Efficient Functional Bioinformatics Tools: Towards Understanding Biological Processes Abstract Introduction Applications
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Arabidopsis Thaliana
Downloaded from genome.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press RESEARCH A Physical Map of Chromosome 2 of Arabidopsis thaliana Eve Ann Zachgo, 2,4 Ming Li Wang, 1'2'4 Julia Dewdney, 1'2 David Bouchez, 3 Christine Carnilleri, 3 Stephen Belmonte, 2 Lu Huang, 2 Maureen Dolan, 2 and Howard M. Goodman 1'2'5 1Department of Genetics, Harvard Medical School and 2Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114; 3Laboratoire de Biologie Cellulaire, Institut National de la Recherche Agronomique (INRA), 78026 Versailles CEDEX, France A yeast artificial chromosome (YAC] physical map of chromosome 2 of Arabidopsis thaliana has been constructed by hybridization of 69 DNA markers and 61 YAC end probes to gridded arrays of YAC clones. Thirty-four YACs in four contigs define the chromosome. Complete closure of the map was not attained because some regions of the chromosome were repetitive or were not represented in the YAC library. Based on the sizes of the YACs and their coverage of the chromosome, the length of chromosome 2 is estimated to be at least 18 Mb. These data provide the means for immediately identifying the YACs containing a genetic locus mapped on Arabidopsis chromosome 2. The small flowering plant Arabidopsis thaliana is ters (Maluszynska and Heslop-Harrison 1991; A1- an excellent model system for metabolic, genetic, bini 1994; Copenhaver et al. 1995). We present and developmental studies in plants. Its haploid here a YAC contig physical map of chromosome nuclear genome is small (-100 Mb), consisting of 2 of A. -
Toolboxes for a Standardised and Systematic Study of Glycans
Campbell et al. BMC Bioinformatics 2014, 15(Suppl 1):S9 http://www.biomedcentral.com/1471-2105/15/S1/S9 RESEARCH Open Access Toolboxes for a standardised and systematic study of glycans Matthew P Campbell1, René Ranzinger2, Thomas Lütteke3, Julien Mariethoz4, Catherine A Hayes5, Jingyu Zhang1, Yukie Akune6, Kiyoko F Aoki-Kinoshita6, David Damerell7,11, Giorgio Carta8, Will S York2, Stuart M Haslam7, Hisashi Narimatsu9, Pauline M Rudd8, Niclas G Karlsson4, Nicolle H Packer1, Frédérique Lisacek4,10* From Integrated Bio-Search: 12th International Workshop on Network Tools and Applications in Biology (NETTAB 2012) Como, Italy. 14-16 November 2012 Abstract Background: Recent progress in method development for characterising the branched structures of complex carbohydrates has now enabled higher throughput technology. Automation of structure analysis then calls for software development since adding meaning to large data collections in reasonable time requires corresponding bioinformatics methods and tools. Current glycobioinformatics resources do cover information on the structure and function of glycans, their interaction with proteins or their enzymatic synthesis. However, this information is partial, scattered and often difficult to find to for non-glycobiologists. Methods: Following our diagnosis of the causes of the slow development of glycobioinformatics, we review the “objective” difficulties encountered in defining adequate formats for representing complex entities and developing efficient analysis software. Results: Various solutions already implemented and strategies defined to bridge glycobiology with different fields and integrate the heterogeneous glyco-related information are presented. Conclusions: Despite the initial stage of our integrative efforts, this paper highlights the rapid expansion of glycomics, the validity of existing resources and the bright future of glycobioinformatics. -
To Find Information About Arabidopsis Genes Leonore Reiser1, Shabari
