| Year |
Citation |
Score |
| 2024 |
Perez AA, Goronzy IN, Blanco MR, Yeh BT, Guo JK, Lopes CS, Ettlin O, Burr A, Guttman M. ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements. Nature Genetics. PMID 39587360 DOI: 10.1038/s41588-024-02000-5 |
0.348 |
|
| 2024 |
Guo JK, Blanco MR, Guttman M. PRC2-RNA interactions: Viewpoint from Jimmy K. Guo, Mario R. Blanco, and Mitchell Guttman. Molecular Cell. 84: 3578-3585. PMID 39366346 DOI: 10.1016/j.molcel.2024.09.007 |
0.413 |
|
| 2024 |
Bhat P, Chow A, Emert B, Ettlin O, Quinodoz SA, Strehle M, Takei Y, Burr A, Goronzy IN, Chen AW, Huang W, Ferrer JLM, Soehalim E, Goh ST, Chari T, ... ... Guttman M, et al. Genome organization around nuclear speckles drives mRNA splicing efficiency. Nature. PMID 38720076 DOI: 10.1038/s41586-024-07429-6 |
0.484 |
|
| 2024 |
Guo JK, Blanco MR, Walkup WG, Bonesteele G, Urbinati CR, Banerjee AK, Chow A, Ettlin O, Strehle M, Peyda P, Amaya E, Trinh V, Guttman M. Denaturing purifications demonstrate that PRC2 and other widely reported chromatin proteins do not appear to bind directly to RNA in vivo. Molecular Cell. PMID 38387462 DOI: 10.1016/j.molcel.2024.01.026 |
0.576 |
|
| 2023 |
Perez AA, Goronzy IN, Blanco MR, Guo JK, Guttman M. ChIP-DIP: A multiplexed method for mapping hundreds of proteins to DNA uncovers diverse regulatory elements controlling gene expression. Biorxiv : the Preprint Server For Biology. PMID 38187704 DOI: 10.1101/2023.12.14.571730 |
0.38 |
|
| 2023 |
Wolin E, Guo JK, Blanco MR, Perez AA, Goronzy IN, Abdou AA, Gorhe D, Guttman M, Jovanovic M. SPIDR: a highly multiplexed method for mapping RNA-protein interactions uncovers a potential mechanism for selective translational suppression upon cellular stress. Biorxiv : the Preprint Server For Biology. PMID 37333139 DOI: 10.1101/2023.06.05.543769 |
0.582 |
|
| 2023 |
Bhat P, Chow A, Emert B, Ettlin O, Quinodoz SA, Takei Y, Huang W, Blanco MR, Guttman M. 3D genome organization around nuclear speckles drives mRNA splicing efficiency. Biorxiv : the Preprint Server For Biology. PMID 36711853 DOI: 10.1101/2023.01.04.522632 |
0.484 |
|
| 2023 |
Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen LL, Chen R, Dean C, Dinger ME, Fitzgerald KA, Gingeras TR, Guttman M, Hirose T, Huarte M, Johnson R, et al. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nature Reviews. Molecular Cell Biology. PMID 36596869 DOI: 10.1038/s41580-022-00566-8 |
0.588 |
|
| 2022 |
Goronzy IN, Quinodoz SA, Jachowicz JW, Ollikainen N, Bhat P, Guttman M. Simultaneous mapping of 3D structure and nascent RNAs argues against nuclear compartments that preclude transcription. Cell Reports. 41: 111730. PMID 36450242 DOI: 10.1016/j.celrep.2022.111730 |
0.802 |
|
| 2022 |
Guo JK, Guttman M. Regulatory non-coding RNAs: everything is possible, but what is important? Nature Methods. 19: 1156-1159. PMID 36203023 DOI: 10.1038/s41592-022-01629-6 |
0.416 |
|
| 2022 |
Jachowicz JW, Strehle M, Banerjee AK, Blanco MR, Thai J, Guttman M. Xist spatially amplifies SHARP/SPEN recruitment to balance chromosome-wide silencing and specificity to the X chromosome. Nature Structural & Molecular Biology. 29: 239-249. PMID 35301492 DOI: 10.1038/s41594-022-00739-1 |
0.793 |
|
| 2022 |
