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Alexander J. Ruthenburg, Ph.D. - Publications

Affiliations: 
2005 Harvard University, Cambridge, MA, United States 
 2010- Molecular Genetics and Cell Biology University of Chicago, Chicago, IL 
Area:
chromatin, biochemistry, chemical biology, structure
Website:
http://mgcb.bsd.uchicago.edu/faculty/ruthenburg/index.html
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34 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Gaurav N, Kanai A, Lachance C, Cox KL, Liu J, Grzybowski AT, Saksouk N, Klein BJ, Komata Y, Asada S, Ruthenburg AJ, Poirier MG, Côté J, Yokoyama A, Kutateladze TG. Guiding the HBO1 complex function through the JADE subunit. Nature Structural & Molecular Biology. PMID 38448574 DOI: 10.1038/s41594-024-01245-2  0.4
2023 Kainth AS, Haddad GA, Hall JM, Ruthenburg AJ. Merging short and stranded long reads improves transcript assembly. Plos Computational Biology. 19: e1011576. PMID 37883581 DOI: 10.1371/journal.pcbi.1011576  0.545
2023 Chi P, Lewis PW, Lu C, Lu J, Ruthenburg AJ, Sabari BR, Shechter D, Wan L, Wang GG. Charles David Allis (1951-2023). Nature Genetics. PMID 36849658 DOI: 10.1038/s41588-023-01331-z  0.676
2022 Zeng Y, Fair BJ, Zeng H, Krishnamohan A, Hou Y, Hall JM, Ruthenburg AJ, Li YI, Staley JP. Profiling lariat intermediates reveals genetic determinants of early and late co-transcriptional splicing. Molecular Cell. PMID 36435176 DOI: 10.1016/j.molcel.2022.11.004  0.55
2020 Oikawa M, Simeone A, Hormanseder E, Teperek M, Gaggioli V, O'Doherty A, Falk E, Sporniak M, D'Santos C, Franklin VNR, Kishore K, Bradshaw CR, Keane D, Freour T, David L, ... ... Ruthenburg AJ, et al. Epigenetic homogeneity in histone methylation underlies sperm programming for embryonic transcription. Nature Communications. 11: 3491. PMID 32661239 DOI: 10.1038/S41467-020-17238-W  0.48
2020 Sun X, Wang Z, Hall JM, Perez-Cervantes C, Ruthenburg AJ, Moskowitz IP, Gribskov M, Yang XH. Chromatin-enriched RNAs mark active and repressive cis-regulation: An analysis of nuclear RNA-seq. Plos Computational Biology. 16: e1007119. PMID 32040509 DOI: 10.1371/Journal.Pcbi.1007119  0.597
2019 Grzybowski AT, Shah RN, Richter WF, Ruthenburg AJ. Native internally calibrated chromatin immunoprecipitation for quantitative studies of histone post-translational modifications. Nature Protocols. PMID 31723301 DOI: 10.1038/S41596-019-0218-7  0.479
2019 Bennett RL, Bele A, Small EC, Will CM, Nabet B, Oyer JA, Huang X, Ghosh RP, Grzybowski AT, Yu T, Zhang Q, Riva A, Lele TP, Schatz GC, Kelleher NL, ... Ruthenburg AJ, et al. A Mutation in Histone H2B Represents a New Class of Oncogenic Driver. Cancer Discovery. PMID 31337617 DOI: 10.1158/2159-8290.Cd-19-0393  0.447
2018 Shah RN, Grzybowski AT, Cornett EM, Johnstone AL, Dickson BM, Boone BA, Cheek MA, Cowles MW, Maryanski D, Meiners MJ, Tiedemann RL, Vaughan RM, Arora N, Sun ZW, Rothbart SB, ... ... Ruthenburg AJ, et al. Examining the Roles of H3K4 Methylation States with Systematically Characterized Antibodies. Molecular Cell. PMID 30244833 DOI: 10.1016/J.Molcel.2018.08.015  0.499
2018 Karki S, Kennedy DE, Mclean K, Grzybowski AT, Maienschein-Cline M, Banerjee S, Xu H, Davis E, Mandal M, Labno C, Powers SE, Le Beau MM, Dinner AR, Singh H, Ruthenburg AJ, et al. Regulated Capture of Vκ Gene Topologically Associating Domains by Transcription Factories. Cell Reports. 24: 2443-2456. PMID 30157436 DOI: 10.1016/J.Celrep.2018.07.091  0.34
