Publications

2023

Andrew J. C. Russell, Jackson A. Weir, Naeem M. Nadaf, Matthew Shabet, Vipin Kumar, Sandeep Kambhampati, Ruth Raichur, Giovanni J. Marrero, Sophia Liu, Karol S. Balderrama, Charles R. Vanderburg, Vignesh Shanmugam, Luyi Tian, Catherine J. Wu, Charles H. Yoon, Evan Z. Macosko, Fei Chen. Slide-tags: scalable, single-nucleus barcoding for multi-modal spatial genomics. Nature 625, 101–109 (2023)

Jonah Langlieb, Nina S Sachdev, Karol S Balderrama, Naeem M Nadaf, Mukund Raj, Evan Murray, James T Webber, Charles Vanderburg, Vahid Gazestani, Daniel Tward, Chris Mezias, Xu Li, Katelyn Flowers, Dylan M Cable, Tabitha Norton, Partha Mitra, Fei Chen, Evan Z Macosko. "The molecular cytoarchitecture of the adult mouse brain." Nature 624, 333-342 (2023)

Sarah M. Mangiameli, Haiqi Chen, Andrew S. Earl, Julie A. Dobkin, Daniel Lesman, Jason D. Buenrostro, Fei Chen. Photoselective sequencing: microscopically guided genomic measurements with subcellular resolution. Nat Methods 20, 686–694 (2023)

Vignesh Shanmugam, Neriman Tokcan, Daniel Chafamo, Sean Sullivan, Haley Martin, Gail A Newton, Mehdi Borji, Naeem Nadaf, Irving Barrera, Dylan Cable, Jackson Weir, Orr Ashenberg, Caroline Uhler, Geraldine Pinkus, Scott Rodig, Margaret A. Shipp, Evan Macosko, Abner Louissaint, Fei Chen, Todd R. Golub. "Genome-Scale High-Resolution Spatial Mapping of the Pro-Tumorigenic Cellular Niche in Classic Hodgkin Lymphoma." Blood 142, 175 (2023)

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 synthesis with RNA sensors by harnessing ADAR." Nature Biotechnology 41.5, 698-707 (2023)

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]
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, cusing 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]
Zhao Y., Bucur O., Irshad H., Chen F., Weins A., Stancu A.L., Oh E-Y., DiStasio M., Torous V., Glass B., Stillman I.E., Schnitt S.J., Beck A.H., Boyden E.S. Nanoscale Imaging of Clinical Specimens Using Pathology-Optimized Expansion Microscopy. Nature Biotechnology. [Publisher link] [PDF]
Chang J.B., Chen F., Yoon Y.G., Jung E. E., Babcock H., Kang J.S., Asano S., Suk H.J., Pak N., Tillberg P.W., Wassie A., Cai D., Boyden E.S. Iterative expansion microscopy. Nature Methods. [Publisher link] [PDF]
Chen F.*, Wassie A.T.*, Cote A.J., Sinha A., Alon S., Asano S., Daugharthy E.R., Chang J.-B., Marblestone A., Church G.M., Raj A., Boyden E.S. Nanoscale Imaging of RNA with Expansion Microscopy. Nature Methods. (*equal contribution) [Publisher link] [PDF]
Tillberg P.W.*, Chen F.*, Piatkevich K.D., Zhao Y., Yu C.-C., English B.P., Gao L., Martorell A., Suk H.-J., Yoshida F., DeGennaro E.M., Roossien D.H., Gong G., Seneviratne U., Tannenbaum S.R., Desimone R., Cai D., Boyden E.S. (2016) Protein-retention expansion microscopy of cells and tissues labeled using standard fluorescent proteins and antibodies. Nature Biotechnology. (*equal contribution) [Publisher link] [PDF]
Zhang Y.S., Chang J.B., Alvarez M.M., Trujillo-de Santiago G., Aleman J., Batzaya B., Kirshnadoss V., Ramanujam A.A., Kazemzadeh-Narbat M., Chen F., Tillberg P.W., Dokmeci M.R., Boyden E.S., Khademhosseini A. Hybrid Microscopy: Enabling Inexpensive High-Performance Imaging through Combined Physical and Optical Magnifications. Scientific Reports. [Publisher link] [PDF]
Chen F.*, Tillberg P.W.*, Boyden E.S. Expansion Microscopy. Science. 347(6221):543-548. (*equal contribution) [Publisher link] [PDF]
Schmidt D., Tillberg P.W.*, Chen F.*, Boyden E.S. A fully genetically encoded protein architecture for optical control of peptide ligand concentration. Nature Communications. (*equal contribution)  [Publisher link] [PDF]