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Items: 41


Expression Atlas of Selaginella moellendorffii Provides Insights into the Evolution of Vasculature, Secondary Metabolism, and Roots.

Ferrari C, Shivhare D, Hansen BO, Pasha A, Esteban E, Provart NJ, Kragler F, Fernie AR, Tohge T, Mutwil M.

Plant Cell. 2020 Jan 27. pii: tpc.00780.2019. doi: 10.1105/tpc.19.00780. [Epub ahead of print]


Inferring biosynthetic and gene regulatory networks from Artemisia annua RNA sequencing data on a credit card-sized ARM computer.

Tan QW, Mutwil M.

Biochim Biophys Acta Gene Regul Mech. 2019 Oct 18:194429. doi: 10.1016/j.bbagrm.2019.194429. [Epub ahead of print]


Gene expression analysis of Cyanophora paradoxa reveals conserved abiotic stress responses between basal algae and flowering plants.

Ferrari C, Mutwil M.

New Phytol. 2020 Feb;225(4):1562-1577. doi: 10.1111/nph.16257. Epub 2019 Nov 11.

4. Comparative Transcriptomic and Co-expression Analyses of Diurnal Gene Expression of the Archaeplastida Kingdom.

Ng JWX, Tan QW, Ferrari C, Mutwil M.

Plant Cell Physiol. 2020 Jan 1;61(1):212-220. doi: 10.1093/pcp/pcz176.


The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation.

Rendón-Anaya M, Ibarra-Laclette E, Méndez-Bravo A, Lan T, Zheng C, Carretero-Paulet L, Perez-Torres CA, Chacón-López A, Hernandez-Guzmán G, Chang TH, Farr KM, Barbazuk WB, Chamala S, Mutwil M, Shivhare D, Alvarez-Ponce D, Mitter N, Hayward A, Fletcher S, Rozas J, Sánchez Gracia A, Kuhn D, Barrientos-Priego AF, Salojärvi J, Librado P, Sankoff D, Herrera-Estrella A, Albert VA, Herrera-Estrella L.

Proc Natl Acad Sci U S A. 2019 Aug 20;116(34):17081-17089. doi: 10.1073/pnas.1822129116. Epub 2019 Aug 6.

6. genomic and transcriptomic database for Plasmodium species.

Tan QW, Mutwil M.

Nucleic Acids Res. 2020 Jan 8;48(D1):D768-D775. doi: 10.1093/nar/gkz662.


Analysis of an improved Cyanophora paradoxa genome assembly.

Price DC, Goodenough UW, Roth R, Lee JH, Kariyawasam T, Mutwil M, Ferrari C, Facchinelli F, Ball SG, Cenci U, Chan CX, Wagner NE, Yoon HS, Weber APM, Bhattacharya D.

DNA Res. 2019 Aug 1;26(4):287-299. doi: 10.1093/dnares/dsz009.


Cellulose Synthesis - Central Components and Their Evolutionary Relationships.

Lampugnani ER, Flores-Sandoval E, Tan QW, Mutwil M, Bowman JL, Persson S.

Trends Plant Sci. 2019 May;24(5):402-412. doi: 10.1016/j.tplants.2019.02.011. Epub 2019 Mar 22. Review.


Appropriate Thiamin Pyrophosphate Levels Are Required for Acclimation to Changes in Photoperiod.

Rosado-Souza L, Proost S, Moulin M, Bergmann S, Bocobza SE, Aharoni A, Fitzpatrick TB, Mutwil M, Fernie AR, Obata T.

Plant Physiol. 2019 May;180(1):185-197. doi: 10.1104/pp.18.01346. Epub 2019 Mar 5.


Correction to: Transcriptomics of manually isolated Amborella trichopoda egg apparatus cells.

Flores-Tornero M, Proost S, Mutwil M, Scutt CP, Dresselhaus T, Sprunck S.

Plant Reprod. 2019 Jun;32(2):229. doi: 10.1007/s00497-019-00367-8.


Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida.

Ferrari C, Proost S, Janowski M, Becker J, Nikoloski Z, Bhattacharya D, Price D, Tohge T, Bar-Even A, Fernie A, Stitt M, Mutwil M.

Nat Commun. 2019 Feb 13;10(1):737. doi: 10.1038/s41467-019-08703-2.


Transcriptomics of manually isolated Amborella trichopoda egg apparatus cells.

Flores-Tornero M, Proost S, Mutwil M, Scutt CP, Dresselhaus T, Sprunck S.

Plant Reprod. 2019 Mar;32(1):15-27. doi: 10.1007/s00497-019-00361-0. Epub 2019 Feb 1. Erratum in: Plant Reprod. 2019 Feb 25;:.


AtRsgA from Arabidopsis thaliana is important for maturation of the small subunit of the chloroplast ribosome.

