Exploration of the Function and Organization of the Yeast Early Secretory Pathway through an Epistatic Miniarray Profile

Schuldiner, Maya, Collins, Sean R., Thompson, Natalie J., Denic, Vladimir, Bhamidipati, Arunashree, Punna, Thanuja, Ihmels, Jan, Andrews, Brenda +4 more·2005·Cell

Cited by (865)

Items 601–700 of 865

  1. Surprising roles for phospholipid binding proteins revealed by high throughput geneticsThis paper is one of a selection of papers published in this special issue entitled “Second International Symposium on Recent Advances in Basic, Clinical, and Social Medicine” and has undergone the Journal's usual peer review process.
    Marissa A. LeBlanc, Christopher R. McMaster · 2010 · Biochemistry and Cell Biology
  2. Metabolism and Roles of Sphingolipids in Yeast Saccharomyces cerevisiae
    Jihui Ren, Yusuf Awni Hannun · 2016 · Springer eBooks
  3. Cellular Consequences of Diminished Protein O-Mannosyltransferase Activity in Baker’s Yeast
    Ewa Zatorska, Lihi Gal, Jaro L. Schmitt, Daniela Bausewein, Maya Schuldiner, Sabine Strahl · 2017 · International Journal of Molecular Sciences
  4. The ATPase activity of Asna1/TRC40 is required for pancreatic progenitor cell survival
    Stefan Norlin, Vishal S. Parekh, Helena Edlund · 2017 · Development
  5. Analysis of Genetic Interactions on a Genome-Wide Scale in Budding Yeast: Diploid-Based Synthetic Lethality Analysis by Microarray
    Pamela B. Meluh, Xuewen Pan, Daniel Yuan, Carol W. Tiffany, Ou Chen, Sharon Sookhai-Mahadeo, Xiaoling Wang, Brian D. Peyser, Rafael A. Irizarry, Forrest A. Spencer et al. · 2008 · Methods in molecular biology
  6. Phenotypic landscape of a fungal meningitis pathogen reveals its unique biology
    Michael J. Boucher, Sanjita Banerjee, Meenakshi Joshi, Angela L. Wei, Manning Y. Huang, Susan Lei, Massimiliano Ciranni, Andrew Condon, Andreas Langen, Thomas D. Goddard et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  7. Advances in CRISPR-enabled genome-wide screens in yeast
    Nicholas R. Robertson, Sang Cheon Lee, Aida Tafrishi, Ian R. Wheeldon · 2025 · FEMS Yeast Research
  8. Deletion of Emc1 in photoreceptor cells causes retinal degeneration in mice
    Xiao Li, Zhilin Jiang, Yujing Su, Kaifang Wang, Xiaoyan Jiang, Kuanxiang Sun, Yeming Yang, Yu Zhou, Xianjun Zhu, Lin Zhang · 2023 · FEBS Journal
  9. Development of a system for discovery of genetic interactions for essential genes in Escherichia coli K-12
    Han Yong, Natsuko Yamamoto, Rikiya Takeuchi, Yi-Ju Hsieh, Tom M Conrad, Kirill A. Datsenko, Toru Nakayashiki, Barry L. Wanner, Hirotada Mori · 2013 · Genes & Genetic Systems
  10. Kinetochore genes are required to fully activate secretory pathway expansion in S. cerevisiae under induced ER stress
    Yee Syuen Low, Peter W. Bircham, David R. Maass, Paul H. Atkinson · 2014 · Molecular BioSystems
  11. The Toxicity of a Novel Antifungal Compound Is Modulated by Endoplasmic Reticulum-Associated Protein Degradation Components
    Shriya Raj, Karthik Krishnan, David S. Askew, Olivier Helynck, Peggy Suzanne, Aurélien Lesnard, Sylvain Rault, Ute Zeidler, Christophe d’Enfert, Jean‐Paul Latgé et al. · 2015 · Antimicrobial Agents and Chemotherapy
