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L. Stirling S. Churchman - Publications

Affiliations: 
Genetics Harvard Medical School, Boston, MA, United States 
Area:
motor mechanism of RNA polymerase
Website:
http://www.fas.harvard.edu/~biophys/L_Stirling_Churchman.htm
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14/58 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
2014 Marquardt S, Escalante-Chong R, Pho N, Wang J, Churchman LS, Springer M, Buratowski S. A Chromatin-Based Mechanism for Limiting Divergent Noncoding Transcription. Cell. 158: 462. PMID 28915368 DOI: 10.1016/j.cell.2014.06.038  0.338
2014 Marquardt S, Escalante-Chong R, Pho N, Wang J, Churchman LS, Springer M, Buratowski S. A chromatin-based mechanism for limiting divergent noncoding transcription. Cell. 157: 1712-23. PMID 24949978 DOI: 10.1016/J.Cell.2014.04.036  0.387
2013 Elting MW, Leslie SR, Churchman LS, Korlach J, McFaul CM, Leith JS, Levene MJ, Cohen AE, Spudich JA. Single-molecule fluorescence imaging of processive myosin with enhanced background suppression using linear zero-mode waveguides (ZMWs) and convex lens induced confinement (CLIC). Optics Express. 21: 1189-202. PMID 23389011 DOI: 10.1364/Oe.21.001189  0.528
2012 Churchman LS, Weissman JS. Native elongating transcript sequencing (NET-seq). Current Protocols in Molecular Biology / Edited by Frederick M. Ausubel ... [Et Al.]. Unit 4.14.1-17. PMID 22470065 DOI: 10.1002/0471142727.Mb0414S98  0.511
2012 Churchman LS, Spudich JA. Single-molecule high-resolution colocalization of single probes. Cold Spring Harbor Protocols. 2012: 242-5. PMID 22301661 DOI: 10.1101/Pdb.Prot067926  0.54
2012 Churchman LS, Spudich JA. Colocalization of fluorescent probes: accurate and precise registration with nanometer resolution. Cold Spring Harbor Protocols. 2012: 141-9. PMID 22301660 DOI: 10.1101/Pdb.Top067918  0.527
2012 Churchman LS, Weissman JS. Visualizing Transcription In Vivo at Nucleotide Resolution using Nascent Transcript Sequencing Biophysical Journal. 102: 611a. DOI: 10.1016/J.Bpj.2011.11.3330  0.534
2011 Terzi N, Churchman LS, Vasiljeva L, Weissman J, Buratowski S. H3K4 trimethylation by Set1 promotes efficient termination by the Nrd1-Nab3-Sen1 pathway. Molecular and Cellular Biology. 31: 3569-83. PMID 21709022 DOI: 10.1128/Mcb.05590-11  0.415
2011 Churchman LS, Weissman JS. Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature. 469: 368-73. PMID 21248844 DOI: 10.1038/Nature09652  0.486
2010 Mortensen KI, Churchman LS, Spudich JA, Flyvbjerg H. Optimized localization analysis for single-molecule tracking and super-resolution microscopy. Nature Methods. 7: 377-81. PMID 20364147 DOI: 10.1038/Nmeth.1447  0.469
2009 Bassik MC, Lebbink RJ, Churchman LS, Ingolia NT, Patena W, LeProust EM, Schuldiner M, Weissman JS, McManus MT. Rapid creation and quantitative monitoring of high coverage shRNA libraries. Nature Methods. 6: 443-5. PMID 19448642 DOI: 10.1038/Nmeth.1330  0.598
2006 Churchman LS, Flyvbjerg H, Spudich JA. A non-Gaussian distribution quantifies distances measured with fluorescence localization techniques. Biophysical Journal. 90: 668-71. PMID 16258038 DOI: 10.1529/Biophysj.105.065599  0.502
2005 Churchman LS, Okten Z, Rock RS, Dawson JF, Spudich JA. Single molecule high-resolution colocalization of Cy3 and Cy5 attached to macromolecules measures intramolecular distances through time. Proceedings of the National Academy of Sciences of the United States of America. 102: 1419-23. PMID 15668396 DOI: 10.1073/Pnas.0409487102  0.634
2004 Okten Z, Churchman LS, Rock RS, Spudich JA. Myosin VI walks hand-over-hand along actin. Nature Structural & Molecular Biology. 11: 884-7. PMID 15286724 DOI: 10.1038/Nsmb815  0.586
Low-probability matches (unlikely to be authored by this person)
