[My Google Scholar Profile](https://scholar.google.com/citations?user=1WY1xDwAAAAJ&hl=en&oi=ao) **93 Peer reviewed publications** Preprints (2026) *** P3\. Wissenberg P, Lee JM, Mutwil M. ORBIT: Orthogonal Rotation for Biological Inter-species Transfer. bioRxiv. 2026. doi: 10.64898/2026.05.04.722193. #bioinformatics #evolution P2\. Koh E, Peh LH, Mutwil M. Kingdom-wide comparative transcriptomics reveals deeply conserved and predictable stress response programs across Viridiplantae. bioRxiv. 2026. doi: 10.64898/2026.04.17.719161. #abiotic_stress #evolution #bioinformatics P1\. Moon J, Koh E, Sun Z, Pei W, Du S, Wang Z, Sunil RS, Tan JY, Tay JH, Tang CCK, Ho BC, Chen L, Cho NJ, Zhang Y, Mutwil M. Unravelling the processes controlling pollen formation and functions with cross-species comparative analysis. bioRxiv. 2026. doi: 10.64898/2026.02.15.705993. #evolution #bioinformatics 2026 *** 93\. Lim PK, Wang R, Lim SC, Antony Velankanni JP, Mutwil M. Constructing gene co-functional and co-regulatory networks from public transcriptomes using condition-specific ensemble co-expression. Nat Commun. 2026. doi: 10.1038/s41467-026-72380-1. PMID: 42062278. #bioinformatics 2025 *** 92\. Lim SC, Itharajula M, Møller MH, Sunil RS, Fo K, Chuah YS, Foo H, Davey EE, Fullwood M, Thibault G, Mutwil M. PlantConnectome: A knowledge graph database encompassing >71,000 plant articles. Plant Cell. 2025 Jul 1;37(7):koaf169. doi: 10.1093/plcell/koaf169. PMID: 40700523; PMCID: PMC12290883. #bioinformatics 91\. Lee JM, Goh JC, Koh E, Mutwil-Anderwald D, Mutwil M. Cross-species analysis of abiotic stress in hydroponic leafy crops reveals conserved regulatory networks and key divergences. Front Plant Sci. 2025 Jul 7;16:1613016. doi: 10.3389/fpls.2025.1613016. PMID: 40692674; PMCID: PMC12277361. #abiotic_stress #bioinformatics #evolution 90\. Ali Z, Tan QW, Lim PK, Chen H, Pfeifer L, Julca I, Lee JM, Classen B, de Vries S, de Vries J, Vinter F, Alvarado C, Layens A, Mizrachi E, Motawie MS, Joergensen B, Ulvskov P, Van de Peer Y, Ho BC, Sibout R, Mutwil M. Comparative transcriptomics in ferns reveals key innovations and divergent evolution of the secondary cell walls. Nat Plants. 2025 May;11(5):1028-1048. doi:10.1038/s41477-025-01978-y. Epub 2025 Apr 23. PMID: 40269175. #evolution #bioinformatics 89\. Zheng S, Blaschek L, Pottier D, Dijkhof LRH, Özmen B, Lim PK, Tan QW, Mutwil M, Hauser AS, Persson S. Pupylation-Based Proximity Labeling Unravels a Comprehensive Protein and Phosphoprotein Interactome of the Arabidopsis TOR Complex. Adv Sci (Weinh). 2025 May;12(19):e2414496. doi: 10.1002/advs.202414496. Epub 2025 Mar 24. PMID: 40126378; PMCID: PMC12097154. #bioinformatics 88\. Kumar MR, Arulprakasam KR, Kutevska AN, Mutwil M, Thibault G. Yeast Knowledge Graphs Database for Exploring Saccharomyces Cerevisiae and Schizosaccharomyces Pombe. J Mol Biol. 2025 May 15;437(10):169072. doi: 10.1016/j.jmb.2025.169072. Epub 2025 Mar 6. PMID: 40057225. #bioinformatics 87\. Brady S, Auge G, Ayalew M, Balasubramanian S, Hamann T, Inze D, Saito K, Brychkova G, Berardini TZ, Friesner J, Ho CH, Hauser MT, Kobayashi M, Lepiniec L, Mähönen AP, Mutwil M, May S, Parry G, Rigas S, Stepanova AN, Williams M, Provart NJ. Arabidopsis research in 2030: Translating the computable plant. Plant J. 2025 Mar;121(5):e70047. doi: 10.1111/tpj.70047. Erratum in: Plant J. 2025 May;122(4):e70221. doi: 10.1111/tpj.70221. PMID: 40028766; PMCID: PMC11874203. #bioinformatics 86\. Low PM, Kong Q, Blaschek L, Ma Z, Lim PK, Yang Y, Quek T, Lim CJR, Singh SK, Crocoll C, Engquist E, Thorsen JS, Pattanaik S, Tee WT, Mutwil M, Miao Y, Yuan L, Xu D, Persson S, Ma W. ZINC FINGER PROTEIN2 suppresses funiculus lignification to ensure seed loading efficiency in Arabidopsis. Dev Cell. 2025 Jun 23;60(12):1719-1729.e6. doi: 10.1016/j.devcel.2025.01.021. Epub 2025 Feb 24. PMID: 39999844. #bioinformatics 85\. Yang Y, Kong Q, Ma Z, Lim PK, Singh SK, Pattanaik S, Mutwil M, Miao Y, Yuan L, Ma W. Phase separation of MYB73 regulates seed oil biosynthesis in Arabidopsis. Plant Physiol. 