Siran Li

Siran Li

Research Assistant Professor

Ph.D., Princeton University, 2015

siranli@cshl.edu | 516-367-5067

Faculty Profile

I develop novel high-throughput, multi-omics methods for single-cell analysis, and apply these methods to understanding complex physiology and disease, including cancer, immunology and neurobiology in humans and other organisms. In cancer, I am working on understanding how the host components interact with a tumor.

Single-cell analyses play an important and unique role in understanding the heterogeneity of a tissue and the interactions between cells. Li’s research focuses on developing high-throughput, multi-omics, single-cell methods and using them to understand the patterns of gene expression and genomic variation of cancer cells and tissues. In spite of rapid advances in single-cell protocols, existing methods still suffer from low coverage, cross-contamination, poor sampling, and high cost. To resolve these problems, Li developed a new platform for single-cell sequencing, in which single-cell nucleic acids are we polymerized into balls of polyacrylamide (BAG-seq). By customizing the choice of Acrydite-modified oligonucleotides, the BAGs can capture DNA or RNA. Once the polymerization is complete, the cell contents are captured and isolated within each BAG, enabling further manipulations without cross contamination. Split-pool barcoding assigns a unique tag to each BAG, enabling a high-throughput low-cost single-cell approach superior to existing single-cell methods. Using BAG-seq, the lab is working on characterizing the host elements in tumors and learning how the host components interact with tumors. In addition, by collaborating with Dr. Dan Levy, Li developed a method of using conventional short-read sequencing to obtain ultra-low-error-rate de novo haplotype-phased sequence assemblies of regions 10 KB in length without reliance on a reference genome.

Selected Publications

Editorial for the Special Issue on Droplet Microfluidics

8 Dec 2020 | Micromachines | 11(12):1086
Brouzes, E, Li, S

Copolymerization of single-cell nucleic acids into balls of acrylamide gel

14 Nov 2019 | Genome Research | 30(1):49-61
Li, S, Kendall, J, Park, S, Wang, Z, Alexander, J, Moffitt, A, Ranade, N, Danyko, C, Gegenhuber, B, Fischer, S, Robinson, B, Lepor, H, Tollkuhn, J, Gillis, J, Brouzes, E, Krasnitz, A, Levy, D, Wigler, M

Impact of Detergents on Membrane Protein Complex Isolation

5 Jan 2018 | Journal of Proteome Research | 17(1):348-358
Lee, Y, Baath, J, Bastle, R, Bhattacharjee, S, Cantoria, M, Dornan, M, Gamero-Estevez, E, Ford, L, Halova, L, Kernan, J, Kurten, C, Li, S, Martinez, J, Sachan, N, Sarr, M, Shan, X, Subramanian, N, Rivera, K, Pappin, D, Lin, S

A microfluidic device and automatic counting system for the study of C. elegans reproductive aging.

21 Jan 2015 | Lab on a Chip | 15(2):524-531
Li, Siran, Stone, Howard, Murphy, Coleen

All Publications

Magnetically Functionalized Hydrogels for High-Throughput Genomic Applications

1 Jan 2023 | Advanced Materials Technologies
Lammertse, E, Li, S, Kendall, J, Kim, C, Morris, P, Ranade, N, Levy, D, Wigler, M, Brouzes, E

Targeted de novo phasing and long-range assembly by template mutagenesis

13 Jul 2022 | Nucleic Acids Research (NAR)
Li, Siran, Park, Sarah, Ye, Catherine, Danyko, Cassidy, Wroten, Matthew, Andrews, Peter, Wigler, Michael, Levy, Dan

Parity-induced changes to mammary epithelial cells control NKT cell expansion and mammary oncogenesis

7 Dec 2021 | Cell Reports | 37(10):110099
Hanasoge Somasundara, Amritha, Moss, Matthew, Feigman, Mary, Chen, Chen, Cyrill, Samantha, Ciccone, Michael, Trousdell, Marygrace, Vollbrecht, Macy, Li, Siran, Kendall, Jude, Beyaz, Semir, Wilkinson, John, Dos Santos, Camila

Intraductal Transplantation Models of Human Pancreatic Ductal Adenocarcinoma Reveal Progressive Transition of Molecular Subtypes.

1 Oct 2020 | Cancer Discovery | 10(10):1566-1589
Miyabayashi, Koji, Baker, Lindsey, Deschênes, Astrid, Traub, Benno, Caligiuri, Giuseppina, Plenker, Dennis, Alagesan, Brinda, Belleau, Pascal, Li, Siran, Kendall, Jude, Jang, Gun, Kawaguchi, Risa, Somerville, Tim, Tiriac, Hervé, Hwang, Chang-Il, Burkhart, Richard, Roberts, Nicholas, Wood, Laura, Hruban, Ralph, Gillis, Jesse, Krasnitz, Alexander, Vakoc, Christopher, Wigler, Michael, Notta, Faiyaz, Gallinger, Steven, Park, Youngkyu, Tuveson, David

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