2023 Publications

Adie, Hylton, and Michael J. Lawes. “Solutions to Fire and Shade: Resprouting, Growing Tall and the Origin of Eurasian Temperate Broadleaved Forest.” Biological Reviews 98, no. 2 (April 2023): 643–61. https://doi.org/10.1111/brv.12923.

Alejandro Salado, Hanumanthrao Kannan, William Rouse Zoe Szajnfarber, and Nirav Merchant Young-Jun Son. “A Reference Architecture for a Policy Test Laboratory.” Acquisition Research Program, 2023.

Arancio, Walter, Nicolina Sciaraffa, and Claudia Coronnello. “MBS: A Genome Browser Annotation Track for High-Confident MicroRNA Binding Sites in Whole Human Transcriptome.” Database 2023 (April 22, 2023): baad015. https://doi.org/10.1093/database/baad015.

Balasubramanian, Vimal Kumar, Albert Rivas-Ubach, Tanya Winkler, Hugh Mitchell, James Moran, and Amir H. Ahkami. “Modulation of Polar Auxin Transport Identifies the Molecular Determinants of Source-Sink Carbon Relationships and Sink Strength in Poplar.” Preprint. Plant Biology, March 13, 2023. https://doi.org/10.1101/2023.03.12.532247.

Benson, Christopher W., Matthew R. Sheltra, Jeff P. Maughan, Eric N. Jellen, Matthew D. Robbins, B. Shaun Bushman, Eric L. Patterson, Nathan D. Hall, and David R. Huff. “Homoeologous Evolution of the Allotetraploid Genome of Poa Annua L.” Preprint. In Review, April 3, 2023. https://doi.org/10.21203/rs.3.rs-2729084/v1.

Bi, Li, Li-Li Han, Shuai Du, Dan-Ting Yu, Ji-Zheng He, Li-Mei Zhang, and Hang-Wei Hu. “Cross-Biome Soil Viruses as an Important Reservoir of Virulence Genes.” Journal of Hazardous Materials 442 (January 2023): 130111. https://doi.org/10.1016/j.jhazmat.2022.130111.

Buck, Ryan, Diego Ortega‐Del Vecchyo, Catherine Gehring, Rhett Michelson, Dulce Flores‐Rentería, Barbara Klein, Amy V. Whipple, and Lluvia Flores‐Rentería. “Sequential Hybridization May Have Facilitated Ecological Transitions in the Southwestern Pinyon Pine Syngameon.” New Phytologist 237, no. 6 (March 2023): 2435–49. https://doi.org/10.1111/nph.18543.

Bunting, Matt, Matthew Nice, Dan Work, Jonathan Sprinkle, and Roman Golota. “WiP Abstract: Edge-Based Privacy of Naturalistic Driving Data Collection.” In Proceedings of the ACM/IEEE 14th International Conference on Cyber-Physical Systems (with CPS-IoT Week 2023), 256–57. San Antonio TX USA: ACM, 2023. https://doi.org/10.1145/3576841.3589623.

Cai, Lirong, Holger Kreft, Amanda Taylor, Pierre Denelle, Julian Schrader, Franz Essl, Mark Van Kleunen, et al. “Global Models and Predictions of Plant Diversity Based on Advanced Machine Learning Techniques.” New Phytologist 237, no. 4 (February 2023): 1432–45. https://doi.org/10.1111/nph.18533.

Cardone, Richard, Smruti Padhy, Steven Black, Sean Cleveland, and Joe Stubbs. “A Decentralized Authorization and Security Framework for Distributed Research Workflows.” arXiv, May 13, 2023. http://arxiv.org/abs/2304.08557.

Chamorro González, Rocío, Thomas Conrad, Maja C. Stöber, Robin Xu, Mădălina Giurgiu, Elias Rodriguez-Fos, Katharina Kasack, et al. “Parallel Sequencing of Extrachromosomal Circular DNAs and Transcriptomes in Single Cancer Cells.” Nature Genetics 55, no. 5 (May 2023): 880–90. https://doi.org/10.1038/s41588-023-01386-y.