2025 Feb 7;197(2):kiae674. doi: 10.1093/plphys/kiae674. PMID: 39704290; PMCID: PMC11803632. #bioinformatics 2024 *** 84\. Sunil RS, Lim SC, Itharajula M, Mutwil M. The gene function prediction challenge: Large language models and knowledge graphs to the rescue. Curr Opin Plant Biol. 2024 Dec;82:102665. doi: 10.1016/j.pbi.2024.102665. Epub 2024 Nov 22. PMID: 39579414. #bioinformatics 83\. Arulprakasam KR, Toh JWS, Foo H, Kumar MR, Kutevska AN, Davey EE, Mutwil M, Thibault G. Harnessing full-text publications for deep insights into C. elegans and Drosophila biomaps. BMC Genomics. 2024 Nov 13;25(1):1080. doi: 10.1186/s12864-024-10997-6. PMID: 39538127; PMCID: PMC11562368. #bioinformatics 82\. Lázaro-Gimeno D, Ferrari C, Delhomme N, Johansson M, Sjölander J, Singh RK, Mutwil M, Eriksson ME. The circadian clock participates in seasonal growth in Norway spruce (Picea abies). Tree Physiol. 2024 Nov 5;44(11):tpae139. doi: 10.1093/treephys/tpae139. PMID: 39488796; PMCID: PMC11586665. #bioinformatics #abiotic_stress 81\. Koh E, Sunil RS, Lam HYI, Mutwil M. Confronting the data deluge: How artificial intelligence can be used in the study of plant stress. Comput Struct Biotechnol J. 2024 Sep 17;23:3454-3466. doi: 10.1016/j.csbj.2024.09.010. PMID: 39415960; PMCID: PMC11480249. #bioinformatics 80\. Brattig-Correia R, Almeida JM, Wyrwoll MJ, Julca I, Sobral D, Misra CS, Di Persio S, Guilgur LG, Schuppe HC, Silva N, Prudêncio P, Nóvoa A, Leocádio AS, Bom J, Laurentino S, Mallo M, Kliesch S, Mutwil M, Rocha LM, Tüttelmann F, Becker JD, Navarro-Costa P. The conserved genetic program of male germ cells uncovers ancient regulators of human spermatogenesis. Elife. 2024 Oct 10;13:RP95774. doi: 10.7554/eLife.95774. PMID: 39388236; PMCID: PMC11466473. #bioinformatics #evolution 79\. Agatha O, Mutwil-Anderwald D, Tan JY, Mutwil M. Plant sesquiterpene lactones. Philos Trans R Soc Lond B Biol Sci. 2024 Nov 18;379(1914):20230350. doi: 10.1098/rstb.2023.0350. Epub 2024 Sep 30. PMID: 39343024; PMCID: PMC11449222. #specialized_metabolism 78\. Zhang Y, Chen K, Tang SC, Cai Y, Nambu A, See YX, Fu C, Raju A, Lebeau B, Ling Z, Chan JJ, Tay Y, Mutwil M, Lakshmanan M, Tucker-Kellogg G, Chng WJ, Tenen DG, Osato M, Tergaonkar V, Fullwood MJ. Super-silencer perturbation by EZH2 and REST inhibition leads to large loss of chromatin interactions and reduction in cancer growth. Nat Struct Mol Biol. 2025 Jan;32(1):137-149. doi: 10.1038/s41594-024-01391-7. Epub 2024 Sep 20. PMID: 39304765; PMCID: PMC11746141. #bioinformatics 77\. Auge G, Sunil RS, Ingle RA, Rahul PV, Mutwil M, Estevez JM. Current challenges for plant biology research in the Global South. New Phytol. 2024 Nov;244(4):1168-1174. doi: 10.1111/nph.20083. Epub 2024 Sep 15. PMID: 39278888. #bioinformatics 76\. Tan QW, Tan E, Mutwil M. [Diurnal.plant.tools in 2024: expanding to Marchantia polymorpha and four angiosperms.](https://pubmed.ncbi.nlm.nih.gov/39219534/)Plant Cell Physiol (IF: 4.93; **Q2**). 