Publications


M. V. Neguembor, J. P. Arcon, D. Buitrago, R. Lema, J. Walther, X. Garate, L. Martin, P. Romero, J. A. Abed, M. Gut, J. Blanc, M. Lakadamyali, C. Wu, I. B. Heath, M. Orozco, P. D. Dans, M. P. Cosma, Nat Struct Mol Biol. 29, 1011–1023 (2022). https://doi.org/10.1038/s41594-022-00839-y 

M. V. Neguembor, L. Martin, Á. Castells-García, P. A. Gómez-García, C. Vicario, D. Carnevali, J. A. Abed, A. Granados, R. Sebastian-Perez, F. Sottile, J. Solon, C. Wu, M. Lakadamyali, M. P. Cosma,. Mol Cell (2021). DOI: 10.1016/j.molcel.2021.06.009.

Huy Q. Nguyen, Shyamtanu Chattoraj, David Castillo, Son C. Nguyen, Guy Nir, Antonios Lioutas, Elliot A. Hershberg, Nuno M. C. Martins, Paul L. Reginato, Mohammed Hannan, Brian J. Beliveau, George M. Church, Evan R. Daugharthy, Marc A. Marti-Renom & C.-ting Wu. Nat Methods 17, 822–832 (2020). https://doi.org/10.1038/s41592-020-0890-0

X inactivation presents two longstanding puzzles: the counting and choice of X chromosomes. Here, we consider counting and choice in the context of pairing, both of the X and of the autosomes.

Nguyen HQ, Lee SD, Wu CT. Trends Genet. 2019 Sep 11. pii: S0168-9525(19)30159-3.DOI: 10.1016/j.tig.2019.07.010

Homologs are paired in Drosophila somatic cells from embryogenesis to adulthood. Using a computational approach for haplotype-resolved Hi-C, the authors reveal highly structured homolog pairing in Drosophila embryos during zygotic genome activation and demonstrate its application to mammalian embryos.

Erceg J, AlHaj Abed J, Goloborodko A, Lajoie BR, Fudenberg G, Abdennur N, Imakaev M, McCole RB, Nguyen SC, Saylor W, Joyce EF, Senaratne TN, Hannan MA, Nir G, Dekker J, Mirny LA, Wu CT. Nat Commun. 2019 Oct 3;10(1):4486. DOI:10.1038/s41467-019-12211-8

Trans-homolog interactions, such as homolog pairing, are highly structured and associated with gene function in Drosophila cells. Here, the authors use haplotype-resolved Hi-C to identify genome-wide trans-homolog interactions in a Drosophila hybrid cell line and investigate complex types of pairing and functional roles.

AlHaj Abed J, Erceg J, Goloborodko A, Nguyen SC, McCole RB, Saylor W, Fudenberg G, Lajoie BR, Dekker J, Mirny LA, Wu CT. Nat Commun. 2019 Oct 3;10(1):4485. DOI:10.1038/s41467-019-12208-

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., et al. (2019).. Plos Biol 17, e3000241.DOI:10.1371/journal.pbio.3000241

Guy Nir, Irene Farabella, Cynthia Pérez Estrada, Carl G. Ebeling, Brian J. Beliveau, Hiroshi M. Sasaki, S. Dean Lee, Son C. Nguyen, Ruth B. McCole, Shyamtanu Chattoraj, Jelena Erceg, Jumana AlHaj Abed, Nuno M. C. Martins, Huy Q. Nguyen, Mohammed A. Hannan, Sheikh Russell, Neva C. Durand, Suhas S. P. Rao, Jocelyn Y. Kishi, Paula Soler-Vila, Michele Di Pierro, José N. Onuchic, Steven P. Callahan, John M. Schreiner, Jeff A. Stuckey, Peng Yin, Erez Lieberman Aiden, Marc A. Marti-Renom, C.-ting Wu. 