Chan, Yen On, Nicholas Dietz, Shuai Zeng, Juexin Wang, Sherry Flint-Garcia, M. Nancy Salazar-Vidal, Mária Škrabišová, Kristin Bilyeu, and Trupti Joshi. “The Allele Catalog Tool: A Web-Based Interactive Tool for Allele Discovery and Analysis.” BMC Genomics 24, no. 1 (March 10, 2023): 107. https://doi.org/10.1186/s12864-023-09161-3.

Chaulagain, Diptee, Elise Schnabel, Ashley Crook, Sagar Bashyal, Lena Maria Müller, and Julia Frugoli. “A Mutation in Mediator Subunit MED16A Suppresses Nodulation and Increases Arbuscule Density in Medicago Truncatula.” Journal of Plant Growth Regulation, May 12, 2023. https://doi.org/10.1007/s00344-023-10993-2.

Chávez Montes, Ricardo A., Mauricio Ulloa, Tammy Biniashvili, Arik Zackay, Nir Kfir, Damar Lopez-Arredondo, and Luis Herrera-Estrella. “Assembly and Annotation of the Gossypium Barbadense L. ‘Pima-S6’ Genome Raise Questions about the Chromosome Structure and Gene Content of Gossypium Barbadense Genomes.” BMC Genomics 24, no. 1 (January 10, 2023): 11. https://doi.org/10.1186/s12864-022-09102-6.

Chivian, Dylan, Sean P. Jungbluth, Paramvir S. Dehal, Elisha M. Wood-Charlson, Richard S. Canon, Benjamin H. Allen, Mikayla M. Clark, et al. “Metagenome-Assembled Genome Extraction and Analysis from Microbiomes Using KBase.” Nature Protocols 18, no. 1 (January 2023): 208–38. https://doi.org/10.1038/s41596-022-00747-x.

Daradur, Jenya, Mohamad Kesserwan, Nowlan H. Freese, Ann E. Loraine, and C. Daniel Riggs. “Genomic Targets of HOP2 Are Enriched for Features Found at Recombination Hotspots.” Preprint. Plant Biology, January 25, 2023. https://doi.org/10.1101/2023.01.25.525520.

Diaz, Rudy, Zheng Wang, and Jeffrey P. Townsend. “Measurement and Meaning in Gene Expression Evolution.” In Transcriptome Profiling, 111–29. Elsevier, 2023. https://doi.org/10.1016/B978-0-323-91810-7.00008-X.

Donovan, Sam, and M. Drew LaMar. “Using Science Education Gateways to Improve Undergraduate STEM Education: The QUBES Platform as a Case Study.” arXiv, January 4, 2023. http://arxiv.org/abs/2301.01760.

Ehsani, Mohammad Reza. “Improving Global Satellite Precipiation Products Utilizing Machine Learning.” PhD Thesis, The University of Arizona, 2023.

Epstein, Ruth, Nikita Sajai, Mateusz Zelkowski, Adele Zhou, Kelly R. Robbins, and Wojciech P. Pawlowski. “Exploring Impact of Recombination Landscapes on Breeding Outcomes.” Proceedings of the National Academy of Sciences 120, no. 14 (April 4, 2023): e2205785119. https://doi.org/10.1073/pnas.2205785119.

George, Nikhil A., and Laura A. Hug. “CRISPR-Resolved Virus-Host Interactions in a Municipal Landfill Include Non-Specific Viruses, Hyper-Targeted Viral Populations, and Interviral Conflicts.” Scientific Reports 13, no. 1 (April 5, 2023): 5611. https://doi.org/10.1038/s41598-023-32078-6.

