Publications
Preprints
Harmonizing the Generation and Pre-publication Stewardship of FAIR Image Data
Bialy, N., Alber, F., Andrews, B., Angelo, M., Beliveau, B., Bintu, L., Boettiger, A., Boehm, U., Brown, C.M., Bukar Maina, M., Chambers, J.J., Cimini, B.A., Eliceiri, K., Errington, R., Faklaris, O., Gaudreault, N., Germain, R., Goscinski, W., Grunwald, D., Halter, M., Hanein, D., Hickey, J., Lacoste, J., Laude, A., Lundberg, E., Ma, J., Malacrdia, L., Moore, J., Nelson, G., Neumann, E. K., Nitschke, R., Onami, S., Pimentel, J.A., Plant, A.L., Radtke, A.J., Sabata, B., Schapiro, D., Schöneberg, J., Spraggins, J.M., Sudar, D., Vierdag, W.-M.A.M., Volkmann, N., Wählby, C., Wang, S., Yaniv, Z., Strambio-De-Castilla, C.
arXiv https://arxiv.org/abs/2401.13022 (2024). PDF
Efficient and highly amplified imaging of nucleic acid targets in cellular and histopathological samples with pSABER
Attar, S., Browning, V.E., Liu, Y., Nichols, E.K., Tsue, A.F., Shechner, D.M., Shendure, J., Lieberman, J.A., Akilesh, S.†, Beliveau, B.J.† [†Co-corresponding authors]
bioRxiv https://www.biorxiv.org/content/10.1101/2022.08.01.502089v2 (2023). PDF SI
Oligonucleotide-directed proximity-interactome mapping (O-MAP): A unified method for discovering RNA-interacting proteins, transcripts and genomic loci in situ
Tsue, A.F., Kania, E.E., Lei, D.Q., Fields, R., McGann, C.C., Hershberg, E.A., Deng, X., Kihiu, M., Ong, S.E., Disteche, C.M., Kugel, S., Beliveau, B.J., Schweppe, D.S., Shechner, D.M.
bioRxiv https://www.biorxiv.org/content/10.1101/2022.08.01.502089v1 (2023). PDF SI
Quantitative multiplexed imaging of chromatin ultrastructure with Decode-PAINT
Sasaki, H.M., Kishi, J.Y., Wu, C.-T., Beliveau, B.J.†, Yin P.† [†Co-corresponding authors]
bioRxiv https://www.biorxiv.org/content/10.1101/2022.08.01.502089v1 (2022). PDF SI
2024
[29] Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes
Aguilar, R., Camplisson, C.K., Lin, Q., Miga, K.H., Noble, W.S.†, Beliveau, B.J.† [†Co-corresponding authors]
Nature Communications 15, 1027 (2024). Journal PDF SI
2023
[28] Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project
Dekker, J., Alber, F., Aufmkolk, S., Beliveau, B.J., Bruneau, B.G., Belmont, A.S., Bintu, L., Boettiger, A., Calandrelli, R., Disteche, C.M., Gilbert, D.M., Gregor, T., Hansen, A.S., Huang, B., Huangfu, D., Kalhor, R., Leslie, C.S., Li, W., Li, Y., Ma, J., Noble, W.S., Park, P.J., Phillips-Cremins, J.E., Pollard. K.S., Rafelski, S.M., Ren, B., Ruan, Y., Shav-Tal, Y., Shen, Y., Shendure, J., Shu, X., Strambio-De-Castillia, C., Vertii, A., Zhang, H., Zong, S.
Molecular Cell 83, https://doi.org/10.1016/j.molcel.2023.06.018 (2023). Journal PDF
[27] Cohesin controls X chromosome structure remodeling and X-reactivation during mouse iPSC-reprogramming
Generoso, S.F., Neguembor, M.V., Hershberg, E.A., Sadreyev, R.I., Kurimoto, K., Yabuta, Y., Ricci, R., Audergon, P., Bauer, M., Saitou, M., Hochedlinger, K., Beliveau, B.J., Cosma, M.P., Lee, J.T., Payer, B.
Proc. Natl. Acad. Sci. USA 120, e2213810120 (2023). Journal PDF SI
2022
[26] Optimized single-nucleus transcriptional profiling by combinatorial indexing
Martin, B.K., Qiu, C., Nichols, E.K., Phung, M., Green-Gladden, R., Srivatsan, S., Blecher-Gonan, R., Beliveau, B.J., Trapnell, C., Cao, J., Shendure, J.
Nature Protocols https://doi.org/10.1038/s41596-022-00752-0 (2022). PDF SI arXiv
[25] An open source 16-channel fluidics system for automating sequential fluorescent in situ hybridization (FISH)-based imaging
Deng, Z., Beliveau, B.J.
