Cable D.M., Murray M., Shanmugam V., Zhang S., Diao M., Chen H., Macosko E.Z., Irizarry R.A. *, †, Chen F. *, † (Nature Methods, 2022) Cell type specific differential expression for spatial transcriptomics. (*,equal contribution; †, Corresponding Author) [Bioarxiv]

Jiang K**., Koob J.**, Chen D.X.**, Krajeski N.R.**, Zhang Y.**, Villger L., Zhou W., Abudayyeh O.O. *, †, Chen F. *, †, Gootenberg J.S. *, †, Programmable eukaryotic protein expression with RNA sensors (*, **equal contribution; †, Corresponding Author) [Bioarxiv]

Zhao T.*, Chiang Z.D.*, Morriss J.W., LaFave L.M., Murray E.M., Del Priore I., Meli K., Lareau C.A., Nadaf M.N., Li J., Earl A.S., Macosko E.Z.,  Jacks T.,  Buenrostro J.D.**,  Chen F.** (Nature, 2022) Spatial genomics enables multi-modal study of clonal heterogeneity in tissues  (*, equal contribution, **, Corresponding Author) [Publisher link]

Cleary* B., Murray M., Alam S., Sinha A., Habibi E., Simonton S., Bezney J., Marshall J., Lander E.S.*, Chen F.*, Regev A.* (Nature Biotechnology, 2021) Compressed sensing for imaging transcriptomics (*, Corresponding Author) [Publisher link]

Cable D.M., Murray M., Zou L.S., Goeva A., Macosko E.Z., Chen F.*, †, Irizarry R.A.*, † (Nature Biotechnology, 2021) Robust decomposition of cell type mixtures in spatial transcriptomics (*,equal contribution; †, Corresponding Author) [Publisher link]

Rodriques S.G.*, Chen L.M*., Liu S., Zhong E.D., Scherrer J.R., Boyden E.S.*†, Chen F.*† (Nature Biotechnology 2021) RNA timestamps identify the age of single molecules in RNA sequencing (**, equal contribution; †, Corresponding Author) [Publisher link]

Alon, S.*, Goodwin, D.R.*, Sinha A.S.*, Wassie A.T.*, Chen, F* et al, (Science 2021) Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems. (*, equal contributions) [Publisher link]

Andrew C. Payne*,  Zachary D. Chiang*,  Paul L. Reginato*,  Sarah M. Mangiameli, Evan M. Murray, Chun-Chen Yao,  Styliani Markoulaki,  Andrew S. Earl,  Ajay S. Labade,  Rudolf Jaenisch,  George M. Church,  Edward S. Boyden†,  Jason D. Buenrostro†,  Fei Chen† (Science, 2020) In situ genome sequencing resolves DNA sequence and structure in intact biological samples. (*,equal contribution; †, Corresponding Author) [Publisher link]

Marshall J.L.*, Doughty B.R.*, Subramanian V., Wang Q., Chen L.M., Rodriques S.G., Zhang K., Guckelberger P., Fulco C.P., Nasser J., Grinkevich E.J., Noel T., Mangiameli S., Greka A., Lander E.S.**, †, Chen F.**, †, Engreitz J.M.**, † (PNAS, 2020) HyPR-seq: Single-cell quantification of chosen RNAs via hybridization and sequencing of DNA probes. (*, **, equal contribution; †, Corresponding Author) [Publisher link]

Stickels R.R.*, Murray M.*, Kumar P., Li J., Marshall J.L., Di Bella D., Arlotta P., Macosko E.Z.**, †, Chen F.**, † (Nature Biotechnology, 2020) Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2 (*, **, equal contribution; †, Corresponding Author) [Publisher link]

Chen H., Liu S., Padula S., Griswold K., Lin A., Zhao T., Marshall J.L., Chen F.* (Nature Biotechnology, 2020) Efficient, continuous mutagenesis in human cells using a pseudo-random DNA editor. (*, Corresponding Author) [Publisher link]

Rodriques S.G.†, Stickels R.R.†, Goeva A., Martin C.A., Murray E., Vanderburg C.R., Welch J., Chen L.M., Chen F.*††, Macosko E.Z.*†† (Science, 2019) Slide-seq: A Scalable Technology for Measuring Genome-Wide Expression at High Spatial Resolution. (†, ††, equal contribution; *, Corresponding Author) [Publisher link]

Asano S.M., Gao. R., Wassie. A.T., Tillberg P.W., Chen F., Boyden E.S. Expansion Microscopy: Protocols for Imaging Proteins and RNA in Cells and Tissues. Current Protocols in Cell Biology. [Publisher link]