UNIT 1.11 Using The Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes Leonore Reiser1, Shabari Subramaniam1, Donghui Li1, and Eva Huala1 1Phoenix Bioinformatics, Redwood City, CA USA ABSTRACT The Arabidopsis Information Resource (TAIR; http://arabidopsis.org) is a comprehensive Web resource of Arabidopsis biology for plant scientists. TAIR curates and integrates information about genes, proteins, gene function, orthologs gene expression, mutant phenotypes, biological materials such as clones and seed stocks, genetic markers, genetic and physical maps, genome organization, images of mutant plants, protein sub-cellular localizations, publications, and the research community. The various data types are extensively interconnected and can be accessed through a variety of Web-based search and display tools. This unit primarily focuses on some basic methods for searching, browsing, visualizing, and analyzing information about Arabidopsis genes and genome, Additionally we describe how members of the community can share data using TAIR’s Online Annotation Submission Tool (TOAST), in order to make their published research more accessible and visible. Keywords: Arabidopsis ● databases ● bioinformatics ● data mining ● genomics INTRODUCTION The Arabidopsis Information Resource (TAIR; http://arabidopsis.org) is a comprehensive Web resource for the biology of Arabidopsis thaliana (Huala et al., 2001; Garcia-Hernandez et al., 2002; Rhee et al., 2003; Weems et al., 2004; Swarbreck et al., 2008, Lamesch, et al., 2010, Berardini et al., 2016). The TAIR database contains information about genes, proteins, gene expression, mutant phenotypes, germplasms, clones, genetic markers, genetic and physical maps, genome organization, publications, and the research community. In addition, seed and DNA stocks from the Arabidopsis Biological Resource Center (ABRC; Scholl et al., 2003) are integrated with genomic data, and can be ordered through TAIR. -
Life with 6000 Genes Author(S): A. Goffeau, B. G. Barrell, H. Bussey, R
Life with 6000 Genes Author(s): A. Goffeau, B. G. Barrell, H. Bussey, R. W. Davis, B. Dujon, H. Feldmann, F. Galibert, J. D. Hoheisel, C. Jacq, M. Johnston, E. J. Louis, H. W. Mewes, Y. Murakami, P. Philippsen, H. Tettelin and S. G. Oliver Source: Science, Vol. 274, No. 5287, Genome Issue (Oct. 25, 1996), pp. 546+563-567 Published by: American Association for the Advancement of Science Stable URL: https://www.jstor.org/stable/2899628 Accessed: 28-08-2019 13:31 UTC REFERENCES Linked references are available on JSTOR for this article: https://www.jstor.org/stable/2899628?seq=1&cid=pdf-reference#references_tab_contents You may need to log in to JSTOR to access the linked references. JSTOR is a not-for-profit service that helps scholars, researchers, and students discover, use, and build upon a wide range of content in a trusted digital archive. We use information technology and tools to increase productivity and facilitate new forms of scholarship. For more information about JSTOR, please contact [email protected]. Your use of the JSTOR archive indicates your acceptance of the Terms & Conditions of Use, available at https://about.jstor.org/terms American Association for the Advancement of Science is collaborating with JSTOR to digitize, preserve and extend access to Science This content downloaded from 152.3.43.41 on Wed, 28 Aug 2019 13:31:29 UTC All use subject to https://about.jstor.org/terms by FISH across the whole genome. A subset of the 37. G. D. Billingsleyet al., Am. J. Hum. Genet. 52, 343 (1994); L. -
Comprehensive Analysis of CRISPR/Cas9-Mediated Mutagenesis in Arabidopsis Thaliana by Genome-Wide Sequencing
International Journal of Molecular Sciences Article Comprehensive Analysis of CRISPR/Cas9-Mediated Mutagenesis in Arabidopsis thaliana by Genome-Wide Sequencing Wenjie Xu 1,2 , Wei Fu 2, Pengyu Zhu 2, Zhihong Li 1, Chenguang Wang 2, Chaonan Wang 1,2, Yongjiang Zhang 2 and Shuifang Zhu 1,2,* 1 College of Plant Protection, China Agricultural University, Beijing 100193 China 2 Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China * Correspondence: [email protected] Received: 9 July 2019; Accepted: 21 August 2019; Published: 23 August 2019 Abstract: The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system has been widely applied in functional genomics research and plant breeding. In contrast to the off-target studies of mammalian cells, there is little evidence for the common occurrence of off-target sites in plants and a great need exists for accurate detection of editing sites. Here, we summarized the precision of CRISPR/Cas9-mediated mutations for 281 targets and found that there is a preference for single nucleotide deletions/insertions and longer deletions starting from 40 nt upstream or ending at 30 nt downstream of the cleavage site, which suggested the candidate sequences for editing sites detection by whole-genome sequencing (WGS). We analyzed the on-/off-target sites of 6 CRISPR/Cas9-mediated Arabidopsis plants by the optimized method. The results showed that the on-target editing frequency ranged from 38.1% to 100%, and one off target at a frequency of 9.8%–97.3% cannot be prevented by increasing the specificity or reducing the expression level of the Cas9 enzyme. -
