Literature DB >> 27730285

Big data mining powers fungal research: recent advances in fission yeast systems biology approaches.

Zhe Wang1,2.   

Abstract

Biology research has entered into big data era. Systems biology approaches therefore become the powerful tools to obtain the whole landscape of how cell separate, grow, and resist the stresses. Fission yeast Schizosaccharomyces pombe is wonderful unicellular eukaryote model, especially studying its division and metabolism can facilitate to understanding the molecular mechanism of cancer and discovering anticancer agents. In this perspective, we discuss the recent advanced fission yeast systems biology tools, mainly focus on metabolomics profiling and metabolic modeling, protein-protein interactome and genetic interaction network, DNA sequencing and applications, and high-throughput phenotypic screening. We therefore hope this review can be useful for interested fungal researchers as well as bioformaticians.

Entities:  

Keywords:  Big data; Omics; Schizosaccharomyces pombe; Systems biology

Mesh:

Year:  2016        PMID: 27730285     DOI: 10.1007/s00294-016-0657-4

Source DB:  PubMed          Journal:  Curr Genet        ISSN: 0172-8083            Impact factor:   3.886


  49 in total

Review 1.  Metabolomics--the link between genotypes and phenotypes.

Authors:  Oliver Fiehn
Journal:  Plant Mol Biol       Date:  2002-01       Impact factor: 4.076

Review 2.  Global strategies to integrate the proteome and metabolome.

Authors:  Alan Saghatelian; Benjamin F Cravatt
Journal:  Curr Opin Chem Biol       Date:  2005-02       Impact factor: 8.822

3.  A parallel proteomic and metabolomic analysis of the hydrogen peroxide- and Sty1p-dependent stress response in Schizosaccharomyces pombe.

Authors:  Mark E Weeks; John Sinclair; Amna Butt; Yuen-Li Chung; Jessica L Worthington; Caroline R M Wilkinson; John Griffiths; Nic Jones; Michael D Waterfield; John F Timms
Journal:  Proteomics       Date:  2006-05       Impact factor: 3.984

4.  Quantitative genetic-interaction mapping in mammalian cells.

Authors:  Assen Roguev; Dale Talbot; Gian Luca Negri; Michael Shales; Gerard Cagney; Sourav Bandyopadhyay; Barbara Panning; Nevan J Krogan
Journal:  Nat Methods       Date:  2013-02-13       Impact factor: 28.547

5.  Unexpected similarities between the Schizosaccharomyces and human blood metabolomes, and novel human metabolites.

Authors:  Romanas Chaleckis; Masahiro Ebe; Tomáš Pluskal; Itsuo Murakami; Hiroshi Kondoh; Mitsuhiro Yanagida
Journal:  Mol Biosyst       Date:  2014-10

6.  A novel function of the mitochondrial transcription factor Mtf1 in fission yeast; Mtf1 regulates the nuclear transcription of srk1.

Authors:  Wenxia Sun; Zhe Wang; Hengyi Jiang; Jing Zhang; Jürg Bähler; Dongrong Chen; Alastair I H Murchie
Journal:  Nucleic Acids Res       Date:  2010-12-07       Impact factor: 16.971

7.  Interconnections Between RNA-Processing Pathways Revealed by a Sequencing-Based Genetic Screen for Pre-mRNA Splicing Mutants in Fission Yeast.

Authors:  Amy Larson; Benjamin Jung Fair; Jeffrey A Pleiss
Journal:  G3 (Bethesda)       Date:  2016-06-01       Impact factor: 3.154

8.  A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human.

Authors:  Tommy V Vo; Jishnu Das; Michael J Meyer; Nicolas A Cordero; Nurten Akturk; Xiaomu Wei; Benjamin J Fair; Andrew G Degatano; Robert Fragoza; Lisa G Liu; Akihisa Matsuyama; Michelle Trickey; Sachi Horibata; Andrew Grimson; Hiroyuki Yamano; Minoru Yoshida; Frederick P Roth; Jeffrey A Pleiss; Yu Xia; Haiyuan Yu
Journal:  Cell       Date:  2016-01-14       Impact factor: 41.582

9.  Global transcriptional responses of fission yeast to environmental stress.

Authors:  Dongrong Chen; W Mark Toone; Juan Mata; Rachel Lyne; Gavin Burns; Katja Kivinen; Alvis Brazma; Nic Jones; Jürg Bähler
Journal:  Mol Biol Cell       Date:  2003-01       Impact factor: 4.138

10.  A genome-wide resource of cell cycle and cell shape genes of fission yeast.

Authors:  Jacqueline Hayles; Valerie Wood; Linda Jeffery; Kwang-Lae Hoe; Dong-Uk Kim; Han-Oh Park; Silvia Salas-Pino; Christian Heichinger; Paul Nurse
Journal:  Open Biol       Date:  2013-05-22       Impact factor: 6.411

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  3 in total

1.  An agent-based model of the fission yeast cell cycle.

Authors:  Carlos Castro; Dora-Luz Flores; David Cervantes-Vásquez; Eunice Vargas-Viveros; Everardo Gutiérrez-López; Franklin Muñoz-Muñoz
Journal:  Curr Genet       Date:  2018-06-18       Impact factor: 3.886

2.  Fission Yeast Schizosaccharomyces pombe: A Unicellular "Micromammal" Model Organism.

Authors:  Aditi Vyas; Anna V Freitas; Zachary A Ralston; Zhaohua Tang
Journal:  Curr Protoc       Date:  2021-06

3.  Assembly of Schizosaccharomyces cryophilus chromosomes and their comparative genomic analyses revealed principles of genome evolution of the haploid fission yeasts.

Authors:  Lajos Ács-Szabó; László Attila Papp; Zsuzsa Antunovics; Matthias Sipiczki; Ida Miklós
Journal:  Sci Rep       Date:  2018-10-02       Impact factor: 4.379

  3 in total

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