List of 61 peer-reviewed articles and book chapters, and 4 preprints
Preprints
1. Z Xinghai, QW Tan, PK Lim, M Mutwil. Multi-omic dissection of ancestral heat stress memory responses in Brachypodium distachyon. https://www.biorxiv.org/content/10.1101/2023.03.04.531132v1
2. Lim PK, Mutwil M. LSTrAP-denovo: Automated Generation of Transcriptome Atlases for Eukaryotic Species Without Genomes. https://www.biorxiv.org/content/10.1101/2023.03.05.530358v1.abstract
3. Feng X, Zheng J, Irisarri I, Yu H, Zheng B, Ali Z, de Vries S, Keller J, Fuerst-Jansen JM, Dadras A, Zegers JMS, Rieseberg TP, Ashok AD, Darienko T, Bierenbroodspot MJ, Gramzow L, Petroll R, Haas FB, Fernandez-Pozo N, Nousias O, Li T, Fitzek E, Grayburn WS, Rittmeier N, Permann C, Ruempler F, Archibald JM, Theissen G, Mower JP, Lorenz M, Buschmann H, von Schwartzenberg K, Boston L, Hayes RD, Daum C, Barry K, Grigoriev IV, Wang X, Li FW, Rensing SA, Ben-Ari J, Keren N, Mosquna A, Holzinger A, Delaux PM, Zhang C, Huang J, Mutwil M, de Vries J, Yin Y. Chromosome-level genomes of multicellular algal sisters to land plants illuminate signaling network evolution. https://www.biorxiv.org/content/10.1101/2023.01.31.526407v1.abstract
4. Dadras A, Fuerst-Jansen JM, Darienko T, Krone D, Scholz P, Rieseberg TP, Irisarri I, Steinkamp R, Hansen M, Buschmann H, Valerius O, Braus GH, Hoecker U, Mutwil M, Ischebeck T, de Vries S, Lorenz M, de Vries J. Environmental gradients reveal stress hubs predating plant terrestrialization. https://www.biorxiv.org/content/10.1101/2022.10.17.512551v2.abstract
2023
61. Lim PK, Julca I, Mutwil M. (2023) Redesigning plant specialized metabolism with supervised machine learning using publicly available reactome data. Comput Struct Biotechnol J (IF: 7.27; Q1). 2023 Jan 18;21:1639-1650.
60. Mutwil M, Fernie AR. (2023) Ancestral genome reconstruction for studies of the green lineage. Mol Plant (IF: 13.16; Q1). 2023 Mar 5:S1674-2052(23)00067-9.
59. Tan QW, Lim PK, Chen Z, Pasha A, Provart N, Arend M, Nikoloski Z, Mutwil M. (2023) Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses. Nat Commun (IF: 14.92; Q1). 2023 Feb 22;14(1):986.
58. Julca I, Mutwil-Anderwald D, Manoj V, Khan Z, Lai SK, Yang LK, Beh IT, Dziekan J, Lim YP, Lim SK, Low YW, Lam YI, Tjia S, Mu Y, Tan QW, Nuc P, Choo LM, Khew G, Shining L, Kam A, Tam JP, Bozdech Z, Schmidt M, Usadel B, Kanagasundaram YS, Alseekh S, Fernie A, Li HY, Mutwil M. (2023) Genomic, transcriptomic, and metabolomic analysis of Oldenlandia corymbosa reveals the biosynthesis and mode of action of anti-cancer metabolites. J Integr Plant Biol (IF: 7.06; Q1). 2023 Feb 21.
57. Julca I, Tan QW, Mutwil M. (2023) Toward kingdom-wide analyses of gene expression. Trends Plant Sci (IF: 18.31; Q1). 2023 Feb;28(2):235-249.
2022
56. Ng JWX, Chua SK, Mutwil M. (2022) Feature importance network reveals novel functional relationships between biological features in Arabidopsis thaliana. Front Plant Sci (IF: 5.75; Q1). 2022 Sep 23;13:944992
55. Lim PK, Zheng X, Goh JC, Mutwil M. (2022) Exploiting plant transcriptomic databases: Resources, tools, and approaches. Plant Commun (Report missing IFs). 2022 Jul 11;3(4):100323. doi: 10.1016/j.xplc.2022.100323. Epub 2022 Apr 9.
54. Villanueva EMF, Lim PK, Lim JJJ, Lim SC, Lau PY, Koh KTS, Tan E, Kairon RS, See WA, Liao JX, Hee KM, Vijay V, Maitra I, Boon CJ, Fo K, Wang YT, Jaya R, Hew LA, Lim YY, Lee WQ, Lee ZQ, Foo H, Dos Santos AL, Mutwil M. (2022) Protist.guru: A Comparative Transcriptomics Database for Protists. J Mol Biol (IF: 5.47; Q1). 2022 Jun 15;434(11):167502.