Quinodoz SA, Bhat P, Chovanec P, Jachowicz JW, Ollikainen N, Detmar E, Soehalim E, Guttman M. SPRITE: a genome-wide method for mapping higher-order 3D interactions in the nucleus using combinatorial split-and-pool barcoding. Nature Protocols. 17: 36-75. PMID 35013617 DOI: 10.1038/s41596-021-00633-y |
0.763 |
|
| 2022 |
Quinodoz SA, Guttman M. Essential Roles for RNA in Shaping Nuclear Organization. Cold Spring Harbor Perspectives in Biology. 14. PMID 34400555 DOI: 10.1101/cshperspect.a039719 |
0.465 |
|
| 2021 |
Markaki Y, Chong JG, Wang Y, Jacobson EC, Luong C, Tan SYX, Jachowicz JW, Strehle M, Maestrini D, Banerjee AK, Mistry BA, Dror I, Dossin F, Schӧneberg J, Heard E, ... Guttman M, et al. Xist nucleates local protein gradients to propagate silencing across the X chromosome. Cell. 184: 6212. PMID 34890555 DOI: 10.1016/j.cell.2021.11.028 |
0.746 |
|
| 2021 |
Markaki Y, Gan Chong J, Wang Y, Jacobson EC, Luong C, Tan SYX, Jachowicz JW, Strehle M, Maestrini D, Banerjee AK, Mistry BA, Dror I, Dossin F, Schöneberg J, Heard E, ... Guttman M, et al. Xist nucleates local protein gradients to propagate silencing across the X chromosome. Cell. PMID 34813726 DOI: 10.1016/j.cell.2021.10.022 |
0.82 |
|
| 2021 |
Quinodoz SA, Jachowicz JW, Bhat P, Ollikainen N, Banerjee AK, Goronzy IN, Blanco MR, Chovanec P, Chow A, Markaki Y, Thai J, Plath K, Guttman M. RNA promotes the formation of spatial compartments in the nucleus. Cell. 184: 5775-5790.e30. PMID 34739832 DOI: 10.1016/j.cell.2021.10.014 |
0.817 |
|
| 2021 |
Arrastia MV, Jachowicz JW, Ollikainen N, Curtis MS, Lai C, Quinodoz SA, Selck DA, Ismagilov RF, Guttman M. Single-cell measurement of higher-order 3D genome organization with scSPRITE. Nature Biotechnology. PMID 34426703 DOI: 10.1038/s41587-021-00998-1 |
0.75 |
|
| 2021 |
Bhat P, Honson D, Guttman M. Nuclear compartmentalization as a mechanism of quantitative control of gene expression. Nature Reviews. Molecular Cell Biology. PMID 34341548 DOI: 10.1038/s41580-021-00387-1 |
0.489 |
|
| 2021 |
Takei Y, Yun J, Zheng S, Ollikainen N, Pierson N, White J, Shah S, Thomassie J, Suo S, Eng CL, Guttman M, Yuan GC, Cai L. Integrated spatial genomics reveals global architecture of single nuclei. Nature. PMID 33505024 DOI: 10.1038/s41586-020-03126-2 |
0.445 |
|
| 2020 |
Banerjee AK, Blanco MR, Bruce EA, Honson DD, Chen LM, Chow A, Bhat P, Ollikainen N, Quinodoz SA, Loney C, Thai J, Miller ZD, Lin AE, Schmidt MM, Stewart DG, ... ... Guttman M, et al. SARS-CoV-2 Disrupts Splicing, Translation, and Protein Trafficking to Suppress Host Defenses. Cell. PMID 33080218 DOI: 10.1016/j.cell.2020.10.004 |
0.462 |
|
| 2020 |
Pandya-Jones A, Markaki Y, Serizay J, Chitiashvili T, Mancia Leon WR, Damianov A, Chronis C, Papp B, Chen CK, McKee R, Wang XJ, Chau A, Sabri S, Leonhardt H, Zheng S, ... Guttman M, et al. A protein assembly mediates Xist localization and gene silencing. Nature. PMID 32908311 DOI: 10.1038/S41586-020-2703-0 |
0.576 |
|
| 2020 |
Strehle M, Guttman M. Xist drives spatial compartmentalization of DNA and protein to orchestrate initiation and maintenance of X inactivation. Current Opinion in Cell Biology. 64: 139-147. PMID 32535328 DOI: 10.1016/j.ceb.2020.04.009 |
0.373 |
|
| 2019 |