Janowski M, Zoschke R, Scharff LB, Martinez Jaime S, Ferrari C, Proost S, Ng Wei Xiong J, Omranian N, Musialak-Lange M, Nikoloski Z, Graf A, Schöttler MA, Sampathkumar A, Vaid N, Mutwil M.

Plant J. 2018 Oct;96(2):404-420. doi: 10.1111/tpj.14040. Epub 2018 Sep 8.


CoNekT: an open-source framework for comparative genomic and transcriptomic network analyses.

Proost S, Mutwil M.

Nucleic Acids Res. 2018 Jul 2;46(W1):W133-W140. doi: 10.1093/nar/gky336.


PhytoNet: comparative co-expression network analyses across phytoplankton and land plants.

Ferrari C, Proost S, Ruprecht C, Mutwil M.

Nucleic Acids Res. 2018 Jul 2;46(W1):W76-W83. doi: 10.1093/nar/gky298.


Ensemble gene function prediction database reveals genes important for complex I formation in Arabidopsis thaliana.

Hansen BO, Meyer EH, Ferrari C, Vaid N, Movahedi S, Vandepoele K, Nikoloski Z, Mutwil M.

New Phytol. 2018 Mar;217(4):1521-1534. doi: 10.1111/nph.14921. Epub 2017 Dec 4.


LSTrAP: efficiently combining RNA sequencing data into co-expression networks.

Proost S, Krawczyk A, Mutwil M.

BMC Bioinformatics. 2017 Oct 10;18(1):444. doi: 10.1186/s12859-017-1861-z.


Revisiting ancestral polyploidy in plants.

Ruprecht C, Lohaus R, Vanneste K, Mutwil M, Nikoloski Z, Van de Peer Y, Persson S.

Sci Adv. 2017 Jul 5;3(7):e1603195. doi: 10.1126/sciadv.1603195. eCollection 2017 Jul.


Expression atlas and comparative coexpression network analyses reveal important genes involved in the formation of lignified cell wall in Brachypodium distachyon.

Sibout R, Proost S, Hansen BO, Vaid N, Giorgi FM, Ho-Yue-Kuang S, Legée F, Cézart L, Bouchabké-Coussa O, Soulhat C, Provart N, Pasha A, Le Bris P, Roujol D, Hofte H, Jamet E, Lapierre C, Persson S, Mutwil M.

New Phytol. 2017 Aug;215(3):1009-1025. doi: 10.1111/nph.14635. Epub 2017 Jun 15.


Phylogenomic analysis of gene co-expression networks reveals the evolution of functional modules.

Ruprecht C, Proost S, Hernandez-Coronado M, Ortiz-Ramirez C, Lang D, Rensing SA, Becker JD, Vandepoele K, Mutwil M.

Plant J. 2017 May;90(3):447-465. doi: 10.1111/tpj.13502. Epub 2017 Mar 23.


Beyond Genomics: Studying Evolution with Gene Coexpression Networks.

Ruprecht C, Vaid N, Proost S, Persson S, Mutwil M.

Trends Plant Sci. 2017 Apr;22(4):298-307. doi: 10.1016/j.tplants.2016.12.011. Epub 2017 Jan 23. Review.


PlaNet: Comparative Co-Expression Network Analyses for Plants.

Proost S, Mutwil M.

Methods Mol Biol. 2017;1533:213-227.


Combined Use of Genome-Wide Association Data and Correlation Networks Unravels Key Regulators of Primary Metabolism in Arabidopsis thaliana.

Wu S, Alseekh S, Cuadros-Inostroza Á, Fusari CM, Mutwil M, Kooke R, Keurentjes JB, Fernie AR, Willmitzer L, Brotman Y.

PLoS Genet. 2016 Oct 19;12(10):e1006363. doi: 10.1371/journal.pgen.1006363. eCollection 2016 Oct.


Tools of the trade: studying molecular networks in plants.

Proost S, Mutwil M.

Curr Opin Plant Biol. 2016 Apr;30:143-50. doi: 10.1016/j.pbi.2016.02.010. Epub 2016 Mar 15. Review.


FamNet: A Framework to Identify Multiplied Modules Driving Pathway Expansion in Plants.

Ruprecht C, Mendrinna A, Tohge T, Sampathkumar A, Klie S, Fernie AR, Nikoloski Z, Persson S, Mutwil M.

Plant Physiol. 2016 Mar;170(3):1878-94. doi: 10.1104/pp.15.01281. Epub 2016 Jan 11.


Salt-Related MYB1 Coordinates Abscisic Acid Biosynthesis and Signaling during Salt Stress in Arabidopsis.

Wang T, Tohge T, Ivakov A, Mueller-Roeber B, Fernie AR, Mutwil M, Schippers JH, Persson S.