HardwareX https://doi.org/10.1016/j.ohx.2022.e00343 (2022). PDF SI bioRxiv
[24] A hybrid open-top light-sheet microscope for multi-scale imaging of cleared tissues
Glaser, A.K.†, Bishop, K.W., Barner L.A., Susaki, E.A., Kubota, S.I., Gao, G., Serafin, R.B., Balaram, P., Turschak, E., Nicovich, P.R., Lai, H., Lucas, L.A.G., Yi, Y., Nichols, E.K., Huang, H., Reder, N.P., Wilson, J.J., Sivakumar, R., Shamskhou, E., Stolfzfus, C.R., Wei, X., Hempton, A.K., Pende, M., Murawala, P., Dodt, H.U., Imaizumi, T., Shendure, J., Beliveau, B.J., Gerner, M.Y., Xin, L., Zhao, H., True, L.D., Reid, C., Chandrashekar, J., Ueda, H.R., Svoboda, K., Liu, J.T.C.† [†Co-corresponding authors]
Nature Methods 19, 613–619 (2022). Journal PDF SI bioRxiv
2021
[23] PaintSHOP enables the interactive design of transcriptome- and genome-scale oligonucleotide FISH experiments
Hershberg, E.A.*, Camplisson, C.K.*, Close, J.L., Attar, S., Chern, R., Liu, Y., Akilesh, S., Nicovich, P.R., Beliveau, B.J. [*Co-first authors]
Nature Methods 18, 937–944 (2021). Journal PDF SI bioRxiv
2020
[22] 3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing
Nguyen, H.Q.*, Chattoraj, S.*, Castillo, D.*, Nguyen, S.C., Nir, G., Lioutas, A., Hershberg, E.A., Martins, N.M.C., Reginato, P.L., Hannan, M., Beliveau, B.J., Church, G.M., Daugharthy, E.R., Marti-Renom, M.A.†, Wu, C.-T.† [*Co-first authors] [†Co-corresponding authors]
Nature Methods 17, 822–832 (2020). Journal PDF SI
[21] Combining Qdot Nanotechnology and DNA Nanotechnology for Sensitive Single-Cell Imaging
Zhou, W., Han, Y., Beliveau, B.J., Gao, X.
Advanced Materials 32, 201908410 (2020). Journal PDF SI
[20] OligoMinerApp: a web-server application for the design of genome-scale oligonucleotide in situ hybridization probes through the flexible OligoMiner environment
Passaro, M., Martinovic, M., Bevilacqua, V., Hershberg, E.A., Rossetti, G., Beliveau, B.J., Bonnal, R.J.P.†, Pagani, M.† [†Co-corresponding authors]
Nucleic Acids Research, gkaa251 (2020). Journal PDF
[19] Pericentromeric heterochromatin is hierarchically organized and spatially contacts H3K9me2/3 islands in euchromatin
Lee, Y.C.G.†, Ogiyama, Y., Martins, N.M.C., Beliveau, B.J., Acevedo, D., Wu, C.-T., Cavalli, G., Karpen, G.H.† [†Co-corresponding authors]
PLoS Genetics 16, e1008673 (2020). Journal PDF SI bioRxiv
2019
[18] Rapid in vitro production of single-stranded DNA
Minev, D.*, Guerra, R.*, Kishi, J.Y., Smith, C., Krieg, E., Said, K., Hornick, A., Sasaki, H.M., Filsinger, G., Beliveau, B.J., Yin, P., Church, G.M., Shih, W.M. [*Co-first authors]
Nucleic Acids Research, gkz998 (2019). Journal PDF SI bioRxiv
[17] Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues
Saka, S.K.*†, Wang, Y.*†, Kishi, J.Y., Zhu, A., Zeng, Y., Xie, W., Kirli, K., Yapp, C., Cicconet, M., Beliveau, B.J., Lapan, S.W., Yin, S., Lin, M., Boyden, E.S., Kaeser, P.S., Pihan, G., Church, G.M., Yin, P.† [*Co-first authors] [†Co-corresponding authors]
Nature Biotechnology 37, 1080–1090 (2019). Journal PDF SI Supp. Protocols bioRxiv
[16] SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues
Kishi, J.Y.*, Lapan, S.W.*, Beliveau, B.J.*†, West, E.R.*, Zhu, A., Sasaki, H.M., Saka, S.K., Wang, Y., Cepko, C.L.†, Yin, P.† [*Co-first authors] [†Co-corresponding authors]
Nature Methods 16, 533–544 (2019). Journal PDF SI Supp. Protocols Sequence List bioRxiv
[15] Islands of retroelements are the major components of Drosophila centromeres
Chang, C.H.*, Chavan, A.*, Palladino, J.*, Wei, X., Martins, N.M.C., Santinello, B., Chen, C.C., Erceg, J., Beliveau, B.J., Wu, C.-T., Larracuente, A.M.†, Mellone, B.† [*Co-first authors] [†Co-corresponding authors]
PLoS Biology 17, e3000241 (2019). Journal PDF SI bioRxiv
2018
[14] Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling
Nir, G.*, Farabella, I.*, Pérez Estrada, C.*, Ebeling, C.G.*, Beliveau, B.J., Sasaki, H.M., Lee, S.H., Nguyen, S.C., McCole, R.B., Chattoraj, S., Erceg, J., AlHaj Abed, J., Martins, N.M.C., Nguyen, H.Q., Hannan, M.A., Russell, S., Durand, N.C., Rao, S.S.P., Kishi, J.Y., Soler-Vila, P., Di Pierro, M., Onuchic, J.N., Callahan, S., Schreiner, J., Stuckey, J.A.†, Yin, P.†, Lieberman Aiden, E.†, Marti-Renom, M.A.†, Wu, C.-T.† [*Co-first authors] [†Co-corresponding authors]
PLoS Genetics 14, e1007872 (2018). Journal PDF SI bioRxiv
[13] OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes
Beliveau, B.J.†, Kishi, J.Y., Nir, G., Sasaki, H.M., Saka, S.K., Nguyen, S.C., Wu, C.-T., Yin, P†. [†Co-corresponding authors]
Proc. Natl. Acad. Sci. USA 115, E2183–E2192 (2018). Journal PDF SI bioRxiv
2017
[12] Multiplexed 3D super-resolution imaging of whole cells using Spinning Disc Confocal Microscopy and DNA-PAINT
Schüder, F., Lara-Gutiérrez, J., Beliveau, B.J., Saka, S.K., Sasaki, H.M., Woehrstein, J.B., Strauss, M.T., Grabmayr, H., Yin, P., Jungmann, R.
