Supervised Contrastive Block Disentanglement

Authors: Makino, Taro, Park, Ji Won, Tagasovska, Natasa, Kudo, Takamasa, Coelho, Paula, Huetter, Jan-Christian, Yao, Heming, Hoeckendorf, Burkhard, Leote, Ana Carolina, Ra, Stephen, Richmond, David, Cho, Kyunghyun, Regev, Aviv, Lopez, Romain

Subject Terms: Computer Science - Machine Learning

Access URL: http://arxiv.org/abs/2502.07281

Context-dependent regulation of lipid accumulation in adipocytes by a HIF1α-PPARγ feedback network

Authors: Kudo, Takamasa, Zhao, Michael L., Jeknić, Stevan, Kovary, Kyle M., LaGory, Edward L., Covert, Markus W., Teruel, Mary N.

Source: In Cell Systems 20 December 2023 14(12):1074-1086

Cell-to-cell variability in Myc dynamics drives transcriptional heterogeneity in cancer cells

Authors: Liu, Chad, Kudo, Takamasa, Ye, Xin, Gascoigne, Karen

Source: In Cell Reports 25 April 2023 42(4)

An optimized reporter of the transcription factor hypoxia-inducible factor 1α reveals complex HIF-1α activation dynamics in single cells

Authors: Jeknić, Stevan, Kudo, Takamasa, Song, Joanna J., Covert, Markus W.

Source: In Journal of Biological Chemistry April 2023 299(4)

A multiplexed epitope barcoding strategy that enables dynamic cellular phenotypic screens

Authors: Kudo, Takamasa, Lane, Keara, Covert, Markus W.

Source: In Cell Systems 18 May 2022 13(5):376-387

A forecast for large-scale, predictive biology: Lessons from meteorology

Authors: Covert, Markus W., Gillies, Taryn E., Kudo, Takamasa, Agmon, Eran

Source: In Cell Systems 16 June 2021 12(6):488-496

Escalating Threat Levels of Bacterial Infection Can Be Discriminated by Distinct MAPK and NF-κB Signaling Dynamics in Single Host Cells

Authors: Lane, Keara, Andres-Terre, Marta, Kudo, Takamasa, Monack, Denise M., Covert, Markus W.

Source: In Cell Systems 27 March 2019 8(3):183-196

Deep learning for cellular image analysis

Authors: Moen, Erick, Bannon, Dylan, Kudo, Takamasa, Graf, William, Covert, Markus, Van Valen, David

Source: Nature methods. 16(12):1233-1246

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100190911223.0x000001&indx=1&recIds=ETOCvdc_100190911223.0x000001

A convex 3D deconvolution algorithm for low photon count fluorescence imaging

Authors: Ikoma, Hayato, Broxton, Michael, Kudo, Takamasa, Wetzstein, Gordon

Source: Scientific reports. 8(1):1-12

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100174802761.0x000001&indx=1&recIds=ETOCvdc_100174802761.0x000001

Robustness of MEK-ERK Dynamics and Origins of Cell-to-Cell Variability in MAPK Signaling

Authors: Filippi, Sarah, Barnes, Chris P., Kirk, Paul D.W., Kudo, Takamasa, Kunida, Katsuyuki, McMahon, Siobhan S., Tsuchiya, Takaho, Wada, Takumi, Kuroda, Shinya, Stumpf, Michael P.H.

Source: In Cell Reports 14 June 2016 15(11):2524-2535

Live-cell measurements of kinase activity in single cells using translocation reporters

Authors: Kudo, Takamasa, Jeknić, Stevan, Macklin, Derek N, Akhter, Sajia, Hughey, Jacob J, Regot, Sergi, Covert, Markus W

Source: Nature protocols. 13(1):155-169

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100132383332.0x000001&indx=1&recIds=ETOCvdc_100132383332.0x000001

Controlling low rates of cell differentiation through noise and ultrahigh feedback

Authors: Ahrends, Robert, Ota, Asuka, Kovary, Kyle M., Kudo, Takamasa, Park, Byung Ouk, Teruel, Mary N.

Source: Science, 2014 Jun . 344(6190), 1384-1389.

