黒田ラボ Kuroda Lab

Welcome to Kuroda Lab.
Ultimate goal of our study is understanding of mechanism of metabolic and signaling networks that regulate various cellular functions including cellular signaling and metabolic regulation at systems level. In these biological processes, the same input stimulation elicits distinct outcomes depending temporal patterns of input, and we are interested in quantitative mechanisms of the encoding/decoding systems via signaling networks that underlie these processing. We use both experimental and computational approaches. Thus, we are trying to understand cellular processes in terms of Systems Biology.
See also our movie of the introduction of Kuroda Lab!

We welcome international phD students via Global Science Graduate Course (GSGC), which provides a monthly scholarship during the phD program. Please visit the website of GSGC.

24.10.22 “iTraNet: integrated Trans-Omics Network Visualization and Analysis” was released.
24.06.18 “Structural robustness and temporal vulnerability of the starvation-responsive metabolic network in liver of healthy and obese mice” has been published in bioRxiv.
24.06.18 “Clarifying obesity-related metabolic abnormalities at the molecular level — Metabolic regulation during feeding in obese mice differs significantly from that during fasting” has been featured in JSTnews.
24.06.11 “Members” updated.
24.05.17 “Publications” updated. “Model selection reveals selective regulation of blood amino acid and lipid metabolism by insulin in humans” has been published in iScience.
24.04.15 “Members” updated.
24.04.08 “Members” updated.
24.03.27 “Seminars”updated (by Dr. Arda Halu; May 22(Wed.), 2024, 22:00~, Zoom)
24.03.21 “Publications” updated. “DNA hypomethylation characterizes genes encoding tissue-dominant functional proteins in liver and skeletal muscle” has been published in Scientific Reports.
24.03.03 “Publications” updated. “Trans-omic analysis reveals opposite metabolic dysregulation between feeding and fasting in liver associated with obesity” has been published in iScience.
23.11.23 “Seminars”updated (by Dr. Cholsoon Jang; Dec. 13(Wed.), 2023, 9:00~, Zoom)
23.10.23 “Seminars”updated (by Dr. Tetsuhiro Hatakeyama; Nov. 2(Thu.), 2023, 16:00~, Zoom and Faculty of Science Bldg.3, 4F, Room 412)
23.10.03 “Members” updated.
23.10.02 Dr. Julio Saez-Rodriguez gave us a wondaful talk in our seminar. ; Sep. 25(Mon.), 2023
23.09.11 “Members” updated.
23.08.24 “Seminars”updated (by Dr. Markus Basan; Sep. 21(Thu.), 2023, 21:00~, Zoom)
23.08.09 Dr. Heather Harrington gave us a wondaful talk in our seminar. ; Aug. 7(Mon.), 2023
23.07.30 Prof. Shinya Kuroda’s talk at the IBS BIMAG 2023 Spring Colloquium is available on YouTube.
23.07.04 “Seminars”updated (by Dr. Jared Rutter; Jul. 4(Tue.), 2023, 9:00~, Zoom)
23.05.02 “Members” updated.
23.04.08 “Members” updated.
23.04.04 “Members” updated.
23.03.06 A lecture in Biomdeical Mathematics Online Colloquium (March, 3rd, 2023) was released in YouTube.
23.02.22 “Publications” updated. “Optogenetic decoding of Akt2-regulated metabolic signaling pathways in skeletal muscle cells using transomics analysis” has been published in Science Signaling.
23.02.18 “Publications” updated. “Features extracted using tensor decomposition reflect the biological features of the temporal patterns of human blood multimodal metabolome” has been published in PLoS ONE.
23.01.31 “Seminars”updated (by Dr. Yumi Konagaya (Ida); Feb. 20(Mon.), 2023, 13:30~, Zoom and Faculty of Science Bldg.3, 4F, Room 412)
23.01.31 “Seminars”updated (by Dr. Hafumi Nishi; Feb. 17(Fri.), 2023, 13:30~, Zoom)
22.08.18 “Seminars”updated (by Dr. Takema Fukatsu; Sep. 02(Fri.), 2022, 16:00~, Zoom)
22.08.18 “Publications” updated. “In vivo transomic analyses of glucose-responsive metabolism in skeletal muscle reveal core differences between the healthy and obese states” has been published in Scientific Reports.
22.06.22 “Seminars”updated (by Dr. Hikari Yoshitane; Jul. 04(Mon.), 2022, 15:00~, Zoom)
22.05.17 “Seminars”updated (by Dr. Kentaro Tomii; Jun. 06(Mon.), 2022, 10:00~, Zoom)
22.04.01 “Publications” updated. “Trans-omics analysis of insulin action reveals a cell growth subnetwork which co-regulates anabolic processes” has been published in iScience.
22.04.01 “Members” updated.
