Koseki J. Kobayashi-Kirschvink

Broad Institute of MIT and Harvard
Klarman Cell Observatory
415 Main Street
Cambridge MA, 02142

I'm Koseki, an incoming Assistant Professor at the University of Chicago, Department of Medicine and the Pritzker School of Molecular Engineering. I'm currently a Post-doctoral Associate at the Broad Institute of MIT and Harvard, working with Drs Aviv Regev and Peter So. My interest lies in combining the strengths of microscopy and genomics through machine learning. I'm especially interested in label-free imaging modalities such as Raman microscopy, and my recent work Raman2RNA showed that genomic profiles could be predicted in live single-cells using deep neural networks. My work has been supported by the Japanese Society of the Promotion of Science (JSPS) overseas research, the Naito Foundation overseas research, and the JSPS graduate research fellowships.

In my spare time I enjoy playing baseball and snowboarding, and recently learned how to sail.

Academic Employment

Postdoctoral Fellow with Dr. Aviv Regev (Broad Institute of MIT and Harvard) and Dr. Peter So (MIT)

Education

Ph.D. in Biophysics, University of Tokyo

B.E. in Applied Physics, University of Tokyo

Select Publications

Koseki J. Kobayashi-Kirschvink, Alex Matlock, Peter So, Jeonwoong Kang, "High-throughput Raman spectroscopy by horizontally shifted collection fibers," Analytical Chemistry, 2024, cover highlight

Johain R. Ounadjela*, Ke Zhang*, Koseki J. Kobayashi-Kirschvink*, …, Fei Chen, Sandra Heider, Jian Shu, "Spatial multiomic landscape of the human placenta at molecular resolution," Nature Medicine, 10.1038/s41591-024-03073-9, 2024

Koseki J. Kobayashi-Kirschvink†, …, Peter So, Tommaso Biancalani†, Jian Shu†, Aviv Regev†, “Raman2RNA: Live-cell label-free prediction of single-cell RNA profiles by Raman microscopy,” Nature Biotechnology, 2024

Ken-ichiro Kamei, Koseki J. Kobayashi-Kirschvink, Takashi Nozoe, Hidenori Nakaoka, Miki Umetani, Yuichi Wakamoto, “Raman spectra and gene expression correspondences reveal global stoichiometry conservation architecture in cells,” bioRxiv (2023)

Charles Comiter, Eeshit Vaishnav, …, Koseki J. Kobayashi-Kirschvink, Jian Shu, Aviv Regev†, “Accelerated multimodal tissue data analysis with SCHAF: the Single-Cell omics from Histology Analysis Framework,” bioRxiv (2023)

Koseki J. Kobayashi-Kirschvink†, Hidenori Nakaoka, Arisa Oda, Ken-ichiro F. Kamei, Kazuki Nosho, Hiroko Fukushima, Yu Kanesaki, Shunsuke Yajima, Haruhiko Masaki, Kunihiro Ohta, Yuichi Wakamoto†: “Linear Regression Links Transcriptomic Data and Cellular Raman Spectra,” Cell Systems (2018)

†Corresponding authors