PLoS Genet. 2018 Dec 28; https://doi.org/10.1371/journal.pgen.1007872

B.J. Beliveau, A.N. Boettiger, G. Nir, B. Bintu, P. Yin, X. Zhuang, C.T. Wu Methods Mol. Biol. 1663 231-252, 2017; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5919218/

Senaratne TN, Joyce EF, Nguyen SC, Wu CT

PLoS Genet. 2016 Aug 19; http://dx.doi.org/10.1371/journal.pgen.1006169

Wang S, Su J-H, Beliveau BJ, Bintu1 B, Moffitt1 JR, Wu CT, Zhuang X.

Science 21 Jul 2016. doi: 10.1126/science.aaf8084

Joyce EF, Erceg J, Wu CT

Curr Opin Genet Dev. 2016 Apr 8;37:119-128. doi: 10.1016/j.gde.2016.03.002 (LINK)

Savova V, Chun S, Sohail M, McCole RB, Witwicki R, Gai L, Lenz TL, Wu CT, Sunyaev SR, Gimelbrant AA.

Nat Genet. 2016 Jan 25. doi: 10.1038/ng.3493. [Epub ahead of print].  PMID: 26808112

Boettiger AN, Bintu B, Moffitt JR, Wang S, Beliveau BJ, Fudenberg G, Imakaev M, Mirny LA, Wu CT, Xiaowei Zhuang X.

Nature 2016 Jan 13. doi: 10.1038/nature16496. Epub 2016 Jan 13 (Pubmed)

Schmidt TL, Beliveau BJ, Uca YO, Theilmann M, Da Cruz F, Wu CT, Shih WM

Nat Commun. 2015 Nov 16;6:8634. doi: 10.1038/ncomms9634. (link)

Pinter SF, Colognori D, Beliveau BJ, Sadreyev RI, Payer B, Yildirim E, Wu CT, Lee JT.

Genetics. 2015 Jun;200(2):537-49. doi: 10.1534/genetics.115.176263. Epub 2015 Apr 9. (pubmed)

Murgha Y, Beliveau B, Semrau K, Schwartz D, Wu CT, Gulari E, Rouillard JM.

Biotechniques. 2015 Jun 1;58(6):301-7. doi: 10.2144/000114298. eCollection 2015 Jun. PMID:26054766

BJ Beliveau, AN Boettiger, MS Avendaño, R Jungmann, RB McCole, EF Joyce, C Kim-Kiselak, F Bantignies, CYFonseka, J Erceg, MA Hannan, HG Hoang, D Colognori, JT Lee, WM Shih, P Yin, X Zhuang, C-t Wu

Nature Communications 2015. May 12; 6:7147. doi: 10.1038/ncomms8147 (pubmed).

McCole RB, Fonseka CY, Koren A, Wu CT.

PLoS Genet. 2014 Oct 23;10(10):e1004646. doi: 10.1371/journal.pgen.1004646

Beliveau BJ, Apostolopoulos N, Wu CT.

Current Protocols in Molecular Biology  2014. 105:14.23.1–14.23.20.

Joyce EF, Apostolopoulos N, Beliveau BJ, Wu CT.

PLoS Genet. 2013 Dec;9(12):e1004013. doi: 10.1371/journal.pgen.1004013. Epub 2013 Dec 19.

Beliveau BJ, Joyce EF, Apostolopoulos N, Yilmaz F, Fonseka CY, McCole RB, Li JB, Senaratne TN, Williams BR, Rouillard JM, Wu CT.

Proc Natl Acad Sci USA. 2012. 109(52):21301-6

Hohl AM, Thompson M, Soshnev AA, Wu J, Morris J, Hsieh T-S, Wu C-t, Geyer PK.

Genetics. 2012 Aug 24 (in press)

Joyce EF, Williams BR, Xie T, Wu C-t.

PLoS Genet 2012. 8(5): e1002667. doi:10.1371/journal.pgen.1002667

Ou SA, Chang E, Lee S, So K, Wu CT, Morris JR.

