley National Laboratory, 1, Cyclotron Road, Berkeley, California 94720, USA
| | - Peter Harrison
- EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Doreen Ware
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York 11724, USA
- USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853, USA
| | - Timothy Tickle
- Data Sciences Platform, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, Baskin School of Engineering, 1156 High Street, Santa Cruz, California 95064, USA
| | - Tony Burdett
- EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Christine G Elsik
- Division of Animal Sciences/Division of Plant Science & Technology/Institute for Data Science & Informatics, University of Missouri, Columbia, Missouri 65211, USA
| | - Christopher K Tuggle
- Bioinformatics and Computational Biology Program, Department of Animal Science, Iowa State University, Ames, Iowa 50011, USA
| | - Nicholas J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
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3
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Jha SG, Borowsky AT, Cole BJ, Fahlgren N, Farmer A, Huang SSC, Karia P, Libault M, Provart NJ, Rice SL, Saura-Sanchez M, Agarwal P, Ahkami AH, Anderton CR, Briggs SP, Brophy JAN, Denolf P, Di Costanzo LF, Exposito-Alonso M, Giacomello S, Gomez-Cano F, Kaufmann K, Ko DK, Kumar S, Malkovskiy AV, Nakayama N, Obata T, Otegui MS, Palfalvi G, Quezada-Rodríguez EH, Singh R, Uhrig RG, Waese J, Van Wijk K, Wright RC, Ehrhardt DW, Birnbaum KD, Rhee SY. Vision, challenges and opportunities for a Plant Cell Atlas. eLife 2021; 10:e66877. [PMID: 34491200 PMCID: PMC8423441 DOI: 10.7554/elife.66877] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 08/26/2021] [Indexed: 02/06/2023] Open
Abstract
With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them.
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Affiliation(s)
- Suryatapa Ghosh Jha
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
| | - Alexander T Borowsky
- Department of Botany and Plant Sciences, University of California, RiversideRiversideUnited States
| | - Benjamin J Cole
- Joint Genome Institute, Lawrence Berkeley National LaboratoryWalnut CreekUnited States
| | - Noah Fahlgren
- Donald Danforth Plant Science CenterSt. LouisUnited States
| | - Andrew Farmer
- National Center for Genome ResourcesSanta FeUnited States
| | | | - Purva Karia
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
- Department of Cell and Systems Biology, University of TorontoTorontoCanada
| | - Marc Libault
- Department of Agronomy and Horticulture, University of Nebraska-LincolnLincolnUnited States
| | - Nicholas J Provart
- Department of Cell and Systems Biology and the Centre for the Analysis of Genome Evolution and Function, University of TorontoTorontoCanada
| | - Selena L Rice
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
| | - Maite Saura-Sanchez
- Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura, Facultad de Agronomía, Universidad de Buenos AiresBuenos AiresArgentina
| | - Pinky Agarwal
- National Institute of Plant Genome ResearchNew DelhiIndia
| | - Amir H Ahkami
- Environmental Molecular Sciences Division, Pacific Northwest National LaboratoryRichlandUnited States
| | - Christopher R Anderton
- Environmental Molecular Sciences Division, Pacific Northwest National LaboratoryRichlandUnited States
| | - Steven P Briggs
- Department of Biological Sciences, University of California, San DiegoSan DiegoUnited States
| | | | | | - Luigi F Di Costanzo
- Department of Agricultural Sciences, University of Naples Federico IINapoliItaly
| | - Moises Exposito-Alonso
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
- Department of Plant Biology, Carnegie Institution for ScienceTübingenGermany
| | | | - Fabio Gomez-Cano
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast LansingUnited States
| | - Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universitaet zu BerlinBerlinGermany
| | - Dae Kwan Ko
- Great Lakes Bioenergy Research Center, Michigan State UniversityEast LansingUnited States
| | - Sagar Kumar
- Department of Plant Breeding & Genetics, Mata Gujri College, Fatehgarh Sahib, Punjabi UniversityPatialaIndia
| | - Andrey V Malkovskiy
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
| | - Naomi Nakayama
- Department of Bioengineering, Imperial College LondonLondonUnited Kingdom
| | - Toshihiro Obata
- Department of Biochemistry, University of Nebraska-LincolnMadisonUnited States
| | - Marisa S Otegui
- Department of Botany, University of Wisconsin-MadisonMadisonUnited States
| | - Gergo Palfalvi
- Division of Evolutionary Biology, National Institute for Basic BiologyOkazakiJapan
| | - Elsa H Quezada-Rodríguez
- Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de MéxicoLeónMexico
| | - Rajveer Singh
- School of Agricultural Biotechnology, Punjab Agricultural UniversityLudhianaIndia
| | - R Glen Uhrig
- Department of Science, University of AlbertaEdmontonCanada
| | - Jamie Waese
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of TorontoTorontoCanada
| | - Klaas Van Wijk
