Papers

Preprints

Large-scale discovery of recombinases for integrating DNA into the human genome
Matthew G Durrant*, Alison Fanton*, Josh Tycko*, Michaela Hinks, Sita S Chandrasekaran, Nicholas T Perry, Julia Schaepe, Peter P Du, Peter Lotfy, Michael C Bassik, Lacramioara Bintu, Ami S Bhatt, Patrick D. Hsu. bioRxiv 2021.11.05.467528; doi: https://doi.org/10.1101/2021.11.05.467528. online article, pdf.

Publications

2017 – present

Dynamic spreading of chromatin-mediated gene silencing and reactivation between neighboring genes in single cells
Lensch S, Herschel MH, Ludwig CH, Sinha J, Hinks MM, Mukund A, Fujimori T, Bintu L (2022). eLife 11:75115 https://doi.org/10.7554/eLife.75115. online article, pdf, GitHub repo.

Temporal signaling, population control, and information processing through chromatin-mediated gene regulation
Mukund A, Bintu L. Journal of Theoretical Biology. Volume 535, 2022, 110977, ISSN 0022-5193, https://doi.org/10.1016/j.jtbi.2021.110977. online article, pdf, supplementary information, GitHub repo.

Nanobody-mediated control of gene expression and epigenetic memory
Van MV, Fujimori T, Bintu L. Nat Commun 12, 537 (2021). https://doi.org/10.1038/s41467-020-20757-1

Direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA mapping (CasKAS)
Georgi K. Marinov, Samuel H. Kim, S. Tansu Bagdatli, Alexandro E. Trevino, Josh Tycko, Tong Wu, Lacramioara Bintu, Michael C. Bassik, Chuan He, Anshul Kundaje, William J. Greenleaf. bioRxiv 2021.04.16.440202; doi: https://doi.org/10.1101/2021.04.16.440202. online article, pdf

High-throughput discovery and characterization of human transcriptional effectors
Tycko J, DelRosso N, Hess GT, Aradhana, Banerjee A, Mukund A, Van MV, Ego BK, Yao D, Spees K, Suzuki P, Marinov GK, Kundaje A, Bassik MC, Bintu L. Cell. 2020 Dec 9:S0092-8674(20)31541-5. doi: 10.1016/j.cell.2020.11.024. Epub ahead of print. PMID: 33326746. online article, pdf

Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements
Tycko J*, Wainberg M*, Marinov GK*, Ursu O, Hess GT, Ego BK, Aradhana, Li A, Truong A, Trevino AE, Spees K, Yao D, Kaplow IM, Greenside PG, Morgens DW, Phanstiel DH, Snyder MP, Bintu L, Greenleaf WJ, Kundaje A, Bassik MC. Nat Commun 104063 (2019). https://doi.org/10.1038/s41467-019-11955-7. online article, pdf

Mapping chromatin modifications at the single-cell level.
Ludwig CH, Bintu L. Development 146, no. 12: dev170217 (2019). online article, pdf

Advancing towards a global mammalian gene regulation model through single-cell analysis and synthetic biology.
Tycko J*, Van MV*, Elowitz MB, & Bintu L. Current Opinion in Biomedical Engineering, 4: 174-193 (2017). online article, pdf

2005 – 2016

Dynamics of epigenetic regulation at the single-cell level.
Bintu L*, Yong J*, Antebi YE, McCue K, Kazuki Y, Uno N, Oshimura M, Elowitz MB. Science, 351 (6274): 720 (2016). online article, pdf, perspective: Keung AJ & Khalil AS.  A unifying model of epigenetic regulation. Science, 351 (6274): 661 (2016).

Molecular Mechanisms of Transcription through Single-Molecule Experiments.
Dangkulwanich M, Ishibashi T, Bintu L, Bustamante C. Chemical reviews, 114 (6) 3203 (2014). online article, pdf

Nucleosomal Elements that Control the Topography of the Barrier to Transcription.
Bintu L*, Ishibashi T*, Dangkulwanich M, Wu Y, Lubkowska L, Kashlev M, Bustamante C. Cell, 151 (4): 738 (2012). online article, pdfCell Video Abstract

Nascent RNA Structure Modulates the Transcriptional Dynamics of RNA Polymerases.
Zamft B, Bintu L, Ishibashi T, Bustamante C. Proceedings of the National Academy of Sciences, 109 (23): 8948 (2012). online article, pdf

The Elongation Rate of RNA Polymerase Determines the Fate of Transcribed Nucleosomes.
Bintu L*, Kopaczynska M*, Hodges C, Lubkowska L, Kashlev M, Bustamante C. Nature Structural & Molecular Biology, 18 (12): 1394 (2011). online article, pdf

Nucleosomal Fluctuations Govern the Transcription Dynamics of RNA Polymerase II.
Hodges C*, Bintu L*, Lubkowska L, Kashlev M, Bustamante C. Science, 325 (5940): 626 (2009). online article, pdf, perspective: Nudging Through a Nucleosome, Otterstrom JJ & van Oijen AM, Science, 325 (5940): 547 (2009)

Transcriptional Regulation by the Numbers 1: Models.
Bintu L, Buchler N, Garcia H, Gerland U, Hwa T, Kondev J, Phillips R. Current Opinion in Genetics & Development, 15(2):116 (2005). online article, pdf

Transcriptional Regulation by the Numbers 2: Applications.
Bintu L, Buchler N, Garcia H, Gerland U, Hwa T, Kondev J, Kuhlman T, Phillips R. Current Opinion in Genetics & Development, 15(2):125 (2005). online article, pdf