Plant Physiol. 2015 Oct;169(2):1027-41. doi: 10.1104/pp.15.00962. Epub 2015 Aug 4.


Elucidating gene function and function evolution through comparison of co-expression networks of plants.

Hansen BO, Vaid N, Musialak-Lange M, Janowski M, Mutwil M.

Front Plant Sci. 2014 Aug 19;5:394. doi: 10.3389/fpls.2014.00394. eCollection 2014. Review.


Towards revealing the functions of all genes in plants.

Rhee SY, Mutwil M.

Trends Plant Sci. 2014 Apr;19(4):212-21. doi: 10.1016/j.tplants.2013.10.006. Epub 2013 Nov 11. Review.


Inferring gene functions through dissection of relevance networks: interleaving the intra- and inter-species views.

Klie S, Mutwil M, Persson S, Nikoloski Z.

Mol Biosyst. 2012 Sep;8(9):2233-41. Epub 2012 Jun 29. Review.


Toward the storage metabolome: profiling the barley vacuole.

Tohge T, Ramos MS, Nunes-Nesi A, Mutwil M, Giavalisco P, Steinhauser D, Schellenberg M, Willmitzer L, Persson S, Martinoia E, Fernie AR.

Plant Physiol. 2011 Nov;157(3):1469-82. doi: 10.1104/pp.111.185710. Epub 2011 Sep 26.


Diverging functions among calreticulin isoforms in higher plants.

Thelin L, Mutwil M, Sommarin M, Persson S.

Plant Signal Behav. 2011 Jun;6(6):905-10. Epub 2011 Jun 1.


PlaNet: combined sequence and expression comparisons across plant networks derived from seven species.

Mutwil M, Klie S, Tohge T, Giorgi FM, Wilkins O, Campbell MM, Fernie AR, Usadel B, Nikoloski Z, Persson S.

Plant Cell. 2011 Mar;23(3):895-910. doi: 10.1105/tpc.111.083667. Epub 2011 Mar 25.


Large-scale co-expression approach to dissect secondary cell wall formation across plant species.

Ruprecht C, Mutwil M, Saxe F, Eder M, Nikoloski Z, Persson S.

Front Plant Sci. 2011 Jul 1;2:23. doi: 10.3389/fpls.2011.00023. eCollection 2011.


Analyzing gene coexpression data by an evolutionary model.

Schütte M, Mutwil M, Persson S, Ebenhöh O.

Genome Inform. 2010;24:154-63.


Assembly of an interactive correlation network for the Arabidopsis genome using a novel heuristic clustering algorithm.

Mutwil M, Usadel B, Schütte M, Loraine A, Ebenhöh O, Persson S.

Plant Physiol. 2010 Jan;152(1):29-43. doi: 10.1104/pp.109.145318. Epub 2009 Nov 4.


Transcriptional wiring of cell wall-related genes in Arabidopsis.

Mutwil M, Ruprecht C, Giorgi FM, Bringmann M, Usadel B, Persson S.

Mol Plant. 2009 Sep;2(5):1015-24. doi: 10.1093/mp/ssp055. Epub 2009 Jul 30.


Co-expression tools for plant biology: opportunities for hypothesis generation and caveats.

Usadel B, Obayashi T, Mutwil M, Giorgi FM, Bassel GW, Tanimoto M, Chow A, Steinhauser D, Persson S, Provart NJ.

Plant Cell Environ. 2009 Dec;32(12):1633-51. doi: 10.1111/j.1365-3040.2009.02040.x. Epub 2009 Aug 27. Review.


Laying down the bricks: logistic aspects of cell wall biosynthesis.

Geisler DA, Sampathkumar A, Mutwil M, Persson S.

Curr Opin Plant Biol. 2008 Dec;11(6):647-52. doi: 10.1016/j.pbi.2008.08.003. Epub 2008 Sep 23. Review.


Functional analysis of the cellulose synthase-like genes CSLD1, CSLD2, and CSLD4 in tip-growing Arabidopsis cells.

Bernal AJ, Yoo CM, Mutwil M, Jensen JK, Hou G, Blaukopf C, Sørensen I, Blancaflor EB, Scheller HV, Willats WG.

Plant Physiol. 2008 Nov;148(3):1238-53. doi: 10.1104/pp.108.121939. Epub 2008 Sep 3.


Cellulose synthesis: a complex complex.

Mutwil M, Debolt S, Persson S.

Curr Opin Plant Biol. 2008 Jun;11(3):252-7. doi: 10.1016/j.pbi.2008.03.007. Epub 2008 May 14. Review.


GeneCAT--novel webtools that combine BLAST and co-expression analyses.

Mutwil M, Obro J, Willats WG, Persson S.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W320-6. doi: 10.1093/nar/gkn292. Epub 2008 May 14.

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