- School of Integrated Plant Science, Plant Biology Section, Cornell UniversityIthacaUnited States
| | - R Clay Wright
- Department of Biological Systems Engineering, Virginia TechBlacksburgUnited States
| | - David W Ehrhardt
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
| | - Kenneth D Birnbaum
- Center for Genomics and Systems Biology, New York UniversityNew YorkUnited States
| | - Seung Y Rhee
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
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Provart NJ, Brady SM, Parry G, Schmitz RJ, Queitsch C, Bonetta D, Waese J, Schneeberger K, Loraine AE. Anno genominis XX: 20 years of Arabidopsis genomics. Plant Cell 2021; 33:832-845. [PMID: 33793861 PMCID: PMC8226293 DOI: 10.1093/plcell/koaa038] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/09/2020] [Indexed: 05/04/2023]
Abstract
Twenty years ago, the Arabidopsis thaliana genome sequence was published. This was an important moment as it was the first sequenced plant genome and explicitly brought plant science into the genomics era. At the time, this was not only an outstanding technological achievement, but it was characterized by a superb global collaboration. The Arabidopsis genome was the seed for plant genomic research. Here, we review the development of numerous resources based on the genome that have enabled discoveries across plant species, which has enhanced our understanding of how plants function and interact with their environments.
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Affiliation(s)
- Nicholas J Provart
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, M5S 3B2, Canada
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, California, 95616, USA
| | - Geraint Parry
- GARNet, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Georgia, 30602, USA
| | - Christine Queitsch
- Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington, 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, 98195, USA
| | - Dario Bonetta
- Faculty of Science, Ontario Tech University, Oshawa, Ontario, L1G 0C5, Canada
| | - Jamie Waese
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, M5S 3B2, Canada
| | - Korbinian Schneeberger
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, D-50829, Cologne, Germany
- Faculty of Biology, LMU Munich, 82152 Munich, Germany
| | - Ann E Loraine
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
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Sullivan A, Purohit PK, Freese NH, Pasha A, Esteban E, Waese J, Wu A, Chen M, Chin CY, Song R, Watharkar SR, Chan AP, Krishnakumar V, Vaughn MW, Town C, Loraine AE, Provart NJ. An 'eFP-Seq Browser' for visualizing and exploring RNA sequencing data. Plant J 2019; 100:641-654. [PMID: 31350781 PMCID: PMC6899666 DOI: 10.1111/tpj.14468] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/25/2019] [Accepted: 07/02/2019] [Indexed: 05/10/2023]
Abstract
Improvements in next-generation sequencing technologies have resulted in dramatically reduced sequencing costs. This has led to an explosion of '-seq'-based methods, of which RNA sequencing (RNA-seq) for generating transcriptomic data is the most popular. By analysing global patterns of gene expression in organs/tissues/cells of interest or in response to chemical or environmental perturbations, researchers can better understand an organism's biology. Tools designed to work with large RNA-seq data sets enable analyses and visualizations to help generate hypotheses about a gene's function. We present here a user-friendly RNA-seq data exploration tool, called the 'eFP-Seq Browser', that shows the read map coverage of a gene of interest in each of the samples along with 'electronic fluorescent pictographic' (eFP) images that serve as visual representations of expression levels. The tool also summarizes the details of each RNA-seq experiment, providing links to archival databases and publications. It automatically computes the reads per kilobase per million reads mapped expression-level summaries and point biserial correlation scores to sort the samples based on a gene's expression level or by how dissimilar the read map profile is from a gene splice variant, to quickly identify samples with the strongest expression level or where alternative splicing might be occurring. Links to the Integrated Genome Browser desktop visualization tool allow researchers to visualize and explore the details of RNA-seq alignments summarized in eFP-Seq Browser as coverage graphs. We present four cases of use of the eFP-Seq Browser for ABI3, SR34, SR45a and U2AF65B, where we examine expression levels and identify alternative splicing. The URL for the browser is https://bar.utoronto.ca/eFP-Seq_Browser/. OPEN RESEARCH BADGES: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. Tool is at https://bar.utoronto.ca/eFP-Seq_Browser/; RNA-seq data at https://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/ and https://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/Klepikova/. Code is available at https://github.com/BioAnalyticResource/eFP-Seq-Browser.
