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Items: 1 to 20 of 27

1.
Protein interaction network revealed by quantitative proteomic analysis links TFIIB to multiple aspects of the transcription cycle
Michael J. O’Brien, Athar Ansari
Biochim Biophys Acta Proteins Proteom. Author manuscript; available in PMC 2024 Feb 16.
Published in final edited form as: Biochim Biophys Acta Proteins Proteom. 2024 Jan 1; 1872(1): 140968. Published online 2023 Oct 19. doi: 10.1016/j.bbapap.2023.140968
PMCID:
PMC10872477
AbstractArticlePDF–1.7M
2.
The social and structural architecture of the yeast protein interactome
André C. Michaelis, Andreas-David Brunner, Maximilian Zwiebel, Florian Meier, Maximilian T. Strauss, Isabell Bludau, Matthias Mann
Nature. 2023; 624(7990): 192–200. Published online 2023 Nov 15. doi: 10.1038/s41586-023-06739-5
PMCID:
PMC10700138
AbstractArticlePDF–20M
3.
New data and collaborations at the Saccharomyces Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources
Stacia R Engel, Edith D Wong, Robert S Nash, Suzi Aleksander, Micheal Alexander, Eric Douglass, Kalpana Karra, Stuart R Miyasato, Matt Simison, Marek S Skrzypek, Shuai Weng, J Michael Cherry
Genetics. 2022 Apr; 220(4): iyab224. Published online 2021 Dec 13. doi: 10.1093/genetics/iyab224
PMCID:
PMC9209811
AbstractArticlePDF–818K
4.
Depletion of the MFAP1/SPP381 Splicing Factor Causes R-Loop-Independent Genome Instability
Irene Salas-Armenteros, Sonia I. Barroso, Ana G. Rondón, Mónica Pérez, Eloisa Andújar, Rosa Luna, Andrés Aguilera
Cell Rep. 2019 Aug 6; 28(6): 1551–1563.e7. Published online 2019 Aug 6. doi: 10.1016/j.celrep.2019.07.010
PMCID:
PMC6693559
AbstractArticle
5.
Systematic Analysis of Complex Genetic Interactions
Elena Kuzmin, Benjamin VanderSluis, Wen Wang, Guihong Tan, Raamesh Deshpande, Yiqun Chen, Matej Usaj, Attila Balint, Mojca Mattiazzi Usaj, Jolanda van Leeuwen, Elizabeth N. Koch, Carles Pons, Andrius J. Dagilis, Michael Pryszlak, Jason Zi Yang Wang, Julia Hanchard, Margot Riggi, Kaicong Xu, Hamed Heydari, Bryan-Joseph San Luis, Ermira Shuteriqi, Hongwei Zhu, Nydia Van Dyk, Sara Sharifpoor, Michael Costanzo, Robbie Loewith, Amy Caudy, Daniel Bolnick, Grant W. Brown, Brenda J. Andrews, Charles Boone, Chad L. Myers
Science. Author manuscript; available in PMC 2018 Nov 4.
Published in final edited form as: Science. 2018 Apr 20; 360(6386): eaao1729. doi: 10.1126/science.aao1729
PMCID:
PMC6215713
AbstractArticlePDF–1.9M
6.
Genome-Wide Mapping of Decay Factor–mRNA Interactions in Yeast Identifies Nutrient-Responsive Transcripts as Targets of the Deadenylase Ccr4
Jason E. Miller, Liye Zhang, Haoyang Jiang, Yunfei Li, B. Franklin Pugh, Joseph C. Reese
G3 (Bethesda) 2018 Jan; 8(1): 315–330. Published online 2017 Nov 20. doi: 10.1534/g3.117.300415
PMCID:
PMC5765359
AbstractArticlePDF–2.2M
7.