  12. New wine in old bottles: current progress on P5 ATPases
    Zhiwen Huang, Zhigang Feng, Yan Zou · 2021 · FEBS Journal
  13. Phenomics approaches to understand genetic networks and gene function in yeast
    Clarence Hue Lok Yeung, Nil Sahin, Brenda Andrews · 2022 · Biochemical Society Transactions
  14. G Protein Signaling Components in Filamentous Fungal Genomes
    Jacqueline A. Servin, Asharie J. Campbell, Katherine A. Borkovich · 2012 · Springer eBooks
  15. Genecentric: a package to uncover graph-theoretic structure in high-throughput epistasis data
    Andrew Gallant, Mark D.M. Leiserson, Maxim Kachalov, Lenore Cowen, Benjamin J. Hescott · 2013 · BMC Bioinformatics
  16. Phenomic Assessment of Genetic Buffering by Kinetic Analysis of Cell Arrays
    John W. Rodgers, Jingyu Guo, John L. Hartman · 2014 · Methods in molecular biology
  17. Differential RNAi screening provides insights into the rewiring of signalling networks during oxidative stress
    Mar Arias-García, Miguel Sánchez‐Álvarez, Heba Sailem, Vicky Bousgouni, Julia Sero, Chris Bakal · 2012 · Molecular BioSystems
  18. Systems Biology of the Endoplasmic Reticulum Stress Response
    Marie-Elaine Caruso, Éric Chevet · 2007 · Springer eBooks
  19. Functional analysis of protein kinase networks in living cells: Beyond “knock-outs” and “knock-downs”
    Hiten D. Madhani · 2006 · Methods
  20. Correction: Genes Confer Similar Robustness to Environmental, Stochastic, and Genetic Perturbations in Yeast
    Ben Lehner · 2010 · PLoS ONE
  21. High-Throughput Quantitative Genetic Interaction Mapping in the Fission Yeast Schizosaccharomyces pombe
    Assen Roguev, Colm J. Ryan, Edgar Hartsuiker, Nevan J. Krogan · 2017 · Cold Spring Harbor Protocols
  22. High-Throughput Robotically Assisted Isolation of Temperature-sensitive Lethal Mutants in Chlamydomonas reinhardtii
    Michal Breker, Kristi Lieberman, Frej Tulin, Frederick R. Cross · 2016 · Journal of Visualized Experiments
  23. Defining substrate requirements for cleavage of farnesylated prelamin A by the integral membrane zinc metalloprotease ZMPSTE24
    Kaitlin M. Wood, Eric D. Spear, Otto W. Mossberg, Kamsi O. Odinammadu, Wenxin Vincent Xu, Susan Michaelis · 2020 · PLoS ONE
  24. Ccr4-not ubiquitin ligase signaling regulates ribosomal protein homeostasis and inhibits 40S ribosomal autophagy
    Daniel L. Johnson, Ravinder Kumar, David G. Kakhniashvili, Lawrence M. Pfeffer, R. Nicholas Laribee · 2024 · Journal of Biological Chemistry
  25. The structure and function of P5A-ATPases
    Ping Li, Viktoria Bågenholm, Per Hägglund, Karin Lindkvist‐Petersson, Kaituo Wang, Pontus Emanuel Gourdon · 2024 · Nature Communications
  26. The Balance of Weak and Strong Interactions in Genetic Networks
    Juan F. Poyatos · 2011 · PLoS ONE
  27. The plasma membrane code
    Anthony H. Futerman, Maya Schuldiner · 2010 · Nature Chemical Biology
  28. Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays
    Alla G. Gagarinova, Mohan Babu, Jack F. Greenblatt, Andrew Emili · 2012 · Journal of Visualized Experiments
