YOSHIMATSU LAB

2024

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34

Saquer, N.; Iqbal, R.; Ellis, J. D.; Yoshimatsu, K.  Infrared spectra prediction using attention-based graph
neural network. Digital Discovery 2024, 3, 602-609. doi:10.1039/D3DD00254C

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33

Ellis, J. D.; Iqbal, R.; Yoshimatsu, K.  Deep Q-Learning-Based Molecular Graph Generation for Chemical Structure Prediction From Infrared Spectra. IEEE Transactions on Artificial Intelligence 2024, 5, 634-646. doi:10.1109/TAI.2023.3287947

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2023

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​32

Koide, H.; Kiyokawa, C.; Okishima, A.; Saito, K.; Yoshimatsu, K.; Fukuta, T.; Hoshino, Y.; Asai, T.; Nishimura, Y.; Miura, Y.; Oku, N.; Shea, K. J.  Design of an Anti-HMGB1 Synthetic Antibody for In Vivo Ischemic/Reperfusion Injury Therapy. Journal of the American Chemical Society 2023, 145, 23143–23151. doi:10.1021/jacs.3c06799

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31

Koide, H.; Saito, K.; Yoshimatsu, K.; Chou, B.; Hoshino, Y.; Yonezawa, S.; Oku, N.; Asai, T.; Shea, K. J.  Cooling-induced, localized release of cytotoxic peptides from engineered polymer nanoparticles in living mice for cancer therapy. Journal of Controlled Release 2023, 355, 745-759. doi:10.1016/j.jconrel.2023.02.020

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2021

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30

Koide, H.; Okishima, A.; Hoshino, Y.; Kamon, Y.; Yoshimatsu, K.; Saito, K.; Yamauchi, I.; Ariizumi, S.; Zhou, Y.; Xiao, T.-H.; Goda, K.; Oku, N.; Asai, T.; Shea, K. J.  Synthetic hydrogel nanoparticles for sepsis therapy. Nature Communications 2021, 12, 5552. doi:10.1038/s41467-021-25847-2

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29

Ellis, J. D.; Iqbal, R.; Yoshimatsu, K.  Verification of the neural network training process for spectrum-based chemical substructure prediction using metamorphic testing. Journal of Computational Science 2021, 55, 101456. doi:10.1016/j.jocs.2021.101456

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28

Yoshimatsu, K.; Fruehauf, K. R.; Zhu, Q.; Weisman, A.; Fan, J.; Xue, M.; Beierle, J. M.; Rose, P. E.; Aral, J.; Epstein, L. F.; Tagari, P.; Miranda, L. P.; Shea, K. J.  Metal-Free Polymer-Based Affinity Medium for Selective Purification of His6-Tagged Proteins. Biomacromolecules 2021, 22, 4, 1695-1705.

doi:10.1021/acs.biomac.1c00119

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27

Odom, T. L.; Blankenship, J. R.; Campos, G.; Mart, D. C.; Liu, W.; Wang, R.; Yoshimatsu, K.  Effect of vortex‐induced physical stress on fluorescent properties of dye‐containing poly(ethylene glycol)‐block‐poly(lactic acid) micelles. Journal of Applied Polymer Science 2021, 138, 4, 49743. doi:10.1002/app.49743

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2020

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26

Ellis, J. D.; Iqbal, R.; Yoshimatsu, K.  A new approach for IR spectra matching using normalized local change. Analytica Chimica Acta 2020, 1103, 49-57. doi:10.1016/j.aca.2019.12.055

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2019

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25

Koide, H.; Fukuta, T.; Okishima, A.; Ariizumi, S.; Kiyokawa, C.; Tsuchida, H.; Nakamoto, M.; Yoshimatsu, K.; Ando, H.; Dewa, T.; Asai, T.; Oku, N.; Hoshino, Y.; Shea, K. J.  Engineering the binding kinetics of synthetic polymer nanoparticles for siRNA delivery. Biomacromolecules 2019, 20, 10, 3648-3657.

doi:10.1021/acs.biomac.9b00611

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24

Yoshida, H.; Kojima, K.; Shiota, M.; Yoshimatsu, K.; Yamazaki, T.; Ferri, S.; Tsugawa, W.; Kamitori, S.; Sode, K.  X-ray structure of the direct electron transfer-type FAD glucose dehydrogenase catalytic subunit complexed with a hitchhiker protein. Acta Crystallographica Section D: Structural Biology 2019, 75, 841-851. 

doi:10.1107/S2059798319010878

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23

Koide, H.; Yoshimatsu, K.; Hoshino, Y.; Ariizumi, S.; Okishima, A.; Ide, T.; Egami, H.; Hamashima, Y.; Nishimura, Y.; Kanazawa, H.; Miura, Y.; Asai, T.; Oku, N.; Shea, K. J.  Sequestering and inhibiting a vascular endothelial growth factor in vivo by systemic administration of a synthetic polymer nanoparticle. 

