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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]

bioRxiv (2023).  PDF  SI

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 (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 (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 (2022).  PDF  SI


[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 


[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 (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 (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




[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


[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 


[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



[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


[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



[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



[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


[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



[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 


[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


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