  29. iMAD, a genetic screening strategy for dissecting complex interactions between a pathogen and its host
    Tamara J. O’Connor, Ralph R. Isberg · 2014 · Nature Protocols
  30. Current Progress in Static and Dynamic Modeling of Biological Networks
    Bernie J. Daigle, Balaji S. Srinivasan, Jason A. Flannick, Antal F. Novak, Serafim Batzoglou · 2010 · Systems biology
  31. The effect of acetaminophen on ubiquitin homeostasis in Saccharomyces cerevisiae
    Angelina Huseinovic, Jolanda S. van Leeuwen, Tibor van Welsem, I.J.E. Stulemeijer, Fred van Leeuwen, Nico P.E. Vermeulen, Jan M. Kooter, J. Chris Vos · 2017 · PLoS ONE
  32. Yeast-Based Screens to Target Alpha-Synuclein Toxicity
    Inês Caldeira Brás, Bilyana Popova, Gerhard H. Braus, Tiago F. Outeiro · 2019 · Methods in molecular biology
  33. Tubular ER Associates With Diacylglycerol-Rich Structures During Lipid Droplet Consumption
    Suriakarthiga Ganesan, Marjan Tavassoli, Brittney N. Shabits, Vanina Zaremberg · 2020 · Frontiers in Cell and Developmental Biology
  34. Functional network motifs defined through integration of protein-protein and genetic interactions
    Amruta Sahoo, Sebastian Pechmann · 2022 · PeerJ
  35. From functional genomics to systems biology
    Sergii Ivakhno · 2007 · FEBS Journal
  36. Using Yeast Genetics to Study Splicing Mechanisms
    Munshi Azad Hossain, Tracy Johnson · 2014 · Methods in molecular biology
  37. Toward the Systems Biology of Vesicle Transport
    Nicole R. Quenneville, Elizabeth Conibear · 2006 · Traffic
  38. A genome-scale CRISPR interference guide library enables comprehensive phenotypic profiling in yeast
    Nicholas J. McGlincy, Zuriah A. Meacham, Kendra Swain, Ryan Yue Muller, Rachel Baum, Nicholas T. Ingolia · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  39. Killer toxin K28 resistance in yeast relies on COG complex-mediated trafficking of the defence factor Ktd1
    Kamilla M. E. Laidlaw, Hatwan H. Nadir, Amy Milburn, Martha S. C. Xelhuantzi, Justas Stanislovas, Alastair Droop, Sandy J. Macdonald, Ilya Andreev, Andrew Leech, Dániel Ungár et al. · 2025 · Journal of Cell Science
  40. An auxin-inducible degron system for conditional mutation in the fungal meningitis pathogen Cryptococcus neoformans
    Manning Y. Huang, Matthew J. Nalley, Patrick C Hecht, Hiten D. Madhani · 2025 · G3 Genes Genomes Genetics
  41. The Ubp3/Bre5 deubiquitylation complex modulates COPII vesicle formation
    Natalia Gómez‐Navarro, Jérôme Boulanger A, Elizabeth A. Miller · 2020 · Traffic
  42. Spf1 and Ste24: quality controllers of transmembrane protein topology in the eukaryotic cell
    Donald J. Tipper, Carol A. Harley · 2023 · Frontiers in Cell and Developmental Biology
  43. An efficient gene targeting system using Δku80 and functional analysis of Cyp51A in Trichophyton rubrum
    Masaki Ishii, Tsuyoshi Yamada, Shinya Ohata · 2024 · AMB Express
  44. A Mathematical Programming Approach to Community Structure Detection in Complex Networks
    Laura Bennett, Songsong Liu, Lazaros G. Papageorgiou, Sophia Tsoka · 2012 · Computer-aided chemical engineering/Computer aided chemical engineering