2024 Sep 2:pcae099. doi: 10.1093/pcp/pcae099 #evolution #bioinformatics 75\. Zheng X, Ali ZM, Lim PK, Mutwil M, Wang Y. Comparative transcriptome database for Camellia sinensis reveals genes related to the cold sensitivity and albino mechanism of 'Anji Baicha'. Physiol Plant. 2024 Jul-Aug;176(4):e14474. doi: 10.1111/ppl.14474. PMID: 39139072. #abiotic_stress #specialized_metabolism 74\. Lim PK, Wang R, Mutwil M. LSTrAP-denovo: Automated Generation of Transcriptome Atlases for Eukaryotic Species Without Genomes. Physiol Plant. 2024 Jul-Aug;176(4):e14407. doi: 10.1111/ppl.14407. PMID: 38973613. #bioinformatics #evolution 73\. Lam HYI, Ong XE, Mutwil M. Large language models in plant biology. Trends Plant Sci. 2024 May 25:S1360-1385(24)00118-3. doi: 10.1016/j.tplants.2024.04.013. Epub ahead of print. PMID: 38797656. #bioinformatics 72\. Zheng X, Lim PK, Mutwil M, Wang Y. A method for mining condition-specific co- expressed genes in Camellia sinensis based on k-means clustering. BMC Plant Biol. 2024 May 8;24(1):373. doi: 10.1186/s12870-024-05086-5. PMID: 38714965; PMCID: PMC11077725. #bioinformatics 71\. Feng X, Zheng J, Irisarri I, Yu H, Zheng B, Ali Z, de Vries S, Keller J, Fürst-Jansen JMR, Dadras A, Zegers JMS, Rieseberg TP, Dhabalia Ashok A, 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, Rümpler 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. Genomes of multicellular algal sisters to land plants illuminate signaling network evolution. Nat Genet. 2024 May;56(5):1018-1031. doi: 10.1038/s41588-024-01737-3. Epub 2024 May 1. PMID: 38693345; PMCID: PMC11096116. #evolution #bioinformatics 70\. Koh E, Goh W, Julca I, Villanueva E, Mutwil M. PEO: Plant Expression Omnibus - a comparative transcriptomic database for 103 Archaeplastida. Plant J. 2024 Mar;117(5):1592-1603. doi: 10.1111/tpj.16566. Epub 2023 Dec 4. PMID: 38050352. #evolution #bioinformatics 69\. Lopez LE, Chuah YS, Encina F, Carignani Sardoy M, Berdion Gabarain V, Mutwil M, Estevez JM. New molecular components that regulate the transcriptional hub in root hairs: coupling environmental signals with endogenous hormones to coordinate growth. J Exp Bot. 2024 Jul 23;75(14):4171-4179. doi: 10.1093/jxb/erad419. PMID: 37875460. #plant_physiology 2023 *** 68\. Siau A, Ang JW, Sheriff O, Hoo R, Loh HP, Tay D, Huang X, Yam XY, Lai SK, Meng W, Julca I, Kwan SS, Mutwil M, Preiser PR. Comparative spatial proteomics of Plasmodium-infected erythrocytes. Cell Rep. 2023 Nov 28;42(11):113419. doi: 10.1016/j.celrep.2023.113419. Epub 2023 Nov 11. PMID: 37952150. #molecular_biology 67\. Poh WH, Ruhazat NS, Yang LK, Shivhare D, Lim PK, Kanagasundaram Y, Rice SA, Mutwil M. Transcriptomic and metabolomic characterization of antibacterial activity of <i>Melastoma dodecandrum</i>. Front Plant Sci. 2023 Sep 13;14:1205725. doi: 10.3389/fpls.2023.1205725. PMID: 37771487; PMCID: PMC10525717. #specialized_metabolism #bioinformatics 66\. Dadras A, Fürst-Jansen JMR, Darienko T, Krone D, Scholz P, Sun S, Herrfurth C, Rieseberg TP, Irisarri I, Steinkamp R, Hansen M, Buschmann H, Valerius O, Braus GH, Hoecker U, Feussner I, Mutwil M, Ischebeck T, de Vries S, Lorenz M, de Vries J. Environmental gradients reveal stress hubs pre-dating plant terrestrialization. Nat Plants. 2023 Sep;9(9):1419-1438. doi: 10.1038/s41477-023-01491-0. Epub 2023 Aug 28. PMID: 37640935; PMCID: PMC10505561. #evolution #bioinformatics 65\. Chan ME, Tan JY, Lee YY, Lee D, Fong YK, Mutwil M, Wong JY, Hong Y. Locally Isolated <i>Trichoderma harzianum</i> Species Have Broad Spectrum Biocontrol Activities against the Wood Rot Fungal Species through Both Volatile Inhibition and Mycoparasitism. J Fungi (Basel). 