53. Lim PK, Davey EE, Wee S, Seetoh WS, Goh JC, Zheng X, Phang SKA, Seah ESK, Ng JWZ, Wee XJH, Quek AJH, Lim JJ, Rodrigues EE, Lee H, Lim CY, Tan WZ, Dan YR, Lee B, Chee SEL, Lim ZZE, Guan JS, Tan IJL, Arong TJ, Mutwil M. (2022) Bacteria.guru: Comparative Transcriptomics and Co-Expression Database for Bacterial Pathogens. J Mol Biol (IF: 5.47; Q1). 2022 Jun 15;434(11):167380.
52. da Fonseca-Pereira P, Pham PA, Cavalcanti JHF, Omena-Garcia RP, Barros JAS, Rosado-Souza L, Vallarino JG, Mutwil M, Avin-Wittenberg T, Nunes-Nesi A, Fernie AR, Araújo WL. (2022) The Arabidopsis electron-transfer flavoprotein:ubiquinone oxidoreductase is required during normal seed development and germination. Plant J (IF: 6.42; Q1). 2022 Jan;109(1):196-214
2021
51. Julca I, Ferrari C, Flores-Tornero M, Proost S, Lindner AC, Hackenberg D, Steinbachová L, Michaelidis C, Gomes Pereira S, Misra CS, Kawashima T, Borg M, Berger F, Goldberg J, Johnson M, Honys D, Twell D, Sprunck S, Dresselhaus T, Becker JD, Mutwil M. (2021) Comparative transcriptomic analysis reveals conserved programmes underpinning organogenesis and reproduction in land plants. Nat Plants (IF: 13.26) [read article]
50. Delli Ponti R, Mutwil M (2021) Structural landscape of the complete genomes of dengue virus serotypes and other viral hemorrhagic fevers. BMC Genomics (IF: 3.97; Q2) [read article]
49. Goh W, Mutwil M (2021) LSTrAP-Kingdom: an automated pipeline to generate annotated gene expression atlases for kingdoms of life. Bioinformatics (IF: 5.61) [read article]
48. Shivhare D, Musialak‑Lange M, Julca I, Gluza P & Mutwil M (2021) Removing auto‑activators from yeast‑two‑hybrid assays by conditional negative selection. Sci. Rep. (IF=3.9) [read article]
47. Delli-Ponti R, Shivhare D, Mutwil M (2021) Using gene expression to study specialized metabolism - a practical guide. Front Plant Sci. (IF=4.4) [read article]
2020
46. Lim JJJ, Koh J, Moo JR, Villanueva EMF, Putri DA, Lim YS, Seetoh WS, Mulupuri S, Ng JWZ, Nguyen NLU, Reji R, Foo H, Zhao MX, Chan TL, Rodrigues EE, Kairon RS, Hee KM, Chee NC, Low AD, Chen ZHX, Lim SC, Lunardi V, Fong TC, Chua CX, Koh KTS, Julca I, Delli-Ponti R, Ng JWX, Mutwil M (2020) Fungi.guru: Comparative genomic and transcriptomic resource for the fungi kingdom. Comput Struct Biotechnol J (IF: 6.018) [read article]
45. Flores-Tornero M, Vogler F, Mutwil M, Potěšil D, Ihnatová I, Zdráhal Z, Sprunck S, Dresselhaus T (2020) Transcriptomic and Proteomic Insights into Amborella trichopoda Male Gametophyte Functions. Plant Physiol (IF: 6.902) [read article]
44. Hew B, Tan QW, Goh W, Ng JWX, Mutwil M (2020) LSTrAP-Crowd: prediction of novel components of bacterial ribosomes with crowd-sourced analysis of RNA sequencing data. BMC Biol (IF: 6.765) [read article]
43. Tan QW, Goh W, Mutwil M (2020) LSTrAP-Cloud: A User-Friendly Cloud Computing Pipeline to Infer Coexpression Networks. Genes (Basel). (IF=3.8) [read article]
42. Mutwil M (2020) Computational approaches to unravel the pathways and evolution of specialized metabolism. Curr Opin Plant Biol. 19;55:38-46. (IF=7.4) [read article]
41. Ferrari C, Shivhare D, Hansen BO, Pasha A, Esteban E, Provart NJ, Kragler F, Fernie AR, Tohge T, Mutwil M (2020) Expression Atlas of Selaginella moellendorffii Provides Insights into the Evolution of Vasculature, Secondary Metabolism, and Roots. Plant Cell. Jan(IF=8.6) [read article]
2019
40. Tan QW, Mutwil M (2019) Inferring biosynthetic and gene regulatory networks from Artemisia annua RNA sequencing data on a credit card-sized ARM computer. Biochim Biophys Acta Gene Regul Mech. Oct (IF=4.5) [read article]
39. Ferrari C, Mutwil M (2019) Gene expression analysis of Cyanophora paradoxa reveals conserved abiotic stress responses between basal algae and flowering plants. New Phytol. Oct(IF=7.3) [read article]