Locdb: Experimental Annotations of Localization for Homo Sapiens and Arabidopsis Thaliana Shruti Rastogi1,* and Burkhard Rost1,2,3
D230–D234 Nucleic Acids Research, 2011, Vol. 39, Database issue Published online 11 November 2010 doi:10.1093/nar/gkq927 LocDB: experimental annotations of localization for Homo sapiens and Arabidopsis thaliana Shruti Rastogi1,* and Burkhard Rost1,2,3 1Department of Biochemistry and Molecular Biophysics, Columbia University, 701 West, 168th Street, New York, NY 10032, USA, 2Technical University Munich, Bioinformatics, Department of Computer Science and Institute of Advanced Studies (IAS) and 3New York Consortium on Membrane Protein Structure (NYCOMPS), TUM Bioinformatics, Boltzmannstr. 3, 85748 Garching, Germany Downloaded from Received August 15, 2010; Revised September 24, 2010; Accepted September 27, 2010 ABSTRACT stepped up to the challenge to increase the amount of annotations (6–15). These data sets capture aspects of LocDB is a manually curated database with protein function and, more generally, of global cellular nar.oxfordjournals.org experimental annotations for the subcellular processes. localizations of proteins in Homo sapiens (HS, UniProt (release 2010_07) (16) constitutes the most human) and Arabidopsis thaliana (AT, thale cress). comprehensive and, arguably, the most accurate Currently, it contains entries for 19 604 UniProt resource with experimental annotations of subcellular proteins (HS: 13 342; AT: 6262). Each database localization. However, even this excellent resource entry contains the experimentally derived locali- remains incomplete for the proteomes from Homo sapiens (HS) and Arabidopsis thaliana (AT): of the zation in Gene Ontology (GO) terminology, the at Medical Center Library, Duke University on January 13, 2011 experimental annotation of localization, localization 20 282 human proteins in Swiss-Prot (17), 14 502 have predictions by state-of-the-art methods and, where annotations of localization (72%), but for only 3720 (18%) these annotations are experimental. -
A Bioinformatics Analysis of the Arabidopsis Thaliana Epigenome Ikhlak Ahmed
A bioinformatics analysis of the arabidopsis thaliana epigenome Ikhlak Ahmed To cite this version: Ikhlak Ahmed. A bioinformatics analysis of the arabidopsis thaliana epigenome. Agricultural sciences. Université Paris Sud - Paris XI, 2011. English. NNT : 2011PA112230. tel-00684391 HAL Id: tel-00684391 https://tel.archives-ouvertes.fr/tel-00684391 Submitted on 2 Apr 2012 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. 2011 PhD Thesis Ikhlak Ahmed Laboratoire: CNRS UMR8197 - INSERM U1024 Institut de Biologie de l'ENS(IBENS) Ecole Doctorale : Sciences Du Végétal A Bioinformatics analysis of the Arabidopsis thaliana Epigenome Supervisors: Dr. Chris Bowler and Dr. Vincent Colot Jury Prof. Dao-Xiu Zhou President Prof. Christian Fankhauser Rapporteur Dr. Raphaël Margueron Rapporteur Dr. Chris Bowler Examiner Dr. Vincent Colot Examiner Dr. Allison Mallory Examiner Dr. Michaël Weber Examiner Acknowledgement I express my deepest gratitude to my supervisors Dr. Chris Bowler and Dr. Vincent Colot for the support, advice and freedom that I enjoyed working with them. I am very thankful to Chris Bowler who trusted in me and gave me the opportunity to come here and work in the excellent possible conditions. I have no words to express my thankfulness to Vincent Colot for his enthusiastic supervision and the incredibly valuable sessions we spent together that shaped my understanding of DNA methylation. -
Mutator-Like Elements in Arabidopsis Thaliana: Structure, Diversity and Evolution
