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A comprehensive thermodynamic model for RNA binding by the Saccharomyces cerevisiae Pumilio protein PUF4.
Published in:
Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-31968-z
By:
- Sadée, Christoph;
- Hagler, Lauren D.;
- Becker, Winston R.;
- Jarmoskaite, Inga;
- Vaidyanathan, Pavanapuresan P.;
- Denny, Sarah K.;
- Greenleaf, William J.;
- Herschlag, Daniel
Publication type:
Article
Diff-seq: A high throughput sequencing-based mismatch detection assay for DNA variant enrichment and discovery.
Published in:
Nucleic Acids Research, 2018, v. 46, n. 7, p. 1, doi. 10.1093/nar/gky022
By:
- Aggeli, Dimitra;
- Karas, Vlad O;
- Sinnott-Armstrong, Nicholas A;
- Varghese, Vici;
- Shafer, Robert W;
- Greenleaf, William J;
- Sherlock, Gavin
Publication type:
Article
High-throughput single-cell chromatin accessibility CRISPR screens enable unbiased identification of regulatory networks in cancer.
Published in:
Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-23213-w
By:
- Pierce, Sarah E.;
- Granja, Jeffrey M.;
- Greenleaf, William J.
Publication type:
Article
Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia.
Published in:
Nature Biotechnology, 2019, v. 37, n. 12, p. 1458, doi. 10.1038/s41587-019-0332-7
By:
- Granja, Jeffrey M.;
- Klemm, Sandy;
- McGinnis, Lisa M.;
- Kathiria, Arwa S.;
- Mezger, Anja;
- Corces, M. Ryan;
- Parks, Benjamin;
- Gars, Eric;
- Liedtke, Michaela;
- Zheng, Grace X. Y.;
- Chang, Howard Y.;
- Majeti, Ravindra;
- Greenleaf, William J.
Publication type:
Article
Challenges and recommendations for epigenomics in precision health.
Published in:
Nature Biotechnology, 2017, v. 35, n. 12, p. 1128, doi. 10.1038/nbt.4030
By:
- Carter, Ava C;
- Chang, Howard Y;
- Church, George;
- Dombkowski, Ashley;
- Ecker, Joseph R;
- Gil, Elad;
- Giresi, Paul G;
- Greely, Henry;
- Greenleaf, William J;
- Hacohen, Nir;
- He, Chuan;
- Hill, David;
- Ko, Justin;
- Kohane, Isaac;
- Kundaje, Anshul;
- Palmer, Megan;
- Snyder, Michael P;
- Tung, Joyce;
- Urban, Alexander;
- Vidal, Marc
Publication type:
Article
Transient acquisition of pluripotency during somatic cell transdifferentiation with iPSC reprogramming factors.
Published in:
Nature Biotechnology, 2015, v. 33, n. 7, p. 769, doi. 10.1038/nbt.3270
By:
- Maza, Itay;
- Caspi, Inbal;
- Zviran, Asaf;
- Chomsky, Elad;
- Rais, Yoach;
- Viukov, Sergey;
- Geula, Shay;
- Buenrostro, Jason D;
- Weinberger, Leehee;
- Krupalnik, Vladislav;
- Hanna, Suhair;
- Zerbib, Mirie;
- Dutton, James R;
- Greenleaf, William J;
- Massarwa, Rada;
- Novershtern, Noa;
- Hanna, Jacob H
Publication type:
Article
Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes.
Published in:
Nature Biotechnology, 2014, v. 32, n. 6, p. 562, doi. 10.1038/nbt.2880
By:
- Buenrostro, Jason D;
- Araya, Carlos L;
- Chircus, Lauren M;
- Layton, Curtis J;
- Chang, Howard Y;
- Snyder, Michael P;
- Greenleaf, William J
Publication type:
Article
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.
Published in:
Nature Methods, 2013, v. 10, n. 12, p. 1213, doi. 10.1038/nmeth.2688
By:
- Buenrostro, Jason D;
- Giresi, Paul G;
- Zaba, Lisa C;
- Chang, Howard Y;
- Greenleaf, William J
Publication type:
Article
Fluorogenic DNDNA sequencing in PDMSDMSDMS microreactors.
Published in:
Nature Methods, 2011, v. 8, n. 7, p. 575, doi. 10.1038/nmeth.1629
By:
- Sims, Peter A.;
- Greenleaf, William J.;
- Duan, Haifeng;
- Xie, X. Sunney
Publication type:
Article
Global mapping of RNA-chromatin contacts reveals a proximity-dominated connectivity model for ncRNA-gene interactions.