2023 Jun 15;9(6):675. doi: 10.3390/jof9060675. PMID: 37367611; PMCID: PMC10301622. 64\. Tan JY, Zhang Z, Izzah HJ, Fong YK, Lee D, Mutwil M, Hong Y. Volatile-Based Diagnosis for Pathogenic Wood-Rot Fungus <i>Fulvifomes siamensis</i> by Electronic Nose (E-Nose) and Solid-Phase Microextraction/Gas Chromatography/Mass Spectrometry. Sensors (Basel). 2023 May 6;23(9):4538. doi: 10.3390/s23094538. PMID: 37177742; PMCID: PMC10181603. 63.\ Hong Y, Tan JY, Xue H, Chow ML, Ali M, Ng A, Leong A, Yeo J, Koh SM, Tang MSY, Lee YY, Choong AMF, Lee SML, Delli Ponti R, Chan PM, Lee D, Wong JY, Mutwil M, Fong YK. A Metagenomic Survey of Wood Decay Fungi in the Urban Trees of Singapore. J Fungi (Basel). 2023 Apr 10;9(4):460. doi: 10.3390/jof9040460. PMID: 37108914; PMCID: PMC10145048. 62\. Lim PK, Julca I, Mutwil M. Redesigning plant specialized metabolism with supervised machine learning using publicly available reactome data. Comput Struct Biotechnol J. 2023 Jan 18;21:1639-1650. doi: 10.1016/j.csbj.2023.01.013. PMID: 36874159; PMCID: PMC9976193. #bioinformatics 61\. Mutwil M, Fernie AR. Ancestral genome reconstruction for studies of the green lineage. Mol Plant. 2023 Apr 3;16(4):657-659. doi: 10.1016/j.molp.2023.03.003. Epub 2023 Mar 5. PMID: 36871157. #bioinformatics #evolution 60\. Tan QW, Lim PK, Chen Z, Pasha A, Provart N, Arend M, Nikoloski Z, Mutwil M. Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses. Nat Commun. 2023 Feb 22;14(1):986. doi: 10.1038/s41467-023-36517-w. PMID: 36813788; PMCID: PMC9946954. #abiotic_stress #bioinformatics #evolution 59\. 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 Y, Alseekh S, Fernie A, Li HY, Mutwil M. Genomic, transcriptomic, and metabolomic analysis of Oldenlandia corymbosa reveals the biosynthesis and mode of action of anti-cancer metabolites. J Integr Plant Biol. 2023 Jun;65(6):1442-1466. doi: 10.1111/jipb.13469. Epub 2023 Apr 4. PMID: 36807520. #abiotic_stress #specialized_metabolism #bioinformatics 58\. Feng X, Zheng J, Irisarri I, Yu H, Zheng B, Ali Z, de Vries S, Keller J, Fürst-Jansen JMR, 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, Rümpler 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, Ari JB, 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. Nat Genet. 2024 May;56(5):1018-1031. doi: 10.1038/s41588-024-01737-3. PMID: 36778228; PMCID: PMC9915684. #evolution #bioinformatics #evolution 57\. Julca I, Tan QW, Mutwil M. Toward kingdom-wide analyses of gene expression. Trends Plant Sci. 2023 Feb;28(2):235-249. doi: 10.1016/j.tplants.2022.09.007. Epub 2022 Nov 4. PMID: 36344371. #bioinformatics #evolution 2022 *** 56\. Ng JWX, Chua SK, Mutwil M. Feature importance network reveals novel functional relationships between biological features in <i>Arabidopsis thaliana</i>. Front Plant Sci. 2022 Sep 23;13:944992. doi: 10.3389/fpls.2022.944992. PMID: 36212273; PMCID: PMC9539877. #bioinformatics 55\. Lim PK, Zheng X, Goh JC, Mutwil M. Exploiting plant transcriptomic databases: Resources, tools, and approaches. Plant Commun. 2022 Jul 11;3(4):100323. doi: 10.1016/j.xplc.2022.100323. Epub 2022 Apr 9. PMID: 35605200; PMCID: PMC9284291. #bioinformatics 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. Protist.guru: A Comparative Transcriptomics Database for Protists. J Mol Biol. 2022 Jun 15;434(11):167502. doi: 10.1016/j.jmb.2022.167502. Epub 2022 Feb 18. PMID: 35389344. #bioinformatics 53\. Lim PK, Davey EE, Wee S, Seetoh WS, Goh JC, Zheng X, Phang SKA, Seah ESK, Ng WZ, 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. Bacteria.guru: Comparative Transcriptomics and Co-Expression Database for Bacterial Pathogens. J Mol Biol. 2022 Jun 15;434(11):167380. doi: 10.1016/j.jmb.2021.167380. Epub 2021 Nov 25. PMID: 34838806. #bioinformatics 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. The Arabidopsis electron-transfer flavoprotein:ubiquinone oxidoreductase is required during normal seed development and germination. Plant J. 2022 Jan;109(1):196-214. doi: 10.1111/tpj.15566. Epub 2021 Nov 22. PMID: 34741366. 