Publications

Google Scholar  Pubmed

Preprints

 

[23] PaintSHOP enables the interactive design of transcriptome- and genome-scale oligonucleotide FISH experiments

Hershberg, E.A., Close, J.L., Camplisson, C.K., Attar, S., Chern, R., Liu, Y., Akilesh, S., Nicovich, P.R., Beliveau, B.J.

bioRxiv, https://doi.org/10.1101/2020.07.05.188797 (2020).  PDF  SI

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 Methodshttps://doi.org/10.1038/s41592-020-0890-0 (2020).  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, 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