Genomic Libraries and a Host Strain Designed for Highly Efficient Two-Hybrid Selection in Yeast

Regulation of RAD53 by the ATM -Like Kinases MEC1 and TEL1 in Yeast Cell Cycle Checkpoint Pathways

Sanchez, Y., Desany, B. A., Jones, W. J., Liu, Q., Wang, B., & Elledge, S. J. (1996) · Science · doi:10.1126/science.271.5247.357 · Cited by 585

A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae

Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., Judson, R. S., Knight, J. R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., et al. (2000) · Nature · doi:10.1038/35001009 · Cited by 4,706

A comprehensive two-hybrid analysis to explore the yeast protein interactome

Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., & Sakaki, Y. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.061034498 · Cited by 3,566

Nutrient-dependent mTORC1 Association with the ULK1–Atg13–FIP200 Complex Required for Autophagy

Hosokawa, N., Hara, T., Kaizuka, T., Kishi, C., Takamura, A., Miura, Y., Iemura, S.-I., Natsume, T., Takehana, K., Yamada, N., et al. (2009) · Molecular Biology of the Cell · doi:10.1091/mbc.e08-12-1248 · Cited by 2,076

Tsg101 and the vacuolar protein sorting pathway are essential for HIV-1 budding

Garrus, J. E., von Schwedler, U. K., Pornillos, O. W., Morham, S. G., Zavitz, K. H., Wang, H. E., Wettstein, D. A., Stray, K. M., Côté, M., Rich, R. L., et al. (2001) · Cell · doi:10.1016/s0092-8674(01)00506-2 · Cited by 1,369

Two Beclin 1-binding proteins, Atg14L and Rubicon, reciprocally regulate autophagy at different stages

Matsunaga, K., Saitoh, T., Tabata, K., Omori, H., Satoh, T., Kurotori, N., Maejima, I., Shirahama-Noda, K., Ichimura, T., Isobe, T., et al. (2009) · Nature Cell Biology · doi:10.1038/ncb1846 · Cited by 1,235

The hMre11/hRad50 Protein Complex and Nijmegen Breakage Syndrome: Linkage of Double-Strand Break Repair to the Cellular DNA Damage Response

Carney, J. P., Maser, R. S., Olivares, H., Davis, E. M., Le Beau, M., Yates, J. R., Hays, L., Morgan, W. F., & Petrini, J. H. J. (1998) · Cell · doi:10.1016/s0092-8674(00)81175-7 · Cited by 1,226

Tor-Mediated Induction of Autophagy via an Apg1 Protein Kinase Complex

Kamada, Y., Funakoshi, T., Shintani, T., Nagano, K., Ohsumi, M., & Ohsumi, Y. (2000) · The Journal of Cell Biology · doi:10.1083/jcb.150.6.1507 · Cited by 1,145

Protein-Protein Interaction Detection: Methods and Analysis

Rao, V. S., Srinivas, K., Sujini, G. N., & Kumar, G. N. S. (2014) · International Journal of Proteomics · doi:10.1155/2014/147648 · Cited by 811

Mitochondria-Anchored Receptor Atg32 Mediates Degradation of Mitochondria via Selective Autophagy

Okamoto, K., Kondo-Okamoto, N., & Ohsumi, Y. (2009) · Developmental Cell · doi:10.1016/j.devcel.2009.06.013 · Cited by 797

Mouse Apg16L, a novel WD-repeat protein, targets to the autophagic isolation membrane with the Apg12-Apg5 conjugate

Mizushima, N., Kuma, A., Kobayashi, Y., Yamamoto, A., Matsubae, M., Takao, T., Natsume, T., Ohsumi, Y., & Yoshimori, T. (2003) · Journal of Cell Science · doi:10.1242/jcs.00381 · Cited by 791

A Suppressor of Two Essential Checkpoint Genes Identifies a Novel Protein that Negatively Affects dNTP Pools

Zhao, X., Muller, E. G. D., & Rothstein, R. (1998) · Molecular Cell · doi:10.1016/s1097-2765(00)80277-4 · Cited by 728

Receptor-mediated selective autophagy degrades the endoplasmic reticulum and the nucleus

Mochida, K., Oikawa, Y., Kimura, Y., Kirisako, H., Hirano, H., Ohsumi, Y., & Nakatogawa, H. (2015) · Nature · doi:10.1038/nature14506 · Cited by 611

Cargo of kinesin identified as JIP scaffolding proteins and associated signaling molecules

Verhey, K. J., Meyer, D., Deehan, R., Blenis, J., Schnapp, B. J., Rapoport, T. A., & Margolis, B. (2001) · The Journal of Cell Biology · doi:10.1083/jcb.152.5.959 · Cited by 609