22.04.01 “Publications” updated. “Quantitative metabolic fluxes regulated by trans-omic networks” has been published in Biochemical Journal.
22.03.25 “Seminars”updated (by Dr. Yuichi Wakamoto; Apr. 27(Wed.), 2022, 16:00~, Zoom)
22.03.06 “Seminars”updated (by Prof. Hideyuki Shimizu; Mar. 30(Wed.), 2022, 16:00~, Zoom)
22.02.10 “Publications” updated. “Multi-omics-based label-free metabolic flux inference reveals obesity-associated dysregulatory mechanisms in liver glucose metabolism” has been published in iScience.
“Four features of temporal patterns characterize similarity among individuals and molecules by glucose ingestion in humans” has been published in npj Systems Biology and Applications.
22.01.31 “Members” updated.
21.12.23 “Seminars”updated (by Prof. Yoshihiro Yamanishi; Mar. 14(Mon.), 2022, 16:00~, Zoom)
21.12.23 “Seminars”updated (by Prof. Shalev Itzkovitz; Mar. 10(Thu.), 2022, 16:00~, Zoom)
21.12.08 “Seminars”updated (by Dr. Shinya Oki; Feb. 10(Thu.), 2022, 16:00~, Zoom)
21.12.08 “Seminars”updated (by Prof. Takashi Ikegami; Dec. 21(Tue.), 2021, 16:00~, Zoom)
21.10.21 “Members” updated.
21.10.13 “Seminars”updated (by Dr. Hiroshi Ochiai; Nov. 16(Tue.), 2021, 16:00~, Zoom)
21.09.30 “Seminars”updated (by Prof. Alexander Hoffmann; Oct. 27(Wed.), 2021, 10:00~, Zoom)
21.09.16 “Publications” updated. “Cell-to-cell variability serves as information not noise” has been published in Current Opinion in Systems Biology.
21.08.27 “Seminars”updated (by Dr. Itoshi Nikaido; Sep. 14(Tue.), 2021, 17:00~, Zoom)
21.08.23 “Seminars”updated (by Mr. Masaki Shirai; Sep. 01(Wed.), 2021, 16:00~, Zoom)
21.06.21 “Research” updated.
21.06.15 “Research” updated.
21.06.07 “Members” updated.
21.04.26 “Members” updated.
21.04.06 “Members” updated.
21.03.22 “Seminars”updated (by Prof. Paola Picotti; May. 17(Mon.), 2021, 16:00~, Zoom)
21.03.22 “Seminars”updated (by Dr. Ryuichiro Nakato; Apr. 13(Tue.), 2021, 14:00~, Zoom)
21.03.09 “Publications” updated. “Trans-omic analysis reveals obesity-associated dysregulation of inter-organ metabolic cycles between the liver and skeletal muscle” has been published in iScience.
20.12.02 “Publications” updated. “Transomics analysis reveals allosteric and gene regulation axes for altered hepatic glucose-responsive metabolism in obesity” has been published in Science Signaling.
20.10.21 “Members” updated.
20.09.22 “Publications” updated. “Trans-omic analysis reveals ROS-dependent pentose phosphate pathway activation after high-frequency electrical stimulation in C2C12 myotubes” has been published in iScience.
20.09.07 “Publications” updated. “Kinetic trans-omic analysis reveals key regulatory mechanisms for insulin-regulated glucose metabolism in adipocytes” has been published in iScience.
20.09.07 “Publications” updated. “Single-Cell Information Analysis Reveals That Skeletal Muscles Incorporate Cell-to-Cell Variability as Information Not Noise.” has been published in Cell Reports.
20.08.11 “Publications” updated. “Monitoring and mathematical modeling of mitochondrial ATP in myotubes at single-cell level reveals two distinct population with different kinetics” has been published in Quantitative Biology.
20.08.11 “Seminars”updated (by Dr. Genshiro Sunagawa ; Sep. 18(Fri.), 2020, 16:00~, Zoom)
20.06.22 “Members” updated.
20.04.27 “Seminars”updated (by Prof. Yoshihiro Taguchi; May. 14(Thu.), 2020, 15:00~, Zoom)
20.04.20 “Members” updated.
20.03.04 “Publications” updated. “Dynamic 13C Flux Analysis Captures the Reorganization of Adipocyte Glucose Metabolism in Response to Insulin ” has been published in iScience.
20.02.17 “Seminars”updated (by Mr. Jumpei F. Yamagishi; Mar. 12(Thu.), 2020, 11:00~, Faculty of Science Bldg.3, 4F, room 412)
19.11.13 “Seminars”updated (by Dr. Shinpei Kawaoka; Nov. 29(Fri.), 2019, 17:00~, Faculty of Science Bldg.3, 4F, room 412)
19.11.13 “Seminars”updated (by Dr. Yuichi Taniguchi; Jan. 15(Wed.), 2020, 17:00~, Faculty of Science Bldg.3, 4F, room 412)
19.10.28 “Members” updated.
