1. Nelson DR, Jaiswal AK, Ismail NS, Mystikou A, Salehi-Ashtiani K. Pan-microalgal dark proteome mapping via interpretable deep learning and synthetic chimeras. Patterns (Cell Press), 2025.
2. Nelson DR, Chaiboonchoe A, Fu W, et al. Multi-omics decipher the molecular mechanisms driving high-lipid production in an artificially-evolved Chlamydomonas mutant. bioRxiv, 2025.
3. Chen J, Qian C, Shu Y, Salehi-Ashtiani K, et al. Bioinspired cell silicification of the model diatom Phaeodactylum tricornutum. Sustainable Horizons, 2025.

1. Nelson DR, Jaiswal AK, Ismail N, et al. LA4SR: illuminating the dark proteome with generative AI. arXiv preprint, 2024.
2. Su Y, Hu J, Xia M, et al. An undiscovered circadian clock to regulate phytoplankton photosynthesis. PNAS Nexus, 2024.
3. Daakour S, Nelson DR, Fu W, et al. Adaptive Evolution Signatures in Prochlorococcus: ORFeome Resources. Microorganisms, 2024.
4. Nelson DR, Mystikou A, Jaiswal AK, et al. Macroalgal deep genomics illuminate multiple paths to aquatic, photosynthetic multicellularity. Molecular Plant, 2024.
5. Alzahmi AS, Daakour S, Nelson D, et al. Enhancing algal production strategies: strain selection, AI-informed cultivation, and mutagenesis. Frontiers in Sustainable Food Systems, 2024.
6. Salehi-Ashtiani K. AlgaGPT: A Transformer-Based Model for Efficient Decontamination of Algal Sequencing Data. PAG 31 Conference, 2024.
7. Nelson DR, Muvunyi R, Hazzouri KM, et al. A near telomere-to-telomere phased reference assembly for the male mountain gorilla. bioRxiv, 2024.
8. Daakour S, Nelson DR, Fu W, et al. Adaptive Evolution Signatures in Prochlorococcus. Preprints, 2024.

1. Salehi-Ashtiani K. Large-Scale Sequencing and Analyses of Micro and Macroalgae Genomes. PAG Australia, 2023.
2. Maseko SB, Brammerloo Y, Van Molle I, et al. Identification of small molecule antivirals against HTLV-1 by targeting the hDLG1-Tax-1 protein-protein interaction. Antiviral Research, 2023.
3. Corominas R, Yang X, Lin GN, et al. Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism. Nature Communications, 2023.

1. Nelson DR, Chaiboonchoe A, Hazzouri KM, et al. Tissue-Specific Transcriptomes Outline Halophyte Adaptive Strategies in the Gray Mangrove. Agronomy, 2022.
2. Hazzouri KM, Sudalaimuthuasari N, Saeed EE, et al. Salt flat microbial diversity and dynamics across salinity gradient. Scientific Reports, 2022.
3. Nelson DR, Al Hrout A, Alzahmi AS, et al. Molecular Mechanisms behind Safranal's Toxicity to HepG2 Cells from Dual Omics. Antioxidants, 2022.
4. Olivet J, Maseko SB, Volkov AN, et al. A systematic approach to identify host targets and rapidly deliver broad-spectrum antivirals. Molecular Therapy, 2022.
5. Maseko SB, Van Molle I, Blibek K, et al. Structural basis for targeting the human T-cell leukemia virus Tax oncoprotein. bioRxiv, 2022.