Copyright 2000 by the Genetics Society of America Mutator-like Elements in Arabidopsis thaliana: Structure, Diversity and Evolution Zhihui Yu, Stephen I. Wright and Thomas E. Bureau Department of Biology, McGill University, Montreal, Quebec, H3A 1B1 Canada Manuscript received May 18, 2000 Accepted for publication September 11, 2000 ABSTRACT While genome-wide surveys of abundance and diversity of mobile elements have been conducted for some class I transposable element families, little is known about the nature of class II transposable elements on this scale. In this report, we present the results from analysis of the sequence and structural diversity of Mutator-like elements (MULEs) in the genome of Arabidopsis thaliana (Columbia). Sequence similarity searches and subsequent characterization suggest that MULEs exhibit extreme structure, sequence, and size heterogeneity. Multiple alignments at the nucleotide and amino acid levels reveal conserved, potentially transposition-related sequence motifs. While many MULEs share common structural features to Mu ele- ments in maize, some groups lack characteristic long terminal inverted repeats. High sequence similarity and phylogenetic analyses based on nucleotide sequence alignments indicate that many of these elements with diverse structural features may remain transpositionally competent and that multiple MULE lineages may have been evolving independently over long time scales. Finally, there is evidence that MULEs are capable of the acquisition of host DNA segments, which may have implications for adaptive evolution, both at the element and host levels. HE Mutator (Mu) system is a diverse family of class ef®cient transposon-tagging tool for maize gene isola- TII transposable elements (TEs) found in maize. tion (Walbot 1992). -
The Embryonic Transcriptome of Arabidopsis Thaliana
bioRxiv preprint doi: https://doi.org/10.1101/479584; this version posted November 27, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Title: The embryonic transcriptome of Arabidopsis thaliana 1,2 1,2 1 Authors: Falko Hofmann , Michael A. Schon and Michael D. Nodine 1 Affiliations: Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter 2 (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria; These authors contributed equally to this work Corresponding author: Michael D. Nodine (email: [email protected]; phone: +43 1 79044-9821) Author ORCID IDs: Falko Hofmann (#0000-0002-5032-0411), Michael A. Schon (#0000-0002-4756-3906) and Michael D. Nodine (#0000-0002-6204-8857) 1 bioRxiv preprint doi: https://doi.org/10.1101/479584; this version posted November 27, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Key Message Arabidopsis embryos possess unique transcriptomes relative to other plant tissues including somatic embryos, and can be partitioned into four transcriptional phases with characteristic biological processes. 2 bioRxiv preprint doi: https://doi.org/10.1101/479584; this version posted November 27, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Cellular differentiation is associated with changes in transcript populations. Accurate quantification of transcriptomes during development can thus provide global insights into differentiation processes including the fundamental specification and differentiation events operating during plant embryogenesis. -
Evolutionary Systems Biology 12 – 14 February 2020 Wellcome
Evolutionary Systems Biology 12 – 14 February 2020 Wellcome Genome Campus, Hinxton, Cambridge, UK Draft Conference Programme Wednesday, 12 February 12:00-13:20 Registration 13:20-13:30 Welcome and introductions Mark Siegal, New York University, USA 13:30-14:30 Keynote lecture Chair: Trisha Wittkopp, University of Michigan, USA Robustness and precision within developmental networks Eileen Furlong EMBL, Germany 14:30-15:30 Session 1: Evolution of Fitness Landscapes Chair: Olivier Tenaillon, INSERM, France 14:30 Understanding genetic interactions and solving protein structures using deep mutagenesis Ben Lehner Centre for Genomic Regulation, Spain 15:00 Latent phenotypic complexity of adaptation in a single condition Dmitri Petrov Stanford University, USA 15:30 Pervasive modulation of a natural genotype-phenotype map by global epistatic modifiers José Aguilar-Rodríguez Stanford University, USA 15:45-16:15 Afternoon tea 16:15-17:15 Session 1b: The diversity of evolutionary systems biology 16:15 The evolution of fitness effects in a long-term experiment with bacteria Alejandro Couce Technical University of Madrid, Spain 16:30 Instraspecific evolution of QR.pax final position in Caenorhabditis elegans Clement Dubois IBENS, France 16:45 Functional optimization governs the rate of protein evolution in multicellular species Dinara Usmanova Columbia University, USA 17:00 Toward an ecology of cancer: Intra-tumor spatial heterogeneity based on multi-region mass spectrometry, single cell copy number sequencing and cyclic immunofluorescence in lung -
