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Q1 Publications

A full list of all publications can be found at Google Scholar

2025

  1. Vavricka, C.J., Mochizuki, M., Yuzawa, S., Murata, M., Yoshida, T., Watanabe, N., Nakatsui, M., Ishii, J., Hara, K., Alper, H.S., Hasunuma, T., Kondo, A., Araki, M. (2025). Genome-scale prediction of gene ontology from yeast mass fingerprints reveals new gene functions useful for engineering microbial production. Life Science Alliance (EMBO Press), 8, e202403154. IF 2.9 (2024 JCR). Q1 in 2023. DOI: 10.26508/lsa.202403154
  2. Chen, J.#, Vavricka, C.J.#,*, Wei, S.#, Nakazawa, Y., Matsumoto, Y., Chen, H., Tang, Y., Liang, J., Chen, J., Huang, Y., Hasunuma, T., Guan, H., Li, J., Liao, C.*, Han, Q.* (2025). 3,4-Dihydroxyphenylacetaldehyde synthase evolved an ordered and distinct active site to promote elastic cuticle formation and blood intake in Aedes aegypti. Nature Communications, 16, 4486. IF 15.7 (2024 JCR). (#First-author, *Corresponding-author). DOI: 10.1038/s41467-025-04486
  3. Hidese, R., Sakai, K., Takenaka, M., Fushimi, K., Kudo, H., Tanaka, K., Nasuno, R., Vavricka, C.J., Kondo, A., Hasunuma, T. (2025). Identification of subfamily specific residues within highly active and promiscuous alcohol dehydrogenases. ACS Catalysis, 15, 11931–11943. IF 13.1 (2024 JCR). DOI: 10.1021/acscatal.5c02764
  4. Zhu, X., Zhang, L., Jiang, L., Chen, H., Tang, Y., Yang, X., Bao, P., Liao, C., Li, J., Vavricka, C.J., Ren, D., Chen, Z., Guo, Y., Han, Q. (2025). Aedes aegypti mosquito evolves two types of prophenoloxidases with diversified functions. Proceedings of the National Academy of Sciences, 122, e2413131122. IF 9.1 (2024 JCR). DOI: 10.1073/pnas.2413131122

2024

  1. Miura, D., Hayashi, W., Hirano, K., Sasaki, I., Tsukakoshi, K., Kakizoe, H., Asai, S., Vavricka, C.J., Takemae, H., Mizutani, T., Tsugawa, W., Sode, K., Ikebukuro, K., Asano, R. (2024). Proximity-unlocked luminescence by sequential enzymatic reactions from antibody and antibody/aptamer (PULSERAA): a platform for detection and visualization of virus-containing spots. Advanced Science, 24, e2403871. IF 14.1 (2024 JCR). DOI: 10.1002/advs.202403871
  2. Takenaka, M., Kamasaka, K., Daryong, K., Tsuchikane, K., Miyazawa, S., Fujihana, S., Hori, Y., Vavricka, C.J., Hosoyama, A., Kawasaki, H., Shirai, T., Araki, M., Nakagawa, A., Minami, H., Kondo, A., Hasunuma, T. (2024). Integrated pathway mining and selection of an artificial CYP79-mediated bypass to improve benzylisoquinoline alkaloid biosynthesis. Microbial Cell Factories, 23, 178. IF 4.9 (2024 JCR). Q1 in Biotechnology & Applied Microbiology. DOI: 10.1186/s12934-024-02453-7

2023

  1. Tanaka, K., Shirai, T., Vavricka, C.J., Matsuda, M., Kondo, A., Hasunuma, T. (2023). Dark accumulation of downstream glycolytic intermediates initiates robust photosynthesis in cyanobacteria. Plant Physiology, 191(4), 2400–2413. IF 6.9 (2024 JCR). DOI: 10.1093/plphys/kiac602
  2. Jagadeesh, V., Yoshida, T., Uraji, M., Okahashi, N., Matsuda, F., Vavricka, C.J., Tsuge, K., Kondo, A. (2023). Simple and rapid non-ribosomal peptide synthetase gene assembly using the SEAM–OGAB method. ACS Synthetic Biology, 12(1), 305–318. IF 3.8 (2024 JCR). Q1 in Biochemical Research Methods. DOI: 10.1021/acssynbio.2c00565