Access URL: http://www.jstor.org/stable/24744702

Robustness and Compensation of Information Transmission of Signaling Pathways

Authors: Uda, Shinsuke, Saito, Takeshi H, Kudo, Takamasa, Kokaji, Toshiya, Tsuchiya, Takaho, Kubota, Hiroyuki, Komori, Yasunori, Ozaki, Yu-ichi, Kuroda, Shinya

Source: Science, 2013 Aug 01. 341(6145), 558-561.

Access URL: http://dx.doi.org/10.1126/science.1234511

Potential Relationships between the Median Nerve Cross-Sectional Area and Physical Characteristics in Unilateral Symptomatic Carpal Tunnel Syndrome Patients.

Authors: Ikumi, Akira, Yoshii, Yuichi, Kudo, Takamasa, Kohyama, Sho, Ogawa, Takeshi, Hara, Yuki, Ishii, Tomoo

Source: Journal of Clinical Medicine; Apr2023, Vol. 12 Issue 7, p2515, 10p

Subject Terms: CARPAL tunnel syndrome, MEDIAN nerve, BODY mass index, NEUROLOGICAL disorders, DISEASE duration

Author Correction: Multiplexed, image-based pooled screens in primary cells and tissues with PerturbView.

Authors: Kudo, Takamasa (AUTHOR), Meireles, Ana M. (AUTHOR), Moncada, Reuben¹ (AUTHOR), Chen, Yushu (AUTHOR), Wu, Ping (AUTHOR), Gould, Joshua (AUTHOR), Hu, Xiaoyu (AUTHOR), Kornfeld, Opher (AUTHOR), Jesudason, Rajiv (AUTHOR), Foo, Conrad (AUTHOR), Höckendorf, Burkhard (AUTHOR), Corrada Bravo, Hector (AUTHOR), Town, Jason P. (AUTHOR), Wei, Runmin (AUTHOR), Rios, Antonio (AUTHOR), Chandrasekar, Vineethkrishna (AUTHOR), Heinlein, Melanie (AUTHOR), Chuong, Amy S. (AUTHOR), Cai, Shuangyi^1,2 (AUTHOR), Lu, Cherry Sakura^1,3 (AUTHOR)

Source: Nature Biotechnology. Feb2025, p1-1.

Subject Terms: *MULTIPLEXING, *TISSUES

PerturbView: scalable image-based perturbation screens in cells and tissues

Authors: Kudo, Takamasa

Source: Nature Reviews Immunology; 20250101, Issue: Preprints p1-1, 1p

An isolated rupture of the flexor digitorum tendon of the index finger following volar locking plate fixation of a distal radius fracture: A case report

Authors: Kudo, Takamasa, Kohyama, Sho, Yoshii, Yuichi

Source: In Trauma Case Reports October 2023 47

Engineered Fluorescent E. coli Lysogens Allow Live-Cell Imaging of Functional Prophage Induction Triggered inside Macrophages

Authors: Bodner, Katie, Melkonian, Arin L., Barth, Angela I.M., Kudo, Takamasa, Tanouchi, Yu, Covert, Markus W.

Source: In Cell Systems 25 March 2020 10(3):254-264

Deep learning multi-shot 3D localization microscopy using hybrid optical—electronic computing

Authors: Ikoma, Hayato, Kudo, Takamasa, Peng, Yifan, Broxton, Michael, Wetzstein, Gordon

Source: Optics letters. 46(24):6023-6023

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN628540389&indx=1&recIds=ETOCRN628540389

Multiplexed, image-based pooled screens in primary cells and tissues with PerturbView.

Authors: Kudo, Takamasa (AUTHOR), Meireles, Ana M. (AUTHOR), Moncada, Reuben¹ (AUTHOR), Chen, Yushu (AUTHOR), Wu, Ping (AUTHOR), Gould, Joshua (AUTHOR), Hu, Xiaoyu (AUTHOR), Kornfeld, Opher (AUTHOR), Jesudason, Rajiv (AUTHOR), Foo, Conrad (AUTHOR), Höckendorf, Burkhard (AUTHOR), Corrada Bravo, Hector (AUTHOR), Town, Jason P. (AUTHOR), Wei, Runmin (AUTHOR), Rios, Antonio (AUTHOR), Chandrasekar, Vineethkrishna (AUTHOR), Heinlein, Melanie (AUTHOR), Chuong, Amy S. (AUTHOR), Cai, Shuangyi^1,2 (AUTHOR), Lu, Cherry Sakura^1,3 (AUTHOR)

Source: Nature Biotechnology. Oct2024, p1-10.