Hartwig, Thomas, Michael Banf, Gisele Passaia Prietsch, Jia-Ying Zhu, Isabel Mora-Ramírez, Jos H. M. Schippers, Samantha J. Snodgrass, et al. “Hybrid Allele-Specific ChIP-Seq Analysis Identifies Variation in Brassinosteroid-Responsive Transcription Factor Binding Linked to Traits in Maize.” Genome Biology 24, no. 1 (May 8, 2023): 108. https://doi.org/10.1186/s13059-023-02909-w.

Henning, Paige M., Eric H. Roalson, Wali Mir, Andrew G. McCubbin, and Joel S. Shore. “Annotation of the Turnera Subulata (Passifloraceae) Draft Genome Reveals the S-Locus Evolved after the Divergence of Turneroideae from Passifloroideae in a Stepwise Manner.” Plants 12, no. 2 (January 7, 2023): 286. https://doi.org/10.3390/plants12020286.

Henry, Erin, Luca Santini, Mark A. J. Huijbregts, and Ana Benítez‐López. “Unveiling the Environmental Drivers of Intraspecific Body Size Variation in Terrestrial Vertebrates.” Global Ecology and Biogeography 32, no. 2 (February 2023): 267–80. https://doi.org/10.1111/geb.13621.

Hoosain, Nisreen, Jeanne Korsman, Peter O Kimathi, Paidamoyo Kachambwa, Rembu Magoba, and Shane L Murray. “AquaSens: Exploring the Use of 16S RRNA next-Generation Sequencing to Determine Bacterial Composition of Various Water Matrices.” Water SA 49, no. 2 (2023): 117–25.

Humphrey, Jack, Sanan Venkatesh, Rahat Hasan, Jake T. Herb, Katia De Paiva Lopes, Fahri Küçükali, Marta Byrska-Bishop, et al. “Integrative Transcriptomic Analysis of the Amyotrophic Lateral Sclerosis Spinal Cord Implicates Glial Activation and Suggests New Risk Genes.” Nature Neuroscience 26, no. 1 (January 2023): 150–62. https://doi.org/10.1038/s41593-022-01205-3.

Jackson, Robert, Esha V Rajadhyaksha, Reid S Loeffler, Caitlyn E Flores, and Koenraad Van Doorslaer. “Characterization of 3D Organotypic Epithelial Tissues Reveals Tonsil-Specific Differences in Tonic Interferon Signaling.” Preprint. Cell Biology, January 21, 2023. https://doi.org/10.1101/2023.01.19.524743.

Joshi, Anand B., Abdul Gaffar, and Sonali Singh. “Security of Medical Images Based on Special Orthogonal Group and Galois Field.” Multimedia Tools and Applications, April 13, 2023. https://doi.org/10.1007/s11042-023-15033-5.

Kang, Jian, Sidharth Sen, Melvin J. Oliver, and Robert E. Sharp. “Comparative Transcriptomics Reveal Metabolic Rather than Genetic Control of Divergent Antioxidant Metabolism in the Primary Root Elongation Zone of Water-Stressed Cotton and Maize.” Antioxidants 12, no. 2 (January 27, 2023): 287. https://doi.org/10.3390/antiox12020287.

Keuler, Rachel. “Assessing the Role of Hybridization in the Evolution of Two Common Lineages of Lichen-Forming Fungi.” These and Dissertations 9888 (2023). https://scholarsarchive.byu.edu/etd/9888.

Khanam, Ruqaiya, and Gitanjali Mehta. “Application of Deep CNN for Image-Based Identification and Classification of Plant Diseases.” In 2023 10th International Conference on Signal Processing and Integrated Networks (SPIN), 224–29. Noida, India: IEEE, 2023. https://doi.org/10.1109/SPIN57001.2023.10116967.

Kruasuwan, Worarat, Karan Lohmaneeratana, John T. Munnoch, Wanwipa Vongsangnak, Chatchawan Jantrasuriyarat, Paul A. Hoskisson, and Arinthip Thamchaipenet. “Transcriptome Landscapes of Salt-Susceptible Rice Cultivar IR29 Associated with a Plant Growth Promoting Endophytic Streptomyces.” Rice 16, no. 1 (December 2023): 6. https://doi.org/10.1186/s12284-023-00622-7.