2022

  1. Vavricka, C.J.#,*, Takahashi, S.#, Watanabe, N., Takenaka, M., Matsuda, M., Yoshida, T., Kiyota, H., Li, J., Minami, H, Ishii, J., Tsuge, K., Araki, M.*, Kondo, A., Hasunuma, T.* (2022). Machine learning discovery of missing links that mediate alternative branches to plant alkaloids. Nature Communications, 13, 1405. IF 15.7 (2024 JCR). (#First-author, *Corresponding-author). DOI: 10.1038/s41467-022-28883-8

2021

  1. Takenaka, M., Yoshida, T., Hori, Y., Bamba, T., Mochizuki, M., Vavricka, C.J., Hattori, T., Hayakawa, Y., Hasunuma, T., Kondo, A. (2021). An ion-pair free LC-MS/MS method for quantitative metabolite profiling of microbial bioproduction systems. Talanta, 222, 121625. IF 5.6 (2024 JCR). DOI: 10.1016/j.talanta.2020.121625
  2. Kato, Y., Oyama, T., Inokuma, K., Vavricka, C.J., Matsuda, M., Hidese, R., Satoh, K., Oono, Y., Chang, J.-S., Hasunuma, T., Kondo, A. (2021). Enhancing carbohydrate repartitioning into lipid and carotenoid by disruption of microalgae starch debranching enzyme. Communications Biology, 4, 450. IF 5.1 (2024 JCR). DOI: 10.1038/s42003-021-01976-8

2020

  1. Vavricka, C.J., Hasunuma, T., Kondo, A. (2020). Dynamic metabolomics for engineering biology: accelerating learning cycles for bioproduction. Trends in Biotechnology, 38(1), 68–82. IF 14.9 (2024 JCR). (First-author). DOI: 10.1016/j.tibtech.2019.07.009
  2. Watanabe, N., Murata, M., Ogawa, T., Vavricka, C.J., Kondo, A., Ogino, C., Araki, M. (2020). Exploration and evaluation of machine-learning-based models for predicting enzymatic reactions. Journal of Chemical Information and Modeling, 60(3), 1833–1843. IF 5.3 (2024 JCR). Q1 in Computer Science—Interdisciplinary Applications. DOI: 10.1021/acs.jcim.9b00877

2019

  1. Vavricka, C.J., Yoshida, T., Kuriya, Y., Takahashi, S., Ogawa, T., Ono, F., Agari, K., Kiyota, H., Li, J., Ishii, J., Tsuge, K., Minami, H., Araki, M., Hasunuma, T., Kondo, A. (2019). Mechanism-based tuning of insect 3,4-dihydroxyphenylacetaldehyde synthase for synthetic bioproduction of benzylisoquinoline alkaloids. Nature Communications, 10, 2015. IF 15.7 (2024 JCR). (First-author). DOI: 10.1038/s41467-019-09610-2
  2. Kato, Y., Fujihara, Y., Vavricka, C.J., Chang, J.-S., Hasunuma, T., Kondo, A. (2019). Light/dark cycling causes delayed lipid accumulation and increased photoperiod-based biomass yield by altering metabolic flux in oleaginous Chlamydomonas sp.. Biotechnology for Biofuels & Bioproducts, 12, 39. IF 4.6 (2024 JCR). Q1 in Biotechnology & Applied Microbiology. DOI: 10.1186/s13068-019-1368-5
  3. Hasunuma, T., Takaki, A., Matsuda, M., Kato, Y., Vavricka, C.J., Kondo, A. (2019). Single-stage astaxanthin production enhances the non-mevalonate pathway and photosynthetic central metabolism in Synechococcus sp. PCC 7002. ACS Synthetic Biology, 8, 2701–2709. IF 3.8 (2024 JCR). Q1 in Biochemical Research Methods.

2018

  1. Hasunuma, T., Matsuda, M., Kato, Y., Vavricka, C.J., Kondo, A. (2018). Temperature enhanced succinate production concurrent with increased central metabolism turnover in the cyanobacterium Synechocystis sp. PCC 6803. Metabolic Engineering, 48, 109–120. IF 6.8 (2024 JCR). DOI: 10.1016/j.ymben.2018.05.013