Journal of Controlled Release 2019, 295, 13-20. doi:10.1016/j.jconrel.2018.12.033

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2018

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22

Miyazaki, R.; Yamazaki, T.; Yoshimatsu, K.; Kojima, K.; Asano, R.; Sode, K.; Tsugawa, W.  Elucidation of the intra- and inter-molecular electron transfer pathways of glucoside 3-dehydrogenase. Bioelectrochemistry 2018, 122, 115-122. doi:10.1016/j.bioelechem.2018.03.001

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2017

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21

Koide, H.; Yoshimatsu, K.; Hoshino, Y.; Lee, S.-H.; Okajima, A.; Ariizumi, S.; Narita, Y.; Yonamine, Y.; Weisman, A. C.; Nishimura, Y.; Oku, N.; Miura, Y.; Shea, K. J.  A polymer nanoparticle with engineered affinity for a vascular endothelial growth factor (VEGF165). Nature Chemistry 2017, 9, 715-722. doi:10.1038/nchem.2749

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2016

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20

Shiota, M.; Yamazaki, T.; Yoshimatsu, K.; Kojima, K.; Tsugawa, W.; Sode, K.  An Fe–S cluster in the conserved Cys-rich region in the catalytic subunit of FAD-dependent dehydrogenase complexes.  

Bioelectrochemistry 2016, 112, 178-183. doi:10.1016/j.bioelechem.2016.01.010

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2015

 

19

Yoshimatsu, K.; Koide, H.; Hoshino, Y.; Shea, K. J.  Preparation of abiotic polymer nanoparticles for sequestration and neutralization of a target peptide toxin.  Nature Protocols 2015, 10, 4, 595–604. doi:10.1038/nprot.2015.032

 

18

Cho, K.; Fasoli, J. B.; Yoshimatsu, K.; Shea, K. J.; Corn, R. M.  Measuring Melittin Uptake into Hydrogel Nanoparticles with Near-Infrared Single Nanoparticle Surface Plasmon Resonance Microscopy.  Analytical Chemistry 2015, 87, 9, 4973-4979. doi:10.1021/acs.analchem.5b00776

 

 

2014

17

Beierle, J. M.; Yoshimatsu, K.; Chou, B.; Mathews, M. A. A.; Lesel, B. K.; Shea, K. J. Polymer Nanoparticle Hydrogels with Autonomous Affinity Switching for the Protection of Proteins from Thermal Stress.  Angewandte Chemie International Edition 2014, 53, 35, 9275–9279. doi:10.1002/anie.201404881

16

Yoshimatsu, K.; Yamazaki, T.; Hoshino, Y.; Rose, P. E.; Epstein, L. F.; Miranda, L. P.; Tagari, P.; Beierle, J. M.; Yonamine, Y.; Shea, K. J.  Epitope Discovery for a Synthetic Polymer Nanoparticle: A New Strategy for Developing a Peptide Tag.  Journal of the American Chemical Society 2014, 136, 4, 1194–1197. doi:10.1021/ja410817p

 

15

Malm, B.; Yoshimatsu, K.; Ye, L.; Krozer, A. Characterization of molecularly imprinted polymer nanoparticles by photon correlation spectroscopy.  Journal of Molecular Recognition 2014, 27, 12, 714–721. doc:10.1002/jmr.2397

 

2013

 

14

Pevarnik, M.; Schiel, M.; Yoshimatsu, K.; Vlassiouk, I. V.; Kwon, J. S.; Shea, K. J.; Siwy, Z. S.  Particle Deformation and Concentration Polarization in Electroosmotic Transport of Hydrogels through Pores.  ACS NANO 2013, 7, 4, 3720–3728. doi:10.1021/nn400774e

 

13

Yonamine, Y.; Yoshimatsu, K.; Lee, S.-H.; Hoshino, Y.; Okahata, Y.; Shea, K. J.  Polymer Nanoparticle–Protein Interface. Evaluation of the Contribution of Positively Charged Functional Groups to Protein Affinity.  ACS Applied Materials & Interfaces 2013, 5, 2, 374–379. doi:10.1021/am302404q