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. Comparative transcriptomic analysis reveals conserved programmes underpinning organogenesis and reproduction in land plants. Nat Plants. 2021 Aug;7(8):1143-1159. doi: 10.1038/s41477-021-00958-2. Epub 2021 Jul PMID: 34253868. #evolution #bioinformatics 50\. Delli Ponti R, Mutwil M. Structural landscape of the complete genomes of dengue virus serotypes and other viral hemorrhagic fevers. BMC Genomics. 2021 May 17;22(1):352. doi: 10.1186/s12864-021-07638-7. PMID: 34000991; PMCID: PMC8127238. #bioinformatics 49\. Shivhare D, Musialak-Lange M, Julca I, Gluza P, Mutwil M. Removing auto- activators from yeast-two-hybrid assays by conditional negative selection. Sci Rep. 2021 Mar 9;11(1):5477. doi: 10.1038/s41598-021-84608-9. PMID: 33750818; PMCID: PMC7943551. #molecular_biology 48\. Goh W, Mutwil M. LSTrAP-Kingdom: an automated pipeline to generate annotated gene expression atlases for kingdoms of life. Bioinformatics. 2021 Sep 29;37(18):3053-3055. doi: 10.1093/bioinformatics/btab168. PMID: 33704421. #bioinformatics 47\. Delli-Ponti R, Shivhare D, Mutwil M. Using Gene Expression to Study Specialized Metabolism-A Practical Guide. Front Plant Sci. 2021 Jan 12;11:625035. doi: 10.3389/fpls.2020.625035. PMID: 33510763; PMCID: PMC7835209. #specialized_metabolism #bioinformatics 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. Fungi.guru: Comparative genomic and transcriptomic resource for the fungi kingdom. Comput Struct Biotechnol J. 2020 Nov 20;18:3788-3795. doi: 10.1016/j.csbj.2020.11.019. PMID: 33304470; PMCID: PMC7718472. #bioinformatics 45\. Flores-Tornero M, Vogler F, Mutwil M, Potěšil D, Ihnatová I, Zdráhal Z, Sprunck S, Dresselhaus T. Transcriptomic and Proteomic Insights into <i>Amborella trichopoda</i> Male Gametophyte Functions. Plant Physiol. 2020 Dec;184(4):1640-1657. doi: 10.1104/pp.20.00837. Epub 2020 Sep 28. PMID: 32989009; PMCID: PMC7723084. #molecular_biology 44\. Hew B, Tan QW, Goh W, Ng JWX, Mutwil M. LSTrAP-Crowd: prediction of novel components of bacterial ribosomes with crowd-sourced analysis of RNA sequencing data. BMC Biol. 2020 Sep 3;18(1):114. doi: 10.1186/s12915-020-00846-9. PMID: 32883264; PMCID: PMC7470450. #bioinformatics 43\. Tan QW, Goh W, Mutwil M. LSTrAP-Cloud: A User-Friendly Cloud Computing Pipeline to Infer Coexpression Networks. Genes (Basel). 2020 Apr 16;11(4):428. doi: 10.3390/genes11040428. PMID: 32316247; PMCID: PMC7230309. #bioinformatics 42\. Mutwil M. Computational approaches to unravel the pathways and evolution of specialized metabolism. Curr Opin Plant Biol. 2020 Jun;55:38-46. doi: 10.1016/j.pbi.2020.01.007. Epub 2020 Mar 19. PMID: 32200228. #specialized_metabolism #bioinformatics 41\. Ferrari C, Shivhare D, Hansen BO, Pasha A, Esteban E, Provart NJ, Kragler F, Fernie A, Tohge T, Mutwil M. Expression Atlas of <i>Selaginella moellendorffii</i> Provides Insights into the Evolution of Vasculature, Secondary Metabolism, and Roots. Plant Cell. 2020 Apr;32(4):853-870. doi: 10.1105/tpc.19.00780. Epub 2020 Jan 27. PMID: 31988262; PMCID: PMC7145505. #bioinformatics #evolution #specialized_metabolism 40\. Tan QW, Mutwil M. 