The Ste20-like kinase Mst2 activates the human large tumor suppressor kinase Lats1

Chan, E. H. Y., Nousiainen, M., Chalamalasetty, R. B., Schäfer, A., Nigg, E. A., & Silljé, H. H. W. (2005) · Oncogene · doi:10.1038/sj.onc.1208445 · Cited by 584

TIN2, a new regulator of telomere length in human cells

Kim, S.-H., Kaminker, P., & Campisi, J. (1999) · Nature Genetics · doi:10.1038/70508 · Cited by 525

Calcineurin acts through the CRZ1/TCN1-encoded transcription factor to regulate gene expression in yeast

Stathopoulos, A. M., & Cyert, M. S. (1997) · Genes & Development · doi:10.1101/gad.11.24.3432 · Cited by 442

Type Iγ phosphatidylinositol phosphate kinase targets and regulates focal adhesions

Ling, K., Doughman, R. L., Firestone, A. J., Bunce, M. W., & Anderson, R. A. (2002) · Nature · doi:10.1038/nature01082 · Cited by 443

The mitochondrial inner membrane protein mitofilin controls cristae morphology

John, G. B., Shang, Y., Li, L., Renken, C., Mannella, C. A., Selker, J. M. L., Rangell, L., Bennett, M. J., & Zha, J. (2005) · Molecular Biology of the Cell · doi:10.1091/mbc.e04-08-0697 · Cited by 440

Drosophila PAR-1 and 14-3-3 Inhibit Bazooka/PAR-3 to Establish Complementary Cortical Domains in Polarized Cells

Benton, R., & Johnston, D. S. (2003) · Cell · doi:10.1016/s0092-8674(03)00938-3 · Cited by 410

Arabidopsis thaliana transcription factors bZIP19 and bZIP23 regulate the adaptation to zinc deficiency

Assunção, A. G. L., Herrero, E., Lin, Y.-F., Huettel, B., Talukdar, S., Smaczniak, C., Immink, R. G. H., van Eldik, M., Fiers, M., Schat, H., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1004788107 · Cited by 379

Mechanism of Cargo Selection in the Cytoplasm to Vacuole Targeting Pathway

Shintani, T., Huang, W.-P., Stromhaug, P. E., & Klionsky, D. J. (2002) · Developmental Cell · doi:10.1016/s1534-5807(02)00373-8 · Cited by 362

Arl8 and SKIP Act Together to Link Lysosomes to Kinesin-1

Rosa-Ferreira, C., & Munro, S. (2011) · Developmental Cell · doi:10.1016/j.devcel.2011.10.007 · Cited by 360

Linking β-Catenin to Androgen-signaling Pathway

Yang, F., Li, X., Sharma, M., Sasaki, C. Y., Longo, D. L., Lim, B., & Sun, Z. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m111962200 · Cited by 342

Drosophila Brain Tumor is a translational repressor

Sonoda, J., & Wharton, R. P. (2001) · Genes & Development · doi:10.1101/gad.870801 · Cited by 329

A Family of Rab27-binding Proteins

Strom, M., Hume, A. N., Tarafder, A. K., Barkagianni, E., & Seabra, M. C. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m202574200 · Cited by 324

Light Controls Growth and Development via a Conserved Pathway in the Fungal Kingdom

Idnurm, A., & Heitman, J. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030095 · Cited by 306

Atg17 Functions in Cooperation with Atg1 and Atg13 in Yeast Autophagy

Kabeya, Y., Kamada, Y., Baba, M., Takikawa, H., Sasaki, M., & Ohsumi, Y. (2005) · Molecular Biology of the Cell · doi:10.1091/mbc.e04-08-0669 · Cited by 304

The Dun1 checkpoint kinase phosphorylates and regulates the ribonucleotide reductase inhibitor Sml1

Zhao, X., & Rothstein, R. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.062502299 · Cited by 290

Atg11 Links Cargo to the Vesicle-forming Machinery in the Cytoplasm to Vacuole Targeting Pathway

Yorimitsu, T., & Klionsky, D. J. (2005) · Molecular Biology of the Cell · doi:10.1091/mbc.e04-11-1035 · Cited by 280

Apg10p, a novel protein‐conjugating enzyme essential for autophagy in yeast

Shintani, T., Mizushima, N., Ogawa, Y., Matsuura, A., Noda, T., & Ohsumi, Y. (1999) · The EMBO Journal · doi:10.1093/emboj/18.19.5234 · Cited by 269