1. Alzahmi A, Daakour S, El Assal DC, et al. High-Throughput Metabolic Profiling for Model Refinements of Microalgae. J. Vis. Exp., 2021.
2. Al-Shehhi MR, Nelson D, Farzanah R, et al. Characterizing algal blooms in a shallow & a deep channel. Ocean and Coastal Management, 2021.
3. Fu W, Dohai B, El Assal DC, et al. Protocol to generate and characterize biofouling transformants of a model marine diatom. STAR Protocols, 2021.
4. Kerselidou D, Dohai BS, Nelson DR, et al. Alternative glycosylation controls endoplasmic reticulum dynamics. Science Advances, 2021.
5. Chen Y, Qi F, Gao F, et al. Hovlinc is a recently evolved class of ribozyme found in human lncRNA. Nature Chemical Biology, 2021.
6. Nelson DR, Hazzouri KM, Lauersen KJ, et al. Large-scale genome sequencing reveals the driving forces of viruses in microalgal evolution. Cell Host & Microbe, 2021.
7. Koussa J, Vitrinel B, Whitney P, et al. Sex-specific glycosylation of secreted immunomodulatory proteins in Brugia malayi. bioRxiv, 2021.
8. Friis G, Vizueta J, Smith EG, et al. A high-quality genome assembly and annotation of the gray mangrove, Avicennia marina. G3 Genes|Genomes|Genetics, 2021.

1. Kerselidou D, Dohai BS, Nelson DR, et al. Exostosin-1 Glycosyltransferase Regulates Endoplasmic Reticulum Architecture. Cold Spring Harbor Laboratory, 2020.
2. Fu W, Chaiboonchoe A, Dohai B, et al. GPCR Genes as Activators of Surface Colonization Pathways in a Model Marine Diatom. iScience, 2020.
3. Wierbowski SD, Vo TV, Falter-Braun P, et al. A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice. PNAS, 2020.
4. Al Shehhi MR, Nelson D, Alkhori RR, et al. Characterizing Algal blooms in a shallow and a deep channel. arXiv preprint, 2020.

1. Fu W, Nelson DR, Mystikou A, et al. Advances in microalgal research and engineering development. Curr. Opin. Biotechnol., 2019.
2. Nelson DR, Chaiboonchoe A, Fu W, et al. Potential for Heightened Sulfur-Metabolic Capacity in Coastal Subtropical Microalgae. iScience/Cell, 2019.
3. Fu W, Gudmundsson S, Wichuk K, et al. Dataset on economic analysis of mass production of algae. Data in Brief, 2019.
4. Fu W, Gudmundsson S, Wichuk K, et al. Sugar-stimulated CO2 sequestration by the green microalga Chlorella vulgaris. Science of The Total Environment, 2019.

1. Al-Hrout A, Chaiboonchoe A, Khraiwesh B, et al. Safranal induces DNA double-strand breakage and ER-stress-mediated cell death in hepatocellular carcinoma cells. Scientific Reports, 2018.
2. Yi Z, Su Y, Bergmann A, et al. Chemical mutagenesis and fluorescence-based high-throughput screening for enhanced accumulation of carotenoids in a model marine diatom. Mar. Drugs, 2018.
3. Hazzouri KM, Khraiwesh B, Amiri KMA, et al. Mapping of HKT1;5 gene in barley using GWAS approach. Frontiers in Plant Science, 2018.

1. Fu W, Chaiboonchoe A, Khraiwesh B, et al. Intracellular spectral recompositioning of light enhances algal photosynthetic efficiency. Science Advances, 2017.
2. Nelson DR, Khraiwesh B, Fu W, et al. The genome and phenome of the green alga Chloroidium sp. UTEX3007 reveal adaptive traits for desert acclimatization. eLife, 2017.
3. Khraiwesh B, Salehi-Ashtiani K. Alternative Poly(A) Tails Meet miRNA Targeting in Caenorhabditis elegans. Genetics, 2017.
4. Fu W, Nelson DR, Yi Z, et al. Bioactive compounds from microalgae: Current development and prospects. Studies in Natural Products Chemistry (Elsevier), 2017.