19.10.11 “Publications” updated. “Robustness against additional noise in cellular information transmission” has been published in Physical Review E.
19.09.09 “Seminars”updated (by Prof. Uwe Sauer; Oct. 18(Fri.), 2019, 17:00~, Faculty of Science Bldg.3, 4F, room 412)
19.09.04 “Publications” updated. “Logical design of oral glucose ingestion pattern minimizing blood glucose in humans” has been published in npj Systems Biology and Applications.
19.08.19 “Seminars”updated (by Dr. Maren Diether; Sep. 02(Mon.), 2019 , 11:00~, Faculty of Science Bldg.3, 4F, room 412)
19.07.30 “Seminars” updated (by Dr. Dorota Badowska; Sep. 03(Tue.), 2019 , 17:00~, Faculty of Science Bldg.3, 4F, room 412)
19.07.29“Seminars” updated (by Prof. Takeshi Inagaki; Sep. 06(Fri.), 2019 , 17:00~, Faculty of Science Bldg.3, 4F, room 412)
19.07.08 “Seminars” updated (by Christopher B. Newgard; Sep 18(Wed.), 2019, Faculty of Science Bldg.3, 4F, room 412)
19.07.01 “Seminars” updated (by Shinsuke Uda; Jul 31 (Wed.) Faculty of Science Bldg.3, 4F, room 412)
19.05.13“Publications” updated. “Rate-oriented trans-omics: integration of multiple omic data on the basis of reaction kinetics” has been published in Current Opinion In Systems Biology.
19.05.13“Publications” updated. “NMDAR-Mediated Ca²⁺ Increase Shows Robust Information Transfer in Dendritic Spines” has been published in Biophysical Journal.
19.04.26 “Seminars” updated (by Takashi Tsuboi; Jun 18 (Tue.) Faculty of Science Bldg.3, 4F, room 412)
19.04.22 “Seminars” updated (by Masahide Kikkawa; May17 (Fri.) Faculty of Science Bldg.3, 4F, room 412)
[ICSB2019] We announce that ICSB2019 (International Conference of Systems Biology) will be held in Okinawa Institute of Science and Technology at 31th Oct. to 5th Nov., 2019. The keynote lectures will be given by Dr. Hiroaki Kitano (SBI) and Dr. Lily Peng (Google). One of the highlight is “Systems Biology meets AI”. We all appreciate if anyone not only from systems biology but also from other fields such as AI. For more detail, visit here.
19.04.04 “Members” updated.
19.01.17 “Seminars” updated (by Yuichi Sakumura; Jan. 17 (Thu.) Faculty of Science Bldg.3, 4F, room 412)
19.01.16 “Seminars” updated (by Momoko Horikoshi; Jan. 16 (Wed.) Faculty of Science Bldg.3, 4F, room 412)
18.12.17 “Publications” updated. “Reconstruction of global regulatory network from signaling to cellular functions using phosphoproteomic data” has been published in Genes to Cells.
18.12.12 “Seminars” updated (by Naoki Honda; Dec. 12 (Wed.) Faculty of Science Bldg.3, 4F, room 412)
18.11.13 “Seminars” updated (by Dr. Ernest Fraenkel; Nov. 13 (Tue.) Faculty of Science Bldg.3, 4F, room 412)
18.11.12 “Seminars” updated (by Dr. Jamey D Young; Nov. 12 (Mon.) Faculty of Science Bldg.3, 4F, room 412)
18.09.19 “Seminars” updated (by Dr. Takeshi Bamba; Sep. 19 (Wed.) Faculty of Science Bldg.3, 4F, room 412)
18.09.10 “Publications” updated. “Trans-omic Analysis Reveals Selective Responses to Induced and Basal Insulin across Signaling, Transcriptional, and Metabolic Networks” has been published in iScience.
18.09.07 “Seminars” updated (by Keigo Morita; Sep. 07 (Fri.) Faculty of Science Bldg.3, 4F, room 412)
18.08.31 “Publications” updated. “Automatic Quantitative Segmentation of Myotubes Reveals Single-cell Dynamics of S6 Kinase Activation” has been published in Cell Structure and Function.