38. Ng JWX, Tan QW, Ferrari C, Mutwil M (2019) Diurnal.plant.tools: comparative transcriptomic and co-expression analyses of diurnal gene expression of the Archaeplastida kingdom. Plant Cell Physiol. Sep (IF=4.7) [read article]
37. 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 (2019) The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation. PNAS. Aug (IF=9.4) [read article]
36. Tan QW, Mutwil M (2019) Malaria.tools-comparative genomic and transcriptomic database for Plasmodium species. Nucleic Acids Res. Aug (IF=11.1) [read article]
35. 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 (2019) Analysis of an improved Cyanophora paradoxa genome assembly. DNA Res. Aug (IF=5.4) [read article]
34. Lampugnani E, Flores-Sandoval E, Tan QW, Mutwil M, Bowman JL, Persson S (2019) Cellulose Synthesis – Central Components and Their Evolutionary Relationships. Trends in Plant Sci. 2019 Mar (IF=13.1) [read article]
33. Rosado-Souza L, Proost S, Moulin M, Bergmann S, Bocobza S, Aharoni A, Fitzpatrick TB, Mutwil M, Fernie AR, Obata T (2019)
Appropriate thiamin pyrophosphate levels are required for acclimation to changes in photoperiod. Plant Physiol. 2019 Mar (IF=5.9) [read article]
32. 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 (2019) Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida. Nat Commun. 13 (IF=12.3) [read article]
31. Flores-Tornero M, Proost S, Mutwil M, Scutt CP, Dresselhaus T, Sprunck S (2019). Transcriptomics of manually isolated Amborella trichopoda egg apparatus cells. Plant Reprod. (IF=2.6) [read article]
2018
30. Janowski M, Zoschke R, Scharff L, 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 (2018). AtRsgA from Arabidopsis thaliana is important for maturation of the small subunit of the chloroplast ribosome. Plant J. 96, 404-420. (IF=5.9) [read article]
29. Proost S, Mutwil M (2018). CoNekT: an open-source framework for comparative genomic and transcriptomic network analyses. Nucleic Acids Res. 46, W133-W140. (IF=10.2) [read article]
28. Ferrari C, Proost S, Ruprecht C, Mutwil M (2018). PhytoNet: Comparative co-expression network analyses across phytoplankton and land plants. Nucleic Acids Res. 46, W76-W83 (IF=10.2) [read article]
27. Hansen BO, Meyer EH, Ferrari C, Vaid N, Movahedi S, Vandepoele K, Nikoloski Z, Mutwil M (2018). Ensemble gene function prediction database reveals genes important for complex I formation in Arabidopsis thaliana. New Phytol. 217, 1521-1534. (IF=7.7) [read article]
2017
26. Proost S, Krawczyk A, Mutwil M (2017). LSTrAP: efficiently combining RNA sequencing data into co-expression networks. BMC Bioinformatics. 18, 444. (IF=2.2) [read article]
25. 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 (2017). Expression atlas and comparative coexpression network analyses reveal important genes involved in the formation of lignified cell wall in Brachypodium distachyon. New Phytol. 215, 1009-1025. (IF=7.7) [read article]
24. Ruprecht C, Lohaus R, Vanneste K, Mutwil M, Nikoloski Z, Van de Peer Y, Persson S (2017). Revisiting ancestral polyploidy in plants. Sci Adv. 3: e1603195. (IF=11.5) [read article]
23. Ruprecht C, Proost S, Hernandez-Coronado M, Ortiz-Ramirez C, Lang D, Rensing SA, Becker JD, Vandepoele K, Mutwil M (2017). Phylogenomic analysis of gene co-expression networks reveals the evolution of functional modules. Plant J. 90, 447-465. (IF=5.9) [read article]
22. Ruprecht C, Vaid N, Proost S, Persson S, Mutwil M (2017). Beyond Genomics: Studying Evolution with Gene Coexpression Networks. Trends Plant Sci. 22, 298-307. (IF=12.2) [read article]
21. Proost S, Mutwil M (2017). PlaNet: Comparative Co-Expression Network Analyses for Plants. Methods Mol Biol. 1533, 213-227. (IF=1.2) [read article]
2008-2016