1. Jijakli K, Khraiwesh B, Fu W, et al. The In Vitro Selection World. Methods, 2016.
2. Chaiboonchoe A, Ghamsari L, Dohai B, et al. Systems level analyses of Chlamydomonas reinhardtii metabolic network. Mol. BioSyst., 2016.
3. Fu W, Khraiwesh B, Liu H, et al. Advances in Biotechnology for Sustainable Development. BioMed Research International, 2016.
4. Wiemann S, Pennacchio C, Hu Y, et al. The ORFeome Collaboration: A genome-scale human ORF-clone resource. Nature Methods, 2016.
5. Chiu CN, Rihel J, Lee DA, et al. A Zebrafish Genetic Screen Identifies Neuromedin U as a Regulator of Sleep/Wake States. Neuron, 2016.
6. Yang X, Coulombe-Huntington J, Kang S, et al. Widespread expansion of protein interaction capabilities by alternative splicing. Cell, 2016.
7. Abdrabu R, Sharma SK, Khraiwesh B, et al. Single Cell Characterization of Microalgal Lipid Contents with Confocal Raman Microscopy. Springer, 2016.
8. Fu W, Chaiboonchoe A, Khraiwesh B, et al. Algal Cell Factories: Approaches, Applications, and Potentials. Mar. Drugs, 2016.

1. Khraiwesh B, Qudeimat E, Thimma M, et al. Genome-wide expression analysis offers new insights into the origin and evolution of Physcomitrella patens stress response. Scientific Reports, 2015.
2. Amin A, Hamza AA, Daoud S, et al. Saffron-Based Crocin Prevents Early Lesions of Liver Cancer. Recent Pat Anticancer Drug Discovery, 2015.
3. Flowers JM, Hazzouri KM, Pham GM, et al. Whole genome re-sequencing reveals extensive natural variation in the model green alga Chlamydomonas reinhardtii. Plant Cell, 2015.
4. Sharma SK, Nelson DR, Abdrabu R, et al. An integrative Raman microscopy-based workflow for rapid in situ analysis of microalgal lipid bodies. Biotechnology for Biofuels, 2015.
5. Sahni N, Yi S, Taipale M, et al. Widespread macromolecular interaction perturbations in human genetic disorders. Cell, 2015.
6. Khraiwesh B, Jijakli K, Swift J, et al. Prospective Applications of Synthetic Biology for Algal Bioproduct Optimization. Springer International Publishing, 2015.
7. Salehi-Ashtiani K, Koussa J, Dohai B, et al. Toward Applications of Genomics and Metabolic Modeling to Improve Algal Biomass Productivity. Springer International Publishing, 2015.
8. Jijakli K, Abdrabu R, Khraiwesh B, et al. Molecular Genetic Techniques for Algal Bioengineering. Springer International Publishing, 2015.
9. Fu W, Wichuk K, Brynjolfsson S. Developing diatoms for value-added products: challenges and opportunities. New Biotechnology, 2015.

2014: Chaiboonchoe A et al. Microalgal metabolic network model refinement (Frontiers); Koussa J et al. Computational Approaches for Microalgal Biofuel (BioMed Res Int); Corominas R et al. Autism-centered interactome network (Nature Communications)

2013: Khraiwesh B & Qudeimat E. Abiotic Stress‐Responsive Small RNA (Wiley); Xin X et al. SH3 interactome conserves general function (Mol Syst Biol)

2012: Djebali S et al. Evidence for transcript networks (PLoS One)

2011: Yang X et al. A public genome-scale lentiviral expression library (Nature Methods); Ghamsari L et al. Genome-wide functional annotation (BMC Genomics); Chang RL et al. Metabolic network reconstruction of Chlamydomonas (Molecular Systems Biology)

2010: Johannessen CM et al. COT drives resistance to RAF inhibition (Nature); Mangone M et al. The landscape of C. elegans 3'UTRs (Science)

2009: Manichaikul A et al. Metabolic network analysis integrated with transcript verification (Nature Methods)

2008: Salehi-Ashtiani K et al. Isoform discovery using targeted cloning (Nature Methods)

2006: Salehi-Ashtiani K et al. A Genome-wide search for ribozymes reveals an HDV-like sequence (Science)

2001: Salehi-Ashtiani K & Szostak JW. In vitro evolution suggests multiple origins for the hammerhead ribozyme (Nature)