Genetics. 2009 Oct;183(2):483-96. Epub 2009 Aug 10.

Griffin R, Sustar A, Bonvin M, Binari R, del Valle Rodriguez A, Hohl AM, Bateman JR, Villalta C, Heffern E, Grunwald D, Bakal C, Desplan C, Schubiger G, Wu CT, Perrimon N.

Nat Methods. 2009 Aug;6(8):600-2. Epub 2009 Jul 26.

Emmons RB, Genetti H, Filandrinos S, Lokere J, Wu CT. 

Genetics. 2009 Aug;182(4):999-1013. Epub 2009 Jun 15.

Chiang CW, Derti A, Schwartz D, Chou MF, Hirschhorn JN, Wu CT.

Genetics. 2008 Dec;180(4):2277-93. Epub 2008 Oct 28.

Bateman JR, Wu CT.

Genetics. 2008 Nov;180(3):1763-6. Epub 2008 Sep 14.

Bateman JR, Wu CT.

Genetics. 2008 Nov;180(3):1329-42. Epub 2008 Sep 14.

Williams BR, Bateman JR, Novikov ND, Wu CT.

Genetics. 2007 Sep;177(1):31-46.

Bateman JR, Wu CT.

Bioessays. 2007 Apr;29(4):382-5.

Lee AM, Wu CT.

Genetics. 2006 Dec;174(4):1867-80. Epub 2006 Oct 22.

Derti A, Roth FP, Church GM, Wu CT.

Nat Genet. 2006 Oct;38(10):1216-20. Epub 2006 Sep 24.

Bateman JR, Lee AM, Wu CT.

Genetics. 2006 Jun;173(2):769-77. Epub 2006 Mar 17.

King IFG, Emmons RB, Francis NJ, Wild B, Müller J, Kingston RE, Wu C-t.

Mol. Cell. Biol. 2005; 25: 6578-91.

Williams BR, Wu CT.

Genetics. 2004 Jul;167(3):1525-8.

Morris JR, Petrov DA, Lee AM, Wu CT.

Genetics. 2004 Aug;167(4):1739-47.

Chen J-L, Huisinga KL, Viering MM, Ou SA, Wu C-t, Geyer PK.

Proc Natl Acad Sci USA 2002; 99: 3723-8.

Dunlap JC, Wu C-t, editors.

Adv Gen 2002; vol 46.

Wu C-t, Dunlap JC.

Adv Gen 2002; 46: xvii-xxiii.

Wu Ct, Morris JR.

Science. 2001 Aug 10;293(5532):1103-5.

Kaplan C, Morris JR, Wu C-t, Winston F.

Genes Dev 2000; 14: 2623-34.

Shao Z, Raible F, Mollaaghababa R, Guyon JR, Wu C-t, Bender W, Kingston RE.

Cell 1999; 98: 37-46.

Wu CT, Morris JR.

Curr Opin Genet Dev. 1999 Apr;9(2):237-46. Review.

Morris JR, Geyer PK, Wu CT.

Genes Dev. 1999 Feb 1;13(3):253-8.

Morris JR, Chen J-l, Filandrinos ST, Dunn RC, Fisk R, Geyer PK, Wu C-t.

Genetics 1999; 151: 633-51.

Morris JR, Chen JL, Geyer PK, Wu CT.

Proc Natl Acad Sci U S A. 1998 Sep 1;95(18):10740-5.

Wu CT, Howe M.

Genetics. 1995 May;140(1):139-81.

Wu CT.

J Cell Biol. 1993 Feb;120(3):587-90. Review.

Wu C-t, Budding M, Griffin MS, Croop JM.

Mol Cell Biol 1991; 11: 3940-8.

Wu C-t, Goldberg ML.

Trends Genet 1989; 5: 189-94.

Wu C-t, Jones RS, Lasko PF, Gelbart WM.

Mol Gen Genet 1989; 218: 559-64.

Gelbart WM, Wu C-t.

Genetics 1982; 102: 179-89.