HURP Is a Ran-Importin β-Regulated Protein that Stabilizes Kinetochore Microtubules in the Vicinity of Chromosomes

Silljé, H. H. W., Nagel, S., Körner, R., & Nigg, E. A. (2006) · Current Biology · doi:10.1016/j.cub.2006.02.070 · Cited by 267

Atg9 Cycles Between Mitochondria and the Pre-Autophagosomal Structure in Yeasts

Reggiori, F., Shintani, T., Chong, H., Nair, U., & Klionsky, D. J. (2005) · Autophagy · doi:10.4161/auto.1.2.1840 · Cited by 266

The Atg1 Kinase Complex Is Involved in the Regulation of Protein Recruitment to Initiate Sequestering Vesicle Formation for Nonspecific Autophagy in Saccharomyces cerevisiae

Cheong, H., Nair, U., Geng, J., & Klionsky, D. J. (2008) · Molecular Biology of the Cell · doi:10.1091/mbc.e07-08-0826 · Cited by 245

The CRL4Cdt2 ubiquitin ligase targets the degradation of p21Cip1 to control replication licensing

Kim, Y., Starostina, N. G., & Kipreos, E. T. (2008) · Genes & Development · doi:10.1101/gad.1703708 · Cited by 240

Apg13p and Vac8p Are Part of a Complex of Phosphoproteins That Are Required for Cytoplasm to Vacuole Targeting

Scott, S. V., Nice, D. C., Nau, J. J., Weisman, L. S., Kamada, Y., Keizer-Gunnink, I., Funakoshi, T., Veenhuis, M., Ohsumi, Y., & Klionsky, D. J. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.m002813200 · Cited by 227

dlk acts as a negative regulator of Notch1 activation through interactions with specific EGF-like repeats

Baladrón, V., Ruiz-Hidalgo, M. J., Nueda, M. L., Díaz-Guerra, M. J. M., García-Ramírez, J. J., Bonvini, E., Gubina, E., & Laborda, J. (2005) · Experimental Cell Research · doi:10.1016/j.yexcr.2004.10.001 · Cited by 226

Golgi coiled-coil proteins contain multiple binding sites for Rab family G proteins

Sinka, R., Gillingham, A. K., Kondylis, V., & Munro, S. (2008) · The Journal of Cell Biology · doi:10.1083/jcb.200808018 · Cited by 190

Atg17 Regulates the Magnitude of the Autophagic Response

Cheong, H., Yorimitsu, T., Reggiori, F., Legakis, J. E., Wang, C.-W., & Klionsky, D. J. (2005) · Molecular Biology of the Cell · doi:10.1091/mbc.e04-10-0894 · Cited by 187

SepF, a novel FtsZ‐interacting protein required for a late step in cell division

Hamoen, L. W., Meile, J., De Jong, W., Noirot, P., & Errington, J. (2006) · Molecular Microbiology · doi:10.1111/j.1365-2958.2005.04987.x · Cited by 180

A Physical Interaction Network of Dengue Virus and Human Proteins

Khadka, S., Vangeloff, A. D., Zhang, C., Siddavatam, P., Heaton, N. S., Wang, L., Sengupta, R., Sahasrabudhe, S., Randall, G., Gribskov, M., et al. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.012187 · Cited by 175

A two-hybrid screen of the yeast proteome for Hsp90 interactors uncovers a novel Hsp90 chaperone requirement in the activity of a stress-activated mitogen-activated protein kinase, Slt2p (Mpk1p).

Millson, S. H., Truman, A. W., King, V., Prodromou, C., Pearl, L. H., & Piper, P. W. (2005) · Eukaryotic Cell · doi:10.1128/ec.4.5.849-860.2005 · Cited by 172

Degradation of Endocytosed Epidermal Growth Factor and Virally Ubiquitinated Major Histocompatibility Complex Class I Is Independent of Mammalian ESCRTII

Bowers, K., Piper, S. C., Edeling, M. A., Gray, S. R., Owen, D. J., Lehner, P. J., & Luzio, J. P. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m508632200 · Cited by 166

TET1 regulates hypoxia-induced epithelial-mesenchymal transition by acting as a co-activator

Tsai, Y.-P., Chen, H.-F., Chen, S.-Y., Cheng, W.-C., Wang, H.-W., Shen, Z.-J., Song, C., Teng, S.-C., He, C., & Wu, K.-J. (2014) · Genome biology · doi:10.1186/s13059-014-0513-0 · Cited by 152

Dual Activators of the Sterol Biosynthetic Pathway of Saccharomyces cerevisiae : Similar Activation/Regulatory Domains but Different Response Mechanisms