Nature Communications 8, 2090 (2017). Journal PDF SI
[11] In situ super-resolution imaging of genomic DNA with OligoSTORM and OligoDNA-PAINT
Beliveau, B.J.*, Boettiger, A.N.*, Nir, G.*, Bintu, B.*, Yin, P., Zhuang, X., Wu, C.-T. [*Co-first authors]
Methods in Molecular Biology 166, 231–252 (2017). Journal PDF
2016
[10] Spatial organization of chromatin domains and compartments in single chromosomes
Wang, S., Su, J.H., Beliveau, B.J., Bintu, B., Moffitt, J.R., Wu, C.-T., Zhuang, X.
Science 353, 598–602 (2016). Journal PDF SI
[9] Super-resolution imaging reveals distinct chromatin folding for different epigenetic states
Boettiger, A.N., Bintu, B., Moffitt, J.R., Wang, S., Beliveau, B.J., Fudenberg, G., Imakaev, M., Mirny, L.A., Wu, C.-T., Zhuang, X.
Nature 529, 418–22 (2016). Journal PDF SI
2015
[8] Scalable amplification of single-stranded oligonucleotides from chip-synthesized oligonucleotide libraries
Schmidt, T.L., Beliveau, B.J., Uca, Y.O., Theilmann, M., Da Cruz, F., Wu, C.-T., Shih, W.M.
Nature Communications 6, 9634 (2015). Journal PDF SI
[7] Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes
Beliveau, B.J., Boettiger, A.B., Avendaño, M.S., Jungmann, R., McCole, R.B., Joyce, E.F., Kim-Kiselak, C., Bantignies, F., Fonseka, C.Y., Erceg, J., Hannan, M.A., Hoang, H.G., Colognori, D., Lee, J.T., Shih, W.M., Yin, P., Zhuang, X., Wu, C.-T.
Nature Communications 6, 8147 (2015). Journal PDF SI
[6] Allelic imbalance is a prevalent and tissue-specific feature of the mouse transcriptome
Pinter, S.F., Colognori, D., Beliveau, B.J., Sadreyev, R.I., Payer, B., Yildirim, E., Wu, C.-T., Lee, J.T.
Genetics 200, 537–49 (2015). Journal PDF SI
[5] Combined in vitro transcription and reverse transcription to amplify and label complex synthetic oligonucleotide probe libraries
Murgha, Y., Beliveau, B., Semrau, K., Schwartz, D., Wu, C.-T., Gulari, E., Rouillard, J.M.
Biotechniques 58, 301–7 (2015). Journal PDF
[4] Avoiding the Ends: Internal Epitope Tagging of Proteins Using Transposon Tn7
Zordan, R.E., Beliveau, B.J., Trow, J.A., Craig, N.L., Cormack, B.P.
Genetics 200, 47–58 (2015). Journal PDF SI
2014
[3] Visualizing genomes with Oligopaint FISH probes
Beliveau, B.J., Apostolopoulos, N.A., Wu, C.-T.
Current Protocols in Molecular Biology 105 Unit 14, 23 (2014). Journal PDF
2013
[2] Germline progenitors escape the widespread phenomenon of homolog pairing during Drosophila development
Joyce, E.F., Apostolopoulos, N., Beliveau, B.J., Wu, C.-T.
PLoS Genetics 9, e1004013 (2013). Journal PDF SI
2012
[1] Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes
Beliveau, B.J.*, Joyce, E.F.*, Apostolopoulos, N., Yilmaz, F., Fonseka, C.Y., McCole, R.B., Chang, Y., Li, J.B., Senaratne, T.N., Williams, B.R., Rouillard, J.M., Wu, C.-T. [*Co-first authors]
Proc. Natl. Acad. Sci. USA 109, 21301–06 (2012). Journal PDF SI