  45. Evaluation of the lower protein limit in the budding yeast Saccharomyces cerevisiae using TIPI-gTOW
    M. Sasabe, Sayumi Shintani, Reiko Kintaka, Kazunari Kaizu, Koji Makanae, Hisao Moriya · 2014 · BMC Systems Biology
  46. Imputing missing values for genetic interaction data
    Yishu Wang, Lin Wang, Dejie Yang, Minghua Deng · 2014 · Methods
  47. Genetic interactions in yeast: is robustness going bust?
    Martin Kupiec, Roded Sharan, Eytan Ruppin · 2007 · Molecular Systems Biology
  48. Mon2 is a negative regulator of the monomeric G protein, Arl1
    Cara Marie Manlandro, V. Palanivel, Emily B. Schorr, Nino Mihatov, Andrew A. Antony, Anne Rosenwald · 2012 · FEMS Yeast Research
  49. High-Throughput Analyses and Curation of Protein Interactions in Yeast
    Shoshana J. Wodak, Jim Vlasblom, Shuye Pu · 2011 · Methods in molecular biology
  50. Chemogenetic E-MAP in Saccharomyces cerevisiae for Identification of Membrane Transporters Operating Lipid Flip Flop
    Hector M. Vazquez, Christine Vionnet, Carole Roubaty, Shamroop Kumar Mallela, Roger Schneiter, Andreas Conzelmann · 2016 · PLoS Genetics
  51. Identification of essential yeast genes involved in polyamine resistance
    Mustapha Aouida, Dindial Ramotar · 2018 · Gene
  52. Proteasome-dependent protein quality control of the peroxisomal membrane protein Pxa1p
    Srishti Devarajan, Matthias Meurer, Carlo W.T. van Roermund, Xiaoli Chen, Ewald H. Hettema, Stephan Kemp, Michael Knop, Chris Williams · 2020 · Biochimica et Biophysica Acta (BBA) - Biomembranes
  53. Organization Principles in Genetic Interaction Networks
    Christopher L. Jacobs, Daniel Segrè · 2012 · Advances in experimental medicine and biology
  54. Quantitative Fitness Analysis Identifies exo1∆ and Other Suppressors or Enhancers of Telomere Defects in Schizosaccharomyces pombe
    Siddharth Narayanan, Marion Dubarry, Conor Lawless, A. Peter Banks, Darren J. Wilkinson, Simon K. Whitehall, David A. Lydall · 2015 · PLoS ONE
  55. Yeast as a Model in High‐Throughput Screening of Small‐Molecule Libraries
    Irene Stefanini, Carlotta De Filippo, Duccio Cavalieri · 2013 · Diversity Oriented Synthesis
  56. Detection of epistatic interactions with Random Forest
    Corinna Lewis Schmalohr, Jan Großbach, Mathieu Clément‐Ziza, Andreas Beyer · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  57. PIPE : a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs
    Sylvain Pitre · 2010
  58. Network dynamics of the yeast methyltransferome
    Guri N. Giaever, Elena Lissina, Corey Nislow · 2019 · Microbial Cell
  59. The Mitogen-Activated Protein Kinase Slt2 Promotes Asymmetric Cell Cycle Arrest and Reduces TORC1-Sch9 Signaling in Yeast Lacking the Protein Phosphatase Ptc1
    Gema González-Rubio, Humberto Martı́n, Marı́a Molina · 2023 · Microbiology Spectrum
  60. Genetic knockdown of genes that are obscure, conserved and essential using CRISPR interference methods in the fission yeast S. pombe
    Ken Ishikawa, Saeko Soejima, Shigeaki Saitoh · 2023 · Journal of Cell Science
  61. Peroxisystem: Harnessing systems cell biology to study peroxisomes
    Maya Schuldiner, Einat Zalckvar · 2015 · Biology of the Cell
  62. Identification of Links Between Cellular Pathways by Genetic Interaction Mapping (GIM)
    Christophe Malabat, Cosmin Saveanu · 2015 · Methods in molecular biology
  63. A Humanized Yeast Phenomic Model of Deoxycytidine Kinase to Predict Genetic Buffering of Nucleoside Analog Cytotoxicity
    Sean M. Santos, Mert Icyuz, Ilya Pound, Doreen William, Jingyu Guo, Brett Allen McKinney, Michael Niederweis, John W. Rodgers, John L. Hartman · 2019 · Genes
  64. Expanding interactome analyses beyond model eukaryotes
    Katherine James, Anil Wipat, Simon Cockell · 2022 · Briefings in Functional Genomics
  65. Genetic Networks
    Michael Costanzo, Anastasia Baryshnikova, Benjamin VanderSluis, Brenda Andrews, Chad L. Myers, Charles M. Boone · 2012 · Elsevier eBooks
  66. A strategy to apply quantitative epistasis analysis on developmental traits
    Marta K. Labocha, Yuan Wang, Boanerges Aleman-meza A, Weiwei Zhong · 2017 · BMC Genetics
  67. Identification of response-modulated genetic interactions by sensitivity-based epistatic analysis
    Cory Batenchuk, Lioudmila Tepliakova, Mads Kærn · 2010 · BMC Genomics
  68. From large-scale assays to mechanistic insights: computational analysis of interactions
    Ariel Jaimovich, Nir Friedman · 2010 · Current Opinion in Biotechnology
  69. The Tail End of Membrane Insertion
    Elisabet C. Mandon, Reid Gilmore · 2007 · Cell
  70. Dissecting the DNA damage response using functional genomics approaches in S. cerevisiae
    Marta Beata Davidson, Grant W. Brown · 2009 · DNA repair
  71. Organellar Protein Complexes of Caco-2 Human Cells Analyzed by Two-Dimensional Blue Native/SDS-PAGE and Mass Spectrometry