A global interaction network maps a wiring diagram of cellular function
Michael Costanzo, Benjamin VanderSluis, Elizabeth N. Koch, Anastasia Baryshnikova, Carles Pons, Guihong Tan, Wen Wang, Matej Usaj, Julia Hanchard, Susan D. Lee, Vicent Pelechano, Erin B. Styles, Maximilian Billmann, Jolanda van Leeuwen, Nydia van Dyk, Zhen-Yuan Lin, Elena Kuzmin, Justin Nelson, Jeff S. Piotrowski, Tharan Srikumar, Sondra Bahr, Yiqun Chen, Raamesh Deshpande, Christoph F. Kurat, Sheena C. Li, Zhijian Li, Mojca Mattiazzi Usaj, Hiroki Okada, Natasha Pascoe, Bryan-Joseph San Luis, Sara Sharifpoor, Emira Shuteriqi, Scott W. Simpkins, Jamie Snider, Harsha Garadi Suresh, Yizhao Tan, Hongwei Zhu, Noel Malod-Dognin, Vuk Janjic, Natasa Przulj, Olga G. Troyanskaya, Igor Stagljar, Tian Xia, Yoshikazu Ohya, Anne-Claude Gingras, Brian Raught, Michael Boutros, Lars M. Steinmetz, Claire L. Moore, Adam P. Rosebrock, Amy A. Caudy, Chad L. Myers, Brenda Andrews, Charles Boone
Science. Author manuscript; available in PMC 2017 Oct 30.
Published in final edited form as: Science. 2016 Sep 23; 353(6306): aaf1420. doi: 10.1126/science.aaf1420
PMCID:
PMC5661885
AbstractArticlePDF–2.6M
8.
The Genetic Landscape of a Cell
Michael Costanzo, Anastasia Baryshnikova, Jeremy Bellay, Yungil Kim, Eric D. Spear, Carolyn S. Sevier, Huiming Ding, Judice L.Y. Koh, Kiana Toufighi, Sara Mostafavi, Jeany Prinz, Robert P. St. Onge, Benjamin VanderSluis, Taras Makhnevych, Franco J. Vizeacoumar, Solmaz Alizadeh, Sondra Bahr, Renee L. Brost, Yiqun Chen, Murat Cokol, Raamesh Deshpande, Zhijian Li, Zhen-Yuan Lin, Wendy Liang, Michaela Marback, Jadine Paw, Bryan-Joseph San Luis, Ermira Shuteriqi, Amy Hin Yan Tong, Nydia van Dyk, Iain M. Wallace, Joseph A. Whitney, Matthew T. Weirauch, Guoqing Zhong, Hongwei Zhu, Walid A. Houry, Michael Brudno, Sasan Ragibizadeh, Balázs Papp, Csaba Pál, Frederick P. Roth, Guri Giaever, Corey Nislow, Olga G. Troyanskaya, Howard Bussey, Gary D. Bader, Anne-Claude Gingras, Quaid D. Morris, Philip M. Kim, Chris A. Kaiser, Chad L. Myers, Brenda J. Andrews, Charles Boone
Science. Author manuscript; available in PMC 2017 Sep 15.
Published in final edited form as: Science. 2010 Jan 22; 327(5964): 425–431. doi: 10.1126/science.1180823
PMCID:
PMC5600254
AbstractArticlePDF–2.4M
9.
Structure of a pre-catalytic spliceosome
Clemens Plaschka, Pei-Chun Lin, Kiyoshi Nagai
Nature. Author manuscript; available in PMC 2017 Nov 22.
Published in final edited form as: Nature. 2017 Jun 29; 546(7660): 617–621. Published online 2017 May 22. doi: 10.1038/nature22799
PMCID:
PMC5503131
AbstractArticlePDF–6.8M
10.
Human MFAP1 is a cryptic ortholog of the Saccharomyces cerevisiae Spp381 splicing factor
Alexander K. C. Ulrich, Markus C. Wahl
BMC Evol Biol. 2017; 17: 91. Published online 2017 Mar 24. doi: 10.1186/s12862-017-0923-1
PMCID:
PMC5364666
AbstractArticlePDF–2.7M
11.
A deep proteomics perspective on CRM1-mediated nuclear export and nucleocytoplasmic partitioning
Koray Kırlı, Samir Karaca, Heinz Jürgen Dehne, Matthias Samwer, Kuan Ting Pan, Christof Lenz, Henning Urlaub, Dirk Görlich
eLife. 2015; 4: e11466. Published online 2015 Dec 17. doi: 10.7554/eLife.11466
PMCID:
PMC4764573
AbstractArticlePDF–5.7M
12.
CryoEM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 Å resolution
Thi Hoang Duong Nguyen, Wojciech P. Galej, Xiao-chen Bai, Chris Oubridge, Andrew J. Newman, Sjors H. W. Scheres, Kiyoshi Nagai
Nature. Author manuscript; available in PMC 2016 Aug 18.