20. Wu S, Alseekh S, Cuadros-Inostroza Á, Fusari CM, Mutwil M, Kooke R, Keurentjes JB, Fernie AR, Willmitzer L, Brotman Y (2016). Combined Use of Genome-Wide Association Data and Correlation Networks Unravels Key Regulators of Primary Metabolism in Arabidopsis thaliana. PLoS Genet. 12: e1006363. doi: 10.1371/journal.pgen.1006363. (IF=5.5) [read article]
19. Proost S, Mutwil M (2016). Tools of the trade: studying molecular networks in plants. Curr Opin Plant Biol. 30, 143-150. (IF=7.4) [read article]
18. Ruprecht C, Mendrinna A, Tohge T, Sampathkumar A, Klie S, Fernie AR, Nikoloski Z, Persson S, Mutwil M (2016). FamNet: A Framework to Identify Multiplied Modules Driving Pathway Expansion in Plants. Plant Physiol. 170, 1878-94. (IF=6.3) [read article]
17. Wang T, Tohge T, Ivakov A, Mueller-Roeber B, Fernie AR, Mutwil M, Schippers JH, Persson S (2015). Salt-Related MYB1 Coordinates Abscisic Acid Biosynthesis and Signaling during Salt Stress in Arabidopsis. Plant Physiol. 169, 1027-41. (IF=6.3) [read article]
16. Hansen BO, Vaid N, Musialak-Lange M, Janowski M, Mutwil M (2014). Elucidating gene function and function evolution through comparison of co-expression networks of plants. Front Plant Sci. 5, 394. (IF=3.7) [read article]
15. Rhee SY, Mutwil M (2014). Towards revealing the functions of all genes in plants. Trends Plant Sci. 19, 212-221. (IF=12.2) [read article]
14. Harrington MJ, Mutwil M, Barrière Y, Sibout R (2012). Molecular Biology of Lignification in Grasses. Chapter in Advances in Botanical Research 61, 77-112. [read article]
13. Klie S, Mutwil M, Persson S, Nikoloski Z. (2012). Inferring gene functions through dissection of relevance networks: interleaving the intra- and inter-species views. Mol Biosyst. 8, 2233-2241. (IF=2.8) [read article]
12. Tohge T, Ramos MS, Nunes-Nesi A, Mutwil M, Giavalisco P, Steinhauser D, Schellenberg M, Willmitzer L, Persson S, Martinoia E, Fernie AR (2011). Toward the storage metabolome: profiling the barley vacuole. Plant Physiol. 157, 1469-1482. (IF=6.3) [read article]
11. Ruprecht C, Mutwil M, Saxe F, Eder M, Nikoloski Z, Persson S (2011). Large-scale co-expression approach to dissect secondary cell wall formation across plant species. Front Plant Sci. 2, 23. (IF=4.4) [read article]
10. Thelin L, Mutwil M, Sommarin M, Persson S (2011). Diverging functions among calreticulin isoforms in higher plants. Plant Signal Behav. 6, 905-910. (IF=1.1) [read article]
9. Mutwil M, Klie S, Tohge T, Giorgi FM, Wilkins O, Campbell MM, Fernie AR, Usadel B, Nikoloski Z, Persson S (2011). PlaNet: combined sequence and expression comparisons across plant networks derived from seven species. Plant Cell. 23, 895-910. (IF=8.5) [read article]
8. Schütte M, Mutwil M, Persson S, Ebenhöh O (2010). Analyzing gene coexpression data by an evolutionary model. Genome Inform. 24, 154-163. [read article]
7. Mutwil M, Usadel B, Schütte M, Loraine A, Ebenhöh O, Persson S (2010). Assembly of an interactive correlation network for the Arabidopsis genome using a novel heuristic clustering algorithm. Plant Physiol. 152, 29-43. (IF=6.3) [read article]
6. Usadel B, Obayashi T, Mutwil M, Giorgi FM, Bassel GW, Tanimoto M, Chow A, Steinhauser D, Persson S, Provart NJ (2009). Co-expression tools for plant biology: opportunities for hypothesis generation and caveats. Plant Cell Environ. 32, 1633-51. (IF=6.2) [read article]
5. Mutwil M, Ruprecht C, Giorgi FM, Bringmann M, Usadel B, Persson S (2009). Transcriptional wiring of cell wall-related genes in Arabidopsis. Mol Plant. 2, 1015-1024. (IF=9.3) [read article]
4. Geisler DA, Sampathkumar A, Mutwil M, Persson S (2008). Laying down the bricks: logistic aspects of cell wall biosynthesis. Curr Opin Plant Biol. 11, 647-652. (IF=7.4) [read article]
3. Bernal AJ, Yoo CM, Mutwil M, Jensen JK, Hou G, Blaukopf C, Sørensen I, Blancaflor EB, Scheller HV, Willats WG (2008). Functional analysis of the cellulose synthase-like genes CSLD1, CSLD2, and CSLD4 in tip-growing Arabidopsis cells. Plant Physiol. 148, 1238-1253. (IF=6.3) [read article]
