Publications

Recent papers

Click here for publications >5 years old or see our Google Scholar page

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

Pre-prints

Wang P, Lehti-Shiu MD, Lotreck S, Segura Abá K, Shiu SH. Prediction of plant complex traits via integration of multi-omics data bioRxiv doi:10.1101/2023.11.14.566971v2

Shiu SH, Lehti-Shiu MD. Evolution of research topics and paradigms in plant sciences. bioRxiv doi: 10.1101/2023.10.02.560457

2023

Lotreck SA, Segura Abá K, Lehti-Shiu MD, Seeger Au, Brown BNI, Ranaweera T, Schumacher A, Ghassemi M, Shiu SH. In a PICKLE: A gold standard entity and relation corpus for the molecular plant sciences. In Silico Plants diad021 doi

Alzohairy SA, Moore BM, Hammerschmidt R, Shiu SH, Hausbeck MK. Lignin biosynthesis gene expression is associated with age-related resistance of winter squash to Phytophthora capsici. J Am Soc Hort Sci 148:240-252 doi

Li Y, Miyani B, Childs KL, Shiu SH, and Xagoraraki I. Effect of wastewater collection and concentration methods on assessment of viral diversity. Sci Total Environ 2023:168128 pubmed

Lee YS, Shiu SH, and Grotewold E. Evolution and diversification of the ACT-like domain associated with plant basic helix–loop–helix transcription factors Proc. Natl. Acad. Sci. USA 120(19):e2219469120 pubmed

US DOE. Artificial Intelligence and Machine Learning for Bioenergy Research: Opportunities and Challenges, DOE/SC-0211. U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy. doi (Shiu Biodesign: Plant group)

Cuddington K, Abbott KC, Adler FR, Aydeniz M, Dale R, Gross LJ, Hastings A, Hobson EA, Karatayev V, Killion A, Madamanchi A, Marrraffini ML, McCombs A, Samyono W, Shiu SH, Watanabe KH, White ER. Challenges and opportunities to build quantitative self-confidence in biologists. Bioscience 73:364 doi

2022

Noble JA, Bielski NV, Liu MJ, DeFalco TA, Stegmann M, Nelson ADL, McNamara K, Sullivan B, Dinh KK, Khuu N, Hancock S, Shiu SH, Zipfel C, Cheung AY, Beilstein MA, Palanivelu R. Evolutionary analysis of the LORELEI gene family in plants reveals regulatory subfunctionalization. Plant Physiol 190(4):2539 pubmed

Ranaweera T, Brown BNI, Wang Pe, Shiu SHe. Temporal Regulation of Cold Transcriptional Response in Switchgrass. Frontier in Plant Sci 13:998400 pubmed

Liu WY, Yu CP, Chang CK, Chen HJ, Li MY, Chen YH, Shiu SH, Ku MSB, Tu SL, Lu MJ, Li WH. Regulators of early maize leaf development inferred from transcriptomes of laser capture microdissection (LCM)-isolated embryonic leaf cells. Proc. Natl. Acad. Sci. USA 119(35):e2208795119 pubmed

Lucker BF, Temple JA, Panchy NL, Benning UF, BibikaPeter JD, Neofotis PG, Weissman JC, Baxter IR, Shiu SH, Kramer DM. Selection-enriched genomic loci (SEGL) reveals genetic loci for environmental adaptation and photosynthetic productivity in Chlamydomonas reinhardtii. Algal Res 64:102709 doi

van Dijk ADJ, Shiu SH, de Ridder D. Editorial: Artificial Intelligence and Machine Learning Applications in Plant Genomics and Genetics. Front Artif Intell. 5:959470 pubmed

Wang Pe, Meng Fe, Donaldson Pu, Horan Su, Panchy NL, Vischulis E, Winship Eu, Conner JK, Shiu SHe, Lehti-Shiu MDe. High throughput measurement of plant fitness traits with an object detection method using Faster R-CNN. New Phytologist 234:1521–1533 pubmed

Wang Pe, Schumacher A and Shiu SHe. Computational prediction of plant metabolic pathways. Current Opinion in Plant Biology 66:102171 pubmed

Moore BM, Lee Y S, Wang PP, Azodi C, Grotewold E, Shiu SH. Modeling temporal and hormonal regulation of plant transcriptional response to wounding. Plant Cell 34(2):867-888 pubmed

Noble JA, Seddon A, Uygun S, Bright A, Smith SE, Shiu SH, Palanivelu R. The SEEL motif and members of the MYB-related REVEILLE transcription factor family are important for the expression of LORELEI in the synergid cells of the Arabidopsis female gametophyte. Plant Reproduction 35(1):61-76 pubmed

2021

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 pubmed

Cusack SA, Wang P, Lotreck SG, Moore BM, Meng F, Conner JK, Krysan PJ, Lehti-Shiu MD, Shiu SH. Predictive models of genetic redundancy in Arabidopsis thaliana. Molecular Biology and Evolution 38(8):3397-3414 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):475-489 pubmed

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

2020

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

2019

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

Click here for publications >5 years old