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Affiliation(s)
- Alexander Sullivan
- Department of Cell and Systems Biology/CAGEFUniversity of TorontoTorontoONCanada
| | - Priyank K. Purohit
- Department of Cell and Systems Biology/CAGEFUniversity of TorontoTorontoONCanada
| | | | - Asher Pasha
- Department of Cell and Systems Biology/CAGEFUniversity of TorontoTorontoONCanada
| | - Eddi Esteban
- Department of Cell and Systems Biology/CAGEFUniversity of TorontoTorontoONCanada
| | - Jamie Waese
- Department of Cell and Systems Biology/CAGEFUniversity of TorontoTorontoONCanada
| | - Alison Wu
- Department of Cell and Systems Biology/CAGEFUniversity of TorontoTorontoONCanada
| | - Michelle Chen
- Department of Cell and Systems Biology/CAGEFUniversity of TorontoTorontoONCanada
| | - Chih Y. Chin
- Department of Cell and Systems Biology/CAGEFUniversity of TorontoTorontoONCanada
| | - Richard Song
- Department of Cell and Systems Biology/CAGEFUniversity of TorontoTorontoONCanada
| | | | | | | | - Matthew W. Vaughn
- Texas Advanced Computing CenterUniversity of Texas at AustinAustinTXUSA
| | | | | | - Nicholas J. Provart
- Department of Cell and Systems Biology/CAGEFUniversity of TorontoTorontoONCanada
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Waese J, Fan J, Pasha A, Yu H, Fucile G, Shi R, Cumming M, Kelley LA, Sternberg MJ, Krishnakumar V, Ferlanti E, Miller J, Town C, Stuerzlinger W, Provart NJ. ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology. Plant Cell 2017; 29:1806-1821. [PMID: 28808136 PMCID: PMC5590499 DOI: 10.1105/tpc.17.00073] [Citation(s) in RCA: 210] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 07/17/2017] [Accepted: 08/09/2017] [Indexed: 05/17/2023]
Abstract
A big challenge in current systems biology research arises when different types of data must be accessed from separate sources and visualized using separate tools. The high cognitive load required to navigate such a workflow is detrimental to hypothesis generation. Accordingly, there is a need for a robust research platform that incorporates all data and provides integrated search, analysis, and visualization features through a single portal. Here, we present ePlant (http://bar.utoronto.ca/eplant), a visual analytic tool for exploring multiple levels of Arabidopsis thaliana data through a zoomable user interface. ePlant connects to several publicly available web services to download genome, proteome, interactome, transcriptome, and 3D molecular structure data for one or more genes or gene products of interest. Data are displayed with a set of visualization tools that are presented using a conceptual hierarchy from big to small, and many of the tools combine information from more than one data type. We describe the development of ePlant in this article and present several examples illustrating its integrative features for hypothesis generation. We also describe the process of deploying ePlant as an "app" on Araport. Building on readily available web services, the code for ePlant is freely available for any other biological species research.
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Affiliation(s)
- Jamie Waese
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Jim Fan
- Department of Computer Science, University of Waterloo, Ontario N2L 3G1, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Hans Yu
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Geoffrey Fucile
- SIB Swiss Institute of Bioinformatics, sciCORE Computing Center, University of Basel, CH-4056 Basel, Switzerland
| | - Ruian Shi
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Matthew Cumming
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | | | | | | | - Erik Ferlanti
- Araport.org/J. Craig Venter Institute, Rockville, Maryland 20850
| | - Jason Miller
- Araport.org/J. Craig Venter Institute, Rockville, Maryland 20850
| | - Chris Town
- Araport.org/J. Craig Venter Institute, Rockville, Maryland 20850
| | - Wolfgang Stuerzlinger
- School of Interactive Arts and Technology, Simon Fraser University, British Columbia V3T 0A3, Canada
| | - Nicholas J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
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7
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Austin RS, Hiu S, Waese J, Ierullo M, Pasha A, Wang TT, Fan J, Foong C, Breit R, Desveaux D, Moses A, Provart NJ. New BAR tools for mining expression data and exploring Cis-elements in Arabidopsis thaliana. Plant J 2016; 88:490-504. [PMID: 27401965 DOI: 10.1111/tpj.13261] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 06/23/2016] [Accepted: 07/01/2016] [Indexed: 05/21/2023]
Abstract
Identifying sets of genes that are specifically expressed in certain tissues or in response to an environmental stimulus is useful for designing reporter constructs, generating gene expression markers, or for understanding gene regulatory networks. We have developed an easy-to-use online tool for defining a desired expression profile (a modification of our Expression Angler program), which can then be used to identify genes exhibiting patterns of expression that match this profile as closely as possible. Further, we have developed another online tool, Cistome, for predicting or exploring cis-elements in the promoters of sets of co-expressed genes identified by such a method, or by other methods. We present two use cases for these tools, which are freely available on the Bio-Analytic Resource at http://BAR.utoronto.ca.