McDonel P, Guttman M. Approaches for Understanding the Mechanisms of Long Noncoding RNA Regulation of Gene Expression. Cold Spring Harbor Perspectives in Biology. 11. PMID 31791999 DOI: 10.1101/Cshperspect.A032151 |
0.532 |
|
| 2019 |
Cerase A, Armaos A, Neumayer C, Avner P, Guttman M, Tartaglia GG. Phase separation drives X-chromosome inactivation: a hypothesis. Nature Structural & Molecular Biology. 26: 331-334. PMID 31061525 DOI: 10.1038/S41594-019-0223-0 |
0.311 |
|
| 2018 |
Munschauer M, Nguyen CT, Sirokman K, Hartigan CR, Hogstrom L, Engreitz JM, Ulirsch JC, Fulco CP, Subramanian V, Chen J, Schenone M, Guttman M, Carr SA, Lander ES. Publisher Correction: The NORAD lncRNA assembles a topoisomerase complex critical for genome stability. Nature. PMID 30279576 DOI: 10.1038/s41586-018-0584-2 |
0.645 |
|
| 2018 |
Munschauer M, Nguyen CT, Sirokman K, Hartigan CR, Hogstrom L, Engreitz JM, Ulirsch JC, Fulco CP, Subramanian V, Chen J, Schenone M, Guttman M, Carr SA, Lander ES. The NORAD lncRNA assembles a topoisomerase complex critical for genome stability. Nature. PMID 30150775 DOI: 10.1038/s41586-018-0453-z |
0.776 |
|
| 2018 |
McHugh CA, Guttman M. RAP-MS: A Method to Identify Proteins that Interact Directly with a Specific RNA Molecule in Cells. Methods in Molecular Biology (Clifton, N.J.). 1649: 473-488. PMID 29130217 DOI: 10.1007/978-1-4939-7213-5_31 |
0.776 |
|
| 2017 |
Blanco MR, Guttman M. Re-evaluating the foundations of lncRNA-Polycomb function. The Embo Journal. 36: 964-966. PMID 28298433 DOI: 10.15252/embj.201796796 |
0.314 |
|
| 2017 |
Szempruch A, Guttman M. Linking Protein and RNA Function within the Same Gene. Cell. 168: 753-755. PMID 28235192 DOI: 10.1016/j.cell.2017.02.014 |
0.464 |
|
| 2016 |
Cirillo D, Blanco M, Armaos A, Buness A, Avner P, Guttman M, Cerase A, Tartaglia GG. Quantitative predictions of protein interactions with long noncoding RNAs. Nature Methods. 14: 5-6. PMID 28032625 DOI: 10.1038/Nmeth.4100 |
0.54 |
|
| 2016 |
Engreitz JM, Haines JE, Perez EM, Munson G, Chen J, Kane M, McDonel PE, Guttman M, Lander ES. Local regulation of gene expression by lncRNA promoters, transcription and splicing. Nature. PMID 27783602 DOI: 10.1038/Nature20149 |
0.656 |
|
| 2016 |
Engreitz JM, Ollikainen N, Guttman M. Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression. Nature Reviews. Molecular Cell Biology. PMID 27780979 DOI: 10.1038/Nrm.2016.126 |
0.576 |
|
| 2016 |
Patil DP, Chen CK, Pickering BF, Chow A, Jackson C, Guttman M, Jaffrey SR. m(6)A RNA methylation promotes XIST-mediated transcriptional repression. Nature. PMID 27602518 DOI: 10.1038/Nature19342 |
0.49 |
|
| 2016 |
Chen CK, Blanco M, Jackson C, Aznauryan E, Ollikainen N, Surka C, Chow A, Cerase A, McDonel P, Guttman M. Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing. Science (New York, N.Y.). PMID 27492478 DOI: 10.1126/Science.Aae0047 |
0.335 |
|
| 2016 |
Van Nostrand EL, Pratt GA, Shishkin AA, Gelboin-Burkhart C, Fang MY, Sundararaman B, Blue SM, Nguyen TB, Surka C, Elkins K, Stanton R, Rigo F, Guttman M, Yeo GW. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nature Methods. PMID 27018577 DOI: 10.1038/Nmeth.3810 |
0.496 |
|
| 2016 |
Chen J, Shishkin AA, Zhu X, Kadri S, Maza I, Guttman M, Hanna JH, Regev A, Garber M. Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs. Genome Biology. 17: 19. PMID 26838501 DOI: 10.1186/S13059-016-0880-9 |