2018 Maganti HB, Jrade H, Cafariello C, Manias Rothberg JL, Porter CJ, Yockell-Lelièvre J, Battaion HL, Khan ST, Howard JP, Li Y, Grzybowski AT, Sabri E, Ruthenburg AJ, Dilworth FJ, Perkins TJ, et al. Targeting the MTF2-MDM2 axis sensitizes refractory acute myeloid leukemia to chemotherapy. Cancer Discovery. PMID 30115703 DOI: 10.1182/Blood-2018-99-117281  0.339
2017 Yang XH, Nadadur RD, Hilvering CR, Bianchi V, Werner M, Mazurek SR, Gadek M, Shen KM, Goldman JA, Tyan L, Bekeny J, Hall JM, Lee N, Perez-Cervantes C, Burnicka-Turek O, ... ... Ruthenburg AJ, et al. Transcription-factor-dependent enhancer transcription defines a gene regulatory network for cardiac rhythm. Elife. 6. PMID 29280435 DOI: 10.7554/Elife.31683  0.597
2017 Chen Z, Notti RQ, Ueberheide BM, Ruthenburg AJ. Quantitative and structural assessment of histone methyllysine analog engagement by cognate binding proteins reveals affinity decrements relative to native counterparts. Biochemistry. PMID 29111671 DOI: 10.1021/Acs.Biochem.7B00926  0.755
2017 Werner MS, Sullivan MA, Shah RN, Nadadur RD, Grzybowski AT, Galat V, Moskowitz IP, Ruthenburg AJ. Chromatin-enriched lncRNAs can act as cell-type specific activators of proximal gene transcription. Nature Structural & Molecular Biology. PMID 28628087 DOI: 10.1038/Nsmb.3424  0.379
2017 Yang XH, Nadadur RD, Hilvering CR, Bianchi V, Werner M, Mazurek SR, Gadek M, Shen KM, Goldman JA, Tyan L, Bekeny J, Hall JM, Lee N, Perez-Cervantes C, Burnicka-Turek O, ... ... Ruthenburg AJ, et al. Author response: Transcription-factor-dependent enhancer transcription defines a gene regulatory network for cardiac rhythm Elife. DOI: 10.7554/Elife.31683.021  0.575
2016 Hattori T, Lai D, Dementieva IS, Montaño SP, Kurosawa K, Zheng Y, Akin LR, Świst-Rosowska KM, Grzybowski AT, Koide A, Krajewski K, Strahl BD, Kelleher NL, Ruthenburg AJ, Koide S. Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation. Proceedings of the National Academy of Sciences of the United States of America. PMID 26862167 DOI: 10.1073/Pnas.1522691113  0.613
2015 Werner MS, Ruthenburg AJ. Nuclear Fractionation Reveals Thousands of Chromatin-Tethered Noncoding RNAs Adjacent to Active Genes. Cell Reports. 12: 1089-98. PMID 26257179 DOI: 10.1016/J.Celrep.2015.07.033  0.403
2015 Rothbart SB, Dickson BM, Raab JR, Grzybowski AT, Krajewski K, Guo AH, Shanle EK, Josefowicz SZ, Fuchs SM, Allis CD, Magnuson TR, Ruthenburg AJ, Strahl BD. An Interactive Database for the Assessment of Histone Antibody Specificity. Molecular Cell. 59: 502-11. PMID 26212453 DOI: 10.1016/J.Molcel.2015.06.022  0.771
2015 Grzybowski AT, Chen Z, Ruthenburg AJ. Calibrating ChIP-Seq with Nucleosomal Internal Standards to Measure Histone Modification Density Genome Wide. Molecular Cell. 58: 886-99. PMID 26004229 DOI: 10.1016/J.Molcel.2015.04.022  0.773
2015 Rothbart SB, Dickson BM, Raab JR, Grzybowski AT, Krajewski K, Guo AH, Shanle EK, Josefowicz SZ, Fuchs SM, Allis CD, Magnuson TR, Ruthenburg AJ, Strahl BD. An Interactive Database for the Assessment of Histone Antibody Specificity Molecular Cell. 59: 502-511. DOI: 10.1016/j.molcel.2015.06.022  0.77