Published in:
Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-41848-9
By:
- Limouse, Charles;
- Smith, Owen K.;
- Jukam, David;
- Fryer, Kelsey A.;
- Greenleaf, William J.;
- Straight, Aaron F.
Publication type:
Article
Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements.
Published in:
Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-11955-7
By:
- Tycko, Josh;
- Wainberg, Michael;
- Marinov, Georgi K.;
- Ursu, Oana;
- Hess, Gaelen T.;
- Ego, Braeden K.;
- Aradhana;
- Li, Amy;
- Truong, Alisa;
- Trevino, Alexandro E.;
- Spees, Kaitlyn;
- Yao, David;
- Kaplow, Irene M.;
- Greenside, Peyton G.;
- Morgens, David W.;
- Phanstiel, Douglas H.;
- Snyder, Michael P.;
- Bintu, Lacramioara;
- Greenleaf, William J.;
- Kundaje, Anshul
Publication type:
Article
Satb1 integrates DNA binding site geometry and torsional stress to differentially target nucleosome-dense regions.
Published in:
Nature Communications, 2019, v. 10, n. 1, p. 1, doi. 10.1038/s41467-019-11118-8
By:
- Ghosh, Rajarshi P.;
- Shi, Quanming;
- Yang, Linfeng;
- Reddick, Michael P.;
- Nikitina, Tatiana;
- Zhurkin, Victor B.;
- Fordyce, Polly;
- Stasevich, Timothy J.;
- Chang, Howard Y.;
- Greenleaf, William J.;
- Liphardt, Jan T.
Publication type:
Article
Joint single-cell DNA accessibility and protein epitope profiling reveals environmental regulation of epigenomic heterogeneity.
Published in:
Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-07115-y
By:
- Chen, Xingqi;
- Litzenburger, Ulrike M.;
- Wei, Yuning;
- Schep, Alicia N.;
- LaGory, Edward L.;
- Choudhry, Hani;
- Giaccia, Amato J.;
- Greenleaf, William J.;
- Chang, Howard Y.
Publication type:
Article
High‐resolution mapping of cancer cell networks using co‐functional interactions.
Published in:
Molecular Systems Biology, 2018, v. 14, n. 12, p. N.PAG, doi. 10.15252/msb.20188594
By:
- Boyle, Evan A;
- Pritchard, Jonathan K;
- Greenleaf, William J
Publication type:
Article
Integrated single-cell transcriptomics and epigenomics reveals strong germinal center–associated etiology of autoimmune risk loci.
Published in:
Science Immunology, 2021, v. 6, n. 64, p. 1, doi. 10.1126/sciimmunol.abh3768
By:
- King, Hamish W.;
- Wells, Kristen L.;
- Shipony, Zohar;
- Kathiria, Arwa S.;
- Wagar, Lisa E.;
- Lareau, Caleb;
- Orban, Nara;
- Capasso, Robson;
- Davis, Mark M.;
- Steinmetz, Lars M.;
- James, Louisa K.;
- Greenleaf, William J.
Publication type:
Article
Epigenomics of human CD8 T cell differentiation and aging.
Published in:
Science Immunology, 2017, v. 2, n. 8, p. 1, doi. 10.1126/sciimmunol.aag0192
By:
- Moskowitz, David M.;
- Zhang, David W.;
- Hu, Bin;
- Le Saux, Sabine;
- Yanes, Rolando E.;
- Zhongde Ye;
- Buenrostro, Jason D.;
- Weyand, Cornelia M.;
- Greenleaf, William J.;
- Goronzy, Jörg J.
Publication type:
Article
Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens.
Published in:
Nature Communications, 2017, v. 8, n. 5, p. 15178, doi. 10.1038/ncomms15178
By:
- Morgens, David W.;
- Wainberg, Michael;
- Boyle, Evan A.;
- Ursu, Oana;
- Araya, Carlos L.;
- Tsui, C. Kimberly;
- Haney, Michael S.;
- Hess, Gaelen T.;
- Han, Kyuho;
- Jeng, Edwin E.;
- Li, Amy;
- Snyder, Michael P.;
- Greenleaf, William J.;
- Kundaje, Anshul;
- Bassik, Michael C.
Publication type:
Article
Genome-wide distribution of 5-hydroxymethyluracil and chromatin accessibility in the Breviolum minutum genome.
Published in:
Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03261-3
By:
- Marinov, Georgi K.;
- Chen, Xinyi;
- Swaffer, Matthew P.;
- Xiang, Tingting;
- Grossman, Arthur R.;
- Greenleaf, William J.