Li, Wenwen, Sizhe Wang, Xiao Chen, Yuanyuan Tian, Zhining Gu, Anna Lopez-Carr, Andrew Schroeder, Kitty Currier, Mark Schildhauer, and Rui Zhu. “GeoGraphVis: A Knowledge Graph and Geovisualization Empowered Cyberinfrastructure to Support Disaster Response and Humanitarian Aid.” ISPRS International Journal of Geo-Information 12, no. 3 (March 7, 2023): 112. https://doi.org/10.3390/ijgi12030112.

Li, Yangjie, Bin Ma, Kexin Hua, Huimin Gong, Rongrong He, Rui Luo, Dingren Bi, Rui Zhou, Paul R. Langford, and Hui Jin. “PPNet: Identifying Functional Association Networks by Phylogenetic Profiling of Prokaryotic Genomes.” Edited by Sébastien P. Faucher. Microbiology Spectrum 11, no. 1 (February 14, 2023): e03871-22. https://doi.org/10.1128/spectrum.03871-22.

Lima, Dayane Cristina, Alejandro Castro Aviles, Ryan Timothy Alpers, Alden Perkins, Dylan L. Schoemaker, Martin Costa, Shawn Kaeppler, et al. “2020-2021 Field Seasons of Maize G x E Project within Maize Genomes to Fields Initiative.” Preprint. In Review, May 11, 2023. https://doi.org/10.21203/rs.3.rs-2908766/v1.

McGarry, Róisín C, Harmanpreet Kaur, Yen-Tung Lin, Guadalupe Lopez Puc, Leor Eshed Williams, Esther Van Der Knaap, and Brian G Ayre. “Altered Expression of SELF-PRUNING Disrupts Homeostasis and Facilitates Signal Delivery to Meristems.” Plant Physiology, February 28, 2023, kiad126. https://doi.org/10.1093/plphys/kiad126.

Mitra, Saptashwa, Maxwell Roselius, Pedro Andrade‐Sanchez, John K. McKay, and Sangmi Lee Pallickara. “Radix+ : High‐throughput Georeferencing and Data Ingestion over Voluminous and Fast‐evolving Phenotyping Sensor Data.” Concurrency and Computation: Practice and Experience 35, no. 8 (April 10, 2023). https://doi.org/10.1002/cpe.7484.

Nguyen, Minh. “Cost-Effective and Performance-Preserving Secured Application Management in Cloud Environments.” PhD Thesis, City University of New York, 2023.

Prather, Ben S., Jason Dexter, Monika Moscibrodzka, Hung-Yi Pu, Thomas Bronzwaer, Jordy Davelaar, Ziri Younsi, et al. “Comparison of Polarized Radiative Transfer Codes Used by the EHT Collaboration.” arXiv, March 21, 2023. http://arxiv.org/abs/2303.12004.

Priyadarshini, Parichita, Smrutirekha Sahu, Gopal Kalwan, Yashwant K. Yadava, Ramawatar Nagar, Vandna Rai, C. Bharadwaj, Kishor Gaikwad, and Pradeep K. Jain. “Unravelling the Mechanism of Fusarium Wilt Resistance in Chickpea Seedlings Using Biochemical Studies and Expression Analysis of NBS-LRR and WRKY Genes.” Physiological and Molecular Plant Pathology 124 (March 2023): 101958. https://doi.org/10.1016/j.pmpp.2023.101958.

Raevskiy, Mikhail, Vladislav Yanvarev, Sascha Jung, Antonio Del Sol, and Yulia A. Medvedeva. “Epi-Impute: Single-Cell RNA-Seq Imputation via Integration with Single-Cell ATAC-Seq.” International Journal of Molecular Sciences 24, no. 7 (March 25, 2023): 6229. https://doi.org/10.3390/ijms24076229.