2016 Mayer A, Churchman LS. Genome-wide profiling of RNA polymerase transcription at nucleotide resolution in human cells with native elongating transcript sequencing. Nature Protocols. 11: 813-33. PMID 27010758 DOI: 10.1038/nprot.2016.047  0.294
2023 Tullius TW, Isaac RS, Ranchalis J, Dubocanin D, Churchman LS, Stergachis AB. RNA polymerases reshape chromatin and coordinate transcription on individual fibers. Biorxiv : the Preprint Server For Biology. PMID 38187631 DOI: 10.1101/2023.12.22.573133  0.29
2021 Drexler HL, Choquet K, Merens HE, Tang PS, Simpson JT, Churchman LS. Revealing nascent RNA processing dynamics with nano-COP. Nature Protocols. PMID 33514943 DOI: 10.1038/s41596-020-00469-y  0.29
2017 Mayer A, Landry HM, Churchman LS. Pause & go: from the discovery of RNA polymerase pausing to its functional implications. Current Opinion in Cell Biology. 46: 72-80. PMID 28363125 DOI: 10.1016/j.ceb.2017.03.002  0.286
2024 Coté A, O'Farrell A, Dardani I, Dunagin M, Coté C, Wan Y, Bayatpour S, Drexler HL, Alexander KA, Chen F, Wassie AT, Patel R, Pham K, Boyden ES, Berger S, ... ... Churchman LS, et al. Post-transcriptional splicing can occur in a slow-moving zone around the gene. Elife. 12. PMID 38577979 DOI: 10.7554/eLife.91357  0.276
2019 Drexler HL, Choquet K, Churchman LS. Splicing Kinetics and Coordination Revealed by Direct Nascent RNA Sequencing through Nanopores. Molecular Cell. 77: 985-998.e8. PMID 31839405 DOI: 10.1016/j.molcel.2019.11.017  0.274
2017 Boswell SA, Snavely A, Landry HM, Churchman LS, Gray JM, Springer M. Total RNA-seq to identify pharmacological effects on specific stages of mRNA synthesis. Nature Chemical Biology. PMID 28263964 DOI: 10.1038/Nchembio.2317  0.267
2015 Mayer A, di Iulio J, Maleri S, Eser U, Vierstra J, Reynolds A, Sandstrom R, Stamatoyannopoulos JA, Churchman LS. Native elongating transcript sequencing reveals human transcriptional activity at nucleotide resolution. Cell. 161: 541-54. PMID 25910208 DOI: 10.1016/J.Cell.2015.03.010  0.25
2017 Winter GE, Mayer A, Buckley DL, Erb MA, Roderick JE, Vittori S, Reyes JM, di Iulio J, Souza A, Ott CJ, Roberts JM, Zeid R, Scott TG, Paulk J, Lachance K, ... ... Churchman LS, et al. BET Bromodomain Proteins Function as Master Transcription Elongation Factors Independent of CDK9 Recruitment. Molecular Cell. PMID 28673542 DOI: 10.1016/J.Molcel.2017.06.004  0.247
2022 Couvillion M, Harlen KM, Lachance KC, Trotta KL, Smith E, Brion C, Smalec BM, Churchman LS. Transcription elongation is finely tuned by dozens of regulatory factors. Elife. 11. PMID 35575476 DOI: 10.7554/eLife.78944  0.242
2017 Mayer A, Churchman LS. A Detailed Protocol for Subcellular RNA Sequencing (subRNA-seq). Current Protocols in Molecular Biology. 120: 4.29.1-4.29.18. PMID 28967997 DOI: 10.1002/cpmb.44  0.239
2020 Stergachis AB, Debo BM, Haugen E, Churchman LS, Stamatoyannopoulos JA. Single-molecule regulatory architectures captured by chromatin fiber sequencing. Science (New York, N.Y.). 368: 1449-1454. PMID 32587015 DOI: 10.1126/Science.Aaz1646  0.239
2016 Harlen KM, Trotta KL, Smith EE, Mosaheb MM, Fuchs SM, Churchman LS. Comprehensive RNA Polymerase II Interactomes Reveal Distinct and Varied Roles for Each Phospho-CTD Residue. Cell Reports. PMID 27239037 DOI: 10.1016/J.Celrep.2016.05.010  0.232
2017 Harlen KM, Churchman LS. Subgenic Pol II interactomes identify region-specific transcription elongation regulators. Molecular Systems Biology. 13: 900. PMID 28043953 DOI: 10.15252/msb.20167279  0.231
2017 Jin Y, Eser U, Struhl K, Churchman LS. The Ground State and Evolution of Promoter Region Directionality. Cell. PMID 28803729 DOI: 10.1016/J.Cell.2017.07.006  0.229