2014 Chen Z, Grzybowski AT, Ruthenburg AJ. Traceless semisynthesis of a set of histone 3 species bearing specific lysine methylation marks. Chembiochem : a European Journal of Chemical Biology. 15: 2071-5. PMID 25155436 DOI: 10.1002/Cbic.201402313  0.778
2013 Hattori T, Taft JM, Swist KM, Luo H, Witt H, Slattery M, Koide A, Ruthenburg AJ, Krajewski K, Strahl BD, White KP, Farnham PJ, Zhao Y, Koide S. Recombinant antibodies to histone post-translational modifications. Nature Methods. 10: 992-5. PMID 23955773 DOI: 10.1038/Nmeth.2605  0.674
2012 Malecek K, Ruthenburg A. Validation of histone-binding partners by peptide pull-downs and isothermal titration calorimetry Methods in Enzymology. 512: 187-220. PMID 22910208 DOI: 10.1016/B978-0-12-391940-3.00009-3  0.479
2011 Werner M, Ruthenburg AJ. The United States of histone ubiquitylation and methylation. Molecular Cell. 43: 5-7. PMID 21726805 DOI: 10.1016/J.Molcel.2011.06.015  0.454
2011 Ruthenburg AJ, Li H, Milne TA, Dewell S, McGinty RK, Yuen M, Ueberheide B, Dou Y, Muir TW, Patel DJ, Allis CD. Recognition of a mononucleosomal histone modification pattern by BPTF via multivalent interactions. Cell. 145: 692-706. PMID 21596426 DOI: 10.1016/J.Cell.2011.03.053  0.649
2010 Milne TA, Kim J, Wang GG, Stadler SC, Basrur V, Whitcomb SJ, Wang Z, Ruthenburg AJ, Elenitoba-Johnson KS, Roeder RG, Allis CD. Multiple interactions recruit MLL1 and MLL1 fusion proteins to the HOXA9 locus in leukemogenesis. Molecular Cell. 38: 853-63. PMID 20541448 DOI: 10.1016/J.Molcel.2010.05.011  0.711
2007 Ruthenburg AJ, Li H, Patel DJ, Allis CD. Multivalent engagement of chromatin modifications by linked binding modules. Nature Reviews. Molecular Cell Biology. 8: 983-94. PMID 18037899 DOI: 10.1038/Nrm2298  0.664
2007 Taverna SD, Li H, Ruthenburg AJ, Allis CD, Patel DJ. How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nature Structural & Molecular Biology. 14: 1025-40. PMID 17984965 DOI: 10.1038/Nsmb1338  0.78
2007 Ruthenburg AJ, Allis CD, Wysocka J. Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark. Molecular Cell. 25: 15-30. PMID 17218268 DOI: 10.1016/J.Molcel.2006.12.014  0.721
2006 Dou Y, Milne TA, Ruthenburg AJ, Lee S, Lee JW, Verdine GL, Allis CD, Roeder RG. Regulation of MLL1 H3K4 methyltransferase activity by its core components. Nature Structural & Molecular Biology. 13: 713-9. PMID 16878130 DOI: 10.1038/Nsmb1128  0.714
2006 Ruthenburg AJ, Wang W, Graybosch DM, Li H, Allis CD, Patel DJ, Verdine GL. Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex. Nature Structural & Molecular Biology. 13: 704-12. PMID 16829959 DOI: 10.1038/Nsmb1119  0.702
2006 Losey HC, Ruthenburg AJ, Verdine GL. Crystal structure of Staphylococcus aureus tRNA adenosine deaminase TadA in complex with RNA. Nature Structural & Molecular Biology. 13: 153-9. PMID 16415880 DOI: 10.1038/Nsmb1047  0.522
2005 Wei H, Ruthenburg AJ, Bechis SK, Verdine GL. Nucleotide-dependent domain movement in the ATPase domain of a human type IIA DNA topoisomerase. The Journal of Biological Chemistry. 280: 37041-7. PMID 16100112 DOI: 10.1074/Jbc.M506520200  0.605
2005 Ruthenburg AJ, Graybosch DM, Huetsch JC, Verdine GL. A superhelical spiral in the Escherichia coli DNA gyrase A C-terminal domain imparts unidirectional supercoiling bias. The Journal of Biological Chemistry. 280: 26177-84. PMID 15897198 DOI: 10.1074/Jbc.M502838200  0.515
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