2. Mutwil M, Obro J, Willats WG, Persson S (2008). GeneCAT--novel webtools that combine BLAST and co-expression analyses. Nucleic Acids Res. 36, W320–6. (IF=10.2) [read article]
1. Mutwil M, Debolt S, Persson S (2008). Cellulose synthesis: a complex complex. Curr Opin Plant Biol. 11, 252-257 (IF=7.4). [read article]
1. Z Xinghai, QW Tan, PK Lim, M Mutwil. Multi-omic dissection of ancestral heat stress memory responses in Brachypodium distachyon. https://www.biorxiv.org/content/10.1101/2023.03.04.531132v1
2. Lim PK, Mutwil M. LSTrAP-denovo: Automated Generation of Transcriptome Atlases for Eukaryotic Species Without Genomes. https://www.biorxiv.org/content/10.1101/2023.03.05.530358v1.abstract
3. Feng X, Zheng J, Irisarri I, Yu H, Zheng B, Ali Z, de Vries S, Keller J, Fuerst-Jansen JM, Dadras A, Zegers JMS, Rieseberg TP, Ashok AD, Darienko T, Bierenbroodspot MJ, Gramzow L, Petroll R, Haas FB, Fernandez-Pozo N, Nousias O, Li T, Fitzek E, Grayburn WS, Rittmeier N, Permann C, Ruempler F, Archibald JM, Theissen G, Mower JP, Lorenz M, Buschmann H, von Schwartzenberg K, Boston L, Hayes RD, Daum C, Barry K, Grigoriev IV, Wang X, Li FW, Rensing SA, Ben-Ari J, Keren N, Mosquna A, Holzinger A, Delaux PM, Zhang C, Huang J, Mutwil M, de Vries J, Yin Y. Chromosome-level genomes of multicellular algal sisters to land plants illuminate signaling network evolution. https://www.biorxiv.org/content/10.1101/2023.01.31.526407v1.abstract
4. Dadras A, Fuerst-Jansen JM, Darienko T, Krone D, Scholz P, Rieseberg TP, Irisarri I, Steinkamp R, Hansen M, Buschmann H, Valerius O, Braus GH, Hoecker U, Mutwil M, Ischebeck T, de Vries S, Lorenz M, de Vries J. Environmental gradients reveal stress hubs predating plant terrestrialization. https://www.biorxiv.org/content/10.1101/2022.10.17.512551v2.abstract
2023
61. Lim PK, Julca I, Mutwil M. (2023) Redesigning plant specialized metabolism with supervised machine learning using publicly available reactome data. Comput Struct Biotechnol J (IF: 7.27; Q1). 2023 Jan 18;21:1639-1650.
60. Mutwil M, Fernie AR. (2023) Ancestral genome reconstruction for studies of the green lineage. Mol Plant (IF: 13.16; Q1). 2023 Mar 5:S1674-2052(23)00067-9.
59. Tan QW, Lim PK, Chen Z, Pasha A, Provart N, Arend M, Nikoloski Z, Mutwil M. (2023) Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses. Nat Commun (IF: 14.92; Q1). 2023 Feb 22;14(1):986.
58. Julca I, Mutwil-Anderwald D, Manoj V, Khan Z, Lai SK, Yang LK, Beh IT, Dziekan J, Lim YP, Lim SK, Low YW, Lam YI, Tjia S, Mu Y, Tan QW, Nuc P, Choo LM, Khew G, Shining L, Kam A, Tam JP, Bozdech Z, Schmidt M, Usadel B, Kanagasundaram YS, Alseekh S, Fernie A, Li HY, Mutwil M. (2023) Genomic, transcriptomic, and metabolomic analysis of Oldenlandia corymbosa reveals the biosynthesis and mode of action of anti-cancer metabolites. J Integr Plant Biol (IF: 7.06; Q1). 2023 Feb 21.
57. Julca I, Tan QW, Mutwil M. (2023) Toward kingdom-wide analyses of gene expression. Trends Plant Sci (IF: 18.31; Q1). 2023 Feb;28(2):235-249.
2022
56. Ng JWX, Chua SK, Mutwil M. (2022) Feature importance network reveals novel functional relationships between biological features in Arabidopsis thaliana. Front Plant Sci (IF: 5.75; Q1). 2022 Sep 23;13:944992
55. Lim PK, Zheng X, Goh JC, Mutwil M. (2022) Exploiting plant transcriptomic databases: Resources, tools, and approaches. Plant Commun (Report missing IFs). 2022 Jul 11;3(4):100323. doi: 10.1016/j.xplc.2022.100323. Epub 2022 Apr 9.
54. Villanueva EMF, Lim PK, Lim JJJ, Lim SC, Lau PY, Koh KTS, Tan E, Kairon RS, See WA, Liao JX, Hee KM, Vijay V, Maitra I, Boon CJ, Fo K, Wang YT, Jaya R, Hew LA, Lim YY, Lee WQ, Lee ZQ, Foo H, Dos Santos AL, Mutwil M. (2022) Protist.guru: A Comparative Transcriptomics Database for Protists. J Mol Biol (IF: 5.47; Q1). 2022 Jun 15;434(11):167502.