Davies, B. S. J., Wang, H. S., & Rine, J. (2005) · Molecular and Cellular Biology · doi:10.1128/mcb.25.16.7375-7385.2005 · Cited by 138

Simian Virus 5 V Protein Acts as an Adaptor, Linking DDB1 to STAT2, To Facilitate the Ubiquitination of STAT1

Precious, B., Childs, K., Fitzpatrick-Swallow, V., Goodbourn, S., & Randall, R. E. (2005) · Journal of Virology · doi:10.1128/jvi.79.21.13434-13441.2005 · Cited by 117

Calcineurin-dependent regulation of Crz1p nuclear export requires Msn5p and a conserved calcineurin docking site

Boustany, L. M., & Cyert, M. S. (2002) · Genes & Development · doi:10.1101/gad.967602 · Cited by 115

The Rab Interacting Lysosomal Protein (RILP) Homology Domain Functions as a Novel Effector Domain for Small GTPase Rab36

Matsui, T., Ohbayashi, N., & Fukuda, M. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.370544 · Cited by 90

p250GAP, a Novel Brain-enriched GTPase-activating Protein for Rho Family GTPases, Is Involved in the N-Methyl-d-aspartate Receptor Signaling

Nakazawa, T., Watabe, A. M., Tezuka, T., Yoshida, Y., Yokoyama, K., Umemori, H., Inoue, A., Okabe, S., Manabe, T., & Yamamoto, T. (2003) · Molecular Biology of the Cell · doi:10.1091/mbc.e02-09-0623 · Cited by 100

Identification and functional analysis of two Ca2+-binding EF-hand motifs in the B″/PR72 subunit of protein phosphatase 2A

Janssens, V., Jordens, J., Stevens, I., Van Hoof, C., Martens, E., De Smedt, H., Engelborghs, Y., Waelkens, E., & Goris, J. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m211717200 · Cited by 89

Cell Cycle-dependent Degradation of the Saccharomyces cerevisiae Spindle Motor Cin8p Requires APCCdh1and a Bipartite Destruction Sequence

Hildebrandt, E. R., & Hoyt, M. A. (2001) · Molecular Biology of the Cell · doi:10.1091/mbc.12.11.3402 · Cited by 87

The yeast transcriptome in aerobic and hypoxic conditions: effects of hap1, rox1, rox3 and srb10 deletions

Becerra, M., Lombardía‐Ferreira, L. J., Hauser, N. C., Hoheisel, J. D., Tizon, B., & Cerdán, M. E. (2002) · Molecular Microbiology · doi:10.1046/j.1365-2958.2002.02724.x · Cited by 85

The Ubiquitin E3 Ligase MARCH7 is Differentially Regulated by the Deubiquitylating Enzymes USP7 and USP9X

Nathan, J. A., Sengupta, S., Wood, S. A., Admon, A., Markson, G., Sanderson, C., & Lehner, P. J. (2008) · Traffic · doi:10.1111/j.1600-0854.2008.00747.x · Cited by 87

YOD1/TRAF6 association balances p62-dependent IL-1 signaling to NF-κB

Schimmack, G., Schorpp, K., Kutzner, K., Gehring, T., Brenke, J. K., Hadian, K., & Krappmann, D. (2017) · eLife · doi:10.7554/elife.22416 · Cited by 84

The Caenorhabditis elegans Aurora B Kinase AIR-2 Phosphorylates and Is Required for the Localization of a BimC Kinesin to Meiotic and Mitotic Spindles

Bishop, J. D., Han, Z., & Schumacher, J. M. (2005) · Molecular Biology of the Cell · doi:10.1091/mbc.e04-08-0682 · Cited by 72

Iron-Induced Dissociation of the Aft1p Transcriptional Regulator from Target Gene Promoters Is an Initial Event in Iron-Dependent Gene Suppression

Ueta, R., Fujiwara, N., Iwai, K., & Yamaguchi-Iwai, Y. (2012) · Molecular and Cellular Biology · doi:10.1128/mcb.00726-12 · Cited by 78

The Divergent Caenorhabditis elegans β-Catenin Proteins BAR-1, WRM-1 and HMP-2 Make Distinct Protein Interactions but Retain Functional Redundancy in Vivo

Natarajan, L., Witwer, N. E., & Eisenmann, D. M. (2001) · Genetics · doi:10.1093/genetics/159.1.159 · Cited by 75

Autophagy genesSmatg8andSmatg4are required for fruiting-body development, vegetative growth and ascospore germination in the filamentous ascomyceteSordaria macrospora

Voigt, O., & Pöggeler, S. (2013) · Autophagy · doi:10.4161/auto.22398 · Cited by 60

