Preprints
(*equal contribution, #co-coresponding)
High-throughput development and characterization of new functional nanobodies for gene regulation and epigenetic control in human cells
Jun Wan*, Abby R. Thurm*, Sage J. Allen, Connor H. Ludwig, Aayan N. Patel, Lacramioara Bintu
bioRxiv 2024.11.01.621523; https://doi.org/10.1101/2024.11.01.621523
Prediction and design of transcriptional repressor domains with large-scale mutational scans and deep learning
Raeline Valbuena*, AkshatKumar Nigam*, Josh Tycko, Peter Suzuki, Kaitlyn Spees, Aradhana, Sophia Arana, Peter Du, Roshni A. Patel, Lacramiora Bintu#, Anshul Kundaje#, Michael C. Bassik#
bioRxiv 2024.09.24 https://doi.org/10.1101/2024.09.21.614253
High-throughput affinity measurements of direct interactions between activation domains and co-activators
Nicole DelRosso*, Peter H. Suzuki*, Daniel Griffith, Jeffrey M. Lotthammer, Borna Novak, Selin Kocalar, Maya U. Sheth, Alex S. Holehouse, Lacramioara Bintu#, Polly Fordyce#
bioRxiv 2024.08.20 https://doi.org/10.1101/2024.08.19.608698
High-throughput discovery of regulatory effector domains in human RNA-binding proteins
Abby R. Thurm, Yaara Finkel, Cecelia Andrews, Xiangmeng S. Cai, Colette Benko, Lacramioara Bintu
bioRxiv 2024.07.19: https://doi.org/10.1101/2024.07.19.604317
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://pmc.ncbi.nlm.nih.gov/articles/PMC10592931/
Peer-reviewed publications
2017 – present
Single-molecule states link transcription factor binding to gene expression
Benjamin R. Doughty*, Michaela M. Hinks*, Julia M. Schaepe*, Georgi K. Marinov, Abby R. Thurm, Carolina Rios-Martinez, Benjamin E. Parks, Yingxuan Tan, Emil Marklund, Danilo Dubocanin, Lacramioara Bintu# & William J. Greenleaf#. Nature (2024). https://doi.org/10.1038/s41586-024-08219-w
Development of compact transcriptional effectors using high-throughput measurements in diverse contexts
Josh Tycko*, Mike V. Van*, Aradhana, Nicole DelRosso, Hanrong Ye, David Yao, Raeline Valbuena, Alun Vaughan-Jackson, Xiaoshu Xu, Connor Ludwig, Kaitlyn Spees, Katherine Liu, Mingxin Gu, Venya Khare, Adi Xiyal Mukund, Peter H. Suzuki, Sophia Arana, Catherine Zhang, Peter P. Du, Thea S. Ornstein, Gaelen T. Hess, Roarke A. Kamber, Lei S. Qi, Ahmad S. Khalil, Lacramioara Bintu#, Michael C. Bassik#. Nature Biotechnology (2024). https://doi.org/10.1038/s41587-024-02442-6
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. Molecular Cell, 2024. DOI: 10.1016/j.molcel.2024.09.015
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*, . Nature Communications 10, 4063 (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, pdf, Cell 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