53. Lim PK, Davey EE, Wee S, Seetoh WS, Goh JC, Zheng X, Phang SKA, Seah ESK, Ng JWZ, Wee XJH, Quek AJH, Lim JJ, Rodrigues EE, Lee H, Lim CY, Tan WZ, Dan YR, Lee B, Chee SEL, Lim ZZE, Guan JS, Tan IJL, Arong TJ, Mutwil M. (2022) Bacteria.guru: Comparative Transcriptomics and Co-Expression Database for Bacterial Pathogens. J Mol Biol (IF: 5.47; Q1). 2022 Jun 15;434(11):167380.
52. da Fonseca-Pereira P, Pham PA, Cavalcanti JHF, Omena-Garcia RP, Barros JAS, Rosado-Souza L, Vallarino JG, Mutwil M, Avin-Wittenberg T, Nunes-Nesi A, Fernie AR, Araújo WL. (2022) The Arabidopsis electron-transfer flavoprotein:ubiquinone oxidoreductase is required during normal seed development and germination. Plant J (IF: 6.42; Q1). 2022 Jan;109(1):196-214
2021
51. Julca I, Ferrari C, Flores-Tornero M, Proost S, Lindner AC, Hackenberg D, Steinbachová L, Michaelidis C, Gomes Pereira S, Misra CS, Kawashima T, Borg M, Berger F, Goldberg J, Johnson M, Honys D, Twell D, Sprunck S, Dresselhaus T, Becker JD, Mutwil M. (2021) Comparative transcriptomic analysis reveals conserved programmes underpinning organogenesis and reproduction in land plants. Nat Plants (IF: 13.26) [read article]
50. Delli Ponti R, Mutwil M (2021) Structural landscape of the complete genomes of dengue virus serotypes and other viral hemorrhagic fevers. BMC Genomics (IF: 3.97; Q2) [read article]
49. Goh W, Mutwil M (2021) LSTrAP-Kingdom: an automated pipeline to generate annotated gene expression atlases for kingdoms of life. Bioinformatics (IF: 5.61) [read article]
48. Shivhare D, Musialak‑Lange M, Julca I, Gluza P & Mutwil M (2021) Removing auto‑activators from yeast‑two‑hybrid assays by conditional negative selection. Sci. Rep. (IF=3.9) [read article]
47. Delli-Ponti R, Shivhare D, Mutwil M (2021) Using gene expression to study specialized metabolism - a practical guide. Front Plant Sci. (IF=4.4) [read article]
2020
46. Lim JJJ, Koh J, Moo JR, Villanueva EMF, Putri DA, Lim YS, Seetoh WS, Mulupuri S, Ng JWZ, Nguyen NLU, Reji R, Foo H, Zhao MX, Chan TL, Rodrigues EE, Kairon RS, Hee KM, Chee NC, Low AD, Chen ZHX, Lim SC, Lunardi V, Fong TC, Chua CX, Koh KTS, Julca I, Delli-Ponti R, Ng JWX, Mutwil M (2020) Fungi.guru: Comparative genomic and transcriptomic resource for the fungi kingdom. Comput Struct Biotechnol J (IF: 6.018) [read article]
45. Flores-Tornero M, Vogler F, Mutwil M, Potěšil D, Ihnatová I, Zdráhal Z, Sprunck S, Dresselhaus T (2020) Transcriptomic and Proteomic Insights into Amborella trichopoda Male Gametophyte Functions. Plant Physiol (IF: 6.902) [read article]
44. Hew B, Tan QW, Goh W, Ng JWX, Mutwil M (2020) LSTrAP-Crowd: prediction of novel components of bacterial ribosomes with crowd-sourced analysis of RNA sequencing data. BMC Biol (IF: 6.765) [read article]
43. Tan QW, Goh W, Mutwil M (2020) LSTrAP-Cloud: A User-Friendly Cloud Computing Pipeline to Infer Coexpression Networks. Genes (Basel). (IF=3.8) [read article]
42. Mutwil M (2020) Computational approaches to unravel the pathways and evolution of specialized metabolism. Curr Opin Plant Biol. 19;55:38-46. (IF=7.4) [read article]
41. Ferrari C, Shivhare D, Hansen BO, Pasha A, Esteban E, Provart NJ, Kragler F, Fernie AR, Tohge T, Mutwil M (2020) Expression Atlas of Selaginella moellendorffii Provides Insights into the Evolution of Vasculature, Secondary Metabolism, and Roots. Plant Cell. Jan(IF=8.6) [read article]
2019
40. Tan QW, Mutwil M (2019) Inferring biosynthetic and gene regulatory networks from Artemisia annua RNA sequencing data on a credit card-sized ARM computer. Biochim Biophys Acta Gene Regul Mech. Oct (IF=4.5) [read article]
39. Ferrari C, Mutwil M (2019) Gene expression analysis of Cyanophora paradoxa reveals conserved abiotic stress responses between basal algae and flowering plants. New Phytol. Oct(IF=7.3) [read article]
38. Ng JWX, Tan QW, Ferrari C, Mutwil M (2019) Diurnal.plant.tools: comparative transcriptomic and co-expression analyses of diurnal gene expression of the Archaeplastida kingdom. Plant Cell Physiol. Sep (IF=4.7) [read article]