———. “Epi-Impute: Single-Cell RNA-Seq Imputation via Integration with Single-Cell ATAC-Seq.” International Journal of Molecular Sciences 24, no. 7 (March 25, 2023): 6229. https://doi.org/10.3390/ijms24076229.

Rawlings, Christopher John, and Robert P. Davey. “From Farm to FAIR: The Trials of Linking and Sharing Wheat Research Data.” In Towards Responsible Plant Data Linkage: Data Challenges for Agricultural Research and Development, edited by Hugh F. Williamson and Sabina Leonelli, 107–23. Cham: Springer International Publishing, 2023. https://doi.org/10.1007/978-3-031-13276-6_6.

Samuels, Mark E., Cassandra Lapointe, Sara Halwas, and Anne C. Worley. “Genomic Sequence of Canadian Chenopodium Berlandieri: A North American Wild Relative of Quinoa.” Plants 12, no. 3 (January 19, 2023): 467. https://doi.org/10.3390/plants12030467.

Sarzaeim, Parisa, Francisco Munoz-Arriola, Diego Jarquin, Hasnat Aslam, and Natalia De Leon Gatti. “CLIM4OMICS: A Geospatially Comprehensive Climate and Multi-OMICS Database for Maize Phenotype Predictability in the U.S. and Canada.” Preprint. ESSD – Land/Biogeosciences and biodiversity, February 1, 2023. https://doi.org/10.5194/essd-2023-11.

Stoy, Kayla S, Joselyne Chavez, Valeria De Las Casas, Venkat Talla, Aileen Berasategui, Levi T Morran, and Nicole M Gerardo. “Evaluating Coevolution in a Horizontally Transmitted Mutualism.” Evolution 77, no. 1 (January 23, 2023): 166–85. https://doi.org/10.1093/evolut/qpac009.

Tabugo, Sharon Rose M., Rose Chinly Mae H. Ortega, Chinee S. Padasas, Carl Nico P. Oñate, Grazzette Anne N. Dablo, Tricksie P. Balatero, Noel John Ian Feben S. Maguate, Joey Genevieve T. Martinez, Nancy Galvez‐Reyes, and Mylene M. Uy. “Conservation Initiatives of Syngnathiformes Species in the Southern Philippines: What Does the Mitochondrial DNA Signature Tell Us?” Aquatic Conservation: Marine and Freshwater Ecosystems 33, no. 3 (March 2023): 231–45. https://doi.org/10.1002/aqc.3924.

Thangavel, Gokilavani, Paulo G. Hofstatter, Raphaël Mercier, and André Marques. “Tracing the Evolution of the Plant Meiotic Molecular Machinery.” Plant Reproduction 36, no. 1 (March 2023): 73–95. https://doi.org/10.1007/s00497-022-00456-1.

Touchette, David, Catherine Maggiori, Ianina Altshuler, Alex Tettenborn, Louis-Jacques Bourdages, Elisse Magnuson, Olivia Blenner-Hassett, Isabelle Raymond-Bouchard, Alex Ellery, and Lyle G. Whyte. “Microbial Characterization of Arctic Glacial Ice Cores with a Semiautomated Life Detection System.” Astrobiology, April 26, 2023, ast.2022.0130. https://doi.org/10.1089/ast.2022.0130.

Tuggle, Christopher K, Jennifer Clarke, Brenda M Murdoch, Eric Lyons, Nicole M Scott, Bedrich Benes, Jacqueline Campbell, et al. “Current Challenges and Future of Agricultural Genomes to Phenomes in the US,” 2023.

Uchenna, Anukwu John, Nwamba Helen Ogochukwu, and Chiaha Ijeoma Emiliana. “DNA Barcoding of Selected Freshwater Fishes in New Calabar River, Rivers State, Nigeria.” Asian Journal of Biotechnology and Bioresource Technology, April 20, 2023, 28–38. https://doi.org/10.9734/ajb2t/2023/v9i1176.