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Affiliation(s)
- Ryan S Austin
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Shu Hiu
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Jamie Waese
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Matthew Ierullo
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Asher Pasha
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Ting Ting Wang
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Jim Fan
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Curtis Foong
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Robert Breit
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Darrell Desveaux
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Alan Moses
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Nicholas J Provart
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
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8
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Waese J, Pasha A, Wang TT, van Weringh A, Guttman DS, Provart NJ. Gene Slider: sequence logo interactive data-visualization for education and research. Bioinformatics 2016; 32:3670-3672. [DOI: 10.1093/bioinformatics/btw525] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 06/27/2016] [Accepted: 08/08/2016] [Indexed: 11/12/2022] Open
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9
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Provart NJ, Alonso J, Assmann SM, Bergmann D, Brady SM, Brkljacic J, Browse J, Chapple C, Colot V, Cutler S, Dangl J, Ehrhardt D, Friesner JD, Frommer WB, Grotewold E, Meyerowitz E, Nemhauser J, Nordborg M, Pikaard C, Shanklin J, Somerville C, Stitt M, Torii KU, Waese J, Wagner D, McCourt P. 50 years of Arabidopsis research: highlights and future directions. New Phytol 2016; 209:921-44. [PMID: 26465351 DOI: 10.1111/nph.13687] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/24/2015] [Indexed: 05/14/2023]
Abstract
922 I. 922 II. 922 III. 925 IV. 925 V. 926 VI. 927 VII. 928 VIII. 929 IX. 930 X. 931 XI. 932 XII. 933 XIII. Natural variation and genome-wide association studies 934 XIV. 934 XV. 935 XVI. 936 XVII. 937 937 References 937 SUMMARY: The year 2014 marked the 25(th) International Conference on Arabidopsis Research. In the 50 yr since the first International Conference on Arabidopsis Research, held in 1965 in Göttingen, Germany, > 54 000 papers that mention Arabidopsis thaliana in the title, abstract or keywords have been published. We present herein a citational network analysis of these papers, and touch on some of the important discoveries in plant biology that have been made in this powerful model system, and highlight how these discoveries have then had an impact in crop species. We also look to the future, highlighting some outstanding questions that can be readily addressed in Arabidopsis. Topics that are discussed include Arabidopsis reverse genetic resources, stock centers, databases and online tools, cell biology, development, hormones, plant immunity, signaling in response to abiotic stress, transporters, biosynthesis of cells walls and macromolecules such as starch and lipids, epigenetics and epigenomics, genome-wide association studies and natural variation, gene regulatory networks, modeling and systems biology, and synthetic biology.
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Affiliation(s)
- Nicholas J Provart
- Department of Cell & Systems Biology/CAGEF, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Jose Alonso
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | | | - Siobhan M Brady
- Department of Plant Biology, University of California, Davis, CA, 95616, USA
| | - Jelena Brkljacic
- Arabidopsis Biological Resource Center, The Ohio State University, Columbus, OH, 43210, USA
| | - John Browse
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164, USA
| | - Clint Chapple
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Vincent Colot
- Departement de Biologie École Normale Supérieure, Biologie Moleculaire des Organismes Photosynthetiques, F-75230, Paris, France
| | - Sean Cutler
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92507, USA
| | - Jeff Dangl
- Department of Biology and Howard Hughes Medical Institute, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - David Ehrhardt
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Joanna D Friesner
- Department of Plant Biology, Agricultural Sustainability Institute, University of California, Davis, CA, 95616, USA
| | - Wolf B Frommer
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Erich Grotewold
- Center for Applied Plant Science, The Ohio State University, Columbus, OH, 43210, USA
| | - Elliot Meyerowitz
- Division of Biology and Biological Engineering and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Jennifer Nemhauser
- Department of Biology, University of Washington, Seattle, WA, 98195, USA
| | - Magnus Nordborg
- Gregor Mendel Institute of Molecular Plant Biology, A-1030, Vienna, Austria
| | - Craig Pikaard
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - John Shanklin
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Chris Somerville
- Energy Biosciences Institute, University of California, Berkeley, CA, 94704, USA
| | - Mark Stitt
- Metabolic Networks Department, Max Planck Institute for Molecular Plant Physiology, D-14476, Potsdam, Germany
| | - Keiko U Torii
- Department of Biology, University of Washington, Seattle, WA, 98195, USA
| | - Jamie Waese
- Department of Cell & Systems Biology/CAGEF, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Peter McCourt
- Department of Cell & Systems Biology/CAGEF, University of Toronto, Toronto, ON, M5S 3B2, Canada
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