2020 Fischer J, Song YS, Yosef N, di Iulio J, Churchman LS, Choder M. The yeast exoribonuclease Xrn1 and associated factors modulate RNA polymerase II processivity in 5' and 3' gene regions. The Journal of Biological Chemistry. PMID 32518159 DOI: 10.1074/Jbc.Ra120.013426  0.22
2023 Choquet K, Baxter-Koenigs AR, Dülk SL, Smalec BM, Rouskin S, Churchman LS. Pre-mRNA splicing order is predetermined and maintains splicing fidelity across multi-intronic transcripts. Nature Structural & Molecular Biology. PMID 37443198 DOI: 10.1038/s41594-023-01035-2  0.219
2015 Padovan-Merhar O, Nair GP, Biaesch AG, Mayer A, Scarfone S, Foley SW, Wu AR, Churchman LS, Singh A, Raj A. Single mammalian cells compensate for differences in cellular volume and DNA copy number through independent global transcriptional mechanisms. Molecular Cell. 58: 339-52. PMID 25866248 DOI: 10.1016/J.Molcel.2015.03.005  0.218
2023 Bergeron D, Faucher-Giguère L, Emmerichs AK, Choquet K, Song KS, Deschamps-Francoeur G, Fafard-Couture É, Rivera A, Couture S, Churchman LS, Heyd F, Abou Elela S, Scott MS. Intronic small nucleolar RNAs regulate host gene splicing through base pairing with their adjacent intronic sequences. Genome Biology. 24: 160. PMID 37415181 DOI: 10.1186/s13059-023-03002-y  0.216
2017 Couvillion MT, Churchman LS. Mitochondrial Ribosome (Mitoribosome) Profiling for Monitoring Mitochondrial Translation In Vivo. Current Protocols in Molecular Biology. 119: 4.28.1-4.28.25. PMID 28678443 DOI: 10.1002/cpmb.41  0.208
2018 Doris SM, Chuang J, Viktorovskaya O, Murawska M, Spatt D, Churchman LS, Winston F. Spt6 Is Required for the Fidelity of Promoter Selection. Molecular Cell. PMID 30318445 DOI: 10.1016/J.Molcel.2018.09.005  0.203
2019 Isaac RS, Churchman LS. The Long and the Short of the RNA Polymerase C-Terminal Domain and Phase Separation. Molecular Cell. 73: 1087-1088. PMID 30901560 DOI: 10.1016/j.molcel.2019.03.004  0.199
2024 Isaac RS, Tullius TW, Hansen KG, Dubocanin D, Couvillion M, Stergachis AB, Churchman LS. Single-nucleoid architecture reveals heterogeneous packaging of mitochondrial DNA. Nature Structural & Molecular Biology. PMID 38347148 DOI: 10.1038/s41594-024-01225-6  0.193
2023 Martell DJ, Merens HE, Caulier A, Fiorini C, Ulirsch JC, Ietswaart R, Choquet K, Graziadei G, Brancaleoni V, Cappellini MD, Scott C, Roberts N, Proven M, Roy NBA, Babbs C, ... ... Churchman LS, et al. RNA polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation. Developmental Cell. PMID 37586368 DOI: 10.1016/j.devcel.2023.07.018  0.183
2017 Harlen KM, Churchman LS. The code and beyond: transcription regulation by the RNA polymerase II carboxy-terminal domain. Nature Reviews. Molecular Cell Biology. 18: 263-273. PMID 28248323 DOI: 10.1038/nrm.2017.10  0.177
2017 Churchman LS. Not Just Noise: Genomics and Genetics Bring Long Noncoding RNAs into Focus. Molecular Cell. 65: 1-2. PMID 28061329 DOI: 10.1016/j.molcel.2016.12.017  0.173
2023 McShane E, Couvillion M, Ietswaart R, Prakash G, Smalec BM, Soto I, Baxter-Koenigs AR, Choquet K, Churchman LS. Regulatory principles of human mitochondrial gene expression revealed by kinetic analysis of the RNA life cycle. Biorxiv : the Preprint Server For Biology. PMID 36824735 DOI: 10.1101/2023.02.09.527880  0.173
2018 Mischo HE, Chun Y, Harlen KM, Smalec BM, Dhir S, Churchman LS, Buratowski S. Cell-Cycle Modulation of Transcription Termination Factor Sen1. Molecular Cell. PMID 29656924 DOI: 10.1016/J.Molcel.2018.03.010  0.166
2023 Kramer NJ, Prakash G, Choquet K, Soto I, Petrova B, Merens HE, Kanarek N, Churchman LS. Genome-wide screens for mitonuclear co-regulators uncover links between compartmentalized metabolism and mitochondrial gene expression. Biorxiv : the Preprint Server For Biology. PMID 36798306 DOI: 10.1101/2023.02.11.528118  0.159