37. 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 (2019) The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation. PNAS. Aug (IF=9.4) [read article]
36. Tan QW, Mutwil M (2019) Malaria.tools-comparative genomic and transcriptomic database for Plasmodium species. Nucleic Acids Res. Aug (IF=11.1) [read article]
35. 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 (2019) Analysis of an improved Cyanophora paradoxa genome assembly. DNA Res. Aug (IF=5.4) [read article]
34. Lampugnani E, Flores-Sandoval E, Tan QW, Mutwil M, Bowman JL, Persson S (2019) Cellulose Synthesis – Central Components and Their Evolutionary Relationships. Trends in Plant Sci. 2019 Mar (IF=13.1) [read article]
33. Rosado-Souza L, Proost S, Moulin M, Bergmann S, Bocobza S, Aharoni A, Fitzpatrick TB, Mutwil M, Fernie AR, Obata T (2019)
Appropriate thiamin pyrophosphate levels are required for acclimation to changes in photoperiod. Plant Physiol. 2019 Mar (IF=5.9) [read article]
32. 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 (2019) Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida. Nat Commun. 13 (IF=12.3) [read article]
31. Flores-Tornero M, Proost S, Mutwil M, Scutt CP, Dresselhaus T, Sprunck S (2019). Transcriptomics of manually isolated Amborella trichopoda egg apparatus cells. Plant Reprod. (IF=2.6) [read article]
2018
30. Janowski M, Zoschke R, Scharff L, 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 (2018). AtRsgA from Arabidopsis thaliana is important for maturation of the small subunit of the chloroplast ribosome. Plant J. 96, 404-420. (IF=5.9) [read article]
29. Proost S, Mutwil M (2018). CoNekT: an open-source framework for comparative genomic and transcriptomic network analyses. Nucleic Acids Res. 46, W133-W140. (IF=10.2) [read article]
28. Ferrari C, Proost S, Ruprecht C, Mutwil M (2018). PhytoNet: Comparative co-expression network analyses across phytoplankton and land plants. Nucleic Acids Res. 46, W76-W83 (IF=10.2) [read article]
27. Hansen BO, Meyer EH, Ferrari C, Vaid N, Movahedi S, Vandepoele K, Nikoloski Z, Mutwil M (2018). Ensemble gene function prediction database reveals genes important for complex I formation in Arabidopsis thaliana. New Phytol. 217, 1521-1534. (IF=7.7) [read article]
2017
26. Proost S, Krawczyk A, Mutwil M (2017). LSTrAP: efficiently combining RNA sequencing data into co-expression networks. BMC Bioinformatics. 18, 444. (IF=2.2) [read article]
25. 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 (2017). Expression atlas and comparative coexpression network analyses reveal important genes involved in the formation of lignified cell wall in Brachypodium distachyon. New Phytol. 215, 1009-1025. (IF=7.7) [read article]
24. Ruprecht C, Lohaus R, Vanneste K, Mutwil M, Nikoloski Z, Van de Peer Y, Persson S (2017). Revisiting ancestral polyploidy in plants. Sci Adv. 3: e1603195. (IF=11.5) [read article]
23. Ruprecht C, Proost S, Hernandez-Coronado M, Ortiz-Ramirez C, Lang D, Rensing SA, Becker JD, Vandepoele K, Mutwil M (2017). Phylogenomic analysis of gene co-expression networks reveals the evolution of functional modules. Plant J. 90, 447-465. (IF=5.9) [read article]
22. Ruprecht C, Vaid N, Proost S, Persson S, Mutwil M (2017). Beyond Genomics: Studying Evolution with Gene Coexpression Networks. Trends Plant Sci. 22, 298-307. (IF=12.2) [read article]
21. Proost S, Mutwil M (2017). PlaNet: Comparative Co-Expression Network Analyses for Plants. Methods Mol Biol. 1533, 213-227. (IF=1.2) [read article]
2008-2016
20. Wu S, Alseekh S, Cuadros-Inostroza Á, Fusari CM, Mutwil M, Kooke R, Keurentjes JB, Fernie AR, Willmitzer L, Brotman Y (2016). Combined Use of Genome-Wide Association Data and Correlation Networks Unravels Key Regulators of Primary Metabolism in Arabidopsis thaliana. PLoS Genet. 12: e1006363. doi: 10.1371/journal.pgen.1006363. (IF=5.5) [read article]