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. 2020 Jun;1863(6):194429. doi: 10.1016/j.bbagrm.2019.194429. Epub 2019 Oct 18. PMID: 31634636. #bioinformatics 39\. Ferrari C, Mutwil M. Gene expression analysis of Cyanophora paradoxa reveals conserved abiotic stress responses between basal algae and flowering plants. New Phytol. 2020 Feb;225(4):1562-1577. doi: 10.1111/nph.16257. Epub 2019 Nov 11. PMID: 31602652. #bioinformatics #abiotic_stress #evolution 38\. Ng JWX, Tan QW, Ferrari C, Mutwil M. Diurnal.plant.tools: Comparative Transcriptomic and Co-expression Analyses of Diurnal Gene Expression of the Archaeplastida Kingdom. Plant Cell Physiol. 2020 Jan 1;61(1):212-220. doi: 10.1093/pcp/pcz176. PMID: 31501868. #evolution #bioinformatics #abiotic_stress 2019 *** 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. The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation. Proc Natl Acad Sci U S A. 2019 Aug 20;116(34):17081-17089. doi: 10.1073/pnas.1822129116. Epub 2019 Aug 6. PMID: 31387975; PMCID: PMC6708331. #abiotic_stress 36\. Tan QW, Mutwil M. Malaria.tools-comparative genomic and transcriptomic database for Plasmodium species. Nucleic Acids Res. 2020 Jan 8;48(D1):D768-D775. doi: 10.1093/nar/gkz662. PMID: 31372645; PMCID: PMC6943069. 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. Analysis of an improved Cyanophora paradoxa genome assembly. DNA Res. 2019 Aug 1;26(4):287-299. doi: 10.1093/dnares/dsz009. PMID: 31098614; PMCID: PMC6704402. 34\. Lampugnani ER, Flores-Sandoval E, Tan QW, Mutwil M, Bowman JL, Persson S. Cellulose Synthesis - Central Components and Their Evolutionary Relationships. Trends Plant Sci. 2019 May;24(5):402-412. doi: 10.1016/j.tplants.2019.02.011. Epub 2019 Mar 22. PMID: 30905522. 33\. Rosado-Souza L, Proost S, Moulin M, Bergmann S, Bocobza SE, Aharoni A, Fitzpatrick TB, Mutwil M, Fernie AR, Obata T. Appropriate Thiamin Pyrophosphate Levels Are Required for Acclimation to Changes in Photoperiod. Plant Physiol. 2019 May;180(1):185-197. doi: 10.1104/pp.18.01346. Epub 2019 Mar 5. PMID: 30837347; PMCID: PMC6501078. 32\. Flores-Tornero M, Proost S, Mutwil M, Scutt CP, Dresselhaus T, Sprunck S. Correction to: Transcriptomics of manually isolated Amborella trichopoda egg apparatus cells. Plant Reprod. 2019 Jun;32(2):229. doi: 10.1007/s00497-019-00367-8. Erratum for: Plant Reprod. 2019 Mar;32(1):15-27. doi: 10.1007/s00497-019-00361-0. PMID: 30805714; PMCID: PMC6500505. 31\. 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. Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida. Nat Commun. 2019 Feb 13;10(1):737. doi: 10.1038/s41467-019-08703-2. PMID: 30760717; PMCID: PMC6374488. 30\. Flores-Tornero M, Proost S, Mutwil M, Scutt CP, Dresselhaus T, Sprunck S. Transcriptomics of manually isolated Amborella trichopoda egg apparatus cells. Plant Reprod. 2019 Mar;32(1):15-27. doi: 10.1007/s00497-019-00361-0. Epub 2019 Feb 1. Erratum in: Plant Reprod. 2019 Jun;32(2):229. doi: 10.1007/s00497-019-00367-8. PMID: 30707279. 2018 *** 29\. 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. AtRsgA from Arabidopsis thaliana is important for maturation of the small subunit of the chloroplast ribosome. Plant J. 2018 Oct;96(2):404-420. doi: 10.1111/tpj.14040. Epub 2018 Sep 8. PMID: 30044525. 28\. Proost S, Mutwil M. CoNekT: an open-source framework for comparative genomic and transcriptomic network analyses. Nucleic Acids Res. 2018 Jul 2;46(W1):W133-W140. doi: 10.1093/nar/gky336. PMID: 29718322; PMCID: PMC6030989. 