0.496 |
|
| 2015 |
McHugh CA, Chen CK, Chow A, Surka CF, Tran C, McDonel P, Pandya-Jones A, Blanco M, Burghard C, Moradian A, Sweredoski MJ, Shishkin AA, Su J, Lander ES, Hess S, ... ... Guttman M, et al. The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. Nature. 521: 232-6. PMID 25915022 DOI: 10.1038/Nature14443 |
0.789 |
|
| 2015 |
Shishkin AA, Giannoukos G, Kucukural A, Ciulla D, Busby M, Surka C, Chen J, Bhattacharyya RP, Rudy RF, Patel MM, Novod N, Hung DT, Gnirke A, Garber M, Guttman M, et al. Simultaneous generation of many RNA-seq libraries in a single reaction. Nature Methods. 12: 323-5. PMID 25730492 DOI: 10.1038/Nmeth.3313 |
0.376 |
|
| 2015 |
Engreitz J, Lander ES, Guttman M. RNA antisense purification (RAP) for mapping RNA interactions with chromatin. Methods in Molecular Biology (Clifton, N.J.). 1262: 183-97. PMID 25555582 DOI: 10.1007/978-1-4939-2253-6_11 |
0.629 |
|
| 2014 |
Quinodoz S, Guttman M. Long noncoding RNAs: an emerging link between gene regulation and nuclear organization. Trends in Cell Biology. 24: 651-63. PMID 25441720 DOI: 10.1016/j.tcb.2014.08.009 |
0.462 |
|
| 2014 |
Engreitz JM, Sirokman K, McDonel P, Shishkin AA, Surka C, Russell P, Grossman SR, Chow AY, Guttman M, Lander ES. RNA-RNA interactions enable specific targeting of noncoding RNAs to nascent Pre-mRNAs and chromatin sites. Cell. 159: 188-99. PMID 25259926 DOI: 10.1016/J.Cell.2014.08.018 |
0.629 |
|
| 2014 |
Schwartz S, Bernstein DA, Mumbach MR, Jovanovic M, Herbst RH, León-Ricardo BX, Engreitz JM, Guttman M, Satija R, Lander ES, Fink G, Regev A. Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA. Cell. 159: 148-62. PMID 25219674 DOI: 10.1016/J.Cell.2014.08.028 |
0.501 |
|
| 2014 |
Rinn J, Guttman M. RNA Function. RNA and dynamic nuclear organization. Science (New York, N.Y.). 345: 1240-1. PMID 25214588 DOI: 10.1126/Science.1252966 |
0.422 |
|
| 2014 |
McHugh CA, Russell P, Guttman M. Methods for comprehensive experimental identification of RNA-protein interactions. Genome Biology. 15: 203. PMID 24467948 DOI: 10.1186/Gb4152 |
0.786 |
|
| 2013 |
Engreitz JM, Pandya-Jones A, McDonel P, Shishkin A, Sirokman K, Surka C, Kadri S, Xing J, Goren A, Lander ES, Plath K, Guttman M. The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science (New York, N.Y.). 341: 1237973. PMID 23828888 DOI: 10.1126/Science.1237973 |
0.52 |
|
| 2013 |
Guttman M, Russell P, Ingolia NT, Weissman JS, Lander ES. Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins. Cell. 154: 240-51. PMID 23810193 DOI: 10.1016/J.Cell.2013.06.009 |
0.633 |
|
| 2013 |
Gifford CA, Ziller MJ, Gu H, Trapnell C, Donaghey J, Tsankov A, Shalek AK, Kelley DR, Shishkin AA, Issner R, Zhang X, Coyne M, Fostel JL, Holmes L, Meldrim J, ... Guttman M, et al. Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Cell. 153: 1149-63. PMID 23664763 DOI: 10.1016/J.Cell.2013.04.037 |
0.636 |
|
| 2013 |
Kirby A, Gnirke A, Jaffe DB, Barešová V, Pochet N, Blumenstiel B, Ye C, Aird D, Stevens C, Robinson JT, Cabili MN, Gat-Viks I, Kelliher E, Daza R, DeFelice M, ... ... Guttman M, et al. Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing. Nature Genetics. 45: 299-303. PMID 23396133 DOI: 10.1038/Ng.2543 |
0.513 |
|
| 2012 |