18.08.06 “Seminars” updated (by Dr. Andre Levchenko; Aug. 06 (Mon.) Faculty of Science Bldg.3, 4F, room 412)
18.07.31 “Seminars” updated (by Dr. Teppei Shimamura; Jul. 31 (Tue.) Faculty of Science Bldg.3, 3F, room 310)
18.07.31 “Seminars” updated (by Dr. Tsuyoshi Osawa; Jul. 31 (Tue.) Faculty of Science Bldg.3, 3F, room 310)
18.07.19 “Seminars” updated (by Dr. Yasuyuki Ohkawa; Jul. 19 (Thu.) Faculty of Science Bldg.3, 4F, room 412)
18.07.17 “Seminars” updated (by Dr. Luonan Chen; Jul. 17 (Tue.) Faculty of Science Bldg.3, 4F, room 412)
18.06.28 “Publications” updated. “In Vivo Decoding Mechanisms of the Temporal Patterns of Blood Insulin by the Insulin-AKT Pathway in the Liver” has been published in Cell Systems.
18.06.08 “Seminars” updated (by Dr. Roy Wollman; July 02 (Mon.) Faculty of Science Bldg.3, 4F, room 412)
18.05.21 “Seminars” updated (by Dr. Shuichi Shimma; June 14 (Thr.) Faculty of Science Bldg.3, 4F, room 412)
18.04.03 “Members” updated.
18.03.14 “Publications” updated. “Increase in hepatic and decrease in peripheral insulin clearance characterize abnormal temporal patterns of serum insulin in diabetic subjects” has been published in npj Systems Biology and Applications.
18.02.23 “Seminars” updated (by Dr. Hiroshi Ohno; Apr 13 (Fri.) Faculty of Science Bldg.3, 4F, room 412)
18.02.05 “Seminars” updated (by Dr. Noboru Mizushima; May 11 (Fri.) Faculty of Science Bldg.3, 4F, room 412)
18.01.15 “Seminars” updated (by Dr. Yukinori Okada; Mar. 09 (Fri.) Faculty of Science Bldg.3, 4F, room 412)
18.01.15 “Publications” updated. “System identification of signaling dependent gene expression with different time-scale data” has been published in PLoS Computational Biology.
18.01.04 “Publications” updated. “Metabolism as a signal generator across trans-omic networks at distinct time scales” has been published in Current Opinion in Systems Biology.
18.01.18 “Seminars” updated (by Dr. Ken-ichi Hironaka; Jan. 18 (Thu.) Faculty of Science Bldg.3, 3F, room 310)
17.12.20 “Publications” updated. “Dynamic Metabolomics Reveals that Insulin Primes the Adipocyte for Glucose Metabolism” has been published in Cell Reports.
17.12.20 “Seminars” updated (by Dr. Eiryo Kawakami; Dec. 20 (Wed.) Faculty of Science Bldg.3, 4F, room 412)
17.12.13 “Seminars” updated (by Dr. Alejandro Granados; Dec. 13 (Wed.) Faculty of Science Bldg.3, 4F, room 310)
17.10.26 “Seminars” updated (by Dr. H. Craig Mak; Nov. 17 (Fri.) Faculty of Science Bldg.3, 3F, room 310)
17.10.12 “Seminars” updated (by Dr. Nen Saito; Oct. 30 (Mon.) Faculty of Science Bldg.3, 4F, room 412)
17.10.04 “Seminars” updated (by Dr. Akinori Awazu; Nov. 13 (Mon.) Faculty of Science Bldg.3, 4F, room 412)
17.05.16 [Registration closed] We organize a symposium entitled CREST Symposium “The 1st International Symposium for Trans-Omics” on 21-22 Nov. 2017 at Koshiba Hall in Univ. of Tokyo. (Details)
17.08.28 “Seminars” updated (by Dr. Hitoshi Shimano; Sep. 29 (Fri.) Faculty of Science Bldg.3, 3F, room 310)
17.08.04 “Seminars” updated (by Dr. Miki Eto; Sep. 06 (Wed.) Faculty of Science Bldg.3, 4F, room 412)
17.07.11 “Seminars” updated (by Dr. Shigeru Kondo; Jul. 20 (Thu.) Faculty of Science Bldg.3, 3F, room 412)
17.06.16 “Seminars” updated (by Dr. Juro Sakai; Sep. 22 (Fri.) Faculty of Science Bldg.3, 4F, room 412)
17.05.16 “Seminars” updated (by Dr. Nobuyoshi Akimitsu; Jun. 08 (Thu.) Faculty of Science Bldg.3, 4F, room 412)
17.03.28 “Seminars” updated (by Dr. Miki Ebisuya; May 18 (Thu.) Faculty of Science Bldg.3, 4F, room 412)
17.03.01 “Publications” updated. “Small-Volume Effect Enables Robust, Sensitive, and Efficient Information Transfer in the Spine” has been published in Biophysical Journal.
17.02.20 “Seminars” updated (by Dr. Katsuhiko Shirahige; Mar. 17 (Fri.) Faculty of Science Bldg.3, 4F, room 412)
17.01.26 “Publications” updated. Our preview of “Metabolism-Centric Trans-Omics” has been published in Cell Systems.