2021 Viktorovskaya O, Chuang J, Jain D, Reim NI, López-Rivera F, Murawska M, Spatt D, Churchman LS, Park PJ, Winston F. Essential histone chaperones collaborate to regulate transcription and chromatin integrity. Genes & Development. PMID 33888559 DOI: 10.1101/gad.348431.121  0.155
2017 Dronamraju R, Jha DK, Eser U, Adams AT, Dominguez D, Choudhury R, Chiang YC, Rathmell WK, Emanuele MJ, Churchman LS, Strahl BD. Set2 methyltransferase facilitates cell cycle progression by maintaining transcriptional fidelity. Nucleic Acids Research. PMID 29294086 DOI: 10.1093/Nar/Gkx1276  0.155
2023 Martell DJ, Merens HE, Fiorini C, Caulier A, Ulirsch JC, Ietswaart R, Choquet K, Graziadei G, Brancaleoni V, Domenica Cappellini M, Scott C, Roberts N, Proven M, Roy NB, Babbs C, ... ... Churchman LS, et al. RNA Polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation. Medrxiv : the Preprint Server For Health Sciences. PMID 36945604 DOI: 10.1101/2023.03.03.23286760  0.151
2023 Kramer NJ, Prakash G, Isaac RS, Choquet K, Soto I, Petrova B, Merens HE, Kanarek N, Churchman LS. Regulators of mitonuclear balance link mitochondrial metabolism to mtDNA expression. Nature Cell Biology. PMID 37770567 DOI: 10.1038/s41556-023-01244-3  0.149
2023 Khitun A, Brion C, Moqtaderi Z, Geisberg JV, Churchman LS, Struhl K. Elongation rate of RNA polymerase II affects pausing patterns across 3' UTRs. The Journal of Biological Chemistry. 105289. PMID 37748648 DOI: 10.1016/j.jbc.2023.105289  0.147
2018 Isaac RS, McShane E, Churchman LS. The Multiple Levels of Mitonuclear Coregulation. Annual Review of Genetics. PMID 30230928 DOI: 10.1146/annurev-genet-120417-031709  0.142
2019 Tye BW, Commins N, Ryazanova LV, Wühr M, Springer M, Pincus D, Churchman LS. Proteotoxicity from aberrant ribosome biogenesis compromises cell fitness. Elife. 8. PMID 30843788 DOI: 10.7554/Elife.43002  0.131
2024 McShane E, Couvillion M, Ietswaart R, Prakash G, Smalec BM, Soto I, Baxter-Koenigs AR, Choquet K, Churchman LS. A kinetic dichotomy between mitochondrial and nuclear gene expression processes. Molecular Cell. PMID 38503286 DOI: 10.1016/j.molcel.2024.02.028  0.13
2016 Couvillion MT, Soto IC, Shipkovenska G, Churchman LS. Synchronized mitochondrial and cytosolic translation programs. Nature. 533: 499-503. PMID 27225121 DOI: 10.1038/Nature18015  0.122
2021 Ietswaart R, Gyori BM, Bachman JA, Sorger PK, Churchman LS. GeneWalk identifies relevant gene functions for a biological context using network representation learning. Genome Biology. 22: 55. PMID 33526072 DOI: 10.1186/s13059-021-02264-8  0.113
2024 Litsios A, Grys BT, Kraus OZ, Friesen H, Ross C, Masinas MPD, Forster DT, Couvillion MT, Timmermann S, Billmann M, Myers C, Johnsson N, Churchman LS, Boone C, Andrews BJ. Proteome-scale movements and compartment connectivity during the eukaryotic cell cycle. Cell. PMID 38452761 DOI: 10.1016/j.cell.2024.02.014  0.11
2022 Soto I, Couvillion M, Hansen KG, McShane E, Moran JC, Barrientos A, Churchman LS. Balanced mitochondrial and cytosolic translatomes underlie the biogenesis of human respiratory complexes. Genome Biology. 23: 170. PMID 35945592 DOI: 10.1186/s13059-022-02732-9  0.105
2014 Gordon JR, Ma Y, Churchman L, Gordon SA, Dawicki W. Regulatory dendritic cells for immunotherapy in immunologic diseases. Frontiers in Immunology. 5: 7. PMID 24550907 DOI: 10.3389/fimmu.2014.00007  0.073
2021 Tye BW, Churchman LS. Hsf1 activation by proteotoxic stress requires concurrent protein synthesis. Molecular Biology of the Cell. mbcE21010014. PMID 34191586 DOI: 10.1091/mbc.E21-01-0014  0.068
2018 Soto IC, Couvillion MT, Churchman LS. Co-regulation of mitochondrial and cytosolic translation programs Biochimica Et Biophysica Acta (Bba) - Bioenergetics. 1859: e20. DOI: 10.1016/J.Bbabio.2018.09.061  0.052
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