Publications

Preprints

(*equal contribution, #co-coresponding)

Single-cell chromatin state transitions during epigenetic memory formation
Taihei Fujimori, Carolina Rios-Martinez, Abby R. Thurm, Michaela M. Hinks, Benjamin R. Doughty, Joydeb Sinha, Derek Le, Antonina Hafner, William J. Greenleaf, Alistair N. Boettiger, Lacramioara Bintu
bioRxiv 2023.10.03: https://doi.org/10.1101/2023.10.03.56061

The H3.3 K36M oncohistone disrupts the establishment of epigenetic memory through loss of DNA methylation
Joydeb Sinha, Jan F. Nickels, Abby R. Thurm, Connor H. Ludwig, Bella N. Archibald, Michaela M. Hinks, Jun Wan, Dong Fang, Lacramioara Bintu
bioRxiv 2023.10.13: https://doi.org/10.1101/2023.10.13.562147

Development of compact transcriptional effectors using high-throughput measurements in diverse contexts
Josh Tycko*, Mike V. Van*, Aradhana, Nicole DelRosso, David Yao, Xiaoshu Xu, Connor Ludwig, Kaitlyn Spees, Katherine Liu, Gaelen T Hess, Mingxin Gu, Adi Xiyal Mukund, Peter H. Suzuki, Roarke A. Kamber, Lei S. Qi, Lacramioara Bintu#, Michael C. Bassik#
bioRxiv 2023.05.12; doi: https://doi.org/10.1101/2023.05.12.540558

Peer-reviewed publications

2017 – present

High-throughput functional characterization of combinations of transcriptional activators and repressors
Adi X Mukund, Josh Tycko, Sage J Allen, Stephanie A Robinson, Cecelia Andrews, Connor H Ludwig, Kaitlyn Spees, Michael C Bassik, Lacramioara Bintu. Cell Systems, 14(9):746–763, 2023. online article

High-throughput discovery and characterization of viral transcriptional effectors in human cells
Connor H. Ludwig, Abby R. Thurm, David W. Morgens, Kevin J. Yang, Josh Tycko, Michael C. Bassik, Britt A. Glaunsinger, Lacramioara Bintu. Cell Systems, 14(6):482-500, 2023. online article

Spatial and temporal organization of the genome: current state and future aims of the 4D Nucleome Project. Review
Dekker J, Alber F, Aufmkolk S, Beliveau BJ, Bruneau BG, Belmont AS, Bintu L, Boettiger A, Calandrelli R, Disteche CM, Gilbert DM, Gregor T, Hansen AS, Huang B, Huangfu D, Kalhor R, Leslie CS, Li W, Li Y, Ma J, William S. Noble WS, Peter J. Park PJ, Jennifer E. Phillips-Cremins JE, Katherine S. Pollard KS, Rafelski SM, Ren B, Ruan Y, Shav-Tal Y, Shen Y, Shendure K, Shu X, Strambio-De-Castillia C, Vertii A, Zhang H, Zhong S Molecular Cell 83, 2023. online article

CasKAS: direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA mapping
Marinov GK, Kim SH, Bagdatli ST, Higashino SI, Trevino AE, Tycko J, Wu T, Bintu L, Bassik MC, He C, Kundaje A, Greenleaf WJ. Genome Biol. 2023 Apr 21;24(1):85. doi: 10.1186/s13059-023-02930-z. PMID: 37085898; PMCID: PMC10120127. online article, pdf

Large-scale mapping and systematic mutagenesis of human transcriptional effector domains
Nicole DelRosso, Josh Tycko, Peter Suzuki, Cecelia Andrews, Aradhana, Adi Mukund, Ivan Liongson, Connor Ludwig, Kaitlyn Spees, Polly Fordyce, Michael C. Bassik, Lacramioara Bintu.
Nature (2023). https://doi.org/10.1038/s41586-023-05906-y, online article, pdf

The sound of silence: Transgene silencing in mammalian cell engineering. Perspective
Alan Cabera*, Hailey I. Edelstein*, Fokion Glykofrydis*, Kasey S. Love*, Sebastian Palacios*, Josh Tycko*, Meng Zhang*, Sarah Lensch, Cara E. Shields, Mark Livingston, Ron Weiss, Huimin Zhao, Karmella A. Haynes, Leonardo Morsut, Yvonne Y. Chen, Ahmad S. Khalil, Wilson W. Wong, James J. Collins, Susan J. Rosser, Karen Polizzi, Michael B. Elowitz, Martin Fussenegger, Isaac B. Hilton, Joshua N. Leonard, Lacramioara Bintu, Kate E. Galloway, Tara L. Deans. Cell Systems, Volume 13, Issue 12, 2022, Pages 950-973, ISSN 2405-4712, online article

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#. Nature Biotechnology (2022). https://doi.org/10.1038/s41587-022-01494-w. online article, pdf.

Dynamic spreading of chromatin-mediated gene silencing and reactivation between neighboring genes in single cells
Lensch S, Herschl 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. Nature Communications 12, 537 (2021). https://doi.org/10.1038/s41467-020-20757-1

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. Nature Communications 104063 (2019). https://doi.org/10.1038/s41467-019-11955-7. online article, pdf

Mapping chromatin modifications at the single-cell level. Review
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. Review
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