Recent papers

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Notation: e: joint first/corresponding, u:undergrad, h:high school student, Bold: lab members.


Peipei Wange, Fanrui Menge, Paityn Donaldsonu, Sarah Horanu, Nicholas L. Panchy, Elyse Vischulis, Eamon Winshipu, Jeffrey K. Conner, Melissa D. Lehti-Shiue, Shin-Han Shiue. High throughput measurement of Arabidopsis thaliana fitness traits using transfer learning. bioRxiv

Moore BM, Lee Y S, Grotewold E, Shiu SH. Modeling gene regulation in response to wounding: temporal variations, hormonal variations, and specialized metabolism pathways induced by wounding. bioRxiv

Noble JA, Liu MCJ, DeFalco TA, Stegmann M, McNamara K, Sullivan B, Dinh KK, Khuu N, Hancock S, Shiu SH, Zipfel C, Beilstein MA, Cheung AY, Palanivelu, R. Conserved Molecular Function and Regulatory Subfunctionalization of the LORELEI Gene Family in Brassicaceae. bioRxiv


Dale R, Oswald S, Jalihal A, Laporte M, Fletcher DM, Hubbard A, Shiu SH, Nelson ADL, Bucksch A. Overcoming the challenges to enhancing experimental plant biology with computational modeling. Frontier in Plant Science 12:687652 doi

Siobhan A. Cusack, Peipei Wang, Serena G. Lotreck, Bethany M. Moore, Fanrui Meng, Jeffrey K. Conner, Patrick J. Krysan, Melissa D. Lehti-Shiu, Shin-Han Shiu. Predictive models of genetic redundancy in Arabidopsis thaliana. Molecular Biology and Evolution 10.1093/molbev/msab111 pubmed

Wang P, Moore BM, Ugyun S, Lehti-Shiu M, Barry C, Shiu SH. Optimizing the use of gene expression data to predict plant metabolic pathway memberships. New Phytologist 231(1):475 pubmed/pdf

Wang PP, Meng FR, Moore BM, Shiu SH. Impact of short-read sequencing on the misassembly of a plant genome. BMC Genomics 22(1):99 pubmed

Baetsen-Young A, Chen H, Shiu SH, Day B. Contrasting transcriptional responses to Fusarium virguliforme infection in symptomatic and asymptomatic hosts. Plant Cell 17;33(2):224-247 pubmed


Liu WY, Lin HH, Yu CP, Chang CK, Chen HJ, Lin JY, Lu MYJ, Tu SL, Shiu SH Wu SH, Ku MSB, Li WH. Maize ANT1 modulates vascular development, chloroplast development, photosynthesis and plant growth. Proc. Natl. Acad. Sci., USA 117(35):21747 pubmed

Moore BM, Wang P, Fan P, Lee Au, Leong B, Lou YR, Schenck C, Sugimoto K, Last R, Lehti-Shiu MD, Barry CS, Shiu SH. Within and cross species predictions of plant specialized metabolism genes using transfer learning. In Silico Plants 2(1):diaa005 doi

Azodi CB, Lloyd JP, Shiu SH. The cis-regulatory codes of response to combined heat and drought stress in Arabidopsis thaliana. Nuc Acid Res-Genomics & Bioinformatics 2(3):lqaa049 doi

Fan P, Wang P, Lou YR, Leong BJ, Moore BM, Schenck CA, Combs R, Cao P, Brandizzi F, Shiu SH, Last RL. Evolution of a plant gene cluster in Solanaceae and emergence of metabolic diversity. eLife 9:e56717 pubmed

Azodi CB, Tang J, Shiu SH. Opening the black box: interpretable machine learning for geneticists. [review] Trends in Genetics 36(6):442 pubmed

Bao Y, Song W, Wang P, Yu X, Li B, Jiang C, Shiu SH, Zhang H, Bassham DC (2020) The plant-specific COST1 protein balances plant growth and drought tolerance via attenuation of autophagy. Proc. Natl. Acad. Sci. USA 117:7482 pumbed

Panchy NL, Lloyd JP, Shiu SH (2020) Improved recovery of cell-cycle gene expression in Saccharomyces cerevisiae from regulatory interactions in multiple omics data. BMC Genomics 21:159 pubmed