Introduction to Bioinformatics (Elective) – SBB1609
SCHOOL OF BIO AND CHEMICAL ENGINEERING DEPARTMENT OF BIOTECHNOLOGY Unit 1 – Introduction to Bioinformatics (Elective) – SBB1609 1 I HISTORY OF BIOINFORMATICS Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biologicaldata. As an interdisciplinary field of science, bioinformatics combines computer science, statistics, mathematics, and engineering to analyze and interpret biological data. Bioinformatics has been used for in silico analyses of biological queries using mathematical and statistical techniques. Bioinformatics derives knowledge from computer analysis of biological data. These can consist of the information stored in the genetic code, but also experimental results from various sources, patient statistics, and scientific literature. Research in bioinformatics includes method development for storage, retrieval, and analysis of the data. Bioinformatics is a rapidly developing branch of biology and is highly interdisciplinary, using techniques and concepts from informatics, statistics, mathematics, chemistry, biochemistry, physics, and linguistics. It has many practical applications in different areas of biology and medicine. Bioinformatics: Research, development, or application of computational tools and approaches for expanding the use of biological, medical, behavioral or health data, including those to acquire, store, organize, archive, analyze, or visualize such data. Computational Biology: The development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems. "Classical" bioinformatics: "The mathematical, statistical and computing methods that aim to solve biological problems using DNA and amino acid sequences and related information.” The National Center for Biotechnology Information (NCBI 2001) defines bioinformatics as: "Bioinformatics is the field of science in which biology, computer science, and information technology merge into a single discipline. -
Embnet Conference 2020 Programme
EMBnet Conference 2020 Bioinformatics Approaches to Precision Research 23-24 September 2020 Zoom Platform - Time 3 pm to 8 pm (CEST) Registration: https://us02web.zoom.us/meeting/register/tZEvd-mupjwiE911qtAnYln4TrNwQlxDMYm4 Programme 1st Day: 23 September 9, 2020 15:00-15:10 Welcome & Programme Presentation Domenica D’Elia & Erik Bongcam-Rudloff 15:10-15:30 Exosomes in breast milk; a beneficial genetic trojan horse from mother to child Dimitrios Vlachakis, Aspasia Efthimiadou, Flora Bacopoulou, Elias Eliopoulos, George P. Chrousos 15:30-15:50 Precision dairy farming – A Phenomenal opportunity Tomas Klingström 15:50-16:10 Genome regulation by long non-coding RNAs Katerina Pierouli, George N. Goulielmos, Elias Eliopoulos, Dimitrios Vlachakis European Molecular Biology Network (EMBnet) and Global Bioinformatics Network since 1988 16:10-16:30 Precision Epidemiology of Multi-drug resistance bacteria: bioinformatics tools J.Donato, L. Lugo, H. Perez, H. Ballen, D. Talero, S. Prada, F.Brion, V. Rincon, L. Falquet, M.T. Reguero, E. Barreto-Hernandez 16:30-16:50 Mechanisms of epigenetic inheritance in children following exposure to abuse E. Damaskopoulou, G.P. Chrousos, E. Eliopoulos, D. Vlachakis 16:50-17:00 Break 17:00-17:20 Genome-wide association studies (GWAS) in an effort to provide insights into the complex interplay of nuclear receptor transcriptional networks and their contribution to the maintenance of homeostasis Thanassis Mitsis, G.P. Chrousos, E. Eliopoulos, D.Vlachakis 17:20-17:40 Computer aided drug design and pharmacophore modelling towards the discovery of novel anti-ebola agents Kalliopi Io Diakou, G.P. Chrousos, E. Eliopoulos, D. Vlachakis 17:40-18:00 3′-Tag RNA-sequencing Andreas Gisel 18:00-18:20 Expression profiling of non-coding RNA in coronaviruses provides clues for virus RNA interference with immune system response Arianna Consiglio, V.F.