ELKS1 localizes the synaptic vesicle priming protein bMunc13-2 to a specific subset of active zones

Kawabe, H., Mitkovski, M., Kaeser, P. S., Hirrlinger, J., Opazo, F., Nestvogel, D., Kalla, S., Fejtova, A., Verrier, S. E., Bungers, S. R., et al. (2017) · Journal of Cell Biology · doi:10.1083/jcb.201606086 · Cited by 50

Rab1A regulates anterograde melanosome transport by recruiting kinesin-1 to melanosomes through interaction with SKIP

Ishida, M., Ohbayashi, N., & Fukuda, M. (2015) · Scientific Reports · doi:10.1038/srep08238 · Cited by 49

Identification of Phospholipid Scramblase 1 as a Novel Interacting Molecule with β-Secretase (β-Site Amyloid Precursor Protein (APP) Cleaving Enzyme (BACE))

Kametaka, S., Shibata, M., Moroe, K., Kanamori, S., Ohsawa, Y., Waguri, S., Sims, P. J., Emoto, K., Umeda, M., & Uchiyama, Y. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m208611200 · Cited by 47

Molecular mechanism for the control of virulent Toxoplasma gondii infections in wild-derived mice

Murillo-León, M., Müller, U. B., Zimmermann, I., Singh, S., Widdershooven, P., Campos, C., Alvarez, C., Könen-Waisman, S., Lukes, N., Ruzsics, Z., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-09200-2 · Cited by 46

Specific interactions of PP2A and PP2A-like phosphatases with the yeast PTPA homologues, Ypa1 and Ypa2

Van HOOF, C., MARTENS, E., LONGIN, S., JORDENS, J., STEVENS, I., JANSSENS, V., & GORIS, J. (2005) · Biochemical Journal · doi:10.1042/bj20040887 · Cited by 42

PIAS3 Interacts with ATF1 and Regulates the Human Ferritin H Gene through an Antioxidant-responsive Element

Iwasaki, K., Hailemariam, K., & Tsuji, Y. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m701477200 · Cited by 41

Functional interactions among members of the meiotic initiation complex in fission yeast

Steiner, S., Kohli, J., & Ludin, K. (2010) · Current Genetics · doi:10.1007/s00294-010-0296-0 · Cited by 34

Rab40C is a novel Varp-binding protein that promotes proteasomal degradation of Varp in melanocytes

Yatsu, A., Shimada, H., Ohbayashi, N., & Fukuda, M. (2015) · Biology Open · doi:10.1242/bio.201411114 · Cited by 28

Systematic analysis of NDUFAF6 in complex I assembly and mitochondrial disease

(2024) · doi:10.1038/s42255-024-01039-2 · Cited by 23

Invasive Californian death caps develop mushrooms unisexually and bisexually

Wang, Y.-W., McKeon, M. C., Elmore, H., Hess, J., Golan, J., Gage, H., Mao, W., Harrow, E., Gonçalves, S. C., Hull, C. M., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-42317-z · Cited by 20

Concurrent remodelling of nucleolar 60S subunit precursors by the Rea1 ATPase and Spb4 RNA helicase

Mitterer, V., Thoms, M., Buschauer, R., Berninghausen, O., Hurt, E., & Beckmann, R. (2023) · eLife · doi:10.7554/elife.84877 · Cited by 13

Barcode fusion genetics-protein-fragment complementation assay (BFG-PCA): tools and resources that expand the potential for binary protein interaction discovery

(2022) · doi:10.1093/nar/gkac045 · Cited by 7

Insects evolved a monomeric histone-fold domain in the CENP-T protein family

Sankaranarayanan, S. R., Ulmer, J., Mørch, A., Ali-Ahmad, A., Sekulić, N., & Drinnenberg, I. A. (2025) · EMBO Reports · doi:10.1038/s44319-025-00603-5 · Cited by 2

Prophage-encoded small protein YqaH counteracts the activities of the replication initiator DnaA in Bacillus subtilis

Ventroux, M., & Noirot-Gros, M.-F. (2022) · Microbiology · doi:10.1099/mic.0.001268 · Cited by 1

A SUMO interacting motif in the replication initiator protein of tomato yellow leaf curl virus is required for viral replication

Gaertner, N. F., Maio, F., Arroyo-Mateos, M., Luna, A. P., Sabarit, B., Kwaaitaal, M., Eltschkner, S., Prins, M., Bejarano, E. R., & van den Burg, H. A. (2025) · Journal of Virology · doi:10.1128/jvi.01286-25 · Cited by 1