2017

  1. Kato, Y., Ho, S.H., Vavricka, C.J., Chang, J.-S., Hasunuma, T., Kondo, A. (2017). Evolutionary engineering of salt-resistant Chlamydomonas sp. strains reveals salinity stress-activated starch-to-lipid biosynthesis switching. Bioresource Technology, 245, 1484–1490. IF 9.0 (2024 JCR). DOI: 10.1016/j.biortech.2017.05.162
  2. Vavricka, C.J.*, Muto, C., Hasunuma, T., Kimura, Y., Araki, M., Wu, Y., Gao, G.F., Ohrui, H., Izumi, M., Kiyota, H.* (2017). Synthesis of sulfo-sialic acid analogues: potent neuraminidase inhibitors in regards to anomeric functionality. Scientific Reports, 7, 8239. IF 3.9 (2024 JCR). (*Corresponding-author). Q1 in Multidisciplinary Sciences. DOI: 10.1038/s41598-017-08868-3

2016

  1. Wu, Y., Gao, F., Qi, J., Bi, Y., Fu, L., Mohan, S., Chen, Y., Li, X., Pinto, B.M., Vavricka, C.J., Tien, P., Gao, G.F. (2016). Resistance to mutant group 2 influenza virus neuraminidases of an oseltamivir-zanamivir hybrid inhibitor. Journal of Virology, 90(23), 10693–10700. IF 3.8 (2024 JCR). Q1 in Virology. DOI: 10.1128/JVI.01664-16

2015

  1. Wu, Y., Vavricka, C.J., Wu, Y., Li, Q., Rudrawar, S., Thomson, R.J., von Itzstein, M., Gao, G.F., Qi, J. (2015). Atypical group 1 neuraminidase pH1N1-N1 bound to a group 1 inhibitor. Protein & Cell, 6, 771–773. IF 12.8 (2024 JCR). DOI: 10.1007/s13238-015-0196-3

2014

  1. Sun, X., Li, Q., Wu, Y., Wang, M., Liu, Y., Qi, J., Vavricka, C.J., Gao, G.F. (2014). Structure of influenza virus N7: the last piece of the neuraminidase 'jigsaw' puzzle. Journal of Virology, 88(16), 9197–9207. IF 3.8 (2024 JCR). Q1 in Virology. DOI: 10.1128/JVI.01213-14
  2. Vavricka, C.J., Han, Q., Mehere, P.V., Christensen, B.M., Li, J. (2014). Tyrosine metabolic enzymes in insects and mammals: a comparative perspective. Insect Science, 21, 13–19. IF 3.0 (2024 JCR). Q1 in Entomology. DOI: 10.1111/1744-7917.12035

2013

  1. Wu, Y.#, Bi, Y.#, Vavricka, C.J.#, Sun, X., Zhang, Y., Gao, F., Zhao, M., Xiao, H., Qin, C., He, J., Liu, J., Yan, J., Qi, J., Gao, G.F. (2013). Characterization of two distinct neuraminidases from avian-origin human-infecting H7N9 influenza viruses. Cell Research, 23, 1347–1355. IF 25.9 (2024 JCR). (#First-author). DOI: 10.1038/cr.2013.144
  2. Vavricka, C.J.#, Liu, Y.#, Kiyota, H., Sriwilaijaroen, N., Qi, J., Tanaka, K., Wu, Y., Li, Q., Li, Y., Yan, J., Suzuki, Y., Gao, G.F. (2013). Influenza neuraminidase operates via a nucleophilic mechanism and can be targeted by covalent inhibitors. Nature Communications, 4, 1491. IF 15.7 (2024 JCR). (#First-author). DOI: 10.1038/ncomms2487
  3. Wu, Y., Qin, G., Gao, F., Liu, Y., Vavricka, C.J., Qi, J., Jiang, H., Yu, K., Gao, G.F. (2013). Induced opening of influenza virus neuraminidase N2 150-loop suggests an important role in inhibitor binding. Scientific Reports, 3, 1551. IF 3.9 (2024 JCR). Q1 in Multidisciplinary Sciences. DOI: 10.1038/srep01551
  4. Li, Q., Qi, J., Wu, Y., Kiyota, H., Tanaka, K., Suhara, Y., Ohrui, H., Suzuki, Y., Vavricka, C.J., Gao, G.F. (2013). Functional and structural analysis of influenza neuraminidase N3 offers further insight into the mechanisms of oseltamivir resistance. Journal of Virology, 87, 10016–10024. IF 3.8 (2024 JCR). Q1 in Virology. DOI: 10.1128/JVI.01017-13

2012

  1. Li, Q., Qi, J., Wu, Y., Vavricka, C.J., Tanaka, K., Suhara, Y., Ohrui, H., Suzuki, Y., Gao, G.F. (2012). Structural and functional characterization of the neuraminidase-like molecule N10 derived from bat influenza A virus. Proceedings of the National Academy of Sciences, 109(46), 18897–18902. IF 9.1 (2024 JCR). DOI: 10.1073/pnas.1211037109