Published in final edited form as: Nature. 2016 Feb 18; 530(7590): 298–302. Published online 2016 Feb 1. doi: 10.1038/nature16940
PMCID:
PMC4762201
AbstractArticlePDF–6.1M
13.
Structural requirements for protein-catalyzed annealing of U4 and U6 RNAs during di-snRNP assembly
Allison L. Didychuk, Eric J. Montemayor, David A. Brow, Samuel E. Butcher
Nucleic Acids Res. 2016 Feb 18; 44(3): 1398–1410. Published online 2015 Dec 15. doi: 10.1093/nar/gkv1374
PMCID:
PMC4756825
AbstractArticlePDF–9.3M
14.
The architecture of the spliceosomal U4/U6.U5 tri-snRNP
Thi Hoang Duong Nguyen, Wojciech P. Galej, Xiao-chen Bai, Christos G. Savva, Andrew J. Newman, Sjors H. W. Scheres, Kiyoshi Nagai
Nature. Author manuscript; available in PMC 2016 Jan 2.
Published in final edited form as: Nature. 2015 Jul 2; 523(7558): 47–52. Published online 2015 Jun 24. doi: 10.1038/nature14548
PMCID:
PMC4536768
AbstractArticlePDF–6.7M
15.
Brr2 plays a role in spliceosomal activation in addition to U4/U6 unwinding
Lingdi Zhang, Xueni Li, Ryan C. Hill, Yan Qiu, Wenzheng Zhang, Kirk C. Hansen, Rui Zhao
Nucleic Acids Res. 2015 Mar 31; 43(6): 3286–3297. Published online 2015 Feb 10. doi: 10.1093/nar/gkv062
PMCID:
PMC4381053
AbstractArticlePDF–5.3M
16.
Sumoylation of the THO complex regulates the biogenesis of a subset of mRNPs
Hugo Bretes, Jérôme O. Rouviere, Thibaut Leger, Marlene Oeffinger, Frédéric Devaux, Valérie Doye, Benoit Palancade
Nucleic Acids Res. 2014 Apr; 42(8): 5043–5058. Published online 2014 Feb 5. doi: 10.1093/nar/gku124
PMCID:
PMC4005672
AbstractArticlePDF–8.1M
17.
Role of the ubiquitin-like protein Hub1 in splice-site usage and alternative splicing
Shravan Kumar Mishra, Tim Ammon, Grzegorz M. Popowicz, Marcin Krajewski, Roland J. Nagel, Manuel Ares, Jr, Tad A. Holak, Stefan Jentsch
Nature. Author manuscript; available in PMC 2013 Mar 4.
Published in final edited form as: Nature. 2011 May 25; 474(7350): 173–178. Published online 2011 May 25. doi: 10.1038/nature10143
PMCID:
PMC3587138
AbstractArticlePDF–1.5M
18.
The nuclear localization of SWI/SNF proteins is subjected to oxygen regulation
Ranita Ghosh Dastidar, Jagmohan Hooda, Ajit Shah, Thai M Cao, Robert Michael Henke, Li Zhang
Cell Biosci. 2012; 2: 30. Published online 2012 Aug 29. doi: 10.1186/2045-3701-2-30
PMCID:
PMC3489556
AbstractArticlePDF–2.4M
19.
Coiled-coil networking shapes cell molecular machinery
Yongqiang Wang, Xinlei Zhang, Hong Zhang, Yi Lu, Haolong Huang, Xiaoxi Dong, Jinan Chen, Jiuhong Dong, Xiao Yang, Haiying Hang, Taijiao Jiang
Mol Biol Cell. 2012 Oct 1; 23(19): 3911–3922. doi: 10.1091/mbc.E12-05-0396
PMCID:
PMC3459866
AbstractArticlePDF–7.0M
20.
Functional wiring of the yeast kinome revealed by global analysis of genetic network motifs
Sara Sharifpoor, Dewald van Dyk, Michael Costanzo, Anastasia Baryshnikova, Helena Friesen, Alison C. Douglas, Ji-Young Youn, Benjamin VanderSluis, Chad L. Myers, Balázs Papp, Charles Boone, Brenda J. Andrews
Genome Res. 2012 Apr; 22(4): 791–801. doi: 10.1101/gr.129213.111
PMCID:
PMC3317160
AbstractArticlePDF–998K

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