David W. Craig Lab
Research Lab Overview
The Craig Lab conducts bioinformatics research within the Department of Integrative Translational Sciences at the Beckman Research Institute of City of Hope. We integrate computational methodologies with experimental benchwork to investigate the molecular mechanisms driving cancer and neurodegenerative diseases.
The Craig Lab primarily focuses on leveraging spatial transcriptomic technologies to integrate single-cell transcriptomics and proteomics with bulk genomics and transcriptomics within their spatial context. This multi-modal molecular approach enables more profound exploration of critical areas in cancer research, including the tumor microenvironment and tumor-associated microbiome. Current projects include:
- Application of Visium, Visium HD, Xenium and CODEX technologies in glioblastoma
- Decoding the tumor microenvironment using deep learning by integrating spatial transcriptomics with histopathology
- Spatial microbiome analysis of solid tumors
The Craig Lab also currently performs bioinformatic analyses of germline and somatic genomic variation to uncover colorectal cancer driver mutations, with a particular focus on Hispanic patient populations.
Additionally, in collaboration with international consortia, the Craig Lab investigates potential biomarkers for early detection and progression of Parkinson’s disease. Our projects utilize bulk and single-cell RNA and ATAC sequencing, as well as both short- and long-read transcriptomic data.
Dr. Craig is a Professor and the Chair of the Department of Integrative Translational Sciences, Deputy Director of Translational Sciences at the Beckman Research Institute of City of Hope, and Associate Director of Data Science in the Comprehensive Cancer Center.
Lab Members
John is a graduate student who joined the Craig Lab in 2023. His
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John is a graduate student who joined the Craig Lab in 2023. His research focuses on integrating multi-omic data — including bulk exome and RNA sequencing, single-cell RNA sequencing and spatial transcriptomics — to decode the tumor microenvironment in glioblastoma. Outside the lab, he enjoys weightlifting, playing basketball and surfing.
Nina is a Ph.D. student who joined the Craig Lab in 2022. She
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Nina is a Ph.D. student who joined the Craig Lab in 2022. She develops deep learning models that integrate histology and spatial transcriptomics to investigate tumor heterogeneity in glioblastoma and other aggressive cancers. She holds a master’s degree in biomedical informatics from University of Southern California and a bachelor’s degree in biochemistry from University of California, Los Angeles. Outside the lab, she enjoys powerlifting and freediving — and hopes to bench 100 kg one day.
Rayyan joined the Craig Lab in 2024 after completing her
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Rayyan joined the Craig Lab in 2024 after completing her bachelor’s degree at University of California, Berkeley, and gaining industry experience. She later earned her master’s degree from University of Southern California. Her research focuses on adapting and integrating spatial transcriptomic technologies for broader applications. Outside the lab, Rayyan is a passionate home cook and enjoys spending time with her husband and their orange cat, Mango.
Bohan joined the Craig Lab in 2022 as a graduate student at
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Bohan joined the Craig Lab in 2022 as a graduate student at University of Southern California. Prior to beginning his Ph.D. at City of Hope, he worked as a bioinformatician at the Molecular Genomics Core of the USC Norris Comprehensive Cancer Center. His research focuses on developing algorithms to analyze spatial transcriptomics data. Outside the lab, he enjoys gaming and reading magical realism novels.
Yonatan joined the Craig Lab as a postdoctoral fellow in 2023. He
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Yonatan joined the Craig Lab as a postdoctoral fellow in 2023. He earned his Ph.D. in Craniofacial Molecular Biology from University of Southern California in 2022, under the mentorship of Dr. Min Yu. His research focuses on integrating somatic data modalities to help interpret germline variants of uncertain significance. In his free time, he enjoys playing basketball and spending time with his family.
Lab Alumni
- Sophia Manjarrez, Ph.D.
- Michelle Webb, M.S., Ph.D.
- Mackenzie Postel, Ph.D.
- Szabolcs Szelinger, Ph.D.
- Alexis Christoforides, M.S.
- Brooke Hjelm, Ph.D.
- Nils Homer, Ph.D.
- Rebecca Halperin, Ph.D.
- Sara Nasser
- Michael Kruer, M.D.
- Ivo Violich
- Ramiyapriya Sivakumar
- Jessica Aldrich
- Tyler Izatt
- Ahmet Kurdoglu
- Waibhav Tembe, Ph.D.
- Shripath Sinari
- Hollie Benson
- Jill Gerber
- Elizabeth Salomon
- Sotirus Mitropanopoulos
- Corrie Panginiban
- Aswin Sekar
- Abe Itty
- David Hilgers
- James Long
- Iviana Malencia
- Shobana Seker
- Daniel Enriquez
- Merideth Sanchez
- Gregory Frantzen
- Carmel McCullough
- Albert Shieh
- Anne Lee
- Kayla Xu
Our Publications
Soni, S., Mittal, P., Lo, J.H., Yang, Y., Smbatyan, G., Lee, K., Wan, J., Kumagai, H., Yen, K., Mehta, H.H., Miller, B., Torres-Gonzalez, L., Battaglin, F., Shah, U.H., Bartolini, M., Zhang, W., Craig, D.W., Millstein, J., Cohen, P., Lenz, H.
Sanjuan-Ruiz, I., Serneels, L., Craessaerts, K., Goate, A., Annaert, W., Chávez-Gutiérrez, L., Shi, Y., Sheikh-Bahaei, N., Jen, J.C., Ramos, E.M., Campan, M., Ward, P.M., Magaki, S., Bartlone, K., Vinters, H.V., Dominantly Inherited Alzheimer Network, Craig, D.W., Ringman, J.M., De Strooper, B.
Xu, K.Y., Violich, I., Hutchins, E., Alsop, E., Nalls, M.A., Moore, A., Blauwendraat, C., Gibbs, J.R., Cookson, M.R., Van Keuren-Jensen, K., Craig, D.W.
Lenz, H., Craig, D.W., Johnson, K.C., Verhaak, R., Bhattacharyya, O., Davis, B., Wesley, C., Byron, S.A., Willman, C., Kelley, L., Claus, E.B., Trent, J., Culver, J.O., Gray, S.W., Church, A.J.
Aparicio, J.G., Stachelek, K., Garcia-Filion, P., Brown, B., Stewart, C., Craig, D.W., Li, W.L., Cobrinik, D., Borchert, M.
Latest Research News
Contact Information
34.1291661, -117.9725847
Duarte, CA 91010