2011

  1. Vavricka, C.J.#, Li, Q.#, Wu, Y.#, Qi, J., Wang, M., Liu, Y., Gao, F., Liu, J., Feng, E., Wang, J., Hong, L., Jiang, H., Gao, G.F. (2011). Structural and functional analysis of laninamivir and its octanoate prodrug reveals group-specific mechanisms of influenza NA inhibition. PLoS Pathogens, 7(10), e1002249. IF 4.9 (2024 JCR). (#First-author). Q1 in Virology / Microbiology / Parasitology. DOI: 10.1371/journal.ppat.1002249
  2. Wang, M., Qi, J., Liu, Y., Vavricka, C.J., Wu, Y., Li, Q., Gao, G.F. (2011). Influenza A virus neuraminidase N5 has an extended 150-cavity. Journal of Virology, 85(16), 8431–8435. IF 3.8 (2024 JCR). Q1 in Virology. DOI: 10.1128/JVI.00540-11
  3. Vavricka, C.J.* (2011). Adventures and lessons of an American biochemist in China. Protein & Cell, 2, 601–603. IF 12.8 (2024 JCR). (*Corresponding author*). DOI: 10.1007/s13238-011-1086-y
  4. Sun, M., Vavricka, C.J., Zhu, B. (2011). What job can a bug give? A controversy over the arsenic-guzzling bacterium cultured by NASA. Protein & Cell, 2, 261–263. IF 12.8 (2024 JCR). DOI: 10.1007/s13238-011-1041-y

2010

  1. Li, Q., Qi, J., Zhang, W., Vavricka, C.J., Shi, Y., Wei, J., Feng, E., Shen, J., Chen, J., Di, L., He, J., Yan, J., Liu, H., Jiang, H., Teng, M., Li, X., Gao, G.F. (2010). The 2009 pandemic H1N1 neuraminidase N1 lacks the 150-cavity in the active site. Nature Structural & Molecular Biology, 17(10), 1266–1268. IF 10.1 (2024 JCR). DOI: 10.1038/nsmb.1909
  2. Liu, J., Wu, P., Gao, F., Qi, J., Kawana-Tachikawa, A., Xie, J., Vavricka, C.J., Iwamoto, A., Li, T., Gao, G.F. (2010). Novel immunodominant peptide presentation strategy: a featured HLA-A*2402 restricted CTL-epitope stabilized by intra-chain hydrogen-bonds from SARS-CoV nucleocapsid protein. Journal of Virology, 84(22), 11849–11857. IF 3.8 (2024 JCR). Q1 in Virology. DOI: 10.1128/JVI.01045-10
  3. Zhang, W., Qi, J., Shi, Y., Qing, L., Gao, F., Sun, Y., Lu, X., Lu, Q., Vavricka, C.J., Liu, D., Yan, J., Gao, G.F. (2010). Crystal structure of the swine-origin A(H1N1)-2009 influenza A virus hemagglutinin (HA) reveals similar antigenicity to that of the 1918 pandemic virus. Protein & Cell, 1(5), 459–467. IF 12.8 (2024 JCR). DOI: 10.1007/s13238-010-0059-1
  4. Vavricka, C.J.*, Christensen, B.M., Li, J. (2010). Melanization in living organisms: a perspective of species evolution. Protein & Cell, 1(9), 830–841. IF 12.8 (2024 JCR). (First-author, *Corresponding author). DOI: 10.1007/s13238-010-0108-9
  5. Mehere, P., Han, Q., Lemkul, J.A., Vavricka, C.J., Robinson, H., Bevan, D.R., Li, J. (2010). Tyrosine aminotransferase: biochemical and structural properties and molecular dynamics simulations. Protein & Cell, 1, 1023–1032. IF 12.8 (2024 JCR). DOI: 10.1007/s13238-010-0137-4
  6. Sun, Y., Shi, Y., Zhang, W., Li, Q., Liu, D., Vavricka, C.J., Yan, J., Gao, G.F. (2010). In silico characterization of the functional and structural modules of the hemagglutinin protein from the swine-origin influenza virus A(H1N1)-2009. Science China Life Sciences, 53, 633–642. IF 9.5 (2024 JCR). DOI: 10.1007/s11427-010-4014-4