Varma, Watan Kishor, and Vipin Kumar. “Analysis of Crop Leaf Image Classification Using Deep Learning Models over Novel Dataset.” In 2023 10th International Conference on Signal Processing and Integrated Networks (SPIN), 14–19. Noida, India: IEEE, 2023. https://doi.org/10.1109/SPIN57001.2023.10116960.

Warren, Derek, Vagner A. Benedito, R Chris Skinner, Ayad Alawadi, Eloisa Vendemiatti, David J. Laub, Casey Showman, Kristen Matak, and Janet C. Tou. “Low-Protein Diets Composed of Protein Recovered from Food Processing Supported Growth, but Induced Mild Hepatic Steatosis Compared with a No-Protein Diet in Young Female Rats.” The Journal of Nutrition, March 2023, S0022316623355019. https://doi.org/10.1016/j.tjnut.2023.03.028.

Zhang, Mujie, Yali Hao, Yi Yi, Shunzhang Liu, Qingyang Sun, Xiaoli Tan, Shan Tang, Xiang Xiao, and Huahua Jian. “Unexplored Diversity and Ecological Functions of Transposable Phages.” The ISME Journal, April 17, 2023. https://doi.org/10.1038/s41396-023-01414-z.

Zhang, Xue, Zhuo Jiang, Xilin Jiao, Yang Yu, Zhenan Wang, Yangyang Hou, Guohua Duan, et al. “Genome Assembly and Comparative Analysis of the Egg Parasitoid Wasp Trichogramma Dendrolimi Shed Light on the Composition and Evolution of Olfactory Receptors and Venoms.” Insects 14, no. 2 (January 31, 2023): 144. https://doi.org/10.3390/insects14020144.

Zhao, Zihao, Chie Amano, Thomas Reinthaler, Federico Baltar, Monica Orellana, and Gerhard Herndl. “Metaproteomic Analysis Decodes the Trophic Basis of Microbes in the Dark Ocean.” Preprint. In Review, April 7, 2023. https://doi.org/10.21203/rs.3.rs-2727130/v1.

Zheng, Kaiyang, Yue Dong, Yantao Liang, Yundan Liu, Xinran Zhang, Wenjing Zhang, Ziyue Wang, et al. “Genomic Diversity and Ecological Distribution of Marine Pseudoalteromonas Phages.” Marine Life Science & Technology, January 20, 2023. https://doi.org/10.1007/s42995-022-00160-z.

Zhou, Andy, Liam D. Kirkpatrick, Izaiah J. Ornelas, Lorenzo J. Washington, Niklas F. C. Hummel, Christopher W. Gee, Sophia N. Tang, Collin R. Barnum, Henrik V. Scheller, and Patrick M. Shih. “A Suite of Constitutive Promoters for Tuning Gene Expression in Plants.” ACS Synthetic Biology, April 21, 2023, acssynbio.3c00075. https://doi.org/10.1021/acssynbio.3c00075.

Zhou, Yifan, Liang Zhou, Shuling Yan, Lanming Chen, Mart Krupovic, and Yongjie Wang. “Diverse Viruses of Marine Archaea Discovered Using Metagenomics.” Environmental Microbiology 25, no. 2 (February 2023): 367–82. https://doi.org/10.1111/1462-2920.16287.

Zimmerman, Amy E., Justin C. Podowski, Gwendolyn E. Gallagher, Maureen L. Coleman, and Jacob R. Waldbauer. “Tracking Nitrogen Allocation to Proteome Biosynthesis in a Marine Microbial Community.” Nature Microbiology 8, no. 3 (January 12, 2023): 498–509. https://doi.org/10.1038/s41564-022-01303-9.

Zuo, Huanyan, Yao Xiao, Jiahao Han, Yuxiu Lin, Cheng Tian, Shu Zhang, Guohua Yuan, Huan Liu, and Zhi Chen. “Phosphorylation of ATF2 Promotes Odontoblastic Differentiation via Intrinsic HAT Activity.” Journal of Genetics and Genomics, February 2023, S1673852723000449. https://doi.org/10.1016/j.jgg.2023.02.005.