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12

Yanagida, M.; Numata, Y.; Yoshimatsu, K.; Satoh, S.; Han, L.  Effective charge collection in dye-sensitized nanocrystalline TiO2.  Advances in Natural Sciences: Nanoscience and Nanotechnology 2013, 4, (1), 015006. doi:10.1088/2043-6262/4/1/015006

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2012

 

11

Yoshimatsu, K.; Lesel, B. K.; Yonamine, Y.; Beierle, J. M.; Hoshino, Y.; Shea, K. J.  Temperature-Responsive “Catch and Release” of Proteins by using Multifunctional Polymer-Based Nanoparticles.  Angewandte Chemie International Edition 2012, 51, 10, 2405–2408. doi:10.1002/anie.201107797  (Highlighted in Materials Today, 2012, 15, 3, 81)
 

10

Yanagida, M.; Numata, Y.; Yoshimatsu, K.; Ochiai, M.; Naito, H.; Han, L. Y.  Structure of electron collection electrode in dye-sensitized nanocrystalline TiO2.  Electrochimica Acta 2013, 87, 309–316. doi:10.1016/j.electacta.2012.09.049

 

9

Trikka, F. A.; Yoshimatsu, K.; Ye, L.; Kyriakidis, D. A.  Molecularly imprinted polymers for histamine recognition in aqueous environment.  Amino Acids 2012, 45, 5, 2113–2124. doi:10.1007/s00726-012-1297-8

 

8

Yoshimatsu, K.; Yamazaki, T.; Chronakis, I. S.; Ye, L.  Influence of Template/Functional Monomer/Cross-Linking Monomer Ratio on Particle Size and Binding Properties of Molecularly Imprinted Nanoparticles.  Journal of Applied Polymer Science 2012, 124, 2, 1249–1255. doi:10.1002/app.35150
 

 

2010

 

7

Suksrichavalit, T.; Yoshimatsu, K.; Prachayasittikul, V.; Bülow, L.; Ye, L.  "Clickable" affinity ligands for effective separation of glycoproteins.  Journal of Chromatography A 2010, 1217, 23, 3635–3641. doi:10.1016/j.chroma.2010.03.050

 

 

2009

 

6

Yoshimatsu, K.; LeJeune, J.; Spivak, D. A.; Ye, L.  Peptide-imprinted polymer microspheres prepared by precipitation polymerization using a single bi-functional monomer.  The Analyst 2009, 134, 4, 719–724. doi:10.1039/b814967d
 

 

2008

 

5

Yoshimatsu, K.; Ye, L.; Stenlund, P.; Chronakis, I. S.  A simple method for preparation of molecularly imprinted nanofiber materials with signal transduction ability.  Chemical Communications 2008, 17, 2022–2024. doi:10.1039/b719586a

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4

Yoshimatsu, K.; Ye, L.; Lindberg, J.; Chronakis, I. S.  Selective molecular adsorption using electrospun nanofiber affinity membranes.  Biosensors and Bioelectronics 2008, 23, 7, 1208–1215. 

doi:10.1016/j.bios.2007.12.002
 

 

3

Reimhult, K.; Yoshimatsu, K.; Risveden, K.; Chen, S.; Ye, L.; Krozer, A.  Characterization of QCM sensor surfaces coated with molecularly imprinted nanoparticles.  Biosensors and Bioelectronics 2008, 23, 12, 1908–1914. 

doi:10.1016/j.bios.2008.02.011

 

 

2007

 

2

Yoshimatsu, K.; Reimhult, K.; Krozer, A.; Mosbach, K.; Sode, K.; Ye, L.  Uniform molecularly imprinted microspheres and nanoparticles prepared by precipitation polymerization: The control of particle size suitable for different analytical applications.  Analytica Chimica Acta 2007, 584, 1, 112–121. 

doi:10.1016/j.aca.2006.11.004
(Ranked 2nd in the Hottest/Most Downloaded Articles in Anal. Chim. Acta during January to March, 2007)
 

 

2006

 

1

Ye, L.; Yoshimatsu, K.; Kolodziej, D.; Francisco, J. D. C.; Dey, E. S.  Preparation of Molecularly Imprinted Polymers in Supercritical Carbon Dioxide.  Journal of Applied Polymer Science 2006, 102, 3, 2863–2867. 

doi:10.1002/app.24648

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