Publication type:
Article
The chromatin landscape of the euryarchaeon Haloferax volcanii.
Published in:
Genome Biology, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s13059-023-03095-5
By:
- Marinov, Georgi K.;
- Bagdatli, S. Tansu;
- Wu, Tong;
- He, Chuan;
- Kundaje, Anshul;
- Greenleaf, William J.
Publication type:
Article
CasKAS: direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA mapping.
Published in:
Genome Biology, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s13059-023-02930-z
By:
- Marinov, Georgi K.;
- Kim, Samuel H.;
- Bagdatli, S. Tansu;
- Higashino, Soon Il;
- Trevino, Alexandro E.;
- Tycko, Josh;
- Wu, Tong;
- Bintu, Lacramioara;
- Bassik, Michael C.;
- He, Chuan;
- Kundaje, Anshul;
- Greenleaf, William J.
Publication type:
Article
The future of sequencing: convergence of intelligent design and market Darwinism.
Published in:
Genome Biology, 2014, v. 15, n. 3, p. 1, doi. 10.1186/gb4168
By:
- Greenleaf, William J.;
- Sidow, Arend
Publication type:
Article
Direct observation of base-pair stepping by RNA polymerase.
Published in:
Nature, 2005, v. 438, n. 7067, p. 460, doi. 10.1038/nature04268
By:
- Abbondanzieri, Elio A.;
- Greenleaf, William J.;
- Shaevitz, Joshua W.;
- Landick, Robert;
- Block, Steven M.
Publication type:
Article
Integration of spatial and single-cell data across modalities with weakly linked features.
Published in:
Nature Biotechnology, 2024, v. 42, n. 7, p. 1096, doi. 10.1038/s41587-023-01935-0
By:
- Chen, Shuxiao;
- Zhu, Bokai;
- Huang, Sijia;
- Hickey, John W.;
- Lin, Kevin Z.;
- Snyder, Michael;
- Greenleaf, William J.;
- Nolan, Garry P.;
- Zhang, Nancy R.;
- Ma, Zongming
Publication type:
Article
Single-cell chromatin accessibility reveals principles of regulatory variation.
Published in:
Nature, 2015, v. 523, n. 7561, p. 486, doi. 10.1038/nature14590
By:
- Buenrostro, Jason D.;
- Wu, Beijing;
- Litzenburger, Ulrike M.;
- Ruff, Dave;
- Gonzales, Michael L.;
- Snyder, Michael P.;
- Chang, Howard Y.;
- Greenleaf, William J.
Publication type:
Article
Unsupervised clustering and epigenetic classification of single cells.
Published in:
Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-04629-3
By:
- Zamanighomi, Mahdi;
- Zhixiang Lin;
- Daley, Timothy;
- Xi Chen;
- Zhana Duren;
- Schep, Alicia;
- Greenleaf, William J.;
- Wing Hung Wong
Publication type:
Article
Single-cell epigenomic variability reveals functional cancer heterogeneity.
Published in:
Genome Biology, 2017, v. 18, p. 1, doi. 10.1186/s13059-016-1133-7
By:
- Litzenburger, Ulrike M.;
- Buenrostro, Jason D.;
- Beijing Wu;
- Ying Shen;
- Sheffield, Nathan C.;
- Kathiria, Arwa;
- Greenleaf, William J.;
- Chang, Howard Y.
Publication type:
Article
Terminal deoxynucleotidyl transferase and CD84 identify human multi-potent lymphoid progenitors.
Published in:
Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-49883-w
By:
- Kim, YeEun;
- Calderon, Ariel A.;
- Favaro, Patricia;
- Glass, David R.;
- Tsai, Albert G.;
- Ho, Daniel;
- Borges, Luciene;
- Greenleaf, William J.;
- Bendall, Sean C.
Publication type:
Article
Molecule by molecule, the physics and chemistry of life: SMB 2007.
Published in:
2007
By:
- Block, Steven M.;
- Larson, Matthew H.;
- Greenleaf, William J.;
- Herbert, Kristina M.;
- Guydosh, Nicholas R.;
- Anthony, Peter C.
Publication type:
Proceeding
Comprehensive sequence-to-function mapping of cofactor-dependent RNA catalysis in the glmS ribozyme.
Published in:
Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-15540-1
By:
- Andreasson, Johan O. L.;
- Savinov, Andrew;
- Block, Steven M.;
- Greenleaf, William J.
Publication type:
Article

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