Schwarz B, Azodi CB, Shiu SH, Bauer P (2020) Putative cis-regulatory elements predict iron deficiency responses in Arabidopsis roots. Plant Physiol 182(3):1420 pubmed

Azodi CB, Pardo J, VanBuren R, de los Campos G, Shiu SH (2020) Transcriptome-based prediction of complex traits in maize. Plant Cell 32:139-151 pubmed


Azodi CB, Bolger Eu, McCarren A, Roantree M, de los Campos G, Shiu SH (2019) Benchmarking algorithms for genomic prediction of complex traits. G3 9(11):3691 pubmed

Uygun Se, Azodi, CBe, Shiu, SH (2019) Cis-regulatory code for predicting plant cell-type specific high salinity response. Plant Physiol. 181(4):1739 pubmed

Lloyd JP, Bowman MJ, Azodi CB, Moghe GD, Childs KL, Shiu SH. Evolutionary characteristics of intergenic transcribed regions indicate rare novel genes and widespread noisy transcription in the Poaceae (2019) Scientific Reports 9:12122 pubmed

Panchy NL, Azodi CB, Winship EFu, Shiu SH (2019) Expression and regulatory asymmetry of retained Arabidopsis thaliana transcription factor genes derived from whole genome duplication. BMC Genomics 19:77 pubmed

Chang YM, Lin HH, Liu WY, Yu CP, Chen HJ, Kao YY, Wu YH, Lin JJ, Li MYJ, Tu SL, Wu SH, Shiu SH, Ku MSB, Li WH (2019) A comparative transcriptomics method to infer gene coexpression networks and its applications to maize and rice leaf transcriptomes. Proc. Natl. Acad. Sci., USA 116(8):3091-3099 pubmed

Moore BM, Wang P, Fan P, Leong B, Schenck C, Lloyd J, Lehti-Shiu MD, Last R, Pichersky E, Shiu SH (2019) Robust predictions of specialized metabolism genes through machine learning. Proc. Natl. Acad. Sci., USA 116(6):2344-2353 pubmed


Wang P, Moore BM, Panchy NL, Meng F, Lehti-Shiu MD, Shiu SH (2018) Factors influencing gene family size variation among related species in a plant family, Solanaceae. Genome Biol. Evol. 10(10):2596–2613 pubmed

Liu MJ, Sugimoto K, Uygun, S, Panchy NL, Campbell M, Yandell M, Howe GA, Shiu SH (2018) Regulatory Divergence In Wound-Responsive Gene Expression In Domesticated And Wild Tomato. Plant Cell 30(7):1445-1460 pubmed

Lloyd JP, Tsai ZTY, Sowers RPu, Panchy NL, Shiu SH (2018) A model-based approach for identifying functional intergenic transcribed regions and non-coding RNAs. Mol. Biol. Evol. 35(6):1422-1436 pubmed

Tsai CH, Uygun S, Roston R, Shiu SH, Benning C (2018) Recovery from N Deprivation Is a Transcriptionally and Functionally Distinct State in Chlamydomonas. Plant Physiol. 176(3):2007-2023 pubmed


Huang CF, Yu CP, Wu YH, Lu MJ, Tu SL, Wu SH, Shiu SH, Ku MSB, Li WH (2017) Elevated auxin biosynthesis and transport underlie high vein density in C4 leaves. Proc. Natl. Acad. Sci., USA 114(33):E6884 pubmed

Uygun Se, Seddon AEe, Azodi C, Shiu SH (2017) Predictive models of spatial transcriptional response to high salinity. Plant Physiol. 174:450-464 pubmed

Tsai ZTY, Lloyd J, Shiu SH (2017) Defining functional, genic regions in the human genome through integration of biochemical, evolutionary, and genetic evidence. Mol. Biol. Evol. 34(7):1788-1798 pubmed

Bennett MS, Shiu SH, Triemer RE. (2017) A rare case of plastid protein-coding gene duplication in the chloroplast genome of Euglena archaeoplastidiata (Euglenophyta). J Phycol. 53(3):493-502 pubmed

Lehti-Shiu MDe, Panchy N, Wang P, Uygun S, Shiu SHe. (2017) Diversity, expansion, and evolutionary novelty of plant DNA-binding transcription factor families. Biochim. Biophys. Acta Gene Regul. Mech. 1860(1):3-20 [Review] pubmed

Click here for publications >5 years old