Garber M, Yosef N, Goren A, Raychowdhury R, Thielke A, Guttman M, Robinson J, Minie B, Chevrier N, Itzhaki Z, Blecher-Gonen R, Bornstein C, Amann-Zalcenstein D, Weiner A, Friedrich D, et al. A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Molecular Cell. 47: 810-22. PMID 22940246 DOI: 10.1016/J.Molcel.2012.07.030 |
0.556 |
|
| 2012 |
Guttman M, Rinn JL. Modular regulatory principles of large non-coding RNAs. Nature. 482: 339-46. PMID 22337053 DOI: 10.1038/nature10887 |
0.521 |
|
| 2011 |
Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, ... ... Guttman M, et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 478: 476-82. PMID 21993624 DOI: 10.1038/Nature10530 |
0.613 |
|
| 2011 |
Guttman M, Donaghey J, Carey BW, Garber M, Grenier JK, Munson G, Young G, Lucas AB, Ach R, Bruhn L, Yang X, Amit I, Meissner A, Regev A, Rinn JL, et al. lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature. 477: 295-300. PMID 21874018 DOI: 10.1038/Nature10398 |
0.52 |
|
| 2011 |
Garber M, Grabherr MG, Guttman M, Trapnell C. Computational methods for transcriptome annotation and quantification using RNA-seq. Nature Methods. 8: 469-77. PMID 21623353 DOI: 10.1038/Nmeth.1613 |
0.403 |
|
| 2011 |
Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP. Integrative genomics viewer. Nature Biotechnology. 29: 24-6. PMID 21221095 DOI: 10.1038/Nbt.1754 |
0.453 |
|
| 2010 |
Loewer S, Cabili MN, Guttman M, Loh YH, Thomas K, Park IH, Garber M, Curran M, Onder T, Agarwal S, Manos PD, Datta S, Lander ES, Schlaeger TM, Daley GQ, et al. Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells. Nature Genetics. 42: 1113-7. PMID 21057500 DOI: 10.1038/Ng.710 |
0.506 |
|
| 2010 |
Huarte M, Guttman M, Feldser D, Garber M, Koziol MJ, Kenzelmann-Broz D, Khalil AM, Zuk O, Amit I, Rabani M, Attardi LD, Regev A, Lander ES, Jacks T, Rinn JL. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell. 142: 409-19. PMID 20673990 DOI: 10.1016/J.Cell.2010.06.040 |
0.539 |
|
| 2010 |
Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nature Biotechnology. 28: 503-10. PMID 20436462 DOI: 10.1038/nbt.1633 |
0.664 |
|
| 2010 |
Ozsolak F, Goren A, Gymrek M, Guttman M, Regev A, Bernstein BE, Milos PM. Digital transcriptome profiling from attomole-level RNA samples. Genome Research. 20: 519-25. PMID 20133332 DOI: 10.1101/Gr.102129.109 |
0.665 |
|
| 2009 |
Amit I, Garber M, Chevrier N, Leite AP, Donner Y, Eisenhaure T, Guttman M, Grenier JK, Li W, Zuk O, Schubert LA, Birditt B, Shay T, Goren A, Zhang X, et al. Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science (New York, N.Y.). 326: 257-63. PMID 19729616 DOI: 10.1126/Science.1179050 |
0.571 |
|
| 2009 |
Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, Thomas K, Presser A, Bernstein BE, van Oudenaarden A, Regev A, Lander ES, Rinn JL. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proceedings of the National Academy of Sciences of the United States of America. 106: 11667-72. PMID 19571010 DOI: 10.1073/Pnas.0904715106 |
0.718 |
|
| 2009 |
Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, Cabili MN, Jaenisch R, Mikkelsen TS, Jacks T, Hacohen N, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature. 458: 223-7. PMID 19182780 DOI: 10.1038/Nature07672 |
0.784 |
|
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