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Items: 1 to 20 of 71

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.
ISW1a modulates cohesin distribution in centromeric and pericentromeric regions
Ireneusz Litwin, Małgorzata Nowicka, Katarzyna Markowska, Ewa Maciaszczyk-Dziubińska, Paulina Tomaszewska, Robert Wysocki, Karol Kramarz
Nucleic Acids Res. 2023 Sep 22; 51(17): 9101–9121. Published online 2023 Jul 24. doi: 10.1093/nar/gkad612
PMCID:
PMC10516642
AbstractArticlePDF–2.8M
4.
Rio1 downregulates centromeric RNA levels to promote the timely assembly of structurally fit kinetochores
Ksenia Smurova, Michela Damizia, Carmela Irene, Stefania Stancari, Giovanna Berto, Giulia Perticari, Maria Giuseppina Iacovella, Ilaria D’Ambrosio, Maria Giubettini, Réginald Philippe, Chiara Baggio, Elisabetta Callegaro, Andrea Casagranda, Alessandro Corsini, Vincenzo Gentile Polese, Anna Ricci, Erik Dassi, Peter De Wulf
Nat Commun. 2023; 14: 3172. Published online 2023 Jun 1. doi: 10.1038/s41467-023-38920-9
PMCID:
PMC10235086
AbstractArticlePDF–2.6M
5.
A systematic proximity ligation approach to studying protein‐substrate specificity identifies the substrate spectrum of the Ssh1 translocon
Nir Cohen, Naama Aviram, Maya Schuldiner
EMBO J. 2023 Jun; 42(11): e113385. Published online 2023 Apr 19. doi: 10.15252/embj.2022113385
PMCID:
PMC10233368
AbstractArticlePDF–1.2M
6.
A synthetic genetic array screen for interactions with the RNA helicase DED1 during cell stress in budding yeast
Sara B Carey, Hannah M List, Ashwin Siby, Paolo Guerra, Timothy A Bolger
G3 (Bethesda) 2023 Jan; 13(1): jkac296. Published online 2022 Nov 21. doi: 10.1093/g3journal/jkac296
PMCID:
PMC9836348
AbstractArticlePDF–857K
7.
A balancing act: interactions within NuA4/TIP60 regulate picNuA4 function in Saccharomyces cerevisiae and humans
Phoebe Y T Lu, Alyssa C Kirlin, Maria J Aristizabal, Hilary T Brewis, Nancy Lévesque, Dheva T Setiaputra, Nikita Avvakumov, Joris J Benschop, Marian Groot Koerkamp, Frank C P Holstege, Nevan J Krogan, Calvin K Yip, Jacques Côté, Michael S Kobor
Genetics. 2022 Nov; 222(3): iyac136. Published online 2022 Sep 6. doi: 10.1093/genetics/iyac136
PMCID:
PMC9630986
AbstractArticlePDF–2.2M
8.
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
9.
Inferring TF activities and activity regulators from gene expression data with constraints from TF perturbation data
Cynthia Z Ma, Michael R Brent
Bioinformatics. 2021 May 1; 37(9): 1234–1245. Published online 2020 Dec 22. doi: 10.1093/bioinformatics/btaa947
PMCID:
PMC8189679
AbstractArticlePDF–1.4M
10.
Transcriptomic Changes Induced by Deletion of Transcriptional Regulator GCR2 on Pentose Sugar Metabolism in Saccharomyces cerevisiae
Minhye Shin, Heeyoung Park, Sooah Kim, Eun Joong Oh, Deokyeol Jeong, Clarissa Florencia, Kyoung Heon Kim, Yong-Su Jin, Soo Rin Kim
Front Bioeng Biotechnol. 2021; 9: 654177. Published online 2021 Mar 25. doi: 10.3389/fbioe.2021.654177
PMCID:
PMC8027353
AbstractArticlePDF–1.3M
11.
Differential activation mechanisms of two isoforms of Gcr1 transcription factor generated from spliced and un-spliced transcripts in Saccharomyces cerevisiae
Seungwoo Cha, Chang Pyo Hong, Hyun Ah Kang, Ji-Sook Hahn
Nucleic Acids Res. 2021 Jan 25; 49(2): 745–759. Published online 2020 Dec 24. doi: 10.1093/nar/gkaa1221
PMCID:
PMC7826247
AbstractArticlePDF–1.3M
12.
Metabolic Changes Induced by Deletion of Transcriptional Regulator GCR2 in Xylose-Fermenting Saccharomyces cerevisiae
Minhye Shin, Soo Rin Kim
Microorganisms. 2020 Oct; 8(10): 1499. Published online 2020 Sep 29. doi: 10.3390/microorganisms8101499
PMCID:
PMC7599485
AbstractArticlePDF–2.7M
13.
A genetic interaction map centered on cohesin reveals auxiliary factors involved in sister chromatid cohesion in S. cerevisiae
Su Ming Sun, Amandine Batté, Mireille Elmer, Sophie C. van der Horst, Tibor van Welsem, Gordon Bean, Trey Ideker, Fred van Leeuwen, Haico van Attikum
J Cell Sci. 2020 May 15; 133(10): jcs237628. Published online 2020 May 22. doi: 10.1242/jcs.237628
PMCID:
PMC7325435
AbstractArticle
14.
Homotypic cooperativity and collective binding are determinants of bHLH specificity and function
Christian A. Shively, Jiayue Liu, Xuhua Chen, Kaiser Loell, Robi D. Mitra
Proc Natl Acad Sci U S A. 2019 Aug 6; 116(32): 16143–16152. Published online 2019 Jul 24. doi: 10.1073/pnas.1818015116
PMCID:
PMC6689977
AbstractArticlePDF–1.8M
15.
Global analysis of genetic circuitry and adaptive mechanisms enabling resistance to the azole antifungal drugs
Harley O’Connor Mount, Nicole M. Revie, Robert T. Todd, Kaitlin Anstett, Cathy Collins, Michael Costanzo, Charles Boone, Nicole Robbins, Anna Selmecki, Leah E. Cowen
PLoS Genet. 2018 Apr; 14(4): e1007319. Published online 2018 Apr 27. doi: 10.1371/journal.pgen.1007319
PMCID:
PMC5922528
AbstractArticlePDF–7.1M
16.
The conserved AU dinucleotide at the 5′ end of nascent U1 snRNA is optimized for the interaction with nuclear cap-binding-complex
Chung-Shu Yeh, Shang-Lin Chang, Jui­-Hui Chen, Hsuan-Kai Wang, Yue-Chang Chou, Chun-Hsiung Wang, Shih-Hsin Huang, Amy Larson, Jeffrey A Pleiss, Wei-Hau Chang, Tien-Hsien Chang
Nucleic Acids Res. 2017 Sep 19; 45(16): 9679–9693. Published online 2017 Jul 13. doi: 10.1093/nar/gkx608
PMCID:
PMC5766165
AbstractArticlePDF–3.0M
17.
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
18.
Protein Moonlighting Revealed by Noncatalytic Phenotypes of Yeast Enzymes
Adriana Espinosa-Cantú, Diana Ascencio, Selene Herrera-Basurto, Jiewei Xu, Assen Roguev, Nevan J. Krogan, Alexander DeLuna
Genetics. 2018 Jan; 208(1): 419–431. Published online 2017 Nov 10. doi: 10.1534/genetics.117.300377
PMCID:
PMC5753873
AbstractArticlePDF–1.5M
19.
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
20.
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

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