    Jean-Paul Lasserre, Loïk Sylvius, Raymonde Joubert‐Caron, Michel Caron, Julie Hardouin · 2010 · Journal of Proteome Research
  72. The Sos-recruitment system as a tool to analyze cellular localization of plant proteins: membrane localization of Arabidopsis thaliana PEPINO/PASTICCINO2
    Sabine Schönhofer‐Merl, Ramón A. Torres‐Ruiz · 2010 · Molecular Genetics and Genomics
  73. Structural and Functional Characterization of Ybr137wp Implicates Its Involvement in the Targeting of Tail-Anchored Proteins to Membranes
    Yi‐Hung Yeh, Tai‐Wen Lin, Yi‐Chuan Li, Jung-Yu Tung, Cheng-Yuan Lin, Chwan‐Deng Hsiao · 2014 · Molecular and Cellular Biology
  74. Synthetic Genetic Interaction (CRISPR-SGI) Profiling in Caenorhabditis elegans
    John A. Calarco, Adam D. Norris · 2018 · BIO-PROTOCOL
  75. The use of high-throughput microscopy in the characterisation of phenotypes associated with the Unfolded Protein Response in Saccharomyces cerevisiae
    Peter W. Bircham · 2014
  76. An E-MAP of the ER
    Elizabeth Conibear · 2005 · Cell
  77. Decoding directional genetic dependencies through orthogonal CRISPR/Cas screens
    Michael Boettcher, Ruilin Tian, James A Blau, Evan Markegard, David Wu, Anne Biton, Noah Zaitlen, Frank P. McCormick, Martin Kampmann, Michael T. McManus · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
  78. Mapping in vivo genetic interactomics through Cpf1 crRNA array screening
    Ryan Dz-Wei Chow, Guangchuan Wang, Adan Codina, Lupeng Ye, Sidi Chen · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
  79. Integrative structure determination of histones H3 and H4 using genetic interactions
    Ignacia Echeverria, Hannes Braberg, Nevan J. Krogan, Andrej Šali · 2022 · FEBS Journal
  80. Transcriptional Regulation Technology for Gene Perturbation in Fission Yeast
    Ken Ishikawa, Shigeaki Saitoh · 2023 · Biomolecules
  81. Time-resolved functional genomics using deep learning reveals global hierarchical control of autophagy
    Nathalia Chica, Aram Nikolai Andersen, Sara Orellana‐Muñoz, Ignacio Garcia, Aurélie Nguéa P, Sigve Nakken, Pilar Ayuda Durán, Linda Håkensbakken, Sebastian Wolfgang Schultz, Eline Rødningen et al. · 2026 · Nature Cell Biology
  82. Imputing and Predicting Quantitative Genetic Interactions in Epistatic MAPs
    Colm J. Ryan, Gerard Cagney, Nevan J. Krogan, Pádraig Cunningham, Derek Greene · 2011 · Methods in molecular biology
  83. Signature-tagged Mutagenesis to Characterize Genes Through Competitive Selection of Bar-coded Genome Libraries
    Julia Oh, Corey Nislow · 2011 · Methods in molecular biology
  84. Application of Distributive Conjugal DNA Transfer in Mycobacterium smegmatis To Establish a Genome-Wide Synthetic Genetic Array
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  85. Using Caenorhabditis elegans to Screen for Tissue-Specific Chaperone Interactions
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  86. Trigenic Synthetic Genetic Array (τ-SGA) Technique for Complex Interaction Analysis
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  87. The box C/D snoRNP assembly factor Bcd1 interacts with the histone chaperone Rtt106 and controls its transcription dependent activity
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  88. Mutational Analysis of the Yeast TRAPP Subunit Trs20p Identifies Roles in Endocytic Recycling and Sporulation
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  89. Metabolism and Roles of Sphingolipids in Yeast Saccharomyces cerevisiae
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  90. A systematic survey of an intragenic epistatic landscape
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  91. High-throughput chemical genomic screening: a step-by-step workflow from plate to phenotype
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  92. Feature Identification of Compensatory Gene Pairs without Sequence Homology in Yeast
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  93. Structural and Functional Characterization of a Caenorhabditis elegans Genetic Interaction Network within Pathways
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  94. Ste24 Protease
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  95. Matrix (factorization) reloaded: flexible methods for imputing genetic interactions with cross-species and side information
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  96. Lipidomic Analysis of Lower Organisms
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  97. Profiling Yeast Deletion Strains Using Sample Multiplexing and Network-Based Analyses
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  98. A Gaussian process-based definition reveals new and bona fide genetic interactions compared to a multiplicative model in the Gram-negative Escherichia coli
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