27\. Ferrari C, Proost S, Ruprecht C, Mutwil M. PhytoNet: comparative co-expression network analyses across phytoplankton and land plants. Nucleic Acids Res. 2018 Jul 2;46(W1):W76-W83. doi: 10.1093/nar/gky298. PMID: 29718316; PMCID: PMC6030924. 26\. Hansen BO, Meyer EH, Ferrari C, Vaid N, Movahedi S, Vandepoele K, Nikoloski Z, Mutwil M. Ensemble gene function prediction database reveals genes important for complex I formation in Arabidopsis thaliana. New Phytol. 2018 Mar;217(4):1521-1534. doi: 10.1111/nph.14921. Epub 2017 Dec 4. PMID: 29205376. 2017 *** 25\. Proost S, Krawczyk A, Mutwil M. LSTrAP: efficiently combining RNA sequencing data into co-expression networks. BMC Bioinformatics. 2017 Oct 10;18(1):444. doi: 10.1186/s12859-017-1861-z. PMID: 29017446; PMCID: PMC5634843. 24\. Ruprecht C, Lohaus R, Vanneste K, Mutwil M, Nikoloski Z, Van de Peer Y, Persson S. Revisiting ancestral polyploidy in plants. Sci Adv. 2017 Jul 5;3(7):e1603195. doi: 10.1126/sciadv.1603195. PMID: 28695205; PMCID: PMC5498109. 23\. 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. Expression atlas and comparative coexpression network analyses reveal important genes involved in the formation of lignified cell wall in Brachypodium distachyon. New Phytol. 2017 Aug;215(3):1009-1025. doi: 10.1111/nph.14635. Epub 2017 Jun 15. PMID: 28617955. 22\. Ruprecht C, Proost S, Hernandez-Coronado M, Ortiz-Ramirez C, Lang D, RensingSA, Becker JD, Vandepoele K, Mutwil M. Phylogenomic analysis of gene co-expression networks reveals the evolution of functional modules. Plant J. 2017 May;90(3):447-465. doi: 10.1111/tpj.13502. Epub 2017 Mar 23. PMID: 28161902. 21\. Ruprecht C, Vaid N, Proost S, Persson S, Mutwil M. Beyond Genomics: StudyingEvolution with Gene Coexpression Networks. Trends Plant Sci. 2017Apr;22(4):298-307. doi: 10.1016/j.tplants.2016.12.011. Epub 2017 Jan 23. PMID:28126286. 20\. Proost S, Mutwil M. PlaNet: Comparative Co-Expression Network Analyses for Plants. Methods Mol Biol. 2017;1533:213-227. doi: 10.1007/978-1-4939-6658-5_12.PMID: 27987173. 2016 *** 19\. Wu S, Alseekh S, Cuadros-Inostroza Á, Fusari CM, Mutwil M, Kooke R, Keurentjes JB, Fernie AR, Willmitzer L, Brotman Y. Combined Use of Genome-WideAssociation Data and Correlation Networks Unravels Key Regulators of PrimaryMetabolism in Arabidopsis thaliana. PLoS Genet. 2016 Oct 19;12(10):e1006363. doi: 10.1371/journal.pgen.1006363. PMID: 27760136; PMCID: PMC5070769. 18\. Proost S, Mutwil M. Tools of the trade: studying molecular networks inplants. Curr Opin Plant Biol. 2016 Apr;30:143-50. doi:10.1016/j.pbi.2016.02.010. Epub 2016 Mar 15. PMID: 26990519. 17\. Ruprecht C, Mendrinna A, Tohge T, Sampathkumar A, Klie S, Fernie AR,Nikoloski Z, Persson S, Mutwil M. FamNet: A Framework to Identify MultipliedModules Driving Pathway Expansion in Plants. Plant Physiol. 2016Mar;170(3):1878-94. doi: 10.1104/pp.15.01281. Epub 2016 Jan 11. PMID: 26754669;PMCID: PMC4775111. 2008-2015 *** 16\. Wang T, Tohge T, Ivakov A, Mueller-Roeber B, Fernie AR, Mutwil M, SchippersJH, Persson S. Salt-Related MYB1 Coordinates Abscisic Acid Biosynthesis andSignaling during Salt Stress in Arabidopsis. Plant Physiol. 2015Oct;169(2):1027-41. doi: 10.1104/pp.15.00962. Epub 2015 Aug 4. PMID: 26243618; PMCID: PMC4587467. 15\. Hansen BO, Vaid N, Musialak-Lange M, Janowski M, Mutwil M. Elucidating genefunction and function evolution through comparison of co-expression networks ofplants. Front Plant Sci. 2014 Aug 19;5:394. doi: 10.3389/fpls.2014.00394. PMID:25191328; PMCID: PMC4137175. 