19. Proost S, Mutwil M (2016). Tools of the trade: studying molecular networks in plants. Curr Opin Plant Biol. 30, 143-150. (IF=7.4) [read article]
18. Ruprecht C, Mendrinna A, Tohge T, Sampathkumar A, Klie S, Fernie AR, Nikoloski Z, Persson S, Mutwil M (2016). FamNet: A Framework to Identify Multiplied Modules Driving Pathway Expansion in Plants. Plant Physiol. 170, 1878-94. (IF=6.3) [read article]
17. Wang T, Tohge T, Ivakov A, Mueller-Roeber B, Fernie AR, Mutwil M, Schippers JH, Persson S (2015). Salt-Related MYB1 Coordinates Abscisic Acid Biosynthesis and Signaling during Salt Stress in Arabidopsis. Plant Physiol. 169, 1027-41. (IF=6.3) [read article]
16. Hansen BO, Vaid N, Musialak-Lange M, Janowski M, Mutwil M (2014). Elucidating gene function and function evolution through comparison of co-expression networks of plants. Front Plant Sci. 5, 394. (IF=3.7) [read article]
15. Rhee SY, Mutwil M (2014). Towards revealing the functions of all genes in plants. Trends Plant Sci. 19, 212-221. (IF=12.2) [read article]
14. Harrington MJ, Mutwil M, Barrière Y, Sibout R (2012). Molecular Biology of Lignification in Grasses. Chapter in Advances in Botanical Research 61, 77-112. [read article]
13. Klie S, Mutwil M, Persson S, Nikoloski Z. (2012). Inferring gene functions through dissection of relevance networks: interleaving the intra- and inter-species views. Mol Biosyst. 8, 2233-2241. (IF=2.8) [read article]
12. Tohge T, Ramos MS, Nunes-Nesi A, Mutwil M, Giavalisco P, Steinhauser D, Schellenberg M, Willmitzer L, Persson S, Martinoia E, Fernie AR (2011). Toward the storage metabolome: profiling the barley vacuole. Plant Physiol. 157, 1469-1482. (IF=6.3) [read article]
11. Ruprecht C, Mutwil M, Saxe F, Eder M, Nikoloski Z, Persson S (2011). Large-scale co-expression approach to dissect secondary cell wall formation across plant species. Front Plant Sci. 2, 23. (IF=4.4) [read article]
10. Thelin L, Mutwil M, Sommarin M, Persson S (2011). Diverging functions among calreticulin isoforms in higher plants. Plant Signal Behav. 6, 905-910. (IF=1.1) [read article]
9. Mutwil M, Klie S, Tohge T, Giorgi FM, Wilkins O, Campbell MM, Fernie AR, Usadel B, Nikoloski Z, Persson S (2011). PlaNet: combined sequence and expression comparisons across plant networks derived from seven species. Plant Cell. 23, 895-910. (IF=8.5) [read article]
8. Schütte M, Mutwil M, Persson S, Ebenhöh O (2010). Analyzing gene coexpression data by an evolutionary model. Genome Inform. 24, 154-163. [read article]
7. Mutwil M, Usadel B, Schütte M, Loraine A, Ebenhöh O, Persson S (2010). Assembly of an interactive correlation network for the Arabidopsis genome using a novel heuristic clustering algorithm. Plant Physiol. 152, 29-43. (IF=6.3) [read article]
6. Usadel B, Obayashi T, Mutwil M, Giorgi FM, Bassel GW, Tanimoto M, Chow A, Steinhauser D, Persson S, Provart NJ (2009). Co-expression tools for plant biology: opportunities for hypothesis generation and caveats. Plant Cell Environ. 32, 1633-51. (IF=6.2) [read article]
5. Mutwil M, Ruprecht C, Giorgi FM, Bringmann M, Usadel B, Persson S (2009). Transcriptional wiring of cell wall-related genes in Arabidopsis. Mol Plant. 2, 1015-1024. (IF=9.3) [read article]
4. Geisler DA, Sampathkumar A, Mutwil M, Persson S (2008). Laying down the bricks: logistic aspects of cell wall biosynthesis. Curr Opin Plant Biol. 11, 647-652. (IF=7.4) [read article]
3. Bernal AJ, Yoo CM, Mutwil M, Jensen JK, Hou G, Blaukopf C, Sørensen I, Blancaflor EB, Scheller HV, Willats WG (2008). Functional analysis of the cellulose synthase-like genes CSLD1, CSLD2, and CSLD4 in tip-growing Arabidopsis cells. Plant Physiol. 148, 1238-1253. (IF=6.3) [read article]
2. Mutwil M, Obro J, Willats WG, Persson S (2008). GeneCAT--novel webtools that combine BLAST and co-expression analyses. Nucleic Acids Res. 36, W320–6. (IF=10.2) [read article]
1. Mutwil M, Debolt S, Persson S (2008). Cellulose synthesis: a complex complex. Curr Opin Plant Biol. 11, 252-257 (IF=7.4). [read article]