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METACLUSTER-an R package for context-specific expression analysis of metabolic gene clusters.
Banf M, Zhao K, Rhee SY. Banf M, et al. Bioinformatics. 2019 Sep 1;35(17):3178-3180. doi: 10.1093/bioinformatics/btz021. Bioinformatics. 2019. PMID: 30657869 Free PMC article.
Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants.
Schläpfer P, Zhang P, Wang C, Kim T, Banf M, Chae L, Dreher K, Chavali AK, Nilo-Poyanco R, Bernard T, Kahn D, Rhee SY. Schläpfer P, et al. Among authors: banf m. Plant Physiol. 2017 Apr;173(4):2041-2059. doi: 10.1104/pp.16.01942. Epub 2017 Feb 22. Plant Physiol. 2017. PMID: 28228535 Free PMC article.
Genomic diversity of a nectar yeast clusters into metabolically, but not geographically, distinct lineages.
Dhami MK, Hartwig T, Letten AD, Banf M, Fukami T. Dhami MK, et al. Among authors: banf m. Mol Ecol. 2018 Apr;27(8):2067-2076. doi: 10.1111/mec.14535. Epub 2018 Mar 23. Mol Ecol. 2018. PMID: 29446179
Enhancing gene regulatory network inference through data integration with markov random fields.
Banf M, Rhee SY. Banf M, et al. Sci Rep. 2017 Feb 1;7:41174. doi: 10.1038/srep41174. Sci Rep. 2017. PMID: 28145456 Free PMC article.
Computational inference of gene regulatory networks: Approaches, limitations and opportunities.
Banf M, Rhee SY. Banf M, et al. Biochim Biophys Acta Gene Regul Mech. 2017 Jan;1860(1):41-52. doi: 10.1016/j.bbagrm.2016.09.003. Epub 2016 Sep 16. Biochim Biophys Acta Gene Regul Mech. 2017. PMID: 27641093 Review.
microProtein Prediction Program (miP3): A Software for Predicting microProteins and Their Target Transcription Factors.
de Klein N, Magnani E, Banf M, Rhee SY. de Klein N, et al. Among authors: banf m. Int J Genomics. 2015;2015:734147. doi: 10.1155/2015/734147. Epub 2015 Apr 28. Int J Genomics. 2015. PMID: 26060811 Free PMC article.
iTAK: A Program for Genome-wide Prediction and Classification of Plant Transcription Factors, Transcriptional Regulators, and Protein Kinases.
Zheng Y, Jiao C, Sun H, Rosli HG, Pombo MA, Zhang P, Banf M, Dai X, Martin GB, Giovannoni JJ, Zhao PX, Rhee SY, Fei Z. Zheng Y, et al. Among authors: banf m. Mol Plant. 2016 Dec 5;9(12):1667-1670. doi: 10.1016/j.molp.2016.09.014. Epub 2016 Oct 5. Mol Plant. 2016. PMID: 27717919 Free article. No abstract available.
Assessment of network module identification across complex diseases.
Choobdar S, Ahsen ME, Crawford J, Tomasoni M, Fang T, Lamparter D, Lin J, Hescott B, Hu X, Mercer J, Natoli T, Narayan R; DREAM Module Identification Challenge Consortium, Subramanian A, Zhang JD, Stolovitzky G, Kutalik Z, Lage K, Slonim DK, Saez-Rodriguez J, Cowen LJ, Bergmann S, Marbach D. Choobdar S, et al. Nat Methods. 2019 Sep;16(9):843-852. doi: 10.1038/s41592-019-0509-5. Epub 2019 Aug 30. Nat Methods. 2019. PMID: 31471613 Free PMC article.
PictureSensation - a mobile application to help the blind explore the visual world through touch and sound.
Banf M, Mikalay R, Watzke B, Blanz V. Banf M, et al. J Rehabil Assist Technol Eng. 2016 Oct 27;3:2055668316674582. doi: 10.1177/2055668316674582. eCollection 2016 Jan-Dec. J Rehabil Assist Technol Eng. 2016. PMID: 31186914 Free PMC article.