14\. Rhee SY, Mutwil M. Towards revealing the functions of all genes in plants.Trends Plant Sci. 2014 Apr;19(4):212-21. doi: 10.1016/j.tplants.2013.10.006.Epub 2013 Nov 11. PMID: 24231067. 13\. Klie S, Mutwil M, Persson S, Nikoloski Z. Inferring gene functions throughdissection of relevance networks: interleaving the intra- and inter-speciesviews. Mol Biosyst. 2012 Sep;8(9):2233-41. doi: 10.1039/c2mb25089f. Epub 2012Jun 29. PMID: 22744313. 12\. Tohge T, Ramos MS, Nunes-Nesi A, Mutwil M, Giavalisco P, Steinhauser D,Schellenberg M, Willmitzer L, Persson S, Martinoia E, Fernie AR. Toward thestorage metabolome: profiling the barley vacuole. Plant Physiol. 2011Nov;157(3):1469-82. doi: 10.1104/pp.111.185710. Epub 2011 Sep 26. PMID:21949213; PMCID: PMC3252150. 11\. Thelin L, Mutwil M, Sommarin M, Persson S. Diverging functions amongcalreticulin isoforms in higher plants. Plant Signal Behav. 2011Jun;6(6):905-10. doi: 10.4161/psb.6.6.15339. Epub 2011 Jun 1. PMID: 21586899;PMCID: PMC3218502. 10\. Mutwil M, Klie S, Tohge T, Giorgi FM, Wilkins O, Campbell MM, Fernie AR,Usadel B, Nikoloski Z, Persson S. PlaNet: combined sequence and expressioncomparisons across plant networks derived from seven species. Plant Cell. 2011Mar;23(3):895-910. doi: 10.1105/tpc.111.083667. Epub 2011 Mar 25. PMID:21441431; PMCID: PMC3082271. 9\. Ruprecht C, Mutwil M, Saxe F, Eder M, Nikoloski Z, Persson S. Large-scaleco-expression approach to dissect secondary cell wall formation across plantspecies. Front Plant Sci. 2011 Jul 1;2:23. doi: 10.3389/fpls.2011.00023. PMID:22639584; PMCID: PMC3355677. 8\. Schütte M, Mutwil M, Persson S, Ebenhöh O. Analyzing gene coexpression databy an evolutionary model. Genome Inform. 2010;24:154-63. PMID: 22081597. 7\. Mutwil M, Usadel B, Schütte M, Loraine A, Ebenhöh O, Persson S. Assembly ofan interactive correlation network for the Arabidopsis genome using a novelheuristic clustering algorithm. Plant Physiol. 2010 Jan;152(1):29-43. doi:10.1104/pp.109.145318. Epub 2009 Nov 4. PMID: 19889879; PMCID: PMC2799344. 6\. Mutwil M, Ruprecht C, Giorgi FM, Bringmann M, Usadel B, Persson S.Transcriptional wiring of cell wall-related genes in Arabidopsis. Mol Plant.2009 Sep;2(5):1015-24. doi: 10.1093/mp/ssp055. Epub 2009 Jul 30. PMID: 19825676. 5\. Usadel B, Obayashi T, Mutwil M, Giorgi FM, Bassel GW, Tanimoto M, Chow A,Steinhauser D, Persson S, Provart NJ. Co-expression tools for plant biology:opportunities for hypothesis generation and caveats. Plant Cell Environ. 2009Dec;32(12):1633-51. doi: 10.1111/j.1365-3040.2009.02040.x. Epub 2009 Aug 27.PMID: 19712066. 4\. Geisler DA, Sampathkumar A, Mutwil M, Persson S. Laying down the bricks: logistic aspects of cell wall biosynthesis. Curr Opin Plant Biol. 2008Dec;11(6):647-52. doi: 10.1016/j.pbi.2008.08.003. Epub 2008 Sep 23. PMID:18818118. 3\. Bernal AJ, Yoo CM, Mutwil M, Jensen JK, Hou G, Blaukopf C, Sørensen I, Blancaflor EB, Scheller HV, Willats WG. Functional analysis of the cellulose synthase-like genes CSLD1, CSLD2, and CSLD4 in tip-growing Arabidopsis cells. Plant Physiol. 2008 Nov;148(3):1238-53. doi: 10.1104/pp.108.121939. Epub 2008Sep 3. PMID: 18768911; PMCID: PMC2577265. 2\. Mutwil M, Debolt S, Persson S. Cellulose synthesis: a complex complex. CurrOpin Plant Biol. 2008 Jun;11(3):252-7. doi: 10.1016/j.pbi.2008.03.007. Epub 2008 May 14. PMID: 18485800. 1\. Mutwil M, Obro J, Willats WG, Persson S. GeneCAT--novel webtools thatcombine BLAST and co-expression analyses. Nucleic Acids Res. 2008 Jul 1;36(WebServer issue):W320-6. doi: 10.1093/nar/gkn292. Epub